201
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Quigley KM, Warner PA, Bay LK, Willis BL. Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral. Heredity (Edinb) 2018; 121:524-536. [PMID: 29453423 PMCID: PMC6221883 DOI: 10.1038/s41437-018-0059-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 12/25/2017] [Accepted: 01/12/2018] [Indexed: 11/12/2022] Open
Abstract
Determining the extent to which Symbiodinium communities in corals are inherited versus environmentally acquired is fundamental to understanding coral resilience and to predicting coral responses to stressors like warming oceans that disrupt this critical endosymbiosis. We examined the fidelity with which Symbiodinium communities in the brooding coral Seriatopora hystrix are vertically transmitted and the extent to which communities are genetically regulated, by genotyping the symbiont communities within 60 larvae and their parents (9 maternal and 45 paternal colonies) using high-throughput sequencing of the ITS2 locus. Unexpectedly, Symbiodinium communities associated with brooded larvae were distinct from those within parent colonies, including the presence of types not detected in adults. Bayesian heritability (h2) analysis revealed that 33% of variability in larval Symbiodinium communities was genetically controlled. Results highlight flexibility in the establishment of larval symbiont communities and demonstrate that symbiont transmission is not exclusively vertical in brooding corals. Instead, we show that Symbiodinium transmission in S. hystrix involves a mixed-mode strategy, similar to many terrestrial invertebrate symbioses. Also, variation in the abundances of common Symbiodinium types among adult corals suggests that microhabitat differences influence the structure of in hospite Symbiodinium communities. Partial genetic regulation coupled with flexibility in the environmentally acquired component of Symbiodinium communities implies that corals with vertical transmission, like S. hystrix, may be more resilient to environmental change than previously thought.
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Affiliation(s)
- Kate M Quigley
- ARC Centre of Excellence for Coral Reef Studies and College of Science and Engineering, James Cook University, Townsville, QLD, Australia. .,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.
| | - Patricia A Warner
- ARC Centre of Excellence for Coral Reef Studies and College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia
| | - Line K Bay
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,Australian Institute of Marine Science, PMB3, Townsville, QLD, Australia
| | - Bette L Willis
- ARC Centre of Excellence for Coral Reef Studies and College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia
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202
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Williams CL, Caraballo-Rodríguez AM, Allaband C, Zarrinpar A, Knight R, Gauglitz JM. Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ddmod.2019.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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203
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Gignoux-Wolfsohn SA, Aronson FM, Vollmer SV. Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral. FEMS Microbiol Ecol 2017. [PMID: 28637338 DOI: 10.1093/femsec/fix080] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Increased bacterial diversity on diseased corals can obscure disease etiology and complicate our understanding of pathogenesis. To untangle microbes that may cause white band disease signs from microbes responding to disease, we inoculated healthy Acropora cervicornis corals with an infectious dose from visibly diseased corals. We sampled these dosed corals and healthy controls over time for sequencing of the bacterial 16S region. Endozoicomonas were associated with healthy fragments from 4/10 colonies, dominating microbiomes before dosing and decreasing over time only in corals that displayed disease signs, suggesting a role in disease resistance. We grouped disease-associated bacteria by when they increased in abundance (primary vs secondary) and whether they originated in the dose (colonizers) or the previously healthy corals (responders). We found that all primary responders increased in all dosed corals regardless of final disease state and are therefore unlikely to cause disease signs. In contrast, primary colonizers in the families Pasteurellaceae and Francisellaceae increased solely in dosed corals that ultimately displayed disease signs, and may be infectious foreign bacteria involved in the development of disease signs. Moving away from a static comparison of diseased and healthy bacterial communities, we provide a framework to identify key players in other coral diseases.
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Affiliation(s)
- Sarah A Gignoux-Wolfsohn
- Department of Ecology, Evolution, & Natural Resources School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8525, USA
| | - Felicia M Aronson
- Marine Science Center, Northeastern University, Nahant, MA 01908, USA
| | - Steven V Vollmer
- Marine Science Center, Northeastern University, Nahant, MA 01908, USA
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204
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Unforeseen swimming and gliding mode of an insect gut symbiont, Burkholderia sp. RPE64, with wrapping of the flagella around its cell body. ISME JOURNAL 2017; 12:838-848. [PMID: 29269839 DOI: 10.1038/s41396-017-0010-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/09/2017] [Accepted: 10/24/2017] [Indexed: 11/08/2022]
Abstract
A bean bug symbiont, Burkholderia sp. RPE64, selectively colonizes the gut crypts by flagella-mediated motility: however, the mechanism for this colonization remains unclear. Here, to obtain clues to this mechanism, we characterized the swimming motility of the Burkholderia symbiont under an advanced optical microscope. High-speed imaging of cells enabled the detection of turn events with up to 5-ms temporal resolution, indicating that cells showed reversal motions (θ ~ 180°) with rapid changes in speed by a factor of 3.6. Remarkably, staining of the flagellar filaments with a fluorescent dye Cy3 revealed that the flagellar filaments wrap around the cell body with a motion like that of a ribbon streamer in rhythmic gymnastics. A motility assay with total internal reflection fluorescence microscopy revealed that the left-handed flagellum wound around the cell body and propelled it forward by its clockwise rotation. We also detected periodic-fluorescent signals of flagella on the glass surface, suggesting that flagella possibly contacted the solid surface directly and produced a gliding-like motion driven by flagellar rotation. Finally, the wrapping motion was also observed in a symbiotic bacterium of the bobtail squid, Aliivibrio fischeri, suggesting that this motility mode may contribute to migration on the mucus-filled narrow passage connecting to the symbiotic organ.
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205
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Savory EA, Fuller SL, Weisberg AJ, Thomas WJ, Gordon MI, Stevens DM, Creason AL, Belcher MS, Serdani M, Wiseman MS, Grünwald NJ, Putnam ML, Chang JH. Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management. eLife 2017; 6:30925. [PMID: 29231813 PMCID: PMC5726852 DOI: 10.7554/elife.30925] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/03/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses. All organisms live in a world teeming with bacteria. Some bacteria are beneficial and, for example, provide their hosts with nutrients. Others cause harm, for example, by stealing nutrients and causing disease. Many bacteria can also gain DNA from other bacteria, and the genes encoded within the new DNA can help them to live with other organisms. This can start the bacteria on an evolutionary path to becoming beneficial or harmful. Rhodococcus are bacteria that live in association with many species of plants, including trees. Most are harmless but some cause disease. Plants infected with harmful Rhodococcus can show deformed growth, which causes major losses to the nursery industry. Savory, Fuller, Weisberg et al. set out to understand how disease-causing Rhodococcus are introduced into nurseries, if they are transferred between nurseries, whether they persist in nurseries, and how to limit their spread. It turns out that harmless Rhodococcus are beneficial to plants. However, if these harmless bacteria gain a certain DNA molecule – called a virulence plasmid – they can convert into harmful bacteria. Further analysis showed that some nurseries repeatedly acquired the harmful bacteria. The pattern of affected nurseries suggested that some might have purchased diseased plants from a common provider. In other cases, the sources remained a mystery. Savory et al. also report that, contrary to previous findings, there is no evidence to support the diagnosis that Rhodococcus without a virulence plasmid are responsible for an unusual growth problem that has plagued the pistachio industry. In recent years, this incorrect diagnosis led to trees being unnecessarily destroyed, worsening the economic losses. These findings suggest that genes moving between bacteria can dramatically change how those bacteria interact with the organisms in which they live. It needs to be shown whether this is an exceptional process, unique to only certain groups of bacteria, or if it is more widespread in nature. These findings could inform future disease management strategies to better protect agricultural systems.
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Affiliation(s)
- Elizabeth A Savory
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Skylar L Fuller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - William J Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Michael I Gordon
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Allison L Creason
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States
| | - Michael S Belcher
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Maryna Serdani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Michele S Wiseman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture and Agricultural Research Service, Corvallis, United States
| | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States.,Center for Genome Research, Oregon State University, Corvallis, United States
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206
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Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome. Arch Med Res 2017; 48:780-789. [DOI: 10.1016/j.arcmed.2018.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/12/2018] [Indexed: 02/06/2023]
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207
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Stress and stability: applying the Anna Karenina principle to animal microbiomes. Nat Microbiol 2017; 2:17121. [DOI: 10.1038/nmicrobiol.2017.121] [Citation(s) in RCA: 402] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 07/03/2017] [Indexed: 02/08/2023]
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208
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Foster KR, Schluter J, Coyte KZ, Rakoff-Nahoum S. The evolution of the host microbiome as an ecosystem on a leash. Nature 2017; 548:43-51. [PMID: 28770836 PMCID: PMC5749636 DOI: 10.1038/nature23292] [Citation(s) in RCA: 484] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 06/20/2017] [Indexed: 12/11/2022]
Abstract
The human body carries vast communities of microbes that provide many benefits. Our microbiome is complex and challenging to understand, but evolutionary theory provides a universal framework with which to analyse its biology and health impacts. Here we argue that to understand a given microbiome feature, such as colonization resistance, host nutrition or immune development, we must consider how hosts and symbionts evolve. Symbionts commonly evolve to compete within the host ecosystem, while hosts evolve to keep the ecosystem on a leash. We suggest that the health benefits of the microbiome should be understood, and studied, as an interplay between microbial competition and host control.
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Affiliation(s)
- Kevin R Foster
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Jonas Schluter
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Katharine Z Coyte
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Division of Infectious Diseases and Division of Gastroenterology, Department of Medicine, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Seth Rakoff-Nahoum
- Division of Infectious Diseases and Division of Gastroenterology, Department of Medicine, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
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209
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Molina-Santiago C, Udaondo Z, Cordero BF, Ramos JL. Interspecies cross-talk between co-cultured Pseudomonas putida and Escherichia coli. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:441-448. [PMID: 28585781 DOI: 10.1111/1758-2229.12553] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/26/2017] [Accepted: 05/28/2017] [Indexed: 06/07/2023]
Abstract
Pseudomonas putida and Escherichia coli are ubiquitous microorganisms that can be isolated from soil rhizosphere, the surface of vegetables, fresh waters and wastewaters - environments in which they likely co-exist. Despite this, the potential interactions between these microbes have not been studied in detail. To analyse these interactions, we carried out RNA-seq transcriptomic analysis of these microbes as monocultures and as co-cultures. Our results show that co-culture of these microbes significantly alters transcriptional profiles. The most dramatic transcriptional changes in both microorganisms were involved in central carbon metabolism, as well as adhesion to surfaces and the activation of drug efflux pumps. We also found that acetate production was one of the mechanisms used by E. coli K-12 MG1655 in response to the presence of P. putida DOT-T1E.
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Affiliation(s)
- Carlos Molina-Santiago
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, E-18008, Spain
| | - Zulema Udaondo
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, E-18008, Spain
| | - Baldo F Cordero
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, E-18008, Spain
| | - Juan L Ramos
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, E-18008, Spain
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210
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Zhou G, Cai L, Yuan T, Tian R, Tong H, Zhang W, Jiang L, Guo M, Liu S, Qian PY, Huang H. Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO 2. Environ Microbiol 2017. [PMID: 28631353 DOI: 10.1111/1462-2920.13840] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Reef-building corals are complex holobionts, harbouring diverse microorganisms that play essential roles in maintaining coral health. However, microbiome development in early life stages of corals remains poorly understood. Here, microbiomes of Acropora gemmifera were analysed during spawning and early developmental stages, and also under different seawater partial pressure of CO2 (pCO2 ) conditions, using amplicon sequencing of 16S rRNA gene for bacteria and archaea and of ITS2 for Symbiodinium. No remarkable microbiome shift was observed in adults before and after spawning. Moreover, microbiomes in eggs were highly similar to those in spawned adults, possibly suggesting a vertical transmission from parents to offspring. However, significant stage-specific changes were found in coral microbiome during development, indicating that host development played a dominant role in shaping coral microbiome. Specifically, Cyanobacteria were particularly abundant in 6-day-old juveniles, but decreased largely in 31-day-old juveniles with a possible subclade shift in Symbiodinium dominance from C2r to D17. Larval microbiome showed changes in elevated pCO2 , while juvenile microbiomes remained rather stable in response to higher pCO2 . This study provides novel insights into the microbiome development during the critical life stages of coral.
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Affiliation(s)
- Guowei Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, Hainan, China.,Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Lin Cai
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Tao Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Renmao Tian
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Haoya Tong
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Weipeng Zhang
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Lei Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Minglan Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Sheng Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Pei-Yuan Qian
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, Hainan, China
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211
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Zepeda EA, Veline RJ, Crook RJ. Rapid Associative Learning and Stable Long-Term Memory in the Squid Euprymna scolopes. THE BIOLOGICAL BULLETIN 2017; 232:212-218. [PMID: 28898600 DOI: 10.1086/693461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Learning and memory in cephalopod molluscs have received intensive study because of cephalopods' complex behavioral repertoire and relatively accessible nervous systems. While most of this research has been conducted using octopus and cuttlefish species, there has been relatively little work on squid. Euprymna scolopes Berry, 1913, a sepiolid squid, is a promising model for further exploration of cephalopod cognition. These small squid have been studied in detail for their symbiotic relationship with bioluminescent bacteria, and their short generation time and successful captive breeding through multiple generations make them appealing models for neurobiological research. However, little is known about their behavior or cognitive ability. Using the well-established "prawn-in-the-tube" assay of learning and memory, we show that within a single 10-min trial E. scolopes learns to inhibit its predatory behavior, and after three trials it can retain this memory for at least 12 d. Rapid learning and very long-term retention were apparent under two different training schedules. To our knowledge, this study is the first demonstration of learning and memory in this species as well as the first demonstration of associative learning in any squid.
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212
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Brown T, Otero C, Grajales A, Rodriguez E, Rodriguez-Lanetty M. Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida (Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank. PeerJ 2017; 5:e3235. [PMID: 28533949 PMCID: PMC5436572 DOI: 10.7717/peerj.3235] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/27/2017] [Indexed: 02/01/2023] Open
Abstract
Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgal Symbiodinium symbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact that E. pallida is likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.
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Affiliation(s)
- Tanya Brown
- Biological Sciences, Florida International University, Miami, FL, USA
| | - Christopher Otero
- Biological Sciences, Florida International University, Miami, FL, USA
| | - Alejandro Grajales
- Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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213
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Carrier TJ, Reitzel AM. The Hologenome Across Environments and the Implications of a Host-Associated Microbial Repertoire. Front Microbiol 2017; 8:802. [PMID: 28553264 PMCID: PMC5425589 DOI: 10.3389/fmicb.2017.00802] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 04/19/2017] [Indexed: 12/20/2022] Open
Abstract
Our understanding of the diverse interactions between hosts and microbes has grown profoundly over the past two decades and, as a product, has revolutionized our knowledge of the life sciences. Through primarily laboratory experiments, the current framework for holobionts and their respective hologenomes aims to decipher the underpinnings and implications of symbioses between host and microbiome. However, the laboratory setting restricts the full spectrum of host-associated symbionts as compared to those found in nature; thus, limiting the potential for a holistic interpretation of the functional roles the microbiome plays in host biology. When holobionts are studied in nature, associated microbial communities vary considerably between conditions, resulting in more microbial associates as part of the "hologenome" across environments than in either environment alone. We review and synthesize empirical evidence suggesting that hosts may associate with a larger microbial network that, in part, corresponds to experiencing diverse environmental conditions. To conceptualize the interactions between host and microbiome in an ecological context, we suggest the "host-associated microbial repertoire," which is the sum of microbial species a host may associate with over the course of its life-history under all encountered environmental circumstances. Furthermore, using examples from both terrestrial and marine ecosystems, we discuss how this concept may be used as a framework to compare the ability of the holobiont to acclimate and adapt to environmental variation, and propose three "signatures" of the concept.
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Affiliation(s)
- Tyler J Carrier
- Department of Biological Sciences, University of North Charlotte at CharlotteCharlotte, NC, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Charlotte at CharlotteCharlotte, NC, USA
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214
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Thompson LR, Nikolakakis K, Pan S, Reed J, Knight R, Ruby EG. Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes. Environ Microbiol 2017; 19:1845-1856. [PMID: 28152560 PMCID: PMC5409853 DOI: 10.1111/1462-2920.13684] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/24/2017] [Accepted: 01/29/2017] [Indexed: 11/30/2022]
Abstract
The marine bacterium Vibrio fischeri is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes, and the establishment of this association involves a number of signaling pathways and transcriptional responses between both partners. We report here the first full RNA-Seq dataset representing host-associated V. fischeri cells from colonized juvenile E. scolopes, as well as comparative transcriptomes under both laboratory and simulated marine planktonic conditions. These data elucidate the broad transcriptional changes that these bacteria undergo during the early stages of symbiotic colonization. We report several previously undescribed and unexpected transcriptional responses within the early stages of this symbiosis, including gene expression patterns consistent with biochemical stresses inside the host, and metabolic patterns distinct from those reported in associations with adult animals. Integration of these transcriptional data with a recently developed metabolic model of V. fischeri provides us with a clearer picture of the metabolic state of symbionts within the juvenile host, including their possible carbon sources. Taken together, these results expand our understanding of the early stages of the squid-vibrio symbiosis, and more generally inform the transcriptional responses underlying the activities of marine microbes during host colonization.
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Affiliation(s)
- Luke R Thompson
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Kiel Nikolakakis
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, USA
| | - Shu Pan
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, USA
| | - Jennifer Reed
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Edward G Ruby
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, USA
- Pacific Biosciences Research Center, University of Hawaii, Manoa, HI, USA
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215
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Pankey MS, Foxall RL, Ster IM, Perry LA, Schuster BM, Donner RA, Coyle M, Cooper VS, Whistler CA. Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria. eLife 2017; 6:e24414. [PMID: 28447935 PMCID: PMC5466423 DOI: 10.7554/elife.24414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/23/2017] [Indexed: 01/14/2023] Open
Abstract
Host immune and physical barriers protect against pathogens but also impede the establishment of essential symbiotic partnerships. To reveal mechanisms by which beneficial organisms adapt to circumvent host defenses, we experimentally evolved ecologically distinct bioluminescent Vibrio fischeri by colonization and growth within the light organs of the squid Euprymna scolopes. Serial squid passaging of bacteria produced eight distinct mutations in the binK sensor kinase gene, which conferred an exceptional selective advantage that could be demonstrated through both empirical and theoretical analysis. Squid-adaptive binK alleles promoted colonization and immune evasion that were mediated by cell-associated matrices including symbiotic polysaccharide (Syp) and cellulose. binK variation also altered quorum sensing, raising the threshold for luminescence induction. Preexisting coordinated regulation of symbiosis traits by BinK presented an efficient solution where altered BinK function was the key to unlock multiple colonization barriers. These results identify a genetic basis for microbial adaptability and underscore the importance of hosts as selective agents that shape emergent symbiont populations.
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Affiliation(s)
- M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Randi L Foxall
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Ian M Ster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
- Graduate Program in Biochemistry, University of New Hampshire, Durham, United States
| | - Lauren A Perry
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Graduate Program in Microbiology, University of New Hampshire, Durham, United States
| | - Brian M Schuster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Rachel A Donner
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Matthew Coyle
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Graduate Program in Microbiology, University of New Hampshire, Durham, United States
| | - Vaughn S Cooper
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Cheryl A Whistler
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
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216
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Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions. Sci Rep 2017; 7:46318. [PMID: 28393904 PMCID: PMC5385879 DOI: 10.1038/srep46318] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/14/2017] [Indexed: 12/16/2022] Open
Abstract
Spaceflight imposes numerous adaptive challenges for terrestrial life. The reduction in gravity, or microgravity, represents a novel environment that can disrupt homeostasis of many physiological processes. Additionally, it is becoming increasingly clear that an organism’s microbiome is critical for host health and examining its resiliency in microgravity represents a new frontier for space biology research. In this study, we examine the impact of microgravity on the interactions between the squid Euprymna scolopes and its beneficial symbiont Vibrio fischeri, which form a highly specific binary mutualism. First, animals inoculated with V. fischeri aboard the space shuttle showed effective colonization of the host light organ, the site of the symbiosis, during space flight. Second, RNA-Seq analysis of squid exposed to modeled microgravity conditions exhibited extensive differential gene expression in the presence and absence of the symbiotic partner. Transcriptomic analyses revealed in the absence of the symbiont during modeled microgravity there was an enrichment of genes and pathways associated with the innate immune and oxidative stress response. The results suggest that V. fischeri may help modulate the host stress responses under modeled microgravity. This study provides a window into the adaptive responses that the host animal and its symbiont use during modeled microgravity.
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217
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Riptortus pedestris and Burkholderia symbiont: an ideal model system for insect–microbe symbiotic associations. Res Microbiol 2017; 168:175-187. [DOI: 10.1016/j.resmic.2016.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 11/28/2016] [Indexed: 01/06/2023]
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218
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Kerwin AH, Nyholm SV. Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs. Environ Microbiol 2017; 19:1463-1475. [DOI: 10.1111/1462-2920.13665] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/07/2016] [Accepted: 01/02/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Allison H. Kerwin
- Department of Molecular and Cell Biology; University of Connecticut; CT 06269 USA
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology; University of Connecticut; CT 06269 USA
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219
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Thornhill DJ, Howells EJ, Wham DC, Steury TD, Santos SR. Population genetics of reef coral endosymbionts (Symbiodinium
, Dinophyceae). Mol Ecol 2017; 26:2640-2659. [DOI: 10.1111/mec.14055] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 01/02/2023]
Affiliation(s)
- D. J. Thornhill
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies; Auburn University; 101 Rouse Life Sciences Building Auburn AL 36849 USA
| | - E. J. Howells
- Center for Genomics and Systems Biology; New York University Abu Dhabi; PO Box 129188 Abu Dhabi United Arab Emirates
| | - D. C. Wham
- Department of Biology; Pennsylvania State University; 208 Mueller Laboratory University Park PA 16802 USA
| | - T. D. Steury
- School of Forestry and Wildlife Sciences; Auburn University; 3301 Forestry and Wildlife Building Auburn AL 36849 USA
| | - S. R. Santos
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies; Auburn University; 101 Rouse Life Sciences Building Auburn AL 36849 USA
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220
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Endosymbiotic calcifying bacteria across sponge species and oceans. Sci Rep 2017; 7:43674. [PMID: 28262822 PMCID: PMC5337934 DOI: 10.1038/srep43674] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/27/2017] [Indexed: 11/17/2022] Open
Abstract
From an evolutionary point of view, sponges are ideal targets to study marine symbioses as they are the most ancient living metazoans and harbour highly diverse microbial communities. A recently discovered association between the sponge Hemimycale columella and an intracellular bacterium that generates large amounts of calcite spherules has prompted speculation on the possible role of intracellular bacteria in the evolution of the skeleton in early animals. To gain insight into this purportedly ancestral symbiosis, we investigated the presence of symbiotic bacteria in Mediterranean and Caribbean sponges. We found four new calcibacteria OTUs belonging to the SAR116 in two orders (Poecilosclerida and Clionaida) and three families of Demospongiae, two additional OTUs in cnidarians and one more in seawater (at 98.5% similarity). Using a calcibacteria targeted probe and CARD-FISH, we also found calcibacteria in Spirophorida and Suberitida and proved that the calcifying bacteria accumulated at the sponge periphery, forming a skeletal cortex, analogous to that of siliceous microscleres in other demosponges. Bacteria-mediated skeletonization is spread in a range of phylogenetically distant species and thus the purported implication of bacteria in skeleton formation and evolution of early animals gains relevance.
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221
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Cleary JL, Condren AR, Zink KE, Sanchez LM. Calling all hosts: Bacterial communication in situ. Chem 2017; 2:334-358. [PMID: 28948238 DOI: 10.1016/j.chempr.2017.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteria are cosmopolitan organisms that in recent years have demonstrated many roles in maintaining host equilibrium. In this review, we discuss three roles bacteria can occupy in a host: pathogenic, symbiotic, and transient, with a specific focus on how bacterial small molecules contribute to homeostasis or dysbiosis. First, we will dissect how small molecules produced by pathogenic bacteria can be used as a source for communication during colonization and as protection against host immune responses. The ability to achieve a higher level of organization through small molecule communication gives pathogenic bacteria an opportunity for increased virulence and fitness. Conversely, in symbiotic relationships with hosts, small molecules are used in the initial acquisition, colonization, and maintenance of this beneficial population. Chemical signals can come from both the host and symbiont, and it is often observed that these interKingdom symbioses result in coevolution of both species involved. Furthermore, the transition from transient to commensal or opportunistic likely relies on molecular mechanisms. The small molecules utilized and produced by transient bacteria are desirable for both the immune and nutritional benefits they provide to the host. Finally, the advantages and disadvantages of modern analytical techniques that are available to researchers in order to study small molecules in situ is an important aspect of this review. It is our opinion that small molecules produced by bacteria are central to many biological processes and a larger focus on uncovering the function and identity of these small molecules is required to gain a deeper understanding of host-microbe associations.
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Affiliation(s)
- Jessica L Cleary
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Alanna R Condren
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Katherine E Zink
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Laura M Sanchez
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
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222
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Doolittle WF. Darwinizing Gaia. J Theor Biol 2017; 434:11-19. [PMID: 28237396 DOI: 10.1016/j.jtbi.2017.02.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/06/2017] [Accepted: 02/13/2017] [Indexed: 11/26/2022]
Abstract
The Gaia hypothesis of James Lovelock was co-developed with and vigorously promoted by Lynn Margulis, but most mainstream Darwinists scorned and still do not accept the notion. They cannot imagine selection for global stability being realized at the level of the individuals or species that make up the biosphere. Here I suggest that we look at the biogeochemical cycles and other homeostatic processes that might confer stability - rather than the taxa (mostly microbial) that implement them - as the relevant units of selection. By thus focusing our attentions on the "song", not the "singers", a Darwinized Gaia might be developed. Our understanding of evolution by natural selection would however need to be stretched to accommodate differential persistence as well as differential reproduction.
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Affiliation(s)
- W Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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223
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Astudillo‐García C, Bell JJ, Webster NS, Glasl B, Jompa J, Montoya JM, Taylor MW. Evaluating the core microbiota in complex communities: A systematic investigation. Environ Microbiol 2017; 19:1450-1462. [DOI: 10.1111/1462-2920.13647] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Carmen Astudillo‐García
- School of Biological SciencesUniversity of AucklandAuckland New Zealand
- Institute of Marine Science, University of AucklandAuckland New Zealand
| | - James J. Bell
- School of Biological SciencesVictoria University of WellingtonWellington New Zealand
| | | | - Bettina Glasl
- AIMS@JCU, Australian Institute of Marine Science, College of Science and EngineeringJames Cook UniversityTownsville Australia
| | - Jamaluddin Jompa
- Research and Development Centre on Marine, Coastal and Small IslandsHasanuddin UniversityMakassar Indonesia
| | - Jose M. Montoya
- Ecological Networks and Global Change Group, Experimental and Theoretical Ecology StationCNRS‐University Paul SabatierMoulis France
| | - Michael W. Taylor
- School of Biological SciencesUniversity of AucklandAuckland New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoveryUniversity of AucklandAuckland New Zealand
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224
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McAnulty SJ, Nyholm SV. The Role of Hemocytes in the Hawaiian Bobtail Squid, Euprymna scolopes: A Model Organism for Studying Beneficial Host-Microbe Interactions. Front Microbiol 2017; 7:2013. [PMID: 28111565 PMCID: PMC5216023 DOI: 10.3389/fmicb.2016.02013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Most, if not all, animals engage in associations with bacterial symbionts. Understanding the mechanisms by which host immune systems and beneficial bacteria communicate is a fundamental question in the fields of immunology and symbiosis. The Hawaiian bobtail squid (Euprymna scolopes) engages in two known symbioses; a binary relationship with the light organ symbiont Vibrio fischeri, and a bacterial consortium within a specialized organ of the female reproductive system, the accessory nidamental gland (ANG). E. scolopes has a well-developed circulatory system that allows immune cells (hemocytes) to migrate into tissues, including the light organ and ANG. In the association with V. fischeri, hemocytes are thought to have a number of roles in the management of symbiosis, including the recognition of non-symbiotic bacteria and the contribution of chitin as a nutrient source for V. fischeri. Hemocytes are hypothesized to recognize bacteria through interactions between pattern recognition receptors and microbe-associated molecular patterns. Colonization by V. fischeri has been shown to affect the bacteria-binding behavior, gene expression, and proteome of hemocytes, indicating that the symbiont can modulate host immune function. In the ANG, hemocytes have also been observed interacting with the residing bacterial community. As a model host, E. scolopes offers a unique opportunity to study how the innate immune system interacts with both a binary and consortial symbiosis. This mini review will recapitulate what is known about the role of hemocytes in the light organ association and offer future directions for understanding how these immune cells interact with multiple types of symbioses.
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Affiliation(s)
- Sarah J McAnulty
- Department of Molecular and Cell Biology, University of Connecticut, Storrs CT, USA
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs CT, USA
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225
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Rouzé H, Lecellier GJ, Saulnier D, Planes S, Gueguen Y, Wirshing HH, Berteaux-Lecellier V. An updated assessment of Symbiodinium spp. that associate with common scleractinian corals from Moorea (French Polynesia) reveals high diversity among background symbionts and a novel finding of clade B. PeerJ 2017; 5:e2856. [PMID: 28168100 PMCID: PMC5289445 DOI: 10.7717/peerj.2856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/02/2016] [Indexed: 12/27/2022] Open
Abstract
The adaptative bleaching hypothesis (ABH) states that, depending on the symbiotic flexibility of coral hosts (i.e., the ability of corals to “switch” or “shuffle” their algal symbionts), coral bleaching can lead to a change in the composition of their associated Symbiodinium community and, thus, contribute to the coral’s overall survival. In order to determine the flexibility of corals, molecular tools are required to provide accurate species delineations and to detect low levels of coral-associated Symbiodinium. Here, we used highly sensitive quantitative (real-time) PCR (qPCR) technology to analyse five common coral species from Moorea (French Polynesia), previously screened using only traditional molecular methods, to assess the presence of low-abundance (background) Symbiodinium spp. Similar to other studies, each coral species exhibited a strong specificity to a particular clade, irrespective of the environment. In addition, however, each of the five species harboured at least one additional Symbiodinium clade, among clades A–D, at background levels. Unexpectedly, and for the first time in French Polynesia, clade B was detected as a coral symbiont. These results increase the number of known coral-Symbiodinium associations from corals found in French Polynesia, and likely indicate an underestimation of the ability of the corals in this region to associate with and/or “shuffle” different Symbiodinium clades. Altogether our data suggest that corals from French Polynesia may favor a trade-off between optimizing symbioses with a specific Symbiodinium clade(s), maintaining associations with particular background clades that may play a role in the ability of corals to respond to environmental change.
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Affiliation(s)
- Héloïse Rouzé
- PSL CRIOBE USR3278 CNRS-EPHE-UPVD, Labex CORAIL , Papetoai , Moorea , French Polynesia
| | - Gaël J Lecellier
- PSL CRIOBE USR3278 CNRS-EPHE-UPVD, Labex CORAIL, Papetoai, Moorea, French Polynesia; Université de Paris Saclay, Departement de Biologie, Versailles-Saint Quentin, Paris, Versailles Cedex, France; Current affiliation: UMR250/9220 ENTROPIE IRD-CNRS-UR, Labex CORAIL, Promenade Roger-Laroque, Noumea cedex, New Caledonia, France
| | - Denis Saulnier
- UMR241 EIO Ifremer-ILM-IRD-UPF, Labex CORAIL , Taravao , French Polynesia
| | - Serge Planes
- PSL CRIOBE USR3278 CNRS-EPHE-UPVD, Labex CORAIL , Papetoai , Moorea , French Polynesia
| | - Yannick Gueguen
- UMR5244 IHPE, CNRS-Ifremer-UM-UPVD, Université de Montpellier , Montpellier , France
| | - Herman H Wirshing
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History , Washington, D.C. , USA
| | - Véronique Berteaux-Lecellier
- PSL CRIOBE USR3278 CNRS-EPHE-UPVD, Labex CORAIL, Papetoai, Moorea, French Polynesia; Current affiliation: UMR250/9220 ENTROPIE IRD-CNRS-UR, Labex CORAIL, Promenade Roger-Laroque, Noumea cedex, New Caledonia, France
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226
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Bongrand C, Koch EJ, Moriano-Gutierrez S, Cordero OX, McFall-Ngai M, Polz MF, Ruby EG. A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior. THE ISME JOURNAL 2016; 10:2907-2917. [PMID: 27128997 PMCID: PMC5148191 DOI: 10.1038/ismej.2016.69] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/14/2016] [Accepted: 03/22/2016] [Indexed: 11/09/2022]
Abstract
Newly hatched Euprymna scolopes squid obtain their specific light-organ symbionts from an array of Vibrio (Allivibrio) fischeri strains present in their environment. Two genetically distinct populations of this squid species have been identified, one in Kaneohe Bay (KB), and another in Maunaloa Bay (MB), Oahu. We asked whether symbionts isolated from squid in each of these populations outcompete isolates from the other population in mixed-infection experiments. No relationship was found between a strain's host source (KB or MB) and its ability to competitively colonize KB or MB juveniles in a mixed inoculum. Instead, two colonization behaviors were identified among the 11 KB and MB strains tested: a 'dominant' outcome, in which one strain outcompetes the other for colonization, and a 'sharing' outcome, in which two strains co-colonize the squid. A genome-level comparison of these and other V. fischeri strains suggested that the core genomic structure of this species is both syntenous and highly conserved over time and geographical distance. We also identified ~250 Kb of sequence, encoding 194 dispersed orfs, that was specific to those strains that expressed the dominant colonization behavior. Taken together, the results indicate a link between the genome content of V. fischeri strains and their colonization behavior when initiating a light-organ symbiosis.
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Affiliation(s)
- Clotilde Bongrand
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Eric J Koch
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Silvia Moriano-Gutierrez
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret McFall-Ngai
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Edward G Ruby
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
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227
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Vecchi M, Vicente F, Guidetti R, Bertolani R, Rebecchi L, Cesari M. Interspecific relationships of tardigrades with bacteria, fungi and protozoans, with a focus on the phylogenetic position ofPyxidium tardigradum(Ciliophora). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Matteo Vecchi
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
| | - Filipe Vicente
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
- Centre of Environmental Biology and Department of Animal Biology; University of Lisbon; Campo Grande C2 1749-016 Lisbon Portugal
| | - Roberto Guidetti
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
| | - Roberto Bertolani
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
| | - Lorena Rebecchi
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
| | - Michele Cesari
- Department of Life Sciences; University of Modena and Reggio Emilia; via Campi 213/d 41125 Modena Italy
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228
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Xu Y, Buss EA, Boucias DG. Impacts of Antibiotic and Bacteriophage Treatments on the Gut-Symbiont-Associated Blissus insularis (Hemiptera: Blissidae). INSECTS 2016; 7:insects7040061. [PMID: 27827869 PMCID: PMC5198209 DOI: 10.3390/insects7040061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/16/2016] [Accepted: 10/28/2016] [Indexed: 12/12/2022]
Abstract
The Southern chinch bug, Blissus insularis, possesses specialized midgut crypts that harbor dense populations of the exocellular symbiont Burkholderia. Oral administration of antibiotics suppressed the gut symbionts in B. insularis and negatively impacted insect host fitness, as reflected by retarded development, smaller body size, and higher susceptibility to an insecticide, bifenthrin. Considering that the antibiotics probably had non-lethal but toxic effects on host fitness, attempts were conducted to reduce gut symbionts using bacteriophage treatment. Soil-lytic phages active against the cultures of specific Burkholderia ribotypes were successfully isolated using a soil enrichment protocol. Characterization of the BiBurk16MC_R phage determined its specificity to the Bi16MC_R_vitro ribotype and placed it within the family Podoviridae. Oral administration of phages to fifth-instar B. insularis, inoculated with Bi16MC_R_vitro as neonates had no deleterious effects on host fitness. However, the ingested phages failed to impact the crypt-associated Burkholderia. The observed inactivity of the phage was likely due to the blockage of the connection between the anterior and posterior midgut regions. These findings suggest that the initial colonization by Burkholderia programs the ontogeny of the midgut, providing a sheltered residence protected from microbial antagonists.
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Affiliation(s)
- Yao Xu
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA.
| | - Eileen A Buss
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA.
| | - Drion G Boucias
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA.
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229
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Abstract
Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ. Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes. Decades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect in situ patterns of diversity with mechanistic in vitro studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative Staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the Staphylococcus species studied, S. saprophyticus, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally, Staphylococcus species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems.
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230
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Hoang KL, Morran LT, Gerardo NM. Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal-Microbe Interactions. Front Microbiol 2016; 7:1444. [PMID: 27679620 PMCID: PMC5020044 DOI: 10.3389/fmicb.2016.01444] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/30/2016] [Indexed: 11/29/2022] Open
Abstract
Microorganisms play a significant role in the evolution and functioning of the eukaryotes with which they interact. Much of our understanding of beneficial host–microbe interactions stems from studying already established associations; we often infer the genotypic and environmental conditions that led to the existing host–microbe relationships. However, several outstanding questions remain, including understanding how host and microbial (internal) traits, and ecological and evolutionary (external) processes, influence the origin of beneficial host–microbe associations. Experimental evolution has helped address a range of evolutionary and ecological questions across different model systems; however, it has been greatly underutilized as a tool to study beneficial host–microbe associations. In this review, we suggest ways in which experimental evolution can further our understanding of the proximate and ultimate mechanisms shaping mutualistic interactions between eukaryotic hosts and microbes. By tracking beneficial interactions under defined conditions or evolving novel associations among hosts and microbes with little prior evolutionary interaction, we can link specific genotypes to phenotypes that can be directly measured. Moreover, this approach will help address existing puzzles in beneficial symbiosis research: how symbioses evolve, how symbioses are maintained, and how both host and microbe influence their partner’s evolutionary trajectories. By bridging theoretical predictions and empirical tests, experimental evolution provides us with another approach to test hypotheses regarding the evolution of beneficial host–microbe associations.
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Affiliation(s)
- Kim L Hoang
- Department of Biology, O. Wayne Rollins Research Center, Emory University Atlanta, GA, USA
| | - Levi T Morran
- Department of Biology, O. Wayne Rollins Research Center, Emory University Atlanta, GA, USA
| | - Nicole M Gerardo
- Department of Biology, O. Wayne Rollins Research Center, Emory University Atlanta, GA, USA
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231
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Eisthen HL, Theis KR. Animal-microbe interactions and the evolution of nervous systems. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150052. [PMID: 26598731 DOI: 10.1098/rstb.2015.0052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Animals ubiquitously interact with environmental and symbiotic microbes, and the effects of these interactions on animal physiology are currently the subject of intense interest. Nevertheless, the influence of microbes on nervous system evolution has been largely ignored. We illustrate here how taking microbes into account might enrich our ideas about the evolution of nervous systems. For example, microbes are involved in animals' communicative, defensive, predatory and dispersal behaviours, and have likely influenced the evolution of chemo- and photosensory systems. In addition, we speculate that the need to regulate interactions with microbes at the epithelial surface may have contributed to the evolutionary internalization of the nervous system.
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Affiliation(s)
- Heather L Eisthen
- Department of Integrative Biology, Michigan State University, 288 Farm Lane Rm 203, East Lansing, MI 48824, USA BEACON Center for the Study of Evolution in Action, 567 Wilson Road Rm 1441, East Lansing, MI 48824, USA
| | - Kevin R Theis
- BEACON Center for the Study of Evolution in Action, 567 Wilson Road Rm 1441, East Lansing, MI 48824, USA Department of Internal Medicine, University of Michigan Medical School, 1150 West Medical Center Drive, MSRB I Rm 1510A, Ann Arbor, MI 48109, USA
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232
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The Histidine Kinase BinK Is a Negative Regulator of Biofilm Formation and Squid Colonization. J Bacteriol 2016; 198:2596-607. [PMID: 26977108 PMCID: PMC5019070 DOI: 10.1128/jb.00037-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/29/2016] [Indexed: 11/22/2022] Open
Abstract
Bacterial colonization of animal epithelial tissue is a dynamic process that relies on precise molecular communication. Colonization of Euprymna scolopes bobtail squid by Vibrio fischeri bacteria requires bacterial aggregation in host mucus as the symbiont transitions from a planktonic lifestyle in seawater to a biofilm-associated state in the host. We have identified a gene, binK (biofilm inhibitor kinase; VF_A0360), which encodes an orphan hybrid histidine kinase that negatively regulates the V. fischeri symbiotic biofilm (Syp) in vivo and in vitro. We identified binK mutants as exhibiting a colonization advantage in a global genetic screen, a phenotype that we confirmed in controlled competition experiments. Bacterial biofilm aggregates in the host are larger in strains lacking BinK, whereas overexpression of BinK suppresses biofilm formation and squid colonization. Signaling through BinK is required for temperature modulation of biofilm formation at 28°C. Furthermore, we present evidence that BinK acts upstream of SypG, the σ54-dependent transcriptional regulator of the syp biofilm locus. The BinK effects are dependent on intact signaling in the RscS-Syp biofilm pathway. Therefore, we propose that BinK antagonizes the signal from RscS and serves as an integral component in V. fischeri biofilm regulation. IMPORTANCE Bacterial lifestyle transitions underlie the colonization of animal hosts from environmental reservoirs. Formation of matrix-enclosed, surface-associated aggregates (biofilms) is common in beneficial and pathogenic associations, but investigating the genetic basis of biofilm development in live animal hosts remains a significant challenge. Using the bobtail squid light organ as a model, we analyzed putative colonization factors and identified a histidine kinase that negatively regulates biofilm formation at the host interface. This work reveals a novel in vivo biofilm regulator that influences the transition of bacteria from their planktonic state in seawater to tight aggregates of cells in the host. The study enriches our understanding of biofilm regulation and beneficial colonization by an animal's microbiome.
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233
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Wolfowicz I, Baumgarten S, Voss PA, Hambleton EA, Voolstra CR, Hatta M, Guse A. Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians. Sci Rep 2016; 6:32366. [PMID: 27582179 PMCID: PMC5007887 DOI: 10.1038/srep32366] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/08/2016] [Indexed: 12/20/2022] Open
Abstract
Symbiosis, defined as the persistent association between two distinct species, is an evolutionary and ecologically critical phenomenon facilitating survival of both partners in diverse habitats. The biodiversity of coral reef ecosystems depends on a functional symbiosis with photosynthetic dinoflagellates of the highly diverse genus Symbiodinium, which reside in coral host cells and continuously support their nutrition. The mechanisms underlying symbiont selection to establish a stable endosymbiosis in non-symbiotic juvenile corals are unclear. Here we show for the first time that symbiont selection patterns for larvae of two Acropora coral species and the model anemone Aiptasia are similar under controlled conditions. We find that Aiptasia larvae distinguish between compatible and incompatible symbionts during uptake into the gastric cavity and phagocytosis. Using RNA-Seq, we identify a set of candidate genes potentially involved in symbiosis establishment. Together, our data complement existing molecular resources to mechanistically dissect symbiont phagocytosis in cnidarians under controlled conditions, thereby strengthening the role of Aiptasia larvae as a powerful model for cnidarian endosymbiosis establishment.
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Affiliation(s)
- Iliona Wolfowicz
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg 69120, Germany
- Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto 4200-465, Portugal
| | - Sebastian Baumgarten
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Philipp A. Voss
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg 69120, Germany
| | | | - Christian R. Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Masayuki Hatta
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo 112-8610, Japan
| | - Annika Guse
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg 69120, Germany
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234
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Li H, Li T, Yao M, Li J, Zhang S, Wirth S, Cao W, Lin Q, Li X. Pika Gut May Select for Rare but Diverse Environmental Bacteria. Front Microbiol 2016; 7:1269. [PMID: 27582734 PMCID: PMC4987353 DOI: 10.3389/fmicb.2016.01269] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/02/2016] [Indexed: 02/01/2023] Open
Abstract
The composition of the mammalian gut bacterial communities can be influenced by the introduction of environmental bacteria in their respective habitats. However, there are no extensive studies examining the interactions between environmental bacteriome and gut bacteriome in wild mammals. Here, we explored the relationship between the gut bacterial communities of pika (Ochotona spp.) and the related environmental bacteria across host species and altitudinal sites using 16S rRNA gene sequencing. Plateau pikas (O. curzoniae) and Daurian pikas (O. daurica) were sampled at five different sites, and plant and soil samples were collected at each site as well. Our data indicated that Plateau pikas and Daurian pikas had distinct bacterial communities. The pika, plant and soil bacterial communities were also distinct. Very little overlap occurred in the pika core bacteria and the most abundant environmental bacteria. The shared OTUs between pikas and environments were present in the environment at relatively low abundance, whereas they were affiliated with diverse bacterial taxa. These results suggested that the pika gut may mainly select for low-abundance but diverse environmental bacteria in a host species-specific manner.
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Affiliation(s)
- Huan Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of SciencesSichuan, China; University of Chinese Academy of SciencesBeijing, China
| | - Tongtong Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Minjie Yao
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Shiheng Zhang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Stephan Wirth
- Leibniz-Center for Agricultural Landscape Research (ZALF), Institute of Landscape Biogeochemistry Müncheberg, Germany
| | - Weidong Cao
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural SciencesBeijing, China; Soil and Fertilizer Institute, Qinghai Academy of Agriculture and Forestry Sciences, Qinghai UniversityXining, China
| | - Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
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235
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The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats. mBio 2016; 7:mBio.00560-16. [PMID: 27460792 PMCID: PMC4981706 DOI: 10.1128/mbio.00560-16] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED For ecosystems vulnerable to environmental change, understanding the spatiotemporal stability of functionally crucial symbioses is fundamental to determining the mechanisms by which these ecosystems may persist. The coral Pachyseris speciosa is a successful environmental generalist that succeeds in diverse reef habitats. The generalist nature of this coral suggests it may have the capacity to form functionally significant microbial partnerships to facilitate access to a range of nutritional sources within different habitats. Here, we propose that coral is a metaorganism hosting three functionally distinct microbial interactions: a ubiquitous core microbiome of very few symbiotic host-selected bacteria, a microbiome of spatially and/or regionally explicit core microbes filling functional niches (<100 phylotypes), and a highly variable bacterial community that is responsive to biotic and abiotic processes across spatial and temporal scales (>100,000 phylotypes). We find that this coral hosts upwards of 170,000 distinct phylotypes and provide evidence for the persistence of a select group of bacteria in corals across environmental habitats of the Great Barrier Reef and Coral Sea. We further show that a higher number of bacteria are consistently associated with corals on mesophotic reefs than on shallow reefs. An increase in microbial diversity with depth suggests reliance by this coral on bacteria for nutrient acquisition on reefs exposed to nutrient upwelling. Understanding the complex microbial communities of host organisms across broad biotic and abiotic environments as functionally distinct microbiomes can provide insight into those interactions that are ubiquitous niche symbioses and those that provide competitive advantage within the hosts' environment. IMPORTANCE Corals have been proposed as the most diverse microbial biosphere. The high variability of microbial communities has hampered the identification of bacteria playing key functional roles that contribute to coral survival. Exploring the bacterial community in a coral with a broad environmental distribution, we found a group of bacteria present across all environments and a higher number of bacteria consistently associated with mesophotic corals (60 to 80 m). These results provide evidence of consistent and ubiquitous coral-bacterial partnerships and support the consideration of corals as metaorganisms hosting three functionally distinct microbiomes: a ubiquitous core microbiome, a microbiome filling functional niches, and a highly variable bacterial community.
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236
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Bourne DG, Morrow KM, Webster NS. Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems. Annu Rev Microbiol 2016; 70:317-40. [PMID: 27482741 DOI: 10.1146/annurev-micro-102215-095440] [Citation(s) in RCA: 346] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.
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Affiliation(s)
- David G Bourne
- Marine Biology and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia 4811; .,Australian Institute of Marine Science, Townsville, Queensland, Australia 4810
| | - Kathleen M Morrow
- Australian Institute of Marine Science, Townsville, Queensland, Australia 4810.,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia 4810
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237
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Martínez-García Á, Martín-Vivaldi M, Ruiz-Rodríguez M, Martínez-Bueno M, Arco L, Rodríguez-Ruano SM, Peralta-Sánchez JM, Soler JJ. The Microbiome of the Uropygial Secretion in Hoopoes Is Shaped Along the Nesting Phase. MICROBIAL ECOLOGY 2016; 72:252-261. [PMID: 27075655 DOI: 10.1007/s00248-016-0765-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/01/2016] [Indexed: 06/05/2023]
Abstract
Microbial symbiont acquisition by hosts may determine the effectiveness of the mutualistic relationships. A mix of vertical and horizontal transmission may be advantageous for hosts by allowing plastic changes of microbial communities depending on environmental conditions. Plasticity is well known for gut microbiota but is poorly understood for other symbionts of wild animals. We here explore the importance of environmental conditions experienced by nestling hoopoes (Upupa epops) during the late nesting phase determining microbiota in their uropygial gland. In cross-fostering experiments of 8 days old nestlings, "sibling-sibling" and "mother-offspring" comparisons were used to explore whether the bacterial community naturally established in the uropygial gland of nestlings could change depending on experimental environmental conditions (i.e., new nest environment). We found that the final microbiome of nestlings was mainly explained by nest of origin. Moreover, cross-fostered nestlings were more similar to their siblings and mothers than to their stepsiblings and stepmothers. We also detected a significant effect of nest of rearing, suggesting that nestling hoopoes acquire most bacterial symbionts during the first days of life but that the microbiome is dynamic and can be modified along the nestling period depending on environmental conditions. Estimated effects of nest of rearing, but also most of those of nest of origin are associated to environmental characteristics of nests, which are extended phenotypes of parents. Thus, natural selection may favor the acquisition of appropriated microbial symbionts for particular environmental conditions found in nests.
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Affiliation(s)
| | | | | | | | - Laura Arco
- Departamento de Zoología Universidad de Granada, E-18071, Granada, Spain
| | | | | | - Juan José Soler
- Estación Experimental de Zonas Áridas (CSIC), E-04120, Almería, Spain.
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238
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Fiorito G, Affuso A, Basil J, Cole A, de Girolamo P, D'Angelo L, Dickel L, Gestal C, Grasso F, Kuba M, Mark F, Melillo D, Osorio D, Perkins K, Ponte G, Shashar N, Smith D, Smith J, Andrews PLR. Guidelines for the Care and Welfare of Cephalopods in Research -A consensus based on an initiative by CephRes, FELASA and the Boyd Group. Lab Anim 2016; 49:1-90. [PMID: 26354955 DOI: 10.1177/0023677215580006] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This paper is the result of an international initiative and is a first attempt to develop guidelines for the care and welfare of cephalopods (i.e. nautilus, cuttlefish, squid and octopus) following the inclusion of this Class of ∼700 known living invertebrate species in Directive 2010/63/EU. It aims to provide information for investigators, animal care committees, facility managers and animal care staff which will assist in improving both the care given to cephalopods, and the manner in which experimental procedures are carried out. Topics covered include: implications of the Directive for cephalopod research; project application requirements and the authorisation process; the application of the 3Rs principles; the need for harm-benefit assessment and severity classification. Guidelines and species-specific requirements are provided on: i. supply, capture and transport; ii. environmental characteristics and design of facilities (e.g. water quality control, lighting requirements, vibration/noise sensitivity); iii. accommodation and care (including tank design), animal handling, feeding and environmental enrichment; iv. assessment of health and welfare (e.g. monitoring biomarkers, physical and behavioural signs); v. approaches to severity assessment; vi. disease (causes, prevention and treatment); vii. scientific procedures, general anaesthesia and analgesia, methods of humane killing and confirmation of death. Sections covering risk assessment for operators and education and training requirements for carers, researchers and veterinarians are also included. Detailed aspects of care and welfare requirements for the main laboratory species currently used are summarised in Appendices. Knowledge gaps are highlighted to prompt research to enhance the evidence base for future revision of these guidelines.
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Affiliation(s)
- Graziano Fiorito
- Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy Association for Cephalopod Research 'CephRes', Italy
| | - Andrea Affuso
- Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy Animal Model Facility - BIOGEM S.C.A.R.L., Ariano Irpino (AV), Italy
| | - Jennifer Basil
- Biology Department, Brooklyn College - CUNY Graduate Center, Brooklyn, NY, USA
| | - Alison Cole
- Association for Cephalopod Research 'CephRes', Italy
| | - Paolo de Girolamo
- Department of Veterinary Medicine and Animal Productions - University of Naples Federico II, Napoli, Italy AISAL - Associazione Italiana per le Scienze degli Animali da Laboratorio, Milano, Italy
| | - Livia D'Angelo
- Department of Veterinary Medicine and Animal Productions - University of Naples Federico II, Napoli, Italy AISAL - Associazione Italiana per le Scienze degli Animali da Laboratorio, Milano, Italy
| | - Ludovic Dickel
- Groupe mémoire et Plasticité comportementale, University of Caen Basse-Normandy, Caen, France
| | - Camino Gestal
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Spain
| | - Frank Grasso
- BioMimetic and Cognitive Robotics, Department of Psychology, Brooklyn College - CUNY, Brooklyn, NY, USA
| | - Michael Kuba
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Felix Mark
- Integrative Ecophysiology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Daniela Melillo
- Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Daniel Osorio
- School of Life Sciences, University of Sussex, Sussex, UK
| | - Kerry Perkins
- School of Life Sciences, University of Sussex, Sussex, UK
| | | | - Nadav Shashar
- Department of Life Sciences, Eilat Campus, Ben-Gurion University of the Negev, Beer, Sheva, Israel
| | - David Smith
- FELASA, Federation for Laboratory Animal Science Associations
| | | | - Paul L R Andrews
- Division of Biomedical Sciences, St George's University of London, London, UK Association for Cephalopod Research 'CephRes', Italy
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239
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Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Bourne DG, Willis BL, Ball EE, Satoh N, Miller DJ. The transcriptomic response of the coral
Acropora digitifera
to a competent
Symbiodinium
strain: the symbiosome as an arrested early phagosome. Mol Ecol 2016; 25:3127-41. [DOI: 10.1111/mec.13659] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/04/2016] [Accepted: 04/14/2016] [Indexed: 12/15/2022]
Affiliation(s)
- A. R. Mohamed
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Comparative Genomics Centre and Department of Molecular and Cell Biology James Cook University Townsville Qld 4811 Australia
- Zoology Department Faculty of Science Benha University Benha 13518 Egypt
- AIMS@JCU Department of Molecular and Cell Biology Australian Institute of Marine Science James Cook University Townsville Qld 4811 Australia
| | - V. Cumbo
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
| | - S. Harii
- Sesoko Station Tropical Biosphere Research Center University of the Ryukyus 3422 Sesoko Motobu Okinawa 905‐0227 Japan
| | - C. Shinzato
- Marine Genomics Unit Okinawa Institute of Science and Technology Promotion Corporation Onna Okinawa 904‐0412 Japan
| | - C. X. Chan
- ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australia
| | - M. A. Ragan
- ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australia
| | - D. G. Bourne
- Australian Institute for Marine Science PMB 3 Townsville Qld 4811 Australia
| | - B. L. Willis
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Department of Marine Ecosystems and Impacts James Cook University Townsville Qld 4811 Australia
| | - E. E. Ball
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Evolution, Ecology and Genetics Research School of Biology Australian National University Canberra ACT 0200 Australia
| | - N. Satoh
- Marine Genomics Unit Okinawa Institute of Science and Technology Promotion Corporation Onna Okinawa 904‐0412 Japan
| | - D. J. Miller
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Comparative Genomics Centre and Department of Molecular and Cell Biology James Cook University Townsville Qld 4811 Australia
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240
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English translation of Heinrich Anton de Bary’s 1878 speech, ‘Die Erscheinung der Symbiose’ (‘De la symbiose’). Symbiosis 2016. [DOI: 10.1007/s13199-016-0409-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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241
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Schwartzman JA, Ruby EG. Stress as a Normal Cue in the Symbiotic Environment. Trends Microbiol 2016; 24:414-424. [PMID: 27004825 DOI: 10.1016/j.tim.2016.02.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 02/06/2023]
Abstract
All multicellular hosts form associations with groups of microorganisms. These microbial communities can be taxonomically diverse and dynamic, and their persistence is due to robust, and sometimes coevolved, host-microbe and microbe-microbe interactions. Chemical and physical sources of stress are prominently situated in this molecular exchange, as cues for cellular responses in symbiotic microbes. Stress in the symbiotic environment may arise from three sources: host tissues, microbe-induced immune responses, or other microbes in the host environment. The responses of microbes to these stresses can be general or highly specialized, and collectively may contribute to the stability of the symbiotic system. In this review, we highlight recent work that emphasizes the role of stress as a cue in the symbiotic environment of plants and animals.
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Affiliation(s)
- Julia A Schwartzman
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Edward G Ruby
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, USA; Kewalo Marine Laboratory, University of Hawaii, Manoa, Honolulu, HI, USA
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242
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Bacterial Community Associated with Organs of Shallow Hydrothermal Vent Crab Xenograpsus testudinatus near Kuishan Island, Taiwan. PLoS One 2016; 11:e0150597. [PMID: 26934591 PMCID: PMC4774926 DOI: 10.1371/journal.pone.0150597] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/16/2016] [Indexed: 01/21/2023] Open
Abstract
Shallow-water hydrothermal vents off Kueishan Island (northeastern Taiwan) provide a unique, sulfur-rich, highly acidic (pH 1.75-4.6) and variable-temperature environment. In this species-poor habitat, the crab Xenograpsus testudinatus is dominant, as it mainly feeds on zooplankton killed by sulfurous plumes. In this study, 16S ribosomal RNA gene amplicon pyrosequencing was used to investigate diversity and composition of bacteria residing in digestive gland, gill, stomach, heart, and mid-gut of X. testudinatus, as well as in surrounding seawater. Dominant bacteria were Gamma- and Epsilonproteobacteria that might be capable of autotrophic growth by oxidizing reduced sulfur compounds and are usually resident in deep-sea hydrothermal systems. Dominant bacterial OTUs in X. testudinatus had both host and potential organ specificities, consistent with a potential trophic symbiotic relationship (nutrient transfer between host and bacteria). We inferred that versatile ways to obtain nutrients may provide an adaptive advantage for X. testudinatus in this demanding environment. To our knowledge, this is the first study of bacterial communities in various organs/tissues of a crustacean in a shallow-water hydrothermal system, and as such, may be a convenient animal model for studying these systems.
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243
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Parkinson JF, Gobin B, Hughes WOH. Heritability of symbiont density reveals distinct regulatory mechanisms in a tripartite symbiosis. Ecol Evol 2016; 6:2053-60. [PMID: 27099709 PMCID: PMC4831439 DOI: 10.1002/ece3.2005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/10/2016] [Accepted: 01/18/2016] [Indexed: 01/08/2023] Open
Abstract
Beneficial eukaryotic–bacterial partnerships are integral to animal and plant evolution. Understanding the density regulation mechanisms behind bacterial symbiosis is essential to elucidating the functional balance between hosts and symbionts. Citrus mealybugs, Planococcus citri (Risso), present an excellent model system for investigating the mechanisms of symbiont density regulation. They contain two obligate nutritional symbionts, Moranella endobia, which resides inside Tremblaya princeps, which has been maternally transmitted for 100–200 million years. We investigate whether host genotype may influence symbiont density by crossing mealybugs from two inbred laboratory‐reared populations that differ substantially in their symbiont density to create hybrids. The density of the M. endobia symbiont in the hybrid hosts matched that of the maternal parent population, in keeping with density being determined either by the symbiont or the maternal genotype. However, the density of the T. princeps symbiont was influenced by the paternal host genotype. The greater dependency of T. princeps on its host may be due to its highly reduced genome. The decoupling of T. princeps and M. endobia densities, in spite of their intimate association, suggests that distinct regulatory mechanisms can be at work in symbiotic partnerships, even when they are obligate and mutualistic.
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Affiliation(s)
| | - Bruno Gobin
- PCS-Ornamental Plant Research Schaessestraat 18 Destelbergen 9070 Belgium
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Lanan MC, Rodrigues PAP, Agellon A, Jansma P, Wheeler DE. A bacterial filter protects and structures the gut microbiome of an insect. ISME JOURNAL 2016; 10:1866-76. [PMID: 26872040 PMCID: PMC5029173 DOI: 10.1038/ismej.2015.264] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 12/02/2015] [Accepted: 12/14/2015] [Indexed: 01/04/2023]
Abstract
Associations with symbionts within the gut lumen of hosts are particularly prone to disruption due to the constant influx of ingested food and non-symbiotic microbes, yet we know little about how partner fidelity is maintained. Here we describe for the first time the existence of a gut morphological filter capable of protecting an animal gut microbiome from disruption. The proventriculus, a valve located between the crop and midgut of insects, functions as a micro-pore filter in the Sonoran Desert turtle ant (Cephalotes rohweri), blocking the entry of bacteria and particles ⩾0.2 μm into the midgut and hindgut while allowing passage of dissolved nutrients. Initial establishment of symbiotic gut bacteria occurs within the first few hours after pupation via oral–rectal trophallaxis, before the proventricular filter develops. Cephalotes ants are remarkable for having maintained a consistent core gut microbiome over evolutionary time and this partner fidelity is likely enabled by the proventricular filtering mechanism. In addition, the structure and function of the cephalotine proventriculus offers a new perspective on organismal resistance to pathogenic microbes, structuring of gut microbial communities, and development and maintenance of host–microbe fidelity both during the animal life cycle and over evolutionary time.
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Affiliation(s)
| | | | - Al Agellon
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Patricia Jansma
- Department of Neuroscience, University of Arizona, Tucson, AZ, USA
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245
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Abstract
Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other 'commodities'. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten 'terms of contract' that 'self-stabilize' trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models-often called 'Walrasian' markets-are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying 'principal-agent' problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists studying cooperation but need to be taken with caution.
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Affiliation(s)
- Peter Hammerstein
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Ronald Noë
- Faculté Psychologie, Université de Strasbourg, Strasbourg 67000, France
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246
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Rebollar EA, Hughey MC, Medina D, Harris RN, Ibáñez R, Belden LK. Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis. ISME JOURNAL 2016; 10:1682-95. [PMID: 26744810 DOI: 10.1038/ismej.2015.234] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/29/2015] [Accepted: 11/06/2015] [Indexed: 01/06/2023]
Abstract
Symbiotic bacteria on amphibian skin can inhibit growth of the fungus Batrachochytrium dendrobatidis (Bd) that has caused dramatic population declines and extinctions of amphibians in the Neotropics. It remains unclear how the amphibians' skin microbiota is influenced by environmental bacterial reservoirs, host-associated factors such as susceptibility to pathogens, and pathogen presence in tropical amphibians. We sampled skin bacteria from five co-occurring frog species that differ in Bd susceptibility at one Bd-naive site, and sampled one of the non-susceptible species from Bd-endemic and Bd-naive sites in Panama. We hypothesized that skin bacterial communities (1) would be distinct from the surrounding environment regardless of the host habitat, (2) would differ between Bd susceptible and non-susceptible species and (3) would differ on hosts in Bd-naive and Bd-endemic sites. We found that skin bacterial communities were enriched in bacterial taxa that had low relative abundances in the environment. Non-susceptible species had very similar skin bacterial communities that were enriched in particular taxa such as the genera Pseudomonas and Acinetobacter. Bacterial communities of Craugastor fitzingeri in Bd-endemic sites were less diverse than in the naive site, and differences in community structure across sites were explained by changes in relative abundance of specific bacterial taxa. Our results indicate that skin microbial structure was associated with host susceptibility to Bd and might be associated to the history of Bd presence at different sites.
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Affiliation(s)
- Eria A Rebollar
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
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247
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Animal–Symbiodinium Symbioses: Foundations of Coral Reef Ecosystems. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2016. [DOI: 10.1007/978-3-319-28068-4_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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248
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Schwartzman JA, Ruby EG. A conserved chemical dialog of mutualism: lessons from squid and vibrio. Microbes Infect 2016; 18:1-10. [PMID: 26384815 PMCID: PMC4715918 DOI: 10.1016/j.micinf.2015.08.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 12/18/2022]
Abstract
Microorganisms shape, and are shaped by, their environment. In host-microbe associations, this environment is defined by tissue chemistry, which reflects local and organism-wide physiology, as well as inflammatory status. We review how, in the squid-vibrio mutualism, both partners shape tissue chemistry, revealing common themes governing tissue homeostasis in animal-microbe associations.
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Affiliation(s)
- Julia A Schwartzman
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Madison, WI 53706, USA
| | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii, Manoa, Honolulu, HI 96813, USA.
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249
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Abstract
With the increasing appreciation for the crucial roles that microbial symbionts play in the development and fitness of plant and animal hosts, there has been a recent push to interpret evolution through the lens of the "hologenome"--the collective genomic content of a host and its microbiome. But how symbionts evolve and, particularly, whether they undergo natural selection to benefit hosts are complex issues that are associated with several misconceptions about evolutionary processes in host-associated microbial communities. Microorganisms can have intimate, ancient, and/or mutualistic associations with hosts without having undergone natural selection to benefit hosts. Likewise, observing host-specific microbial community composition or greater community similarity among more closely related hosts does not imply that symbionts have coevolved with hosts, let alone that they have evolved for the benefit of the host. Although selection at the level of the symbiotic community, or hologenome, occurs in some cases, it should not be accepted as the null hypothesis for explaining features of host-symbiont associations.
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250
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Pontarotti G. Extended inheritance from an organizational point of view. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2015; 37:430-448. [PMID: 26452777 DOI: 10.1007/s40656-015-0088-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 09/14/2015] [Indexed: 06/05/2023]
Abstract
In this paper, I argue that the increasing data about non-genetic inheritance requires the construction of a new conceptual framework that should complement the inclusive approaches already discussed in the literature. More precisely, I hold that this framework should be epistemologically relevant for evolutionary biologists in capturing the limits of extended inheritance and in reassessing the boundaries of biological systems that transmit traits to their offspring. I outline the first elements of an organizational account of extended inheritance. In this account, the category of inherited factors is neither restricted to genes nor extended to stable resources related to trans-generational similarities. Instead, it includes persisting constitutive elements appearing as difference makers for heterogeneous organizational constraints, namely for heterogeneous constitutive parts whose specific role is to harness flows of matter and energy across generations of clearly delimited extended organized systems. This both inclusive and restrictive framework opens an additional way to apprehend how extended inheritance may affect evolutionary trajectories.
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