1
|
Septer AN, Visick KL. Lighting the way: how the Vibrio fischeri model microbe reveals the complexity of Earth's "simplest" life forms. J Bacteriol 2024; 206:e0003524. [PMID: 38695522 PMCID: PMC11112999 DOI: 10.1128/jb.00035-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024] Open
Abstract
Vibrio (Aliivibrio) fischeri's initial rise to fame derived from its alluring production of blue-green light. Subsequent studies to probe the mechanisms underlying this bioluminescence helped the field discover the phenomenon now known as quorum sensing. Orthologs of quorum-sensing regulators (i.e., LuxR and LuxI) originally identified in V. fischeri were subsequently uncovered in a plethora of bacterial species, and analogous pathways were found in yet others. Over the past three decades, the study of this microbe has greatly expanded to probe the unique role of V. fischeri as the exclusive symbiont of the light organ of the Hawaiian bobtail squid, Euprymna scolopes. Buoyed by this optically amenable host and by persistent and insightful researchers who have applied novel and cross-disciplinary approaches, V. fischeri has developed into a robust model for microbe-host associations. It has contributed to our understanding of how bacteria experience and respond to specific, often fluxing environmental conditions and the mechanisms by which bacteria impact the development of their host. It has also deepened our understanding of numerous microbial processes such as motility and chemotaxis, biofilm formation and dispersal, and bacterial competition, and of the relevance of specific bacterial genes in the context of colonizing an animal host. Parallels in these processes between this symbiont and bacteria studied as pathogens are readily apparent, demonstrating functional conservation across diverse associations and permitting a reinterpretation of "pathogenesis." Collectively, these advances built a foundation for microbiome studies and have positioned V. fischeri to continue to expand the frontiers of our understanding of the microbial world inside animals.
Collapse
Affiliation(s)
- Alecia N. Septer
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Karen L. Visick
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| |
Collapse
|
2
|
Bosch TCG, Blaser MJ, Ruby E, McFall-Ngai M. A new lexicon in the age of microbiome research. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230060. [PMID: 38497258 PMCID: PMC10945402 DOI: 10.1098/rstb.2023.0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/04/2023] [Indexed: 03/19/2024] Open
Abstract
At a rapid pace, biologists are learning the many ways in which resident microbes influence, and sometimes even control, their hosts to shape both health and disease. Understanding the biochemistry behind these interactions promises to reveal completely novel and targeted ways of counteracting disease processes. However, in our protocols and publications, we continue to describe these new results using a language that originated in a completely different context. This language developed when microbial interactions with hosts were perceived to be primarily pathogenic, as threats that had to be vanquished. Biomedicine had one dominating thought: winning this war against microorganisms. Today, we know that beyond their defensive roles, host tissues, especially epithelia, are vital to ensuring association with the normal microbiota, the communities of microbes that persistently live with the host. Thus, we need to adopt a language that better encompasses the newly appreciated importance of host-microbiota associations. We also need a language that frames the onset and progression of pathogenic conditions within the context of the normal microbiota. Such a reimagined lexicon should make it clear, from the very nature of its words, that microorganisms are primarily vital to our health, and only more rarely the cause of disease. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
Collapse
Affiliation(s)
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Edward Ruby
- California Institute of Technology, Pasadena, CA 91125, USA
| | | |
Collapse
|
3
|
Martignoni MM, Tyson RC, Kolodny O, Garnier J. Mutualism at the leading edge: insights into the eco-evolutionary dynamics of host-symbiont communities during range expansion. J Math Biol 2024; 88:24. [PMID: 38308102 DOI: 10.1007/s00285-023-02037-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 09/04/2023] [Accepted: 12/14/2023] [Indexed: 02/04/2024]
Abstract
The evolution of mutualism between host and symbiont communities plays an essential role in maintaining ecosystem function and should therefore have a profound effect on their range expansion dynamics. In particular, the presence of mutualistic symbionts at the leading edge of a host-symbiont community should enhance its propagation in space. We develop a theoretical framework that captures the eco-evolutionary dynamics of host-symbiont communities, to investigate how the evolution of resource exchange may shape community structure during range expansion. We consider a community with symbionts that are mutualistic or parasitic to various degrees, where parasitic symbionts receive the same amount of resource from the host as mutualistic symbionts, but at a lower cost. The selective advantage of parasitic symbionts over mutualistic ones is increased with resource availability (i.e. with host density), promoting mutualism at the range edges, where host density is low, and parasitism at the population core, where host density is higher. This spatial selection also influences the speed of spread. We find that the host growth rate (which depends on the average benefit provided by the symbionts) is maximal at the range edges, where symbionts are more mutualistic, and that host-symbiont communities with high symbiont density at their core (e.g. resulting from more mutualistic hosts) spread faster into new territories. These results indicate that the expansion of host-symbiont communities is pulled by the hosts but pushed by the symbionts, in a unique push-pull dynamic where both the host and symbionts are active and tightly-linked players.
Collapse
Affiliation(s)
- Maria M Martignoni
- Department of Ecology, Evolution and Behavior, A. Silberman Institute of Life Sciences, Faculty of Sciences, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Rebecca C Tyson
- CMPS Department (Mathematics), University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, A. Silberman Institute of Life Sciences, Faculty of Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jimmy Garnier
- Laboratory of Mathematics, CNRS, Université Savoie-Mont Blanc, Université Grenoble Alpes, Chambery, France
| |
Collapse
|
4
|
Quinn A, El Chazli Y, Escrig S, Daraspe J, Neuschwander N, McNally A, Genoud C, Meibom A, Engel P. Host-derived organic acids enable gut colonization of the honey bee symbiont Snodgrassella alvi. Nat Microbiol 2024; 9:477-489. [PMID: 38225461 PMCID: PMC11343714 DOI: 10.1038/s41564-023-01572-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/30/2023] [Indexed: 01/17/2024]
Abstract
Diverse bacteria can colonize the animal gut using dietary nutrients or by engaging in microbial crossfeeding interactions. Less is known about the role of host-derived nutrients in enabling gut bacterial colonization. Here we examined metabolic interactions within the evolutionary ancient symbiosis between the honey bee (Apis mellifera) and the core gut microbiota member Snodgrassella alvi. This betaproteobacterium is incapable of metabolizing saccharides, yet colonizes the honey bee gut in the presence of a sugar-only diet. Using comparative metabolomics, 13C-tracers and nanoscale secondary ion mass spectrometry (NanoSIMS), we show in vivo that S. alvi grows on host-derived organic acids, including citrate, glycerate and 3-hydroxy-3-methylglutarate, which are actively secreted by the host into the gut lumen. S. alvi also modulates tryptophan metabolism in the gut by converting kynurenine to anthranilate. These results suggest that S. alvi is adapted to a specific metabolic niche in the honey bee gut that depends on host-derived nutritional resources.
Collapse
Affiliation(s)
- Andrew Quinn
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yassine El Chazli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Stéphane Escrig
- Laboratory for Biological Geochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Neuschwander
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aoife McNally
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Christel Genoud
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
5
|
Mondal S, Somani J, Roy S, Babu A, Pandey AK. Insect Microbial Symbionts: Ecology, Interactions, and Biological Significance. Microorganisms 2023; 11:2665. [PMID: 38004678 PMCID: PMC10672782 DOI: 10.3390/microorganisms11112665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 11/26/2023] Open
Abstract
The guts of insect pests are typical habitats for microbial colonization and the presence of bacterial species inside the gut confers several potential advantages to the insects. These gut bacteria are located symbiotically inside the digestive tracts of insects and help in food digestion, phytotoxin breakdown, and pesticide detoxification. Different shapes and chemical assets of insect gastrointestinal tracts have a significant impact on the structure and makeup of the microbial population. The number of microbial communities inside the gastrointestinal system differs owing to the varying shape and chemical composition of digestive tracts. Due to their short generation times and rapid evolutionary rates, insect gut bacteria can develop numerous metabolic pathways and can adapt to diverse ecological niches. In addition, despite hindering insecticide management programs, they still have several biotechnological uses, including industrial, clinical, and environmental uses. This review discusses the prevalent bacterial species associated with insect guts, their mode of symbiotic interaction, their role in insecticide resistance, and various other biological significance, along with knowledge gaps and future perspectives. The practical consequences of the gut microbiome and its interaction with the insect host may lead to encountering the mechanisms behind the evolution of pesticide resistance in insects.
Collapse
Affiliation(s)
- Sankhadeep Mondal
- Deparment of Entomology, Tea Research Association, Tocklai Tea Research Institute, Jorhat 785008, Assam, India; (S.M.)
| | - Jigyasa Somani
- Deparment of Entomology, Tea Research Association, Tocklai Tea Research Institute, Jorhat 785008, Assam, India; (S.M.)
| | - Somnath Roy
- Deparment of Entomology, Tea Research Association, Tocklai Tea Research Institute, Jorhat 785008, Assam, India; (S.M.)
| | - Azariah Babu
- Deparment of Entomology, Tea Research Association, Tocklai Tea Research Institute, Jorhat 785008, Assam, India; (S.M.)
| | - Abhay K. Pandey
- Deparment of Mycology & Microbiology, Tea Research Association, North Bengal Regional R & D Centre, Nagrakata, Jalpaiguri 735225, West Bengal, India
| |
Collapse
|
6
|
Wollmuth EM, Angert ER. Microbial circadian clocks: host-microbe interplay in diel cycles. BMC Microbiol 2023; 23:124. [PMID: 37161348 PMCID: PMC10173096 DOI: 10.1186/s12866-023-02839-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Circadian rhythms, observed across all domains of life, enable organisms to anticipate and prepare for diel changes in environmental conditions. In bacteria, a circadian clock mechanism has only been characterized in cyanobacteria to date. These clocks regulate cyclical patterns of gene expression and metabolism which contribute to the success of cyanobacteria in their natural environments. The potential impact of self-generated circadian rhythms in other bacterial and microbial populations has motivated extensive research to identify novel circadian clocks. MAIN TEXT Daily oscillations in microbial community composition and function have been observed in ocean ecosystems and in symbioses. These oscillations are influenced by abiotic factors such as light and the availability of nutrients. In the ocean ecosystems and in some marine symbioses, oscillations are largely controlled by light-dark cycles. In gut systems, the influx of nutrients after host feeding drastically alters the composition and function of the gut microbiota. Conversely, the gut microbiota can influence the host circadian rhythm by a variety of mechanisms including through interacting with the host immune system. The intricate and complex relationship between the microbiota and their host makes it challenging to disentangle host behaviors from bacterial circadian rhythms and clock mechanisms that might govern the daily oscillations observed in these microbial populations. CONCLUSIONS While the ability to anticipate the cyclical behaviors of their host would likely be enhanced by a self-sustained circadian rhythm, more evidence and further studies are needed to confirm whether host-associated heterotrophic bacteria possess such systems. In addition, the mechanisms by which heterotrophic bacteria might respond to diel cycles in environmental conditions has yet to be uncovered.
Collapse
Affiliation(s)
- Emily M Wollmuth
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA
| | - Esther R Angert
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA.
| |
Collapse
|
7
|
Abstract
Developmental processes in animals are influenced by colonization and/or signaling from microbial symbionts. Here, we show that bacteria from the environment are linked to development of a symbiotic organ that houses a bacterial consortium in female Hawaiian bobtail squid, Euprymna scolopes. In addition to the well-characterized light organ association with the bioluminescent bacterium Vibrio fischeri, female E. scolopes house a simple bacterial community in a reproductive organ, the accessory nidamental gland (ANG). In order to understand the influences of bacteria on ANG development, squid were raised in the laboratory under conditions where exposure to environmental microorganisms was experimentally manipulated. Under conditions where hosts were exposed to depleted environmental bacteria, ANGs were completely absent or stunted, a result independent of the presence of the light organ symbiont V. fischeri. When squid were raised in the laboratory with substrate from the host's natural environment containing the native microbiota, normal ANG development was observed, and the bacterial communities were similar to wild-caught animals. Analysis of the bacterial communities from ANGs and substrates of wild-caught and laboratory-raised animals suggests that certain bacterial groups, namely, the Verrucomicrobia, are linked to ANG development. The ANG community composition was also experimentally manipulated. Squid raised with natural substrate supplemented with a specific ANG bacterial strain, Leisingera sp. JC1, had high proportions of this strain in the ANG, suggesting that once ANG development is initiated, specific strains can be introduced and subsequently colonize the organ. Overall, these data suggest that environmental bacteria are required for development of the ANG in E. scolopes. IMPORTANCE Microbiota have profound effects on animal and plant development. Hosts raised axenically or without symbionts often suffer negative outcomes resulting in developmental defects or reduced organ function. Using defined experimental conditions, we demonstrate that environmental bacteria are required for the formation of a female-specific symbiotic organ in the Hawaiian bobtail squid, Euprymna scolopes. Although nascent tissues from this organ that are involved with bacterial recruitment formed initially, the mature organ failed to develop and was absent or severely reduced in sexually mature animals that were not exposed to microbiota from the host's natural environment. This is the first example of complete organ development relying on exposure to symbiotic bacteria in an animal host. This study broadens the use of E. scolopes as a model organism for studying the influence of beneficial bacteria on animal development.
Collapse
|
8
|
Rinsky M, Weizman E, Ben-Asher HW, Eyal G, Zhu B, Levy O. Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis. SCIENCE ADVANCES 2022; 8:eabo6467. [PMID: 36112690 PMCID: PMC9481131 DOI: 10.1126/sciadv.abo6467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/02/2022] [Indexed: 05/25/2023]
Abstract
Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.
Collapse
Affiliation(s)
- Mieka Rinsky
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eviatar Weizman
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hiba Waldman Ben-Asher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gal Eyal
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland St. Lucia, Queensland 4072, Australia
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| |
Collapse
|
9
|
Beneficial commensal bacteria promote Drosophila growth by down-regulating the expression of peptidoglycan recognition proteins. iScience 2022; 25:104357. [PMID: 35601912 PMCID: PMC9121327 DOI: 10.1016/j.isci.2022.104357] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/24/2021] [Accepted: 04/29/2022] [Indexed: 11/22/2022] Open
|
10
|
Nocturnal Acidification: A Coordinating Cue in the Euprymna scolopes- Vibrio fischeri Symbiosis. Int J Mol Sci 2022; 23:ijms23073743. [PMID: 35409100 PMCID: PMC8999011 DOI: 10.3390/ijms23073743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
The Vibrio fischeri–Euprymna scolopes symbiosis has become a powerful model for the study of specificity, initiation, and maintenance between beneficial bacteria and their eukaryotic partner. In this invertebrate model system, the bacterial symbionts are acquired every generation from the surrounding seawater by newly hatched squid. These symbionts colonize a specialized internal structure called the light organ, which they inhabit for the remainder of the host’s lifetime. The V. fischeri population grows and ebbs following a diel cycle, with high cell densities at night producing bioluminescence that helps the host avoid predation during its nocturnal activities. Rhythmic timing of the growth of the symbionts and their production of bioluminescence only at night is critical for maintaining the symbiosis. V. fischeri symbionts detect their population densities through a behavior termed quorum-sensing, where they secrete and detect concentrations of autoinducer molecules at high cell density when nocturnal production of bioluminescence begins. In this review, we discuss events that lead up to the nocturnal acidification of the light organ and the cues used for pre-adaptive behaviors that both host and symbiont have evolved. This host–bacterium cross talk is used to coordinate networks of regulatory signals (such as quorum-sensing and bioluminescence) that eventually provide a unique yet stable environment for V. fischeri to thrive and be maintained throughout its life history as a successful partner in this dynamic symbiosis.
Collapse
|
11
|
Vibrio spp.: Life Strategies, Ecology, and Risks in a Changing Environment. DIVERSITY 2022. [DOI: 10.3390/d14020097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vibrios are ubiquitous bacteria in aquatic systems, especially marine ones, and belong to the Gammaproteobacteria class, the most diverse class of Gram-negative bacteria. The main objective of this review is to update the information regarding the ecology of Vibrio species, and contribute to the discussion of their potential risk in a changing environment. As heterotrophic organisms, Vibrio spp. live freely in aquatic environments, from marine depths to the surface of the water column, and frequently may be associated with micro- and macroalgae, invertebrates, and vertebrates such as fish, or live in symbiosis. Some Vibrio spp. are pathogenic to humans and animals, and there is evidence that infections caused by vibrios are increasing in the world. This rise may be related to global changes in human behavior (increases in tourism, maritime traffic, consumption of seafood, aquaculture production, water demand, pollution), and temperature. Most likely in the future, Vibrio spp. in water and in seafood will be monitored in order to safeguard human and animal health. Regulators of the microbiological quality of water (marine and freshwater) and food for human and animal consumption, professionals involved in marine and freshwater production chains, consumers and users of aquatic resources, and health professionals will be challenged to anticipate and mitigate new risks.
Collapse
|
12
|
Smith DS, Houck C, Lee A, Simmons TB, Chester ON, Esdaile A, Symes SJK, Giles DK. Polyunsaturated fatty acids cause physiological and behavioral changes in Vibrio alginolyticus and Vibrio fischeri. Microbiologyopen 2021; 10:e1237. [PMID: 34713610 PMCID: PMC8494716 DOI: 10.1002/mbo3.1237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/08/2021] [Indexed: 11/06/2022] Open
Abstract
Vibrio alginolyticus and Vibrio (Aliivibrio) fischeri are Gram-negative bacteria found globally in marine environments. During the past decade, studies have shown that certain Gram-negative bacteria, including Vibrio species (cholerae, parahaemolyticus, and vulnificus) are capable of using exogenous polyunsaturated fatty acids (PUFAs) to modify the phospholipids of their membrane. Moreover, exposure to exogenous PUFAs has been shown to affect certain phenotypes that are important factors of virulence. The purpose of this study was to investigate whether V. alginolyticus and V. fischeri are capable of responding to exogenous PUFAs by remodeling their membrane phospholipids and/or altering behaviors associated with virulence. Thin-layer chromatography (TLC) analyses and ultra-performance liquid chromatography-electrospray ionization mass spectrometry (UPLC/ESI-MS) confirmed incorporation of all PUFAs into membrane phosphatidylglycerol and phosphatidylethanolamine. Several growth phenotypes were identified when individual fatty acids were supplied in minimal media and as sole carbon sources. Interestingly, several PUFAs acids inhibited growth of V. fischeri. Significant alterations to membrane permeability were observed depending on fatty acid supplemented. Strikingly, arachidonic acid (20:4) reduced membrane permeability by approximately 35% in both V. alginolyticus and V. fischeri. Biofilm assays indicated that fatty acid influence was dependent on media composition and temperature. All fatty acids caused decreased swimming motility in V. alginolyticus, while only linoleic acid (18:2) significantly increased swimming motility in V. fischeri. In summary, exogenous fatty acids cause a variety of changes in V. alginolyticus and V. fischeri, thus adding these bacteria to a growing list of Gram-negatives that exhibit versatility in fatty acid utilization and highlighting the potential for environmental PUFAs to influence phenotypes associated with planktonic, beneficial, and pathogenic associations.
Collapse
Affiliation(s)
- David S. Smith
- Department of Biology, Geology, and Environmental ScienceChattanoogaTennesseeUSA
| | - Carina Houck
- Department of Biology, Geology, and Environmental ScienceChattanoogaTennesseeUSA
| | - Allycia Lee
- Department of Chemistry and PhysicsThe University of Tennessee at ChattanoogaChattanoogaTennesseeUSA
| | - Timothy B. Simmons
- Department of Biology, Geology, and Environmental ScienceChattanoogaTennesseeUSA
| | - Olivia N. Chester
- Department of Biology, Geology, and Environmental ScienceChattanoogaTennesseeUSA
| | - Ayanna Esdaile
- Department of Biology, Geology, and Environmental ScienceChattanoogaTennesseeUSA
| | - Steven J. K. Symes
- Department of Chemistry and PhysicsThe University of Tennessee at ChattanoogaChattanoogaTennesseeUSA
| | - David K. Giles
- Department of Biology, Geology, and Environmental ScienceChattanoogaTennesseeUSA
| |
Collapse
|
13
|
Nyholm SV, McFall-Ngai MJ. A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner. Nat Rev Microbiol 2021; 19:666-679. [PMID: 34089010 PMCID: PMC8440403 DOI: 10.1038/s41579-021-00567-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 01/08/2023]
Abstract
For more than 30 years, the association between the Hawaiian bobtail squid, Euprymna scolopes, and the bioluminescent bacterium Vibrio fischeri has been studied as a model system for understanding the colonization of animal epithelia by symbiotic bacteria. The squid-vibrio light-organ system provides the exquisite resolution only possible with the study of a binary partnership. The impact of this relationship on the partners' biology has been broadly characterized, including their ecology and evolutionary biology as well as the underlying molecular mechanisms of symbiotic dynamics. Much has been learned about the factors that foster initial light-organ colonization, and more recently about the maturation and long-term maintenance of the association. This Review synthesizes the results of recent research on the light-organ association and also describes the development of new horizons for E. scolopes as a model organism that promises to inform biology and biomedicine about the basic nature of host-microorganism interactions.
Collapse
Affiliation(s)
- Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
| | - Margaret J McFall-Ngai
- Pacific Biosciences Research Center, Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, HI, USA.
| |
Collapse
|
14
|
Brooks JF, Behrendt CL, Ruhn KA, Lee S, Raj P, Takahashi JS, Hooper LV. The microbiota coordinates diurnal rhythms in innate immunity with the circadian clock. Cell 2021; 184:4154-4167.e12. [PMID: 34324837 PMCID: PMC8967342 DOI: 10.1016/j.cell.2021.07.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 04/23/2021] [Accepted: 06/28/2021] [Indexed: 02/08/2023]
Abstract
Environmental light cycles entrain circadian feeding behaviors in animals that produce rhythms in exposure to foodborne bacteria. Here, we show that the intestinal microbiota generates diurnal rhythms in innate immunity that synchronize with feeding rhythms to anticipate microbial exposure. Rhythmic expression of antimicrobial proteins was driven by daily rhythms in epithelial attachment by segmented filamentous bacteria (SFB), members of the mouse intestinal microbiota. Rhythmic SFB attachment was driven by the circadian clock through control of feeding rhythms. Mechanistically, rhythmic SFB attachment activated an immunological circuit involving group 3 innate lymphoid cells. This circuit triggered oscillations in epithelial STAT3 expression and activation that produced rhythmic antimicrobial protein expression and caused resistance to Salmonella Typhimurium infection to vary across the day-night cycle. Thus, host feeding rhythms synchronize with the microbiota to promote rhythms in intestinal innate immunity that anticipate exogenous microbial exposure.
Collapse
Affiliation(s)
- John F Brooks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cassie L Behrendt
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kelly A Ruhn
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Syann Lee
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; The Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; The Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
15
|
Wasilko NP, Ceron JS, Baker ER, Cecere AG, Wollenberg MS, Miyashiro TI. Vibrio fischeri imports and assimilates sulfate during symbiosis with Euprymna scolopes. Mol Microbiol 2021; 116:926-942. [PMID: 34212439 DOI: 10.1111/mmi.14780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/24/2022]
Abstract
Sulfur is in cellular components of bacteria and is, therefore, an element necessary for growth. However, mechanisms by which bacteria satisfy their sulfur needs within a host are poorly understood. Vibrio fischeri is a bacterial symbiont that colonizes, grows, and produces bioluminescence within the light organ of the Hawaiian bobtail squid, which provides an experimental platform for investigating sulfur acquisition in vivo. Like other γ-proteobacteria, V. fischeri fuels sulfur-dependent anabolic processes with intracellular cysteine. Within the light organ, the abundance of a ΔcysK mutant, which cannot synthesize cysteine through sulfate assimilation, is attenuated, suggesting sulfate import is necessary for V. fischeri to establish symbiosis. Genes encoding sulfate-import systems of other bacteria that assimilate sulfate were not identified in the V. fischeri genome. A transposon mutagenesis screen implicated YfbS as a sulfate importer. YfbS is necessary for growth on sulfate and in the marine environment. During symbiosis, a ΔyfbS mutant is attenuated and strongly expresses sulfate-assimilation genes, which is a phenotype associated with sulfur-starved cells. Together, these results suggest V. fischeri imports sulfate via YfbS within the squid light organ, which provides insight into the molecular mechanisms by which bacteria harvest sulfur in vivo.
Collapse
Affiliation(s)
- Nathan P Wasilko
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Josue S Ceron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Emily R Baker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Andrew G Cecere
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | | | - Tim I Miyashiro
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
16
|
Paredes GF, Viehboeck T, Lee R, Palatinszky M, Mausz MA, Reipert S, Schintlmeister A, Maier A, Volland JM, Hirschfeld C, Wagner M, Berry D, Markert S, Bulgheresi S, König L. Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces. mSystems 2021; 6:e0118620. [PMID: 34058098 PMCID: PMC8269255 DOI: 10.1128/msystems.01186-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.
Collapse
Affiliation(s)
- Gabriela F. Paredes
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Tobias Viehboeck
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Raymond Lee
- Washington State University, School of Biological Sciences, Pullman, Washington, USA
| | - Marton Palatinszky
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Michaela A. Mausz
- University of Warwick, School of Life Sciences, Coventry, United Kingdom
| | - Siegfried Reipert
- University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Vienna, Austria
| | - Arno Schintlmeister
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, Center for Microbiology and Environmental Systems Science, Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Vienna, Austria
| | - Andreas Maier
- University of Vienna, Faculty of Geosciences, Geography, and Astronomy, Department of Geography and Regional Research, Geoecology, Vienna, Austria
| | - Jean-Marie Volland
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Claudia Hirschfeld
- University of Greifswald, Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Greifswald, Germany
| | - Michael Wagner
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Aalborg University, Department of Chemistry and Bioscience, Aalborg, Denmark
| | - David Berry
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Stephanie Markert
- University of Greifswald, Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Greifswald, Germany
| | - Silvia Bulgheresi
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Lena König
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| |
Collapse
|
17
|
A lasting symbiosis: how Vibrio fischeri finds a squid partner and persists within its natural host. Nat Rev Microbiol 2021; 19:654-665. [PMID: 34089008 DOI: 10.1038/s41579-021-00557-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2021] [Indexed: 01/10/2023]
Abstract
As our understanding of the human microbiome progresses, so does the need for natural experimental animal models that promote a mechanistic understanding of beneficial microorganism-host interactions. Years of research into the exclusive symbiosis between the Hawaiian bobtail squid, Euprymna scolopes, and the bioluminescent bacterium Vibrio fischeri have permitted a detailed understanding of those bacterial genes underlying signal exchange and rhythmic activities that result in a persistent, beneficial association, as well as glimpses into the evolution of symbiotic competence. Migrating from the ambient seawater to regions deep inside the light-emitting organ of the squid, V. fischeri experiences, recognizes and adjusts to the changing environmental conditions. Here, we review key advances over the past 15 years that are deepening our understanding of these events.
Collapse
|
18
|
Christensen DG, Visick KL. Vibrio fischeri: Laboratory Cultivation, Storage, and Common Phenotypic Assays. ACTA ACUST UNITED AC 2021; 57:e103. [PMID: 32497392 DOI: 10.1002/cpmc.103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Vibrio fischeri is a nonpathogenic organism related to pathogenic Vibrio species that can be readily grown and stored with common laboratory equipment. In this article, protocols for routine growth, storage, and phenotypic assessment of V. fischeri, as well as recipes for useful media, are included. Specifically, this article describes procedures and considerations for growth of this microbe in complex and minimal media. It also describes assays for biofilm formation, motility, and bioluminescence, three commonly assessed phenotypes of V. fischeri. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Growth of V. fischeri from frozen stocks Basic Protocol 2: Growth of V. fischeri in rich, undefined liquid medium Alternate Protocol 1: Growth of V. fischeri in minimal medium Basic Protocol 3: Storage of V. fischeri in frozen stocks Basic Protocol 4: Biofilm assay on solid agar Alternate Protocol 2: Biofilm assay in shaking liquid culture Alternate Protocol 3: Biofilm assay in static liquid culture Basic Protocol 5: Motility assay Basic Protocol 6: Luminescence assay.
Collapse
Affiliation(s)
- David G Christensen
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois
| | - Karen L Visick
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois
| |
Collapse
|
19
|
Cohen SK, Aschtgen MS, Lynch JB, Koehler S, Chen F, Escrig S, Daraspe J, Ruby EG, Meibom A, McFall-Ngai M. Tracking the cargo of extracellular symbionts into host tissues with correlated electron microscopy and nanoscale secondary ion mass spectrometry imaging. Cell Microbiol 2021; 22:e13177. [PMID: 32185893 DOI: 10.1111/cmi.13177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/18/2020] [Accepted: 01/23/2020] [Indexed: 12/14/2022]
Abstract
Extracellular bacterial symbionts communicate biochemically with their hosts to establish niches that foster the partnership. Using quantitative ion microprobe isotopic imaging (nanoscale secondary ion mass spectrometry [NanoSIMS]), we surveyed localization of 15 N-labelled molecules produced by the bacterium Vibrio fischeri within the cells of the symbiotic organ of its host, the Hawaiian bobtail squid, and compared that with either labelled non-specific species or amino acids. In all cases, two areas of the organ's epithelia were significantly more 15 N enriched: (a) surface ciliated cells, where environmental symbionts are recruited, and (b) the organ's crypts, where the symbiont population resides in the host. Label enrichment in all cases was strongest inside host cell nuclei, preferentially in the euchromatin regions and the nucleoli. This permissiveness demonstrated that uptake of biomolecules is a general mechanism of the epithelia, but the specific responses to V. fischeri cells recruited to the organ's surface are due to some property exclusive to this species. Similarly, in the organ's deeper crypts, the host responds to common bacterial products that only the specific symbiont can present in that location. The application of NanoSIMS allows the discovery of such distinct modes of downstream signalling dependent on location within the host and provides a unique opportunity to study the microbiogeographical patterns of symbiotic dialogue.
Collapse
Affiliation(s)
- Stephanie K Cohen
- Laboratory of Biological Geochemistry, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marie-Stéphanie Aschtgen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jonathan B Lynch
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Sabrina Koehler
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Fangmin Chen
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Stéphane Escrig
- Laboratory of Biological Geochemistry, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Anders Meibom
- Laboratory of Biological Geochemistry, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
20
|
Nourabadi N, Nishiguchi MK. pH Adaptation Drives Diverse Phenotypes in a Beneficial Bacterium-Host Mutualism. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.611411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abiotic variation can influence the evolution of specific phenotypes that contribute to the diversity of bacterial strains observed in the natural environment. Environmentally transmitted symbiotic bacteria are particularly vulnerable to abiotic fluctuations, given that they must accommodate the transition between the free-living state and the host's internal environment. This type of life history strategy can strongly influence the success of a symbiont, and whether adapting to changes outside the host will allow a greater capacity to survive in symbiosis with the host partner. One example of how environmental breadth is advantageous to the symbiosis is the beneficial association between Vibrio fischeri and sepiolid squids (Cephalopoda: Sepiolidae). Since Vibrio bacteria are environmentally transmitted, they are subject to a wide variety of abiotic variables prior to infecting juvenile squids and must be poised to survive in the host light organ. In order to better understand how a changing abiotic factor (e.g., pH) influences the diversification of symbionts and their eventual symbiotic competence, we used an experimental evolution approach to ascertain how pH adaptation affects symbiont fitness. Results show that low pH adapted Vibrio strains have more efficient colonization rates compared to their ancestral strains. In addition, growth rates had significant differences compared to ancestral strains (pH 6.5–6.8, and 7.2). Bioluminescence production (a marker for symbiont competence) of pH evolved strains also improved at pH 6.5–7.2. Results imply that the evolution and diversification of Vibrio strains adapted to low pH outside the squid improves fitness inside the squid by allowing a higher success rate for host colonization and symbiotic competence.
Collapse
|
21
|
McFall-Ngai M, Bosch TCG. Animal development in the microbial world: The power of experimental model systems. Curr Top Dev Biol 2020; 141:371-397. [PMID: 33602493 PMCID: PMC8211120 DOI: 10.1016/bs.ctdb.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The development of powerful model systems has been a critical strategy for understanding the mechanisms underlying the progression of an animal through its ontogeny. Here we provide two examples that allow deep and mechanistic insight into the development of specific animal systems. Species of the cnidarian genus Hydra have provided excellent models for studying host-microbe interactions and how metaorganisms function in vivo. Studies of the Hawaiian bobtail squid Euprymna scolopes and its luminous bacterial partner Vibrio fischeri have been used for over 30 years to understand the impact of a broad array of levels, from ecology to genomics, on the development and persistence of symbiosis. These examples provide an integrated perspective of how developmental processes work and evolve within the context of a microbial world, a new view that opens vast horizons for developmental biology research. The Hydra and the squid systems also lend an example of how profound insights can be discovered by taking advantage of the "experiments" that evolution had done in shaping conserved developmental processes.
Collapse
Affiliation(s)
- Margaret McFall-Ngai
- Pacific Biosciences Research Center, Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, HI, United States.
| | - Thomas C G Bosch
- Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| |
Collapse
|
22
|
The cytokine MIF controls daily rhythms of symbiont nutrition in an animal-bacterial association. Proc Natl Acad Sci U S A 2020; 117:27578-27586. [PMID: 33067391 DOI: 10.1073/pnas.2016864117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The recent recognition that many symbioses exhibit daily rhythms has encouraged research into the partner dialogue that drives these biological oscillations. Here we characterized the pivotal role of the versatile cytokine macrophage migration inhibitory factor (MIF) in regulating a metabolic rhythm in the model light-organ symbiosis between Euprymna scolopes and Vibrio fischeri As the juvenile host matures, it develops complex daily rhythms characterized by profound changes in the association, from gene expression to behavior. One such rhythm is a diurnal shift in symbiont metabolism triggered by the periodic provision of a specific nutrient by the mature host: each night the symbionts catabolize chitin released from hemocytes (phagocytic immune cells) that traffic into the light-organ crypts, where the population of V. fischeri cells resides. Nocturnal migration of these macrophage-like cells, together with identification of an E. scolopes MIF (EsMIF) in the light-organ transcriptome, led us to ask whether EsMIF might be the gatekeeper controlling the periodic movement of the hemocytes. Western blots, ELISAs, and confocal immunocytochemistry showed EsMIF was at highest abundance in the light organ. Its concentration there was lowest at night, when hemocytes entered the crypts. EsMIF inhibited migration of isolated hemocytes, whereas exported bacterial products, including peptidoglycan derivatives and secreted chitin catabolites, induced migration. These results provide evidence that the nocturnal decrease in EsMIF concentration permits the hemocytes to be drawn into the crypts, delivering chitin. This nutritional function for a cytokine offers the basis for the diurnal rhythms underlying a dynamic symbiotic conversation.
Collapse
|
23
|
The noncoding small RNA SsrA is released by Vibrio fischeri and modulates critical host responses. PLoS Biol 2020; 18:e3000934. [PMID: 33141816 PMCID: PMC7665748 DOI: 10.1371/journal.pbio.3000934] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/13/2020] [Accepted: 09/22/2020] [Indexed: 01/13/2023] Open
Abstract
The regulatory noncoding small RNAs (sRNAs) of bacteria are key elements influencing gene expression; however, there has been little evidence that beneficial bacteria use these molecules to communicate with their animal hosts. We report here that the bacterial sRNA SsrA plays an essential role in the light-organ symbiosis between Vibrio fischeri and the squid Euprymna scolopes. The symbionts load SsrA into outer membrane vesicles, which are transported specifically into the epithelial cells surrounding the symbiont population in the light organ. Although an SsrA-deletion mutant (ΔssrA) colonized the host to a normal level after 24 h, it produced only 2/10 the luminescence per bacterium, and its persistence began to decline by 48 h. The host's response to colonization by the ΔssrA strain was also abnormal: the epithelial cells underwent premature swelling, and host robustness was reduced. Most notably, when colonized by the ΔssrA strain, the light organ differentially up-regulated 10 genes, including several encoding heightened immune-function or antimicrobial activities. This study reveals the potential for a bacterial symbiont's sRNAs not only to control its own activities but also to trigger critical responses promoting homeostasis in its host. In the absence of this communication, there are dramatic fitness consequences for both partners.
Collapse
|
24
|
Koch EJ, Moriano-Gutierrez S, Ruby EG, McFall-Ngai M, Liebeke M. The impact of persistent colonization by Vibrio fischeri on the metabolome of the host squid Euprymna scolopes. J Exp Biol 2020; 223:jeb212860. [PMID: 32616546 PMCID: PMC7473655 DOI: 10.1242/jeb.212860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/24/2020] [Indexed: 12/27/2022]
Abstract
Associations between animals and microbes affect not only the immediate tissues where they occur, but also the entire host. Metabolomics, the study of small biomolecules generated during metabolic processes, provides a window into how mutualistic interactions shape host biochemistry. The Hawaiian bobtail squid, Euprymna scolopes, is amenable to metabolomic studies of symbiosis because the host can be reared with or without its species-specific symbiont, Vibrio fischeri In addition, unlike many invertebrates, the host squid has a closed circulatory system. This feature allows a direct sampling of the refined collection of metabolites circulating through the body, a focused approach that has been highly successful with mammals. Here, we show that rearing E. scolopes without its natural symbiont significantly affected one-quarter of the more than 100 hemolymph metabolites defined by gas chromatography mass spectrometry analysis. Furthermore, as in mammals, which harbor complex consortia of bacterial symbionts, the metabolite signature oscillated on symbiont-driven daily rhythms and was dependent on the sex of the host. Thus, our results provide evidence that the population of even a single symbiont species can influence host hemolymph biochemistry as a function of symbiotic state, host sex and circadian rhythm.
Collapse
Affiliation(s)
- Eric J Koch
- Kewalo Marine Laboratory, University of Hawaii at Mānoa, Honolulu, HI 96813, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Silvia Moriano-Gutierrez
- Kewalo Marine Laboratory, University of Hawaii at Mānoa, Honolulu, HI 96813, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii at Mānoa, Honolulu, HI 96813, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Margaret McFall-Ngai
- Kewalo Marine Laboratory, University of Hawaii at Mānoa, Honolulu, HI 96813, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| |
Collapse
|
25
|
Eickhoff MJ, Bassler BL. Vibrio fischeri siderophore production drives competitive exclusion during dual-species growth. Mol Microbiol 2020; 114:244-261. [PMID: 32259318 PMCID: PMC7541421 DOI: 10.1111/mmi.14509] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/21/2020] [Accepted: 03/28/2020] [Indexed: 12/15/2022]
Abstract
When two or more bacterial species inhabit a shared niche, often, they must compete for limited nutrients. Iron is an essential nutrient that is especially scarce in the marine environment. Bacteria can use the production, release, and re-uptake of siderophores, small molecule iron chelators, to scavenge iron. Siderophores provide fitness advantages to species that employ them by enhancing iron acquisition, and moreover, by denying iron to competitors incapable of using the siderophore-iron complex. Here, we show that cell-free culture fluids from the marine bacterium Vibrio fischeri ES114 prevent the growth of other vibrio species. Mutagenesis reveals the aerobactin siderophore as the inhibitor. Our analysis reveals a gene, that we name aerE, encodes the aerobactin exporter, and LuxT is a transcriptional activator of aerobactin production. In co-culture, under iron-limiting conditions, aerobactin production allows V. fischeri ES114 to competitively exclude Vibrio harveyi, which does not possess aerobactin production and uptake genes. In contrast, V. fischeri ES114 mutants incapable of aerobactin production lose in competition with V. harveyi. Introduction of iutA, encoding the aerobactin receptor, together with fhuCDB, encoding the aerobactin importer are sufficient to convert V. harveyi into an "aerobactin cheater."
Collapse
Affiliation(s)
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
26
|
Saad MM, Eida AA, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3878-3901. [PMID: 32157287 PMCID: PMC7450670 DOI: 10.1093/jxb/eraa111] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/05/2023]
Abstract
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.
Collapse
Affiliation(s)
- Maged M Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette Cedex, France
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| |
Collapse
|
27
|
Wu P, Cheng J, Chen L, Xiang J, Pan Y, Zhang Y, Zheng T, Liu N, Chu W, Zhang J. Nr1d1 affects autophagy in the skeletal muscles of juvenile Nile tilapia by regulating the rhythmic expression of autophagy-related genes. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:891-907. [PMID: 32072342 DOI: 10.1007/s10695-019-00757-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Autophagy is an important evolutionary conserved process in eukaryotic organisms for the turnover of intracellular substances. Recent studies revealed that autophagy displays circadian rhythms in mice and zebrafish. To date, there is no report focused on the rhythmic changes of autophagy in fish skeletal muscles upon nutritional deprivation. In this study, we examined the circadian rhythms of 158 functional genes in tilapia muscle in response to starvation. We found that 12 genes were involved in autophagy changed their rhythm after starvation. Among these genes, Atg4c, Bnip3la, Lc3a, Lc3b, Lc3c, and Ulk1a exhibited a daily rhythmicity in tilapia muscle, and Atg4b, becn1, bnip3la, bnip3lb, Lc3a, and ulk1b were significantly upregulated in response to starvation. The number of autophagosomes was dramatically increased in fasted fish, indicating that nutritional signals affect not only the muscular clock system but also its autophagy behavior. Administration of GSK4112, an activator of Nr1d1, altered rhythmic expression of both circadian clock genes and autophagy genes in tilapia muscle. Taken together, these findings provide evidence that nutritional deficiency affects both circadian regulation and autophagy activities in skeletal muscle.
Collapse
Affiliation(s)
- Ping Wu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Jia Cheng
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Lin Chen
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Jing Xiang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Yaxiong Pan
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Yongzhan Zhang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China
| | - Tao Zheng
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China
| | - Naiyuan Liu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China
| | - Wuying Chu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China.
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China.
| | - Jianshe Zhang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, Hunan, China.
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China.
| |
Collapse
|
28
|
Interactions of Symbiotic Partners Drive the Development of a Complex Biogeography in the Squid-Vibrio Symbiosis. mBio 2020; 11:mBio.00853-20. [PMID: 32457244 PMCID: PMC7251207 DOI: 10.1128/mbio.00853-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The complexity, inaccessibility, and time scales of initial colonization of most animal microbiomes present challenges for the characterization of how the bacterial symbionts influence the form and function of tissues in the minutes to hours following the initial interaction of the partners. Here, we use the naturally occurring binary squid-vibrio association to explore this phenomenon. Imaging of the spatiotemporal landscape of this symbiosis during its onset provides a window into the impact of differences in both host-tissue maturation and symbiont strain phenotypes on the establishment of a dynamically stable symbiotic system. These data provide evidence that the symbionts shape the host-tissue landscape and that tissue maturation impacts the influence of strain-level differences on the daily rhythms of the symbiosis, the competitiveness for colonization, and antibiotic sensitivity. Microbes live in complex microniches within host tissues, but how symbiotic partners communicate to create such niches during development remains largely unexplored. Using confocal microscopy and symbiont genetics, we characterized the shaping of host microenvironments during light organ colonization of the squid Euprymna scolopes by the bacterium Vibrio fischeri. During embryogenesis, three pairs of invaginations form sequentially on the organ’s surface, producing pores that lead to interior compressed tubules at different stages of development. After hatching, these areas expand, allowing V. fischeri cells to enter and migrate ∼120 μm through three anatomically distinct regions before reaching blind-ended crypt spaces. A dynamic gatekeeper, or bottleneck, connects these crypts with the migration path. Once V. fischeri cells have entered the crypts, the bottlenecks narrow, and colonization by the symbiont population becomes spatially restricted. The actual timing of constriction and restriction varies with crypt maturity and with different V. fischeri strains. Subsequently, starting with the first dawn following colonization, the bottleneck controls a lifelong cycle of dawn-triggered expulsions of most of the symbionts into the environment and a subsequent regrowth in the crypts. Unlike other developmental phenotypes, bottleneck constriction is not induced by known microbe-associated molecular patterns (MAMPs) or by V. fischeri-produced bioluminescence, but it does require metabolically active symbionts. Further, while symbionts in the most mature crypts have a higher proportion of live cells and a greater likelihood of expulsion at dawn, they have a lower resistance to antibiotics. The overall dynamics of these distinct microenvironments reflect the complexity of the host-symbiont dialogue.
Collapse
|
29
|
Cohen ML, Mashanova EV, Jagannathan SV, Soto W. Adaptation to pH stress by Vibrio fischeri can affect its symbiosis with the Hawaiian bobtail squid ( Euprymna scolopes). MICROBIOLOGY-SGM 2020; 166:262-277. [PMID: 31967537 PMCID: PMC7376262 DOI: 10.1099/mic.0.000884] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many microorganisms engaged in host-microbe interactions pendulate between a free-living phase and a host-affiliated stage. How adaptation to stress during the free-living phase affects host-microbe associations is unclear and understudied. To explore this topic, the symbiosis between Hawaiian bobtail squid (Euprymna scolopes) and the luminous bacterium Vibrio fischeri was leveraged for a microbial experimental evolution study. V. fischeri experienced adaptation to extreme pH while apart from the squid host. V. fischeri was serially passaged for 2000 generations to the lower and upper pH growth limits for this microorganism, which were pH 6.0 and 10.0, respectively. V. fischeri was also serially passaged for 2000 generations to vacillating pH 6.0 and 10.0. Evolution to pH stress both facilitated and impaired symbiosis. Microbial evolution to acid stress promoted squid colonization and increased bioluminescence for V. fischeri, while symbiont adaptation to alkaline stress diminished these two traits. Oscillatory selection to acid and alkaline stress also improved symbiosis for V. fischeri, but the facilitating effects were less than that provided by microbial adaptation to acid stress. In summary, microbial adaptation to harsh environments amid the free-living phase may impact the evolution of host-microbe interactions in ways that were not formerly considered.
Collapse
Affiliation(s)
- Meagan Leah Cohen
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Ekaterina Vadimovna Mashanova
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Sveta Vivian Jagannathan
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - William Soto
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| |
Collapse
|
30
|
Aschtgen MS, Brennan CA, Nikolakakis K, Cohen S, McFall-Ngai M, Ruby EG. Insights into flagellar function and mechanism from the squid-vibrio symbiosis. NPJ Biofilms Microbiomes 2019; 5:32. [PMID: 31666982 PMCID: PMC6814793 DOI: 10.1038/s41522-019-0106-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Flagella are essential and multifunctional nanomachines that not only move symbionts towards their tissue colonization site, but also play multiple roles in communicating with the host. Thus, untangling the activities of flagella in reaching, interacting, and signaling the host, as well as in biofilm formation and the establishment of a persistent colonization, is a complex problem. The squid-vibrio system offers a unique model to study the many ways that bacterial flagella can influence a beneficial association and, generally, other bacteria-host interactions. Vibrio fischeri is a bioluminescent bacterium that colonizes the Hawaiian bobtail squid, Euprymna scolopes. Over the last 15 years, the structure, assembly, and functions of V. fischeri flagella, including not only motility and chemotaxis, but also biofilm formation and symbiotic signaling, have been revealed. Here we discuss these discoveries in the perspective of other host-bacteria interactions.
Collapse
Affiliation(s)
- Marie-Stephanie Aschtgen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, 171 76 Sweden
| | - Caitlin A. Brennan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Kiel Nikolakakis
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Natural and Applied Sciences, University of Wisconsin – Green Bay, Green Bay, WI 54311 USA
| | - Stephanie Cohen
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, and Center for Advanced Surface Analysis, Institute of Earth Sciences, Université de Lausanne, CH-1015 Lausanne, Switzerland
- Kewalo Marine Laboratory, University of Hawaii-Manoa, Honolulu, HI 96813 USA
| | | | - Edward G. Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa, Honolulu, HI 96813 USA
| |
Collapse
|
31
|
Lynch JB, Schwartzman JA, Bennett BD, McAnulty SJ, Knop M, Nyholm SV, Ruby EG. Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis. J Bacteriol 2019; 201:e00319-19. [PMID: 31331976 PMCID: PMC6755730 DOI: 10.1128/jb.00319-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/03/2019] [Indexed: 12/31/2022] Open
Abstract
Outer membrane vesicles (OMVs) are continuously produced by Gram-negative bacteria and are increasingly recognized as ubiquitous mediators of bacterial physiology. In particular, OMVs are powerful effectors in interorganismal interactions, driven largely by their molecular contents. These impacts have been studied extensively in bacterial pathogenesis but have not been well documented within the context of mutualism. Here, we examined the proteomic composition of OMVs from the marine bacterium Vibrio fischeri, which forms a specific mutualism with the Hawaiian bobtail squid, Euprymna scolopes We found that V. fischeri upregulates transcription of its major outer membrane protein, OmpU, during growth at an acidic pH, which V. fischeri experiences when it transitions from its environmental reservoir to host tissues. We used comparative genomics and DNA pulldown analyses to search for regulators of ompU and found that differential expression of ompU is governed by the OmpR, H-NS, and ToxR proteins. This transcriptional control combines with nutritional conditions to govern OmpU levels in OMVs. Under a host-encountered acidic pH, V. fischeri OMVs become more potent stimulators of symbiotic host development in an OmpU-dependent manner. Finally, we found that symbiotic development could be stimulated by OMVs containing a homolog of OmpU from the pathogenic species Vibrio cholerae, connecting the role of a well-described virulence factor with a mutualistic element. This work explores the symbiotic effects of OMV variation, identifies regulatory machinery shared between pathogenic and mutualistic bacteria, and provides evidence of the role that OMVs play in animal-bacterium mutualism.IMPORTANCE Beneficial bacteria communicate with their hosts through a variety of means. These communications are often carried out by a combination of molecules that stimulate responses from the host and are necessary for development of the relationship between these organisms. Naturally produced bacterial outer membrane vesicles (OMVs) contain many of those molecules and can stimulate a wide range of responses from recipient organisms. Here, we describe how a marine bacterium, Vibrio fischeri, changes the makeup of its OMVs under conditions that it experiences as it goes from its free-living lifestyle to associating with its natural host, the Hawaiian bobtail squid. This work improves our understanding of how bacteria change their signaling profile as they begin to associate with their beneficial partner animals.
Collapse
Affiliation(s)
- Jonathan B Lynch
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Julia A Schwartzman
- Department of Medical Microbiology & Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - Brittany D Bennett
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Sarah J McAnulty
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Mirjam Knop
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Edward G Ruby
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin, Madison, Wisconsin, USA
| |
Collapse
|
32
|
Lee SJ, Morse D, Hijri M. Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms. MYCORRHIZA 2019; 29:403-412. [PMID: 31190278 DOI: 10.1007/s00572-019-00903-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.
Collapse
Affiliation(s)
- Soon-Jae Lee
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - David Morse
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada.
| |
Collapse
|
33
|
Mushegian AA, Tougeron K. Animal-Microbe Interactions in the Context of Diapause. THE BIOLOGICAL BULLETIN 2019; 237:180-191. [PMID: 31714855 DOI: 10.1086/706078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Dormancy and diapause are key adaptations in many organisms, enabling survival of temporarily or seasonally unsuitable environmental conditions. In this review, we examine how our understanding of programmed developmental and metabolic arrest during diapause intersects with the increasing body of knowledge about animal co-development and co-evolution with microorganisms. Host-microbe interactions are increasingly understood to affect a number of metabolic, physiological, developmental, and behavioral traits and to mediate adaptations to various environments. Therefore, it is timely to consider how microbial factors might affect the expression and evolution of diapause in a changing world. We examine how a range of host-microbe interactions, from pathogenic to mutualistic, may have an impact on diapause phenotypes. Conversely, we examine how the discontinuities that diapause introduces into animal host generations can affect the ecology of microbial communities and the evolution of host-microbe interactions. We discuss these issues as they relate to physiology, evolution of development, local adaptation, disease ecology, and environmental change. Finally, we outline research questions that bridge the historically distinct fields of seasonal ecology and host-microbe interactions.
Collapse
|
34
|
Wein T, Romero Picazo D, Blow F, Woehle C, Jami E, Reusch TB, Martin WF, Dagan T. Currency, Exchange, and Inheritance in the Evolution of Symbiosis. Trends Microbiol 2019; 27:836-849. [DOI: 10.1016/j.tim.2019.05.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/19/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022]
|
35
|
Rader B, McAnulty SJ, Nyholm SV. Persistent symbiont colonization leads to a maturation of hemocyte response in the Euprymna scolopes/Vibrio fischeri symbiosis. Microbiologyopen 2019; 8:e858. [PMID: 31197972 PMCID: PMC6813443 DOI: 10.1002/mbo3.858] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/10/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023] Open
Abstract
The binary association between the squid, Euprymna scolopes, and its symbiont, Vibrio fischeri, serves as a model system to study interactions between beneficial bacteria and the innate immune system. Previous research demonstrated that binding of the squid's immune cells, hemocytes, to V. fischeri is altered if the symbiont is removed from the light organ, suggesting that host colonization alters hemocyte recognition of V. fischeri. To investigate the influence of symbiosis on immune maturation during development, we characterized hemocyte binding and phagocytosis of V. fischeri and nonsymbiotic Vibrio harveyi from symbiotic (sym) and aposymbiotic (apo) juveniles, and wild-caught and laboratory-raised sym and apo adults. Our results demonstrate that while light organ colonization by V. fischeri did not alter juvenile hemocyte response, these cells bound a similar number of V. fischeri and V. harveyi yet phagocytosed only V. harveyi. Our results also indicate that long-term colonization altered the adult hemocyte response to V. fischeri but not V. harveyi. All hemocytes from adult squid, regardless of apo or sym state, both bound and phagocytosed a similar number of V. harveyi while hemocytes from both wild-caught and sym-raised adults bound significantly fewer V. fischeri, although more V. fischeri were phagocytosed by hemocytes from wild-caught animals. In contrast, hemocytes from apo-raised squid bound similar numbers of both V. fischeri and V. harveyi, although more V. harveyi cells were engulfed, suggesting that blood cells from apo-raised adults behaved similarly to juvenile hosts. Taken together, these data suggest that persistent colonization by the light organ symbiont is required for hemocytes to differentially bind and phagocytose V. fischeri. The cellular immune system of E. scolopes likely possesses multiple mechanisms at different developmental stages to promote a specific and life-long interaction with the symbiont.
Collapse
Affiliation(s)
- Bethany Rader
- Department of MicrobiologySouthern Illinois UniversityCarbondaleIllinois
| | - Sarah J. McAnulty
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticut
| | - Spencer V. Nyholm
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticut
| |
Collapse
|
36
|
Leach WB, Carrier TJ, Reitzel AM. Diel patterning in the bacterial community associated with the sea anemone Nematostella vectensis. Ecol Evol 2019; 9:9935-9947. [PMID: 31534705 PMCID: PMC6745676 DOI: 10.1002/ece3.5534] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/11/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Microbes can play an important role in the physiology of animals by providing essential nutrients, inducing immune pathways, and influencing the specific species that compose the microbiome through competitive or facilitatory interactions. The community of microbes associated with animals can be dynamic depending on the local environment, and factors that influence the composition of the microbiome are essential to our understanding of how microbes may influence the biology of their animal hosts. Regularly repeated changes in the environment, such as diel lighting, can result in two different organismal responses: a direct response to the presence and absence of exogenous light and endogenous rhythms resulting from a molecular circadian clock, both of which can influence the associated microbiota. Here, we report how diel lighting and a potential circadian clock impacts the diversity and relative abundance of bacteria in the model cnidarian Nematostella vectensis using an amplicon-based sequencing approach. Comparisons of bacterial communities associated with anemones cultured in constant darkness and in light:dark conditions revealed that individuals entrained in the dark had a more diverse microbiota. Overall community composition showed little variation over a 24-hr period in either treatment; however, abundances of individual bacterial OTUs showed significant cycling in each treatment. A comparative analysis of genes involved in the innate immune system of cnidarians showed differential expression between lighting conditions in N. vectensis, with significant up-regulation during long-term darkness for a subset of genes. Together, our studies support a hypothesis that the bacterial community associated with this species is relatively stable under diel light conditions when compared with static conditions and that particular bacterial members may have time-dependent abundance that coincides with the diel photoperiod in an otherwise stable community.
Collapse
Affiliation(s)
- Whitney B. Leach
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Tyler J. Carrier
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Adam M. Reitzel
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| |
Collapse
|
37
|
Natural Strain Variation Reveals Diverse Biofilm Regulation in Squid-Colonizing Vibrio fischeri. J Bacteriol 2019; 201:JB.00033-19. [PMID: 30782630 DOI: 10.1128/jb.00033-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/07/2019] [Indexed: 12/17/2022] Open
Abstract
The mutualistic symbiont Vibrio fischeri builds a symbiotic biofilm during colonization of squid hosts. Regulation of the exopolysaccharide component, termed Syp, has been examined in strain ES114, where production is controlled by a phosphorelay that includes the inner membrane hybrid histidine kinase RscS. Most strains that lack RscS or encode divergent RscS proteins cannot colonize a squid host unless RscS from a squid symbiont is heterologously expressed. In this study, we examine V. fischeri isolates worldwide to understand the landscape of biofilm regulation during beneficial colonization. We provide a detailed study of three distinct evolutionary groups of V. fischeri and find that while the RscS-Syp biofilm pathway is required in one of the groups, two other groups of squid symbionts require Syp independent of RscS. Mediterranean squid symbionts, including V. fischeri SR5, colonize without an RscS homolog encoded by their genome. Additionally, group A V. fischeri strains, which form a tightly related clade of Hawaii isolates, have a frameshift in rscS and do not require the gene for squid colonization or competitive fitness. These same strains have a frameshift in sypE, and we provide evidence that this group A sypE allele leads to an upregulation in biofilm activity. Thus, this work describes the central importance of Syp biofilm in colonization of diverse isolates and demonstrates that significant evolutionary transitions correspond to regulatory changes in the syp pathway.IMPORTANCE Biofilms are surface-associated, matrix-encased bacterial aggregates that exhibit enhanced protection to antimicrobial agents. Previous work has established the importance of biofilm formation by a strain of luminous Vibrio fischeri bacteria as the bacteria colonize their host, the Hawaiian bobtail squid. In this study, expansion of this work to many natural isolates revealed that biofilm genes are universally required, yet there has been a shuffling of the regulators of those genes. This work provides evidence that even when bacterial behaviors are conserved, dynamic regulation of those behaviors can underlie evolution of the host colonization phenotype. Furthermore, this work emphasizes the importance of investigating natural diversity as we seek to understand molecular mechanisms in bacteria.
Collapse
|
38
|
Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression. Proc Natl Acad Sci U S A 2019; 116:7990-7999. [PMID: 30833394 DOI: 10.1073/pnas.1819897116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The colonization of an animal's tissues by its microbial partners creates networks of communication across the host's body. We used the natural binary light-organ symbiosis between the squid Euprymna scolopes and its luminous bacterial partner, Vibrio fischeri, to define the impact of colonization on transcriptomic networks in the host. A night-active predator, E. scolopes coordinates the bioluminescence of its symbiont with visual cues from the environment to camouflage against moon and starlight. Like mammals, this symbiosis has a complex developmental program and a strong day/night rhythm. We determined how symbiont colonization impacted gene expression in the light organ itself, as well as in two anatomically remote organs: the eye and gill. While the overall transcriptional signature of light organ and gill were more alike, the impact of symbiosis was most pronounced and similar in light organ and eye, both in juvenile and adult animals. Furthermore, the presence of a symbiosis drove daily rhythms of transcription within all three organs. Finally, a single mutation in V. fischeri-specifically, deletion of the lux operon, which abrogates symbiont luminescence-reduced the symbiosis-dependent transcriptome of the light organ by two-thirds. In addition, while the gills responded similarly to light-organ colonization by either the wild-type or mutant, luminescence was required for all of the colonization-associated transcriptional responses in the juvenile eye. This study defines not only the impact of symbiont colonization on the coordination of animal transcriptomes, but also provides insight into how such changes might impact the behavior and ecology of the host.
Collapse
|
39
|
Abstract
Animal–microbe associations are critical drivers of evolutionary innovation, yet the origin of specialized symbiotic organs remains largely unexplored. We analyzed the genome of Euprymna scolopes, a model cephalopod, and observed large-scale genomic reorganizations compared with the ancestral bilaterian genome. We report distinct evolutionary signatures within the two symbiotic organs of E. scolopes, the light organ (LO) and the accessory nidamental gland (ANG). The LO evolved through subfunctionalization of genes expressed in the eye, indicating a deep evolutionary link between these organs. Alternatively, the ANG was enriched in novel, species-specific orphan genes suggesting these two tissues originated via different evolutionary strategies. These analyses represent the first genomic insights into the evolution of multiple symbiotic organs within a single animal host. Microbes have been critical drivers of evolutionary innovation in animals. To understand the processes that influence the origin of specialized symbiotic organs, we report the sequencing and analysis of the genome of Euprymna scolopes, a model cephalopod with richly characterized host–microbe interactions. We identified large-scale genomic reorganization shared between E. scolopes and Octopus bimaculoides and posit that this reorganization has contributed to the evolution of cephalopod complexity. To reveal genomic signatures of host–symbiont interactions, we focused on two specialized organs of E. scolopes: the light organ, which harbors a monoculture of Vibrio fischeri, and the accessory nidamental gland (ANG), a reproductive organ containing a bacterial consortium. Our findings suggest that the two symbiotic organs within E. scolopes originated by different evolutionary mechanisms. Transcripts expressed in these microbe-associated tissues displayed their own unique signatures in both coding sequences and the surrounding regulatory regions. Compared with other tissues, the light organ showed an abundance of genes associated with immunity and mediating light, whereas the ANG was enriched in orphan genes known only from E. scolopes. Together, these analyses provide evidence for different patterns of genomic evolution of symbiotic organs within a single host.
Collapse
|
40
|
Helmkampf M, Bellinger MR, Frazier M, Takabayashi M. Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata. Ecol Evol 2019; 9:378-392. [PMID: 30680121 PMCID: PMC6341978 DOI: 10.1002/ece3.4756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022] Open
Abstract
Reef-building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA-seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai'i Island with contrasting environmental conditions. We found that transcriptome-wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (F ST = 0.046) and among corals harboring alternative symbiont clades (F ST = 0.036), suggesting that site-related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.
Collapse
Affiliation(s)
- Martin Helmkampf
- Tropical Conservation Biology and Environmental ScienceUniversity of Hawaiʻi at HiloHiloHawaii
| | - M. Renee Bellinger
- Tropical Conservation Biology and Environmental ScienceUniversity of Hawaiʻi at HiloHiloHawaii
| | - Monika Frazier
- Tropical Conservation Biology and Environmental ScienceUniversity of Hawaiʻi at HiloHiloHawaii
| | - Misaki Takabayashi
- Tropical Conservation Biology and Environmental ScienceUniversity of Hawaiʻi at HiloHiloHawaii
- Okinawa Institute of Science and TechnologyOnna-son, OkinawaJapan
| |
Collapse
|
41
|
Nighttime activities and peripheral clock oscillations depend on Wolbachia endosymbionts in flies. Sci Rep 2018; 8:15432. [PMID: 30337547 PMCID: PMC6194088 DOI: 10.1038/s41598-018-33522-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022] Open
Abstract
Wolbachia are ubiquitous bacterial endosymbionts of arthropods and affect host gene expression. Although Wolbachia infections were suggested to modulate sleep in flies, their influence on the circadian clock remained obscure. Here, we screened bacterial symbionts in a laboratory Drosophila melanogaster colony, and observed widespread infections of wMel strain Wolbachia. We established a Wolbachia-free strain from a clock gene reporter strain, period-luciferase (per-luc). Temperature (19-29 °C)-compensated free-running periods were detected regardless of infections which may reflect the lack of wMel infections in central circadian pacemaker neurons. However, locomotor activity levels during the night or subjective night were significantly amplified in uninfected flies. Moreover, the behavioral phenotype of F1 offspring of an uninfected female and infected male resembled that of uninfected flies. This trait is consistent with maternal transmission of Wolbachia infection. Interestingly, per-luc activities in headless bodies, as an index of peripheral circadian oscillators, were severely damped in uninfected flies. Additionally, circadian amplitudes of PER immunoreactivities in Malpighian tubules were reduced in uninfected flies. These results demonstrate that Wolbachia boost fly peripheral clock oscillations and diurnal behavioral patterns. Genetic mechanisms underlying behavioral rhythms have been widely analyzed using mutant flies whereas screening of Wolbachia will be necessary for future studies.
Collapse
|
42
|
Persistent Interactions with Bacterial Symbionts Direct Mature-Host Cell Morphology and Gene Expression in the Squid-Vibrio Symbiosis. mSystems 2018; 3:mSystems00165-18. [PMID: 30320217 PMCID: PMC6172772 DOI: 10.1128/msystems.00165-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/28/2018] [Indexed: 11/20/2022] Open
Abstract
In horizontally transmitted symbioses, structural, biochemical, and molecular features both facilitate host colonization by specific symbionts and mediate their persistent carriage. In the association between the squid Euprymna scolopes and its luminous bacterial partner Vibrio fischeri, the symbionts interact with two epithelial fields; they interact (i) transiently with the superficial ciliated field that potentiates colonization and regresses within days of colonization and (ii) persistently with the cells that line the internal crypts, whose ultrastructure changes in response to the symbionts. Development of the association creates conditions that promote the symbiotic partner over the lifetime of the host. To determine whether light organ maturation requires continuous interactions with V. fischeri or only the signaling that occurs during its initiation, we compared 4-week-old squid that were uncolonized with those colonized either persistently by wild-type V. fischeri or transiently by a V. fischeri mutant that triggers early events in morphogenesis but does not persist. Microscopic analysis of the light organs showed that, while morphogenesis of the superficial ciliated field is greatly accelerated by V. fischeri colonization, its eventual outcome is largely independent of colonization state. In contrast, the symbiont-induced changes in crypt cell shape require persistent host-symbiont interaction, reflected in the similarity between uncolonized and transiently colonized animals. Transcriptomic analyses reflected the microscopy results; host gene expression at 4 weeks was due primarily to the persistent interactions of host and symbiont cells. Further, the transcriptomic signature of specific pathways reflected the daily rhythm of symbiont release and regrowth and required the presence of the symbionts. IMPORTANCE A long-term relationship between symbiotic partners is often characterized by development and maturation of host structures that harbor the symbiont cells over the host's lifetime. To understand the mechanisms involved in symbiosis maintenance more fully, we studied the mature bobtail squid, whose light-emitting organ, under experimental conditions, can be transiently or persistently colonized by Vibrio fischeri or remain uncolonized. Superficial anatomical changes in the organ were largely independent of symbiosis. However, both the microanatomy of cells with which symbionts interact and the patterns of gene expression in the mature animal were due principally to the persistent interactions of host and symbiont cells rather than to a response to early colonization events. Further, the characteristic pronounced daily rhythm on the host transcriptome required persistent V. fischeri colonization of the organ. This experimental study provides a window into how persistent symbiotic colonization influences the form and function of host animal tissues.
Collapse
|
43
|
Baker LY, Hobby CR, Siv AW, Bible WC, Glennon MS, Anderson DM, Symes SJ, Giles DK. Pseudomonas aeruginosa responds to exogenous polyunsaturated fatty acids (PUFAs) by modifying phospholipid composition, membrane permeability, and phenotypes associated with virulence. BMC Microbiol 2018; 18:117. [PMID: 30217149 PMCID: PMC6137939 DOI: 10.1186/s12866-018-1259-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 09/05/2018] [Indexed: 12/20/2022] Open
Abstract
Background Pseudomonas aeruginosa, a common opportunistic pathogen, is known to cause infections in a variety of compromised human tissues. An emerging mechanism for microbial survival is the incorporation of exogenous fatty acids to alter the cell’s membrane phospholipid profile. With these findings, we show that exogenous fatty acid exposure leads to changes in bacterial membrane phospholipid structure, membrane permeability, virulence phenotypes and consequent stress responses that may influence survival and persistence of Pseudomonas aeruginosa. Results Thin-layer chromatography and ultra performance liquid chromatography / ESI-mass spectrometry indicated alteration of bacterial phospholipid profiles following growth in the presence of polyunsaturated fatty acids (PUFAs) (ranging in carbon length and unsaturation). The exogenously supplied fatty acids were incorporated into the major bacterial phospholipids phosphatidylethanolamine and phosphatidylglycerol. The incorporation of fatty acids increased membrane permeability as judged by both accumulation and exclusion of ethidium bromide. Individual fatty acids were identified as modifying resistance to the cyclic peptide antibiotics polymyxin B and colistin, but not the beta-lactam imipenem. Biofilm formation was increased by several PUFAs and significant fluctuations in swimming motility were observed. Conclusions Our results emphasize the relevance and complexity of exogenous fatty acids in the membrane physiology and pathobiology of a medically important pathogen. P. aeruginosa exhibits versatility with regard to utilization of and response to exogenous fatty acids, perhaps revealing potential strategies for prevention and control of infection. Electronic supplementary material The online version of this article (10.1186/s12866-018-1259-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Lyssa Y Baker
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Chelsea R Hobby
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Andrew W Siv
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - William C Bible
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Michael S Glennon
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Derek M Anderson
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Steven J Symes
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - David K Giles
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA.
| |
Collapse
|
44
|
Patelunas AJ, Nishiguchi MK. Vascular architecture in the bacteriogenic light organ of Euprymna tasmanica (Cephalopoda: Sepiolidae). INVERTEBRATE BIOLOGY : A QUARTERLY JOURNAL OF THE AMERICAN MICROSCOPICAL SOCIETY AND THE DIVISION OF INVERTEBRATE ZOOLOGY/ASZ 2018; 137:240-249. [PMID: 30853777 PMCID: PMC6405259 DOI: 10.1111/ivb.12223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Symbiosis between southern dumpling squid, Euprymna tasmanica (Cephalopoda: Sepiolidae), and its luminescent symbiont, the bacterium Vibrio fischeri, provides an experimentally tractable system to examine interactions between the eukaryotic host and its bacterial partner. Luminescence emitted by the symbiotic bacteria provides light for the squid in a behavior termed "counter-illumination," which allows the squid to mask its shadow amidst downwelling moonlight. Although this association is beneficial, light generated from the bacteria requires large quantities of oxygen to maintain this energy-consuming reaction. Therefore, we examined the vascular network within the light organ of juveniles of E. tasmanica with and without V. fischeri. Vessel type, diameter, and location of vessels were measured. Although differences between symbiotic and aposymbiotic squid demonstrated that the presence of V. fischeri does not significantly influence the extent of vascular branching at early stages of symbiotic development, these finding do provide an atlas of blood vessel distribution in the organ. Thus, these results provide a framework to understand how beneficial bacteria influence the development of a eukaryotic closed vascular network and provide insight to the evolutionary developmental dynamics that form during mutualistic interactions.
Collapse
|
45
|
Harke MJ, Frischkorn KR, Haley ST, Aylward FO, Zehr JP, Dyhrman ST. Periodic and coordinated gene expression between a diazotroph and its diatom host. ISME JOURNAL 2018; 13:118-131. [PMID: 30116042 DOI: 10.1038/s41396-018-0262-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/28/2018] [Accepted: 07/28/2018] [Indexed: 01/30/2023]
Abstract
In the surface ocean, light fuels photosynthetic carbon fixation of phytoplankton, playing a critical role in ecosystem processes including carbon export to the deep sea. In oligotrophic oceans, diatom-diazotroph associations (DDAs) play a keystone role in ecosystem function because diazotrophs can provide otherwise scarce biologically available nitrogen to the diatom host, fueling growth and subsequent carbon sequestration. Despite their importance, relatively little is known about the nature of these associations in situ. Here we used metatranscriptomic sequencing of surface samples from the North Pacific Subtropical Gyre (NPSG) to reconstruct patterns of gene expression for the diazotrophic symbiont Richelia and we examined how these patterns were integrated with those of the diatom host over day-night transitions. Richelia exhibited significant diel signals for genes related to photosynthesis, N2 fixation, and resource acquisition, among other processes. N2 fixation genes were significantly co-expressed with host nitrogen uptake and metabolism, as well as potential genes involved in carbon transport, which may underpin the exchange of nitrogen and carbon within this association. Patterns of expression suggested cell division was integrated between the host and symbiont across the diel cycle. Collectively these data suggest that symbiont-host physiological ecology is strongly interconnected in the NPSG.
Collapse
Affiliation(s)
- Matthew J Harke
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Kyle R Frischkorn
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA. .,Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA.
| |
Collapse
|
46
|
An Iterative, Synthetic Approach To Engineer a High-Performance PhoB-Specific Reporter. Appl Environ Microbiol 2018; 84:AEM.00603-18. [PMID: 29752265 DOI: 10.1128/aem.00603-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/03/2018] [Indexed: 11/20/2022] Open
Abstract
Transcriptional reporters are common tools for analyzing either the transcription of a gene of interest or the activity of a specific transcriptional regulator. Unfortunately, the latter application has the shortcoming that native promoters did not evolve as optimal readouts for the activity of a particular regulator. We sought to synthesize an optimized transcriptional reporter for assessing PhoB activity, aiming for maximal "on" expression when PhoB is active, minimal background in the "off" state, and no control elements for other regulators. We designed specific sequences for promoter elements with appropriately spaced PhoB-binding sites, and at 19 additional intervening nucleotide positions for which we did not predict sequence-specific effects, the bases were randomized. Eighty-three such constructs were screened in Vibrio fischeri, enabling us to identify bases at particular randomized positions that significantly correlated with high-level "on" or low-level "off" expression. A second round of promoter design rationally constrained 13 additional positions, leading to a reporter with high-level PhoB-dependent expression, essentially no background, and no other known regulatory elements. As expressed reporters, we used both stable and destabilized variants of green fluorescent protein (GFP), the latter of which has a half-life of 81 min in V. fischeri In culture, PhoB induced the reporter when phosphate was depleted to a concentration below 10 μM. During symbiotic colonization of its host squid, Euprymna scolopes, the reporter indicated heterogeneous phosphate availability in different light-organ microenvironments. Finally, testing this construct in other members of the Proteobacteria demonstrated its broader utility. The results illustrate how a limited ability to predict synthetic promoter-reporter performance can be overcome through iterative screening and reengineering.IMPORTANCE Transcriptional reporters can be powerful tools for assessing when a particular regulator is active; however, native promoters may not be ideal for this purpose. Optimal reporters should be specific to the regulator being examined and should maximize the difference between the "on" and "off" states; however, these properties are distinct from the selective pressures driving the evolution of natural promoters. Synthetic promoters offer a promising alternative, but our understanding often does not enable fully predictive promoter design, and the large number of alternative sequence possibilities can be intractable. In a synthetic promoter region with over 34 billion sequence variants, we identified bases correlated with favorable performance by screening only 83 candidates, allowing us to rationally constrain our design. We thereby generated an optimized reporter that is induced by PhoB and used it to explore the low-phosphate response of V. fischeri This promoter design strategy will facilitate the engineering of other regulator-specific reporters.
Collapse
|
47
|
Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes. mBio 2018; 9:mBio.01033-18. [PMID: 29946051 PMCID: PMC6020299 DOI: 10.1128/mbio.01033-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diverse marine fish and squid form symbiotic associations with extracellular bioluminescent bacteria. These symbionts are typically free-living bacteria with large genomes, but one known lineage of symbionts has undergone genomic reduction and evolution of host dependence. It is not known why distinct evolutionary trajectories have occurred among different luminous symbionts, and not all known lineages previously had genome sequences available. In order to better understand patterns of evolution across diverse bioluminescent symbionts, we de novo sequenced the genomes of bacteria from a poorly studied interaction, the extracellular symbionts from the "lures" of deep-sea ceratioid anglerfishes. Deep-sea anglerfish symbiont genomes are reduced in size by about 50% compared to free-living relatives. They show a striking convergence of genome reduction and loss of metabolic capabilities with a distinct lineage of obligately host-dependent luminous symbionts. These losses include reductions in amino acid synthesis pathways and abilities to utilize diverse sugars. However, the symbiont genomes have retained a number of categories of genes predicted to be useful only outside the host, such as those involved in chemotaxis and motility, suggesting that they may persist in the environment. These genomes contain very high numbers of pseudogenes and show massive expansions of transposable elements, with transposases accounting for 28 and 31% of coding sequences in the symbiont genomes. Transposon expansions appear to have occurred at different times in each symbiont lineage, indicating either independent evolutions of reduction or symbiont replacement. These results suggest ongoing genomic reduction in extracellular luminous symbionts that is facilitated by transposon proliferations.IMPORTANCE Many female deep-sea anglerfishes possess a "lure" containing luminous bacterial symbionts. Here we show that unlike most luminous symbionts, these bacteria are undergoing an evolutionary transition toward small genomes with limited metabolic capabilities. Comparative analyses of the symbiont genomes indicate that this transition is ongoing and facilitated by transposon expansions. This transition may have occurred independently in different symbiont lineages, although it is unclear why. Genomic reduction is common in bacteria that only live within host cells but less common in bacteria that, like anglerfish symbionts, live outside host cells. Since multiple evolutions of genomic reduction have occurred convergently in luminous bacteria, they make a useful system with which to understand patterns of genome evolution in extracellular symbionts. This work demonstrates that ecological factors other than an intracellular lifestyle can lead to dramatic gene loss and evolutionary changes and that transposon expansions may play important roles in this process.
Collapse
|
48
|
Maire J, Vincent-Monégat C, Masson F, Zaidman-Rémy A, Heddi A. An IMD-like pathway mediates both endosymbiont control and host immunity in the cereal weevil Sitophilus spp. MICROBIOME 2018; 6:6. [PMID: 29310713 PMCID: PMC5759881 DOI: 10.1186/s40168-017-0397-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/28/2017] [Indexed: 05/08/2023]
Abstract
Many insects developing on nutritionally unbalanced diets have evolved symbiotic associations with vertically transmitted intracellular bacteria (endosymbionts) that provide them with metabolic components, thereby improving the host's abilities to thrive on such poor ecological niches. While host-endosymbiont coevolutionary constraints are known to entail massive genomic changes in the microbial partner, host's genomic evolution remains elusive, particularly with regard to the immune system. In the cereal weevil Sitophilus spp., which houses Sodalis pierantonius, endosymbionts are secluded in specialized host cells, the bacteriocytes that group together as an organ, the bacteriome. We previously reported that at standard conditions, the bacteriome highly expresses the coleoptericin A (colA) antimicrobial peptide (AMP), which was shown to prevent endosymbiont escape from the bacteriocytes. However, following the insect systemic infection by pathogens, the bacteriome upregulates a cocktail of AMP encoding genes, including colA. The regulations that allow these contrasted immune responses remain unknown. In this short report, we provide evidence that an IMD-like pathway is conserved in two sibling species of cereal weevils, Sitophilus oryzae and Sitophilus zeamais. RNA interference (RNAi) experiments showed that imd and relish genes are essential for (i) colA expression in the bacteriome under standard conditions, (ii) AMP up-regulation in the bacteriome following a systemic immune challenge, and (iii) AMP systemic induction following an immune challenge. Histological analyses also showed that relish inhibition by RNAi resulted in endosymbiont escape from the bacteriome, strengthening the involvement of an IMD-like pathway in endosymbiont control. We conclude that Sitophilus' IMD-like pathway mediates both the bacteriome immune program involved in endosymbiont seclusion within the bacteriocytes and the systemic and local immune responses to exogenous challenges. This work provides a striking example of how a conserved immune pathway, initially described as essential in pathogen clearance, also functions in the control of mutualistic associations.
Collapse
Affiliation(s)
- Justin Maire
- Univ Lyon, INSA-Lyon, INRA, BF2i, UMR0203, F-69621, Villeurbanne, France
| | | | - Florent Masson
- Univ Lyon, INSA-Lyon, INRA, BF2i, UMR0203, F-69621, Villeurbanne, France
- Present address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA-Lyon, INRA, BF2i, UMR0203, F-69621, Villeurbanne, France
| | - Abdelaziz Heddi
- Univ Lyon, INSA-Lyon, INRA, BF2i, UMR0203, F-69621, Villeurbanne, France.
| |
Collapse
|
49
|
Schwartz WJ. Embodied Clocks. J Biol Rhythms 2017; 32:503-504. [PMID: 29249193 DOI: 10.1177/0748730417748381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
50
|
Peyer SM, Heath-Heckman EAC, McFall-Ngai MJ. Characterization of the cell polarity gene crumbs during the early development and maintenance of the squid-vibrio light organ symbiosis. Dev Genes Evol 2017; 227:375-387. [PMID: 28105525 PMCID: PMC5519459 DOI: 10.1007/s00427-017-0576-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/13/2017] [Indexed: 11/26/2022]
Abstract
The protein Crumbs is a determinant of apical-basal cell polarity and plays a role in apoptosis of epithelial cells and their protection against photodamage. Using the squid-vibrio system, a model for development of symbiotic partnerships, we examined the modulation of the crumbs gene in host epithelial tissues during initiation and maintenance of the association. The extracellular luminous symbiont Vibrio fischeri colonizes the apical surfaces of polarized epithelia in deep crypts of the Euprymna scolopes light organ. During initial colonization each generation, symbiont harvesting is potentiated by the biochemical and biophysical activity of superficial ciliated epithelia, which are several cell layers from the crypt epithelia where the symbionts reside. Within hours of crypt colonization, the symbionts induce the cell death mediated regression of the remote superficial ciliated fields. However, the crypt cells directly interacting with the symbiont are protected from death. In the squid host, we characterized the gene and encoded protein during light organ morphogenesis and in response to symbiosis. Features of the protein sequence and structure, phylogenetic relationships, and localization patterns in the eye supported assignment of the squid protein to the Crumbs family. In situ hybridization revealed that the crumbs transcript shows opposite expression at the onset of symbiosis in the two different regions of the light organ: elevated levels in the superficial epithelia were attenuated whereas low levels in the crypt epithelia were turned up. Although a rhythmic association in which the host controls the symbiont population over the day-night cycle begins in the juvenile upon colonization, cycling of crumbs was evident only in the adult organ with peak expression coincident with maximum symbiont population and luminescence. Our results provide evidence that crumbs responds to symbiont cues that induce developmental apoptosis and to symbiont population dynamics correlating with luminescence-based stress throughout the duration of the host-microbe association.
Collapse
Affiliation(s)
- Suzanne M Peyer
- School of Medicine and Public Health, Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, 53706, USA.
- McPherson Eye Research Institute, University of Wisconsin, Madison, WI, 53706, USA.
| | - Elizabeth A C Heath-Heckman
- School of Medicine and Public Health, Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, 53706, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Margaret J McFall-Ngai
- School of Medicine and Public Health, Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, 53706, USA.
- McPherson Eye Research Institute, University of Wisconsin, Madison, WI, 53706, USA.
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
| |
Collapse
|