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Williams CE, Fontaine SS. Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes. Comp Biochem Physiol A Mol Integr Physiol 2024; 296:111690. [PMID: 38964709 DOI: 10.1016/j.cbpa.2024.111690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
Comparative physiologists often compare physiological traits across organisms to understand the selective pressures influencing their evolution in different environments. Traditionally focused on the organisms themselves, comparative physiology has more recently incorporated studies of the microbiome-the communities of microbes living in and on animals that influence host physiology. In this commentary, we describe the utility of applying a comparative framework to study the microbiome, particularly in understanding how hosts vary in their dependence on microbial communities for physiological function, a concept we term the "microbial dependence continuum". This hypothesis suggests that hosts exist on a spectrum ranging from high to low reliance on their microbiota. Certain physiological traits may be highly dependent on microbes for proper function in some species but microbially independent in others. Comparative physiology can elucidate the selective pressures driving species along this continuum. Here, we discuss the microbial dependence continuum in detail and how comparative physiology can be useful to study it. Then, we discuss two example traits, herbivory and flight, where comparative physiology has helped reveal the selective pressures influencing host dependence on microbial communities. Lastly, we discuss useful experimental approaches for studying the microbial dependence continuum in a comparative physiology context.
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Affiliation(s)
- Claire E Williams
- University of Nevada, Department of Biology, 1664 N Virginia St, Reno, NV 89557, USA.
| | - Samantha S Fontaine
- Kent State University, Department of Biological Sciences, 800 E Summit St, Kent, OH, USA. https://twitter.com/sammiefontaine
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2
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Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 PMCID: PMC11323152 DOI: 10.1016/j.mib.2024.102496] [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: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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3
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Wilde J, Slack E, Foster KR. Host control of the microbiome: Mechanisms, evolution, and disease. Science 2024; 385:eadi3338. [PMID: 39024451 DOI: 10.1126/science.adi3338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus on how hosts affect their microbiomes. Hosts exert control over their symbionts through diverse mechanisms, including immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable hosts to shape the ecology and evolution of microbiomes and generate natural selection for microbial traits that benefit the host. Our microbiomes result from a perpetual tension between host control and symbiont evolution, and we can leverage the host's evolved abilities to regulate the microbiota to prevent and treat disease. The study of host control will be central to our ability to both understand and manipulate microbiotas for better health.
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Affiliation(s)
- Jacob Wilde
- Department of Biology, University of Oxford, Oxford, UK
| | - Emma Slack
- Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Basel Institute for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
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4
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McAtamney A, Ferranti A, Ludvik DA, Yildiz FH, Mandel MJ, Hayward T, Sanchez LM. Microbial metabolomics' latest SICRIT: Soft ionization by Chemical Reaction in-Transfer mass spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.604007. [PMID: 39071417 PMCID: PMC11275794 DOI: 10.1101/2024.07.17.604007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Microbial metabolomics studies are a common approach to identifying microbial strains that have a capacity to produce new chemistries both in vitro and in situ. A limitation to applying microbial metabolomics to the discovery of new chemical entities is the rediscovery of known compounds, or "known unknowns." One contributing factor to this rediscovery is the majority of laboratories use one ionization source-electrospray ionization (ESI)-to conduct metabolomics studies. Although ESI is an efficient, widely adopted ionization method, its widespread use may contribute to the re-identification of known metabolites. Here, we present the use of a dielectric barrier discharge ionization (DBDI) for microbial metabolomics applications through the use of soft ionization chemical reaction in-transfer (SICRIT). Additionally, we compared SICRIT to ESI using two different Vibrio species-Vibrio fischeri, a symbiotic marine bacterium, and Vibrio cholerae, a pathogenic bacterium. Overall, we found that the SICRIT source ionizes a different set of metabolites than ESI, and it has the ability to ionize lipids more efficiently than ESI in positive mode. This work highlights the value of using more than one ionization source for the detection of metabolites.
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Affiliation(s)
- Allyson McAtamney
- 1156 High St, Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Denise A. Ludvik
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Mark J. Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Laura M. Sanchez
- 1156 High St, Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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5
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Piedl K, Aylward FO, Mevers E. The Microbiota of Moon Snail Egg Collars is Shaped by Host-Specific Factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602920. [PMID: 39071397 PMCID: PMC11275906 DOI: 10.1101/2024.07.10.602920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Moon Snails lay eggs using a mixture of mucus and sediment to form an egg mass commonly referred to as an egg collar. These collars do not appear to experience micro-biofouling or predation and this observation led us to hypothesize that the egg collars possess a chemically-rich microbiota that protect the egg collars from pathogens. Herein, we sought to gain an understanding of the bacterial composition of the egg collars by amplifying and sequencing the 16S rRNA gene from egg collar and sediment samples collected at four distinct geographical regions in SW Florida. Relative abundance and non-metric multidimensional scaling plots revealed distinct differences in the bacterial composition between the egg collar and sediment samples. In addition, the egg collars had a lower α-diversity than the sediment, with specific genera being significantly enriched in the egg collars. Analysis of microorganisms consistent across two seasons suggests that Flavobacteriaceae make up a large portion of the core microbiota (36 - 58% of 16S sequences). We also investigated the natural product potential of the egg collar microbiota by sequencing a core biosynthetic gene, the adenylation domains (AD), within the gene clusters of non-ribosomal peptide synthetase (NRPS). AD sequences matched multiple modules within known bioactive NRPs biosynthetic gene clusters, suggesting production is possible within the egg collar system and lays the foundation for future studies into the chemical and ecological role of this microbiota.
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Affiliation(s)
- Karla Piedl
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Emily Mevers
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia, USA
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6
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Gilbert SF. Inter-kingdom communication and the sympoietic way of life. Front Cell Dev Biol 2024; 12:1427798. [PMID: 39071805 PMCID: PMC11275584 DOI: 10.3389/fcell.2024.1427798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
Organisms are now seen as holobionts, consortia of several species that interact metabolically such that they sustain and scaffold each other's existence and propagation. Sympoiesis, the development of the symbiotic relationships that form holobionts, is critical for our understanding the origins and maintenance of biodiversity. Rather than being the read-out of a single genome, development has been found to be sympoietic, based on multigenomic interactions between zygote-derived cells and symbiotic microbes. These symbiotic and sympoietic interactions are predicated on the ability of cells from different kingdoms of life (e.g., bacteria and animals) to communicate with one another and to have their chemical signals interpreted in a manner that facilitates development. Sympoiesis, the creation of an entity by the interactions of other entities, is commonly seen in embryogenesis (e.g., the creation of lenses and retinas through the interaction of brain and epidermal compartments). In holobiont sympoiesis, interactions between partners of different domains of life interact to form organs and biofilms, wherein each of these domains acts as the environment for the other. If evolution is forged by changes in development, and if symbionts are routinely involved in our development, then changes in sympoiesis can constitute an important factor in evolution.
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Affiliation(s)
- Scott F. Gilbert
- Department of Biology, Swarthmore College, Swarthmore, PA, United States
- Evolutionary Phenomics Group, Biotechnology Institute, University of Helsinki, Helsinki, Finland
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7
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Yang L, Lawhorn S, Bongrand C, Kosmopoulos JC, Kuwabara J, VanNieuwenhze M, Mandel MJ, McFall-Ngai M, Ruby E. Bacterial growth dynamics in a rhythmic symbiosis. Mol Biol Cell 2024; 35:ar79. [PMID: 38598294 PMCID: PMC11238090 DOI: 10.1091/mbc.e24-01-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
The symbiotic relationship between the bioluminescent bacterium Vibrio fischeri and the bobtail squid Euprymna scolopes serves as a valuable system to investigate bacterial growth and peptidoglycan (PG) synthesis within animal tissues. To better understand the growth dynamics of V. fischeri in the crypts of the light-emitting organ of its juvenile host, we showed that, after the daily dawn-triggered expulsion of most of the population, the remaining symbionts rapidly proliferate for ∼6 h. At that point the population enters a period of extremely slow growth that continues throughout the night until the next dawn. Further, we found that PG synthesis by the symbionts decreases as they enter the slow-growing stage. Surprisingly, in contrast to the most mature crypts (i.e., Crypt 1) of juvenile animals, most of the symbiont cells in the least mature crypts (i.e., Crypt 3) were not expelled and, instead, remained in the slow-growing state throughout the day, with almost no cell division. Consistent with this observation, the expression of the gene encoding the PG-remodeling enzyme, L,D-transpeptidase (LdtA), was greatest during the slowly growing stage of Crypt 1 but, in contrast, remained continuously high in Crypt 3. Finally, deletion of the ldtA gene resulted in a symbiont that grew and survived normally in culture, but was increasingly defective in competing against its parent strain in the crypts. This result suggests that remodeling of the PG to generate additional 3-3 linkages contributes to the bacterium's fitness in the symbiosis, possibly in response to stresses encountered during the very slow-growing stage.
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Affiliation(s)
- Liu Yang
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - Susannah Lawhorn
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - Clotilde Bongrand
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - James C. Kosmopoulos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Jill Kuwabara
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | | | - Mark J. Mandel
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706
| | - Margaret McFall-Ngai
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Edward Ruby
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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8
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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.
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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
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9
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Nanes Sarfati D, Xue Y, Song ES, Byrne A, Le D, Darmanis S, Quake SR, Burlacot A, Sikes J, Wang B. Coordinated wound responses in a regenerative animal-algal holobiont. Nat Commun 2024; 15:4032. [PMID: 38740753 DOI: 10.1038/s41467-024-48366-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Animal regeneration involves coordinated responses across cell types throughout the animal body. In endosymbiotic animals, whether and how symbionts react to host injury and how cellular responses are integrated across species remain unexplored. Here, we study the acoel Convolutriloba longifissura, which hosts symbiotic Tetraselmis sp. green algae and can regenerate entire bodies from tissue fragments. We show that animal injury causes a decline in the photosynthetic efficiency of the symbiotic algae, alongside two distinct, sequential waves of transcriptional responses in acoel and algal cells. The initial algal response is characterized by the upregulation of a cohort of photosynthesis-related genes, though photosynthesis is not necessary for regeneration. A conserved animal transcription factor, runt, is induced after injury and required for acoel regeneration. Knockdown of Cl-runt dampens transcriptional responses in both species and further reduces algal photosynthetic efficiency post-injury. Our results suggest that the holobiont functions as an integrated unit of biological organization by coordinating molecular networks across species through the runt-dependent animal regeneration program.
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Affiliation(s)
| | - Yuan Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Eun Sun Song
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | | | - Daniel Le
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Adrien Burlacot
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - James Sikes
- Department of Biology, University of San Francisco, San Francisco, CA, USA.
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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10
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Ludington WB. The importance of host physical niches for the stability of gut microbiome composition. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230066. [PMID: 38497267 PMCID: PMC10945397 DOI: 10.1098/rstb.2023.0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/04/2023] [Indexed: 03/19/2024] Open
Abstract
Gut bacteria are prevalent throughout the Metazoa and form complex microbial communities associated with food breakdown, nutrient provision and disease prevention. How hosts acquire and maintain a consistent bacterial flora remains mysterious even in the best-studied animals, including humans, mice, fishes, squid, bugs, worms and flies. This essay visits the evidence that hosts have co-evolved relationships with specific bacteria and that some of these relationships are supported by specialized physical niches that select, sequester and maintain microbial symbionts. Genetics approaches could uncover the mechanisms for recruiting and maintaining the stable and consistent members of the microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- William B. Ludington
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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11
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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'.
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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
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12
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Li R, Zarate D, Avila-Magaña V, Li J. Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve. Proc Biol Sci 2024; 291:20232408. [PMID: 38807516 DOI: 10.1098/rspb.2023.2408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/05/2024] [Indexed: 05/30/2024] Open
Abstract
Photosymbioses between heterotrophic hosts and autotrophic symbionts are evolutionarily prevalent and ecologically significant. However, the molecular mechanisms behind such symbioses remain less elucidated, which hinders our understanding of their origin and adaptive evolution. This study compared gene expression patterns in a photosymbiotic bivalve (Fragum sueziense) and a closely related non-symbiotic species (Trigoniocardia granifera) under different light conditions to detect potential molecular pathways involved in mollusc photosymbiosis. We discovered that the presence of algal symbionts greatly impacted host gene expression in symbiont-containing tissues. We found that the host immune functions were suppressed under normal light compared with those in the dark. In addition, we found that cilia in the symbiont-containing tissues play important roles in symbiont regulation or photoreception. Interestingly, many potential photosymbiosis genes could not be annotated or do not exhibit orthologues in T. granifera transcriptomes, indicating unique molecular functions in photosymbiotic bivalves. Overall, we found both novel and known molecular mechanisms involved in animal-algal photosymbiosis within bivalves. Given that many of the molecular pathways are shared among distantly related host lineages, such as molluscs and cnidarians, it indicates that parallel and/or convergent evolution is instrumental in shaping host-symbiont interactions and responses in these organisms.
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Affiliation(s)
- Ruiqi Li
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, USA
| | - Daniel Zarate
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, USA
| | | | - Jingchun Li
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, USA
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13
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Rohner PT, Moczek AP. Vertically inherited microbiota and environment modifying behaviours conceal genetic variation in dung beetle life history. Proc Biol Sci 2024; 291:20240122. [PMID: 38628120 PMCID: PMC11021930 DOI: 10.1098/rspb.2024.0122] [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: 01/15/2024] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feed back on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating (i) physical environmental modifications and (ii) the vertical inheritance of microbes, we assess how environment modifying behaviour and microbiome transmission shape heritable variation and evolutionary potential. We found that depriving larvae of symbionts and environment modifying behaviours increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that are less amenable to organismal manipulation or restructuring. Our findings also suggest that intact microbiomes, which are commonly thought to increase genetic variation of their hosts, may instead reduce and conceal heritable variation. More broadly, our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.
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Affiliation(s)
- Patrick T. Rohner
- Department of Ecology, Behavior, and Evolution, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Armin P. Moczek
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
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14
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Chen L, Li D, Shen Y, Li Z, Hao H, Ke C, Meng Z, Feng D. Microbiota characterization of the green mussel Perna viridis at the tissue scale and its relationship with the environment. Front Microbiol 2024; 15:1366305. [PMID: 38680921 PMCID: PMC11047130 DOI: 10.3389/fmicb.2024.1366305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024] Open
Abstract
Research on the microbiota associated with marine invertebrates is important for understanding host physiology and the relationship between the host and the environment. In this study, the microbiota of the green mussel Perna viridis was characterized at the tissue scale using 16S rRNA gene high-throughput sequencing and compared with the microbiota of the surrounding environment. Different mussel tissues were sampled, along with two environmental samples (the mussel's attachment substratum and seawater). The results showed that the phyla Proteobacteria, Bacteroidetes, and Spirochaetae were dominant in mussel tissues. The bacterial community composition at the family level varied among the tissues of P. viridis. Although the microbiota of P. viridis clearly differed from that of the surrounding seawater, the composition and diversity of the microbial community of the foot and outer shell surface were similar to those of the substratum, indicating their close relationship with the substratum. KEGG prediction analysis indicated that the bacteria harbored by P. viridis were enriched in the degradation of aromatic compounds, osmoregulation, and carbohydrate oxidation and fermentation, processes that may be important in P. viridis physiology. Our study provides new insights into the tissue-scale characteristics of mussel microbiomes and the intricate connection between mussels and their environment.
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Affiliation(s)
- Liying Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dai Li
- China Nuclear Power Engineering Co., Ltd, Beijing, China
| | - Yawei Shen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhuo Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huanhuan Hao
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhang Meng
- China Nuclear Power Engineering Co., Ltd, Beijing, China
| | - Danqing Feng
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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15
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McFall-Ngai M. Symbiosis takes a front and center role in biology. PLoS Biol 2024; 22:e3002571. [PMID: 38578728 PMCID: PMC10997088 DOI: 10.1371/journal.pbio.3002571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
All animals and plants likely require interactions with microbes, often in strong, persistent symbiotic associations. While the recognition of this phenomenon has been slow in coming, it will impact most, if not all, subdisciplines of biology.
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Affiliation(s)
- Margaret McFall-Ngai
- Biosphere Sciences and Engineering, Carnegie Institution for Science, and Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
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16
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Vijayan N, McAnulty SJ, Sanchez G, Jolly J, Ikeda Y, Nishiguchi MK, Réveillac E, Gestal C, Spady BL, Li DH, Burford BP, Kerwin AH, Nyholm SV. Evolutionary history influences the microbiomes of a female symbiotic reproductive organ in cephalopods. Appl Environ Microbiol 2024; 90:e0099023. [PMID: 38315021 PMCID: PMC10952459 DOI: 10.1128/aem.00990-23] [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: 06/14/2023] [Accepted: 12/09/2023] [Indexed: 02/07/2024] Open
Abstract
Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis, P = 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%) Opitutae (Verrucomicrobia) and Ruegeria (Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test r = 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.
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Affiliation(s)
- Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sarah J. McAnulty
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
- Graduate School of Integrated Science for Life, Hiroshima University, Hiroshima, Japan
| | - Jeffrey Jolly
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Yuzuru Ikeda
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of Ryukyus, Ryukyus, Japan
| | - Michele K. Nishiguchi
- Department of Molecular and Cell Biology, University of California, Merced, California, USA
| | - Elodie Réveillac
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS–La Rochelle Université, La Rochelle, France
| | - Camino Gestal
- Institute of Marine Research (IIM), CSIC, Vigo, Spain
| | - Blake L. Spady
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- U.S. National Oceanic and Atmospheric Administration, National Environmental Satellite Data and Information Service, Center for Satellite Applications and Research, Coral Reef Watch, College Park, Maryland, USA
| | - Diana H. Li
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, USA
| | - Benjamin P. Burford
- Institute of Marine Sciences, University of California, affiliated with the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - Allison H. Kerwin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Biology, McDaniel College, Westminster, Maryland, USA
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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17
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Fung BL, Esin JJ, Visick KL. Vibrio fischeri: a model for host-associated biofilm formation. J Bacteriol 2024; 206:e0037023. [PMID: 38270381 PMCID: PMC10882983 DOI: 10.1128/jb.00370-23] [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: 01/26/2024] Open
Abstract
Multicellular communities of adherent bacteria known as biofilms are often detrimental in the context of a human host, making it important to study their formation and dispersal, especially in animal models. One such model is the symbiosis between the squid Euprymna scolopes and the bacterium Vibrio fischeri. Juvenile squid hatch aposymbiotically and selectively acquire their symbiont from natural seawater containing diverse environmental microbes. Successful pairing is facilitated by ciliary movements that direct bacteria to quiet zones on the surface of the squid's symbiotic light organ where V. fischeri forms a small aggregate or biofilm. Subsequently, the bacteria disperse from that aggregate to enter the organ, ultimately reaching and colonizing deep crypt spaces. Although transient, aggregate formation is critical for optimal colonization and is tightly controlled. In vitro studies have identified a variety of polysaccharides and proteins that comprise the extracellular matrix. Some of the most well-characterized matrix factors include the symbiosis polysaccharide (SYP), cellulose polysaccharide, and LapV adhesin. In this review, we discuss these components, their regulation, and other less understood V. fischeri biofilm contributors. We also highlight what is currently known about dispersal from these aggregates and host cues that may promote it. Finally, we briefly describe discoveries gleaned from the study of other V. fischeri isolates. By unraveling the complexities involved in V. fischeri's control over matrix components, we may begin to understand how the host environment triggers transient biofilm formation and dispersal to promote this unique symbiotic relationship.
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Affiliation(s)
- Brittany L. Fung
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Jeremy J. Esin
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Karen L. Visick
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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18
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Meyerowitz JT, Larsson EM, Murray RM. Development of Cell-Free Transcription-Translation Systems in Three Soil Pseudomonads. ACS Synth Biol 2024; 13:530-537. [PMID: 38319019 DOI: 10.1021/acssynbio.3c00468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
In vitro transcription-translation (TX-TL) can enable faster engineering of biological systems. This speed-up can be significant, especially in difficult-to-transform chassis. This work shows the successful development of TX-TL systems using three soil-derived wild-type Pseudomonads known to promote plant growth: Pseudomonas synxantha, Pseudomonas chlororaphis, and Pseudomonas aureofaciens. All three species demonstrated multiple sonication, runoff, and salt conditions producing detectable protein synthesis. One of these new TX-TL systems, P. synxantha, demonstrated a maximum protein yield of 2.5 μM at 125 proteins per DNA template, a maximum protein synthesis rate of 20 nM/min, and a range of DNA concentrations with a linear correspondence with the resulting protein synthesis. A set of different constitutive promoters driving mNeonGreen expression were tested in TX-TL and integrated into the genome, showing similar normalized strengths for in vivo and in vitro fluorescence. This correspondence between the TX-TL-derived promoter strength and the in vivo promoter strength indicates that these lysate-based cell-free systems can be used to characterize and engineer biological parts without genomic integration, enabling a faster design-build-test cycle.
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Affiliation(s)
- Joseph T Meyerowitz
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| | - Elin M Larsson
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
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19
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Rogers TF, Yalçın G, Briseno J, Vijayan N, Nyholm SV, Simakov O. Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes. Sci Data 2024; 11:40. [PMID: 38184621 PMCID: PMC10771462 DOI: 10.1038/s41597-023-02903-8] [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: 08/15/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024] Open
Abstract
Coleoid cephalopods possess numerous complex, species-specific morphological and behavioural adaptations, e.g., a uniquely structured nervous system that is the largest among the invertebrates. The Hawaiian bobtail squid (Euprymna scolopes) is one of the most established cephalopod species. With its recent publication of the chromosomal-scale genome assembly and regulatory genomic data, it also emerges as a key model for cephalopod gene regulation and evolution. However, the latest genome assembly has been lacking a native gene model set. Our manuscript describes the generation of new long-read transcriptomic data and, made using this combined with a plethora of publicly available transcriptomic and protein sequence data, a new reference annotation for E. scolopes.
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Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria.
| | - Gözde Yalçın
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - John Briseno
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
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20
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Mazel F, Pitteloud C, Guisan A, Pellissier L. Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets. ISME COMMUNICATIONS 2024; 4:ycad013. [PMID: 38374896 PMCID: PMC10875604 DOI: 10.1093/ismeco/ycad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Camille Pitteloud
- Département de la mobilité, du territoire et de l'environnement, Service des forêts, de la nature et du paysage, Sion 1950, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne 1015, Switzerland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
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21
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Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Santos CP, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin CB. Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology. Integr Comp Biol 2023; 63:1226-1239. [PMID: 37370232 PMCID: PMC10755191 DOI: 10.1093/icb/icad087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.
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Affiliation(s)
- Tom Baden
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - John Briseño
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Gabrielle Coffing
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Sophie Cohen-Bodénès
- Laboratoire des Systèmes Perceptifs, Département d'Etudes Cognitives, Ecole Normale Supérieure, PSL University, CNRS, 75005 Paris, France
| | - Amy Courtney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Dominick Dickerson
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Gül Dölen
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Camino Gestal
- Laboratory of Marine Molecular Pathobiology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo 36208, Spain
| | | | - Elizabeth Heath-Heckman
- Departments of Integrative Biology and Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaz Hua
- Department of Ecology and Evolution, University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Ryosuke Kimbara
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan
| | - Mirela Król
- Adam Mickiewicz University in Poznań, Poznań 61-712, Poland
| | - Zdeněk Lajbner
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | - Nicolás Lichilín
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, P.O. Box 129188 Abu Dhabi, United Arab Emirates
| | - Matthew J McCoy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michele K Nishiguchi
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Spencer V Nyholm
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Eve Otjacques
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
- Division of Biosphere Sciences and Engineering, Carnegie Institution for Science, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Pedro Antonio Pérez-Ferrer
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Judit R Pungor
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Thea F Rogers
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Joshua J C Rosenthal
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
| | - Lisa Rouressol
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Noelle Rubas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii Manoa, Honolulu, HI 96822, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Catarina Pereira Santos
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
| | - Darrin T Schultz
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Jeremea O Songco-Casey
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Ian Erik Stewart
- Neural Circuits and Behaviour Lab, Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Surangkana Tuanapaya
- Laboratory of genetics and applied breeding of molluscs, Fisheries College, Ocean University of China, Qingdao 266100, China
| | - Nidhi Vijayan
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | | | - Lucia Zifcakova
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | | | - Willem Weertman
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Caroline B Albertin
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
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22
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Griem-Krey H, Petersen C, Hamerich IK, Schulenburg H. The intricate triangular interaction between protective microbe, pathogen and host determines fitness of the metaorganism. Proc Biol Sci 2023; 290:20232193. [PMID: 38052248 PMCID: PMC10697802 DOI: 10.1098/rspb.2023.2193] [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: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
The microbiota shapes host biology in numerous ways. One example is protection against pathogens, which is likely critical for host fitness in consideration of the ubiquity of pathogens. The host itself can affect abundance of microbiota or pathogens, which has usually been characterized in separate studies. To date, however, it is unclear how the host influences the interaction with both simultaneously and how this triangular interaction determines fitness of the host-microbe assemblage, the so-called metaorganism. To address this current knowledge gap, we focused on a triangular model interaction, consisting of the nematode Caenorhabditis elegans, its protective symbiont Pseudomonas lurida MYb11 and its pathogen Bacillus thuringiensis Bt679. We combined the two microbes with C. elegans mutants with altered immunity and/or microbial colonization, and found that (i) under pathogen stress, immunocompetence has a larger influence on metaorganism fitness than colonization with the protective microbe; (ii) in almost all cases, MYb11 still improves fitness; and (iii) disruption of p38 MAPK signalling, which contributes centrally to immunity against Bt679, completely reverses the protective effect of MYb11, which further reduces nematode survival and fitness upon infection with Bt679. Our study highlights the complex interplay between host, protective microbe and pathogen in shaping metaorganism biology.
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Affiliation(s)
- Hanne Griem-Krey
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel 24118, Germany
| | - Carola Petersen
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel 24118, Germany
| | - Inga K. Hamerich
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel 24118, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel 24118, Germany
- Antibiotic resistance group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
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23
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Wiesmann CL, Wang NR, Zhang Y, Liu Z, Haney CH. Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals. FEMS Microbiol Rev 2023; 47:fuac048. [PMID: 36521845 PMCID: PMC10719066 DOI: 10.1093/femsre/fuac048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/17/2023] Open
Abstract
Regardless of the outcome of symbiosis, whether it is pathogenic, mutualistic or commensal, bacteria must first colonize their hosts. Intriguingly, closely related bacteria that colonize diverse hosts with diverse outcomes of symbiosis have conserved host-association and virulence factors. This review describes commonalities in the process of becoming host associated amongst bacteria with diverse lifestyles. Whether a pathogen, commensal or mutualist, bacteria must sense the presence of and migrate towards a host, compete for space and nutrients with other microbes, evade the host immune system, and change their physiology to enable long-term host association. We primarily focus on well-studied taxa, such as Pseudomonas, that associate with diverse model plant and animal hosts, with far-ranging symbiotic outcomes. Given the importance of opportunistic pathogens and chronic infections in both human health and agriculture, understanding the mechanisms that facilitate symbiotic relationships between bacteria and their hosts will help inform the development of disease treatments for both humans, and the plants we eat.
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Affiliation(s)
- Christina L Wiesmann
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nicole R Wang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yue Zhang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhexian Liu
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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24
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Alker AT, Farrell MV, Aspiras AE, Dunbar TL, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine bacteria reveals functional insights during bacteria-stimulated metamorphosis. mBio 2023; 14:e0150223. [PMID: 37530556 PMCID: PMC10470607 DOI: 10.1128/mbio.01502-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023] Open
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm, Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for testing the genetic tractability of marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts resulted in the successful conjugation of 12 marine strains from the Alphaproteobacteria and Gammaproteobacteria classes. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with potential implications for environmental restoration and biotechnology. IMPORTANCE Marine Proteobacteria are attractive targets for genetic engineering due to their ability to produce a diversity of bioactive metabolites and their involvement in host-microbe symbioses. Modular cloning toolkits have become a standard for engineering model microbes, such as Escherichia coli, because they enable innumerable mix-and-match DNA assembly and engineering options. However, such modular tools have not yet been applied to most marine bacterial species. In this work, we adapt a modular plasmid toolkit for use in a set of 12 marine bacteria from the Gammaproteobacteria and Alphaproteobacteria classes. We demonstrate the utility of this genetic toolkit by engineering a marine Pseudoalteromonas bacterium to study their association with its host animal Hydroides elegans. This work provides a proof of concept that modular genetic tools can be applied to diverse marine bacteria to address basic science questions and for biotechnology innovations.
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Affiliation(s)
- Amanda T. Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Morgan V. Farrell
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Alpher E. Aspiras
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Tiffany L. Dunbar
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Andriy Fedoriouk
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Jeffrey E. Jones
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Sama R. Mikhail
- Department of Biology, San Diego State University, San Diego, California, USA
| | | | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Nicholas J. Shikuma
- Department of Biology, San Diego State University, San Diego, California, USA
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25
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Bapteste E, Huneman P, Keller L, Teulière J, Lopez P, Teeling EC, Lindner AB, Baudisch A, Ludington WB, Franceschi C. Expanding evolutionary theories of ageing to better account for symbioses and interactions throughout the Web of Life. Ageing Res Rev 2023; 89:101982. [PMID: 37321383 PMCID: PMC10771319 DOI: 10.1016/j.arr.2023.101982] [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: 04/14/2023] [Revised: 05/26/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023]
Abstract
How, when, and why organisms age are fascinating issues that can only be fully addressed by adopting an evolutionary perspective. Consistently, the main evolutionary theories of ageing, namely the Mutation Accumulation theory, the Antagonistic Pleiotropy theory, and the Disposable Soma theory, have formulated stimulating hypotheses that structure current debates on both the proximal and ultimate causes of organismal ageing. However, all these theories leave a common area of biology relatively under-explored. The Mutation Accumulation theory and the Antagonistic Pleiotropy theory were developed under the traditional framework of population genetics, and therefore are logically centred on the ageing of individuals within a population. The Disposable Soma theory, based on principles of optimising physiology, mainly explains ageing within a species. Consequently, current leading evolutionary theories of ageing do not explicitly model the countless interspecific and ecological interactions, such as symbioses and host-microbiomes associations, increasingly recognized to shape organismal evolution across the Web of Life. Moreover, the development of network modelling supporting a deeper understanding on the molecular interactions associated with ageing within and between organisms is also bringing forward new questions regarding how and why molecular pathways associated with ageing evolved. Here, we take an evolutionary perspective to examine the effects of organismal interactions on ageing across different levels of biological organisation, and consider the impact of surrounding and nested systems on organismal ageing. We also apply this perspective to suggest open issues with potential to expand the standard evolutionary theories of ageing.
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Affiliation(s)
- Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
| | - Philippe Huneman
- Institut d'Histoire et de Philosophie des Sciences et des Techniques (CNRS/ Université Paris I Sorbonne), Paris, France
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
| | - Annette Baudisch
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, 5230 Odense M, Denmark
| | - William B Ludington
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; Department of Applied Mathematics and Laboratory of Systems Medicine of Aging, Lobachevsky University, Nizhny Novgorod 603950, Russia
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26
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Rouressol L, Briseno J, Vijayan N, Chen GY, Ritschard EA, Sanchez G, Nyholm SV, McFall-Ngai MJ, Simakov O. Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid. iScience 2023; 26:107091. [PMID: 37426346 PMCID: PMC10329180 DOI: 10.1016/j.isci.2023.107091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Light organs (LO) with symbiotic bioluminescent bacteria are hallmarks of many bobtail squid species. These organs possess structural and functional features to modulate light, analogous to those found in coleoid eyes. Previous studies identified four transcription factors and modulators (SIX, EYA, PAX6, DAC) associated with both eyes and light organ development, suggesting co-option of a highly conserved gene regulatory network. Using available topological, open chromatin, and transcriptomic data, we explore the regulatory landscape around the four transcription factors as well as genes associated with LO and shared LO/eye expression. This analysis revealed several closely associated and putatively co-regulated genes. Comparative genomic analyses identified distinct evolutionary origins of these putative regulatory associations, with the DAC locus showing a unique topological and evolutionarily recent organization. We discuss different scenarios of modifications to genome topology and how these changes may have contributed to the evolutionary emergence of the light organ.
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Affiliation(s)
- Lisa Rouressol
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - John Briseno
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Grischa Y. Chen
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - Elena A. Ritschard
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, NA, Italy
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Margaret J. McFall-Ngai
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
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27
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Essock-Burns T, Lawhorn S, Wu L, McClosky S, Moriano-Gutierrez S, Ruby EG, McFall-Ngai MJ. Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership. MICROBIOME 2023; 11:68. [PMID: 37004104 PMCID: PMC10064550 DOI: 10.1186/s40168-023-01509-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Many animals and plants acquire their coevolved symbiotic partners shortly post-embryonic development. Thus, during embryogenesis, cellular features must be developed that will promote both symbiont colonization of the appropriate tissues, as well as persistence at those sites. While variation in the degree of maturation occurs in newborn tissues, little is unknown about how this variation influences the establishment and persistence of host-microbe associations. RESULTS The binary symbiosis model, the squid-vibrio (Euprymna scolopes-Vibrio fischeri) system, offers a way to study how an environmental gram-negative bacterium establishes a beneficial, persistent, extracellular colonization of an animal host. Here, we show that bacterial symbionts occupy six different colonization sites in the light-emitting organ of the host that have both distinct morphologies and responses to antibiotic treatment. Vibrio fischeri was most resilient to antibiotic disturbance when contained within the smallest and least mature colonization sites. We show that this variability in crypt development at the time of hatching allows the immature sites to act as a symbiont reservoir that has the potential to reseed the more mature sites in the host organ when they have been cleared by antibiotic treatment. This strategy may produce an ecologically significant resiliency to the association. CONCLUSIONS The data presented here provide evidence that the evolution of the squid-vibrio association has been selected for a nascent organ with a range of host tissue maturity at the onset of symbiosis. The resulting variation in physical and chemical environments results in a spectrum of host-symbiont interactions, notably, variation in susceptibility to environmental disturbance. This "insurance policy" provides resiliency to the symbiosis during the critical period of its early development. While differences in tissue maturity at birth have been documented in other animals, such as along the infant gut tract of mammals, the impact of this variation on host-microbiome interactions has not been studied. Because a wide variety of symbiosis characters are highly conserved over animal evolution, studies of the squid-vibrio association have the promise of providing insights into basic strategies that ensure successful bacterial passage between hosts in horizontally transmitted symbioses. Video Abstract.
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Affiliation(s)
- Tara Essock-Burns
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i, Mānoa, Honolulu, HI, USA
- Present address: Carnegie Institution for Science, Division of Biosphere Sciences and Engineering, Pasadena, CA, USA
| | - Susannah Lawhorn
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i, Mānoa, Honolulu, HI, USA
| | - Leo Wu
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i, Mānoa, Honolulu, HI, USA
| | - Sawyer McClosky
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i, Mānoa, Honolulu, HI, USA
| | - Silvia Moriano-Gutierrez
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i, Mānoa, Honolulu, HI, USA
- Present address: Department of Fundamental Biology, University of Lausanne, Lausanne, Switzerland
| | - Edward G Ruby
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i, Mānoa, Honolulu, HI, USA
- Present address: Carnegie Institution for Science, Division of Biosphere Sciences and Engineering, Pasadena, CA, USA
| | - Margaret J McFall-Ngai
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i, Mānoa, Honolulu, HI, USA.
- Present address: Carnegie Institution for Science, Division of Biosphere Sciences and Engineering, Pasadena, CA, USA.
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28
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Ma Y, He J, Sieber M, von Frieling J, Bruchhaus I, Baines JF, Bickmeyer U, Roeder T. The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity. Commun Biol 2023; 6:289. [PMID: 36934156 PMCID: PMC10024726 DOI: 10.1038/s42003-023-04671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/07/2023] [Indexed: 03/20/2023] Open
Abstract
The close association between animals and their associated microbiota is usually beneficial for both partners. Here, we used a simple marine model invertebrate, the flatworm Macrostomum lignano, to characterize the host-microbiota interaction in detail. This analysis revealed that the different developmental stages each harbor a specific microbiota. Studies with gnotobiotic animals clarified the physiological significance of the microbiota. While no fitness benefits were mediated by the microbiota when food was freely available, animals with microbiota showed significantly increased fitness with a reduced food supply. The microbiota of M. lignano shows circadian rhythmicity, affecting both the total bacterial load and the behavior of specific taxa. Moreover, the presence of the worm influences the composition of the bacterial consortia in the environment. In summary, the Macrostomum-microbiota system described here can serve as a general model for host-microbe interactions in marine invertebrates.
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Affiliation(s)
- Yuanyuan Ma
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Jinru He
- Kiel University, Zoological Institute, Cell and Developmental Biology, Kiel, Germany
| | - Michael Sieber
- Max-Planck Institute for Evolutionary Biology, Dept. Evolutionary Theory, Plön, Germany
| | - Jakob von Frieling
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Iris Bruchhaus
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John F Baines
- Kiel University, Medical Faculty, Institute for Experimental Medicine, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, Group Evolutionary Medicine, Plön, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institute, Biosciences, Ecological Chemistry, Bremerhaven, Germany
| | - Thomas Roeder
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany.
- German Center for Lung Research (DZL), Airway Research Center North, Kiel, Germany.
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29
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Guo Y, Meng L, Wang M, Zhong Z, Li D, Zhang Y, Li H, Zhang H, Seim I, Li Y, Jiang A, Ji Q, Su X, Chen J, Fan G, Li C, Liu S. Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves. BMC Biol 2023; 21:51. [PMID: 36882766 PMCID: PMC9993606 DOI: 10.1186/s12915-023-01551-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution. RESULTS We present a hologenome of Conchocele bisecta (Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers of C. bisecta, and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent in C. bisecta. Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance in C. bisecta. CONCLUSIONS Thus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.
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Affiliation(s)
- Yang Guo
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lingfeng Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minxiao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Denghui Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Yuli Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Aijun Jiang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Qianyue Ji
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xiaoshan Su
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. .,BGI-Shenzhen, Shenzhen, 518083, China.
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,College of Marine Science, University of Chinese Academy of Sciences, Qingdao, 266400, China. .,South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. .,Qingdao Key Laboratory of Marine Genomics, BGI-qingdao, Qingdao, China.
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30
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Rossetto V, Moore-Machacek A, Woods DF, Galvão HM, Shanahan RM, Hickey A, O'Leary N, O'Gara F, McGlacken GP, Reen FJ. Structural modification of the Pseudomonas aeruginosa alkylquinoline cell-cell communication signal, HHQ, leads to benzofuranoquinolines with anti-virulence behaviour in ESKAPE pathogens. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36862576 DOI: 10.1099/mic.0.001303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Microbial populations have evolved intricate networks of negotiation and communication through which they can coexist in natural and host ecosystems. The nature of these systems can be complex and they are, for the most part, poorly understood at the polymicrobial level. The Pseudomonas Quinolone Signal (PQS) and its precursor 4-hydroxy-2-heptylquinoline (HHQ) are signal molecules produced by the important nosocomial pathogen
Pseudomonas aeruginosa
. They are known to modulate the behaviour of co-colonizing bacterial and fungal pathogens such as Bacillus atropheaus, Candida albicans and Aspergillus fumigatus. While the structural basis for alkyl-quinolone signalling within
P. aeruginosa
has been studied extensively, less is known about how structural derivatives of these molecules can influence multicellular behaviour and population-level decision-making in other co-colonizing organisms. In this study, we investigated a suite of small molecules derived initially from the HHQ framework, for anti-virulence activity against ESKAPE pathogens, at the species and strain levels. Somewhat surprisingly, with appropriate substitution, loss of the alkyl chain (present in HHQ and PQS) did not result in a loss of activity, presenting a more easily accessible synthetic framework for investigation. Virulence profiling uncovered significant levels of inter-strain variation among the responses of clinical and environmental isolates to small-molecule challenge. While several lead compounds were identified in this study, further work is needed to appreciate the extent of strain-level tolerance to small-molecule anti-infectives among pathogenic organisms.
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Affiliation(s)
- Veronica Rossetto
- Faculty of Science and Technology, Universidade do Algarve, Algarve, Portugal.,School of Microbiology, University College Cork, Cork, Ireland
| | | | - David F Woods
- School of Microbiology, University College Cork, Cork, Ireland
| | - Helena M Galvão
- Faculty of Science and Technology, Universidade do Algarve, Algarve, Portugal
| | - Rachel M Shanahan
- School of Chemistry and Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
| | - Aobha Hickey
- School of Chemistry and Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
| | - Niall O'Leary
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O'Gara
- School of Microbiology, University College Cork, Cork, Ireland.,Biomerit Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Gerard P McGlacken
- School of Chemistry and Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| | - F Jerry Reen
- School of Microbiology, University College Cork, Cork, Ireland.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
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31
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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.
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32
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Sanchez S, Ng WL. Motility Control as a Possible Link Between Quorum Sensing to Surface Attachment in Vibrio Species. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:65-75. [PMID: 36792871 DOI: 10.1007/978-3-031-22997-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
In this chapter, we discuss motility control as a possible link between quorum sensing (QS) to surface attachment in Vibrio species. QS regulates a variety of behaviors that are important for the life cycle of many bacterial species, including virulence factor production, biofilm formation, or metabolic homeostasis. Therefore, without QS, many species of bacteria cannot survive in their natural environments. Here, we summarize several QS systems in different Vibrio species and discuss some of emerging features that suggest QS is intimately connected to motility control. Finally, we speculate the connection between motility and QS is critical for Vibrio species to detect solid surfaces for surface attachment.
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Affiliation(s)
- Sandra Sanchez
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, USA
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, USA.
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33
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Guckes KR, Miyashiro TI. The type-VI secretion system of the beneficial symbiont Vibrio fischeri. MICROBIOLOGY (READING, ENGLAND) 2023; 169:10.1099/mic.0.001302. [PMID: 36809081 PMCID: PMC9972734 DOI: 10.1099/mic.0.001302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The mutualistic symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the marine bacterium Vibrio fischeri is a powerful experimental system for determining how intercellular interactions impact animal-bacterial associations. In nature, this symbiosis features multiple strains of V. fischeri within each adult animal, which indicates that different strains initially colonize each squid. Various studies have demonstrated that certain strains of V. fischeri possess a type-VI secretion system (T6SS), which can inhibit other strains from establishing symbiosis within the same host habitat. The T6SS is a bacterial melee weapon that enables a cell to kill adjacent cells by translocating toxic effectors via a lancet-like apparatus. This review describes the progress that has been made in understanding the factors that govern the structure and expression of the T6SS in V. fischeri and its effect on the symbiosis.
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Alker AT, Aspiras AE, Dunbar TL, Farrell MV, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526474. [PMID: 36778221 PMCID: PMC9915575 DOI: 10.1101/2023.01.31.526474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea , which stimulates the metamorphosis of the model tubeworm, Hydroides elegans . Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for rapidly creating and iteratively testing genetic tractability by modifying marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts enabled the successful transformation of twelve marine strains across two Proteobacteria classes, four orders and ten genera. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with broader implications for environmental restoration and biotechnology.
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Juhas M. Communication Between Microorganisms. BRIEF LESSONS IN MICROBIOLOGY 2023:27-41. [DOI: 10.1007/978-3-031-29544-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Ganesan R, Wierz JC, Kaltenpoth M, Flórez LV. How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts. Microbiol Mol Biol Rev 2022; 86:e0012621. [PMID: 36301103 PMCID: PMC9769632 DOI: 10.1128/mmbr.00126-21] [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: 01/01/2023] Open
Abstract
Beneficial associations with bacteria are widespread across animals, spanning a range of symbiont localizations, transmission routes, and functions. While some of these associations have evolved into obligate relationships with permanent symbiont localization within the host, the majority require colonization of every host generation from the environment or via maternal provisions. Across the broad diversity of host species and tissue types that beneficial bacteria can colonize, there are some highly specialized strategies for establishment yet also some common patterns in the molecular basis of colonization. This review focuses on the mechanisms underlying the early stage of beneficial bacterium-invertebrate associations, from initial contact to the establishment of the symbionts in a specific location of the host's body. We first reflect on general selective pressures that can drive the transition from a free-living to a host-associated lifestyle in bacteria. We then cover bacterial molecular factors for colonization in symbioses from both model and nonmodel invertebrate systems where these have been studied, including terrestrial and aquatic host taxa. Finally, we discuss how interactions between multiple colonizing bacteria and priority effects can influence colonization. Taking the bacterial perspective, we emphasize the importance of developing new experimentally tractable systems to derive general insights into the ecological factors and molecular adaptations underlying the origin and establishment of beneficial symbioses in animals.
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Affiliation(s)
- Ramya Ganesan
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Jürgen C. Wierz
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura V. Flórez
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Plant and Environmental Sciences, Section for Organismal Biology, University of Copenhagen, Copenhagen, Denmark
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Song J, Li B, Zeng L, Ye Z, Wu W, Hu B. A Mini-Review on Reflectins, from Biochemical Properties to Bio-Inspired Applications. Int J Mol Sci 2022; 23:ijms232415679. [PMID: 36555320 PMCID: PMC9779258 DOI: 10.3390/ijms232415679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Some cephalopods (squids, octopuses, and cuttlefishes) produce dynamic structural colors, for camouflage or communication. The key to this remarkable capability is one group of specialized cells called iridocytes, which contain aligned membrane-enclosed platelets of high-reflective reflectins and work as intracellular Bragg reflectors. These reflectins have unusual amino acid compositions and sequential properties, which endows them with functional characteristics: an extremely high reflective index among natural proteins and the ability to answer various environmental stimuli. Based on their unique material composition and responsive self-organization properties, the material community has developed an impressive array of reflectin- or iridocyte-inspired optical systems with distinct tunable reflectance according to a series of internal and external factors. More recently, scientists have made creative attempts to engineer mammalian cells to explore the function potentials of reflectin proteins as well as their working mechanism in the cellular environment. Progress in wide scientific areas (biophysics, genomics, gene editing, etc.) brings in new opportunities to better understand reflectins and new approaches to fully utilize them. The work introduced the composition features, biochemical properties, the latest developments, future considerations of reflectins, and their inspiration applications to give newcomers a comprehensive understanding and mutually exchanged knowledge from different communities (e.g., biology and material).
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Affiliation(s)
- Junyi Song
- Correspondence: (J.S.); (B.H.); Tel.: +86-18969697729 (J.S.); +86-13308492461 (B.H.)
| | | | | | | | | | - Biru Hu
- Correspondence: (J.S.); (B.H.); Tel.: +86-18969697729 (J.S.); +86-13308492461 (B.H.)
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Schmittmann L, Rahn T, Busch K, Fraune S, Pita L, Hentschel U. Stability of a dominant sponge-symbiont in spite of antibiotic-induced microbiome disturbance. Environ Microbiol 2022; 24:6392-6410. [PMID: 36250983 DOI: 10.1111/1462-2920.16249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 10/13/2022] [Indexed: 01/12/2023]
Abstract
Marine sponges are known for their complex and stable microbiomes. However, the lack of a gnotobiotic sponge-model and experimental methods to manipulate both the host and the microbial symbionts currently limit our mechanistic understanding of sponge-microbial symbioses. We have used the North Atlantic sponge species Halichondria panicea to evaluate the use of antibiotics to generate gnotobiotic sponges. We further asked whether the microbiome can be reestablished via recolonization with the natural microbiome. Experiments were performed in marine gnotobiotic facilities equipped with a custom-made, sterile, flow-through aquarium system. Bacterial abundance dynamics were monitored qualitatively and quantitatively by 16 S rRNA gene amplicon sequencing and qPCR, respectively. Antibiotics induced dysbiosis by favouring an increase of opportunistic, antibiotic-resistant bacteria, resulting in more complex, but less specific bacteria-bacteria interactions than in untreated sponges. The abundance of the dominant symbiont, Candidatus Halichondribacter symbioticus, remained overall unchanged, reflecting its obligately symbiotic nature. Recolonization with the natural microbiome could not reverse antibiotic-induced dysbiosis. However, single bacterial taxa that were transferred, successfully recolonized the sponge and affected bacteria-bacteria interactions. By experimentally manipulating microbiome composition, we could show the stability of a sponge-symbiont clade despite microbiome dysbiosis. This study contributes to understanding both host-bacteria and bacteria-bacteria interactions in the sponge holobiont.
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Affiliation(s)
- Lara Schmittmann
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - Tanja Rahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - Sebastian Fraune
- Heinrich-Heine-University, Zoology and Organismic Interactions, Düsseldorf, Germany
| | - Lucía Pita
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany.,Institut de Ciències del Mar - CSIC, Marine Biology and Oceanography, Marine Biogeochemistry, Atmosphere and Climate, Barcelona, Spain
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany.,Christian-Albrechts-University Kiel, Kiel, Germany
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Gundlach KA, Nawroth J, Kanso E, Nasrin F, Ruby EG, McFall-Ngai M. Ciliated epithelia are key elements in the recruitment of bacterial partners in the squid-vibrio symbiosis. Front Cell Dev Biol 2022; 10:974213. [PMID: 36340026 PMCID: PMC9632347 DOI: 10.3389/fcell.2022.974213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/07/2022] [Indexed: 11/28/2022] Open
Abstract
The Hawaiian bobtail squid, Euprymna scolopes, harvests its luminous symbiont, Vibrio fischeri, from the surrounding seawater within hours of hatching. During embryogenesis, the host animal develops a nascent light organ with ciliated fields on each lateral surface. We hypothesized that these fields function to increase the efficiency of symbiont colonization of host tissues. Within minutes of hatching from the egg, the host’s ciliated fields shed copious amounts of mucus in a non-specific response to bacterial surface molecules, specifically peptidoglycan (PGN), from the bacterioplankton in the surrounding seawater. Experimental manipulation of the system provided evidence that nitric oxide in the mucus drives an increase in ciliary beat frequency (CBF), and exposure to even small numbers of V. fischeri cells for short periods resulted in an additional increase in CBF. These results indicate that the light-organ ciliated fields respond specifically, sensitively, and rapidly, to the presence of nonspecific PGN as well as symbiont cells in the ambient seawater. Notably, the study provides the first evidence that this induction of an increase in CBF occurs as part of a thus far undiscovered initial phase in colonization of the squid host by its symbiont, i.e., host recognition of V. fischeri cues in the environment within minutes. Using a biophysics-based mathematical analysis, we showed that this rapid induction of increased CBF, while accelerating bacterial advection, is unlikely to be signaled by V. fischeri cells interacting directly with the organ surface. These overall changes in CBF were shown to significantly impact the efficiency of V. fischeri colonization of the host organ. Further, once V. fischeri has fully colonized the host tissues, i.e., about 12–24 h after initial host-symbiont interactions, the symbionts drove an attenuation of mucus shedding from the ciliated fields, concomitant with an attenuation of the CBF. Taken together, these findings offer a window into the very first interactions of ciliated surfaces with their coevolved microbial partners.
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Affiliation(s)
- Katrina A. Gundlach
- Kewalo Marine Laboratory, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
| | - Janna Nawroth
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Eva Kanso
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA, United States
| | - Farzana Nasrin
- Department of Mathematics, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
| | - Edward G. Ruby
- Kewalo Marine Laboratory, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
| | - Margaret McFall-Ngai
- Kewalo Marine Laboratory, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
- *Correspondence: Margaret McFall-Ngai,
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Suria AM, Smith S, Speare L, Chen Y, Chien I, Clark EG, Krueger M, Warwick AM, Wilkins H, Septer AN. Prevalence and diversity of type VI secretion systems in a model beneficial symbiosis. Front Microbiol 2022; 13:988044. [PMID: 36187973 PMCID: PMC9515649 DOI: 10.3389/fmicb.2022.988044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
The type VI secretion system (T6SS) is widely distributed in diverse bacterial species and habitats where it is required for interbacterial competition and interactions with eukaryotic cells. Previous work described the role of a T6SS in the beneficial symbiont, Vibrio fischeri, during colonization of the light organ of Euprymna scolopes squid. However, the prevalence and diversity of T6SSs found within the distinct symbiotic structures of this model host have not yet been determined. Here, we analyzed 73 genomes of isolates from squid light organs and accessory nidamental glands (ANGs) and 178 reference genomes. We found that the majority of these bacterial symbionts encode diverse T6SSs from four distinct classes, and most share homology with T6SSs from more distantly related species, including pathogens of animals and humans. These findings indicate that T6SSs with shared evolutionary histories can be integrated into the cellular systems of host-associated bacteria with different effects on host health. Furthermore, we found that one T6SS in V. fischeri is located within a genomic island with high genomic plasticity. Five distinct genomic island genotypes were identified, suggesting this region encodes diverse functional potential that natural selection can act on. Finally, analysis of newly described T6SSs in roseobacter clade ANG isolates revealed a novel predicted protein that appears to be a fusion of the TssB-TssC sheath components. This work underscores the importance of studying T6SSs in diverse organisms and natural habitats to better understand how T6SSs promote the propagation of bacterial populations and impact host health.
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Affiliation(s)
- Andrea M. Suria
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stephanie Smith
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lauren Speare
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Yuzhou Chen
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Iris Chien
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Emily Grace Clark
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Madelyn Krueger
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alexander M. Warwick
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Hannah Wilkins
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alecia N. Septer
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,*Correspondence: Alecia N. Septer,
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Vroom MM, Troncoso-Garcia A, Duscher AA, Foster JS. Modeled microgravity alters apoptotic gene expression and caspase activity in the squid-vibrio symbiosis. BMC Microbiol 2022; 22:202. [PMID: 35982413 PMCID: PMC9389742 DOI: 10.1186/s12866-022-02614-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022] Open
Abstract
Background Spaceflight is a novel and profoundly stressful environment for life. One aspect of spaceflight, microgravity, has been shown to perturb animal physiology thereby posing numerous health risks, including dysregulation of normal developmental pathways. Microgravity can also negatively impact the interactions between animals and their microbiomes. However, the effects of microgravity on developmental processes influenced by beneficial microbes, such as apoptosis, remains poorly understood. Here, the binary mutualism between the bobtail squid, Euprymna scolopes, and the gram-negative bacterium, Vibrio fischeri, was studied under modeled microgravity conditions to elucidate how this unique stressor alters apoptotic cell death induced by beneficial microbes. Results Analysis of the host genome and transcriptome revealed a complex network of apoptosis genes affiliated with extrinsic/receptor-mediated and intrinsic/stress-induced apoptosis. Expression of apoptosis genes under modeled microgravity conditions occurred earlier and at high levels compared to gravity controls, in particular the expression of genes encoding initiator and executioner caspases. Functional assays of these apoptotic proteases revealed heightened activity under modeled microgravity; however, these increases could be mitigated using caspase inhibitors. Conclusions The outcomes of this study indicated that modeled microgravity alters the expression of both extrinsic and intrinsic apoptosis gene expression and that this process is mediated in part by caspases. Modeled microgravity-associated increases of caspase activity can be pharmacologically inhibited suggesting that perturbations to the normal apoptosis signaling cascade can be mitigated, which may have broader implications for maintaining animal-microbial homeostasis in spaceflight. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02614-x.
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Affiliation(s)
- Madeline M Vroom
- Department of Microbiology and Cell Science, Space Life Science Lab, University of Florida, Merritt Island, FL, 32953, USA
| | - Angel Troncoso-Garcia
- Department of Microbiology and Cell Science, Space Life Science Lab, University of Florida, Merritt Island, FL, 32953, USA
| | - Alexandrea A Duscher
- Department of Microbiology and Cell Science, Space Life Science Lab, University of Florida, Merritt Island, FL, 32953, USA
| | - Jamie S Foster
- Department of Microbiology and Cell Science, Space Life Science Lab, University of Florida, Merritt Island, FL, 32953, USA.
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A peptidoglycan-recognition protein orchestrates the first steps of symbiont recruitment in the squid-vibrio symbiosis. Symbiosis 2022; 87:31-43. [DOI: 10.1007/s13199-022-00855-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Drerup C. The behavioural ecology of Sepiolidae (Cephalopoda: Sepiolida): a review. MOLLUSCAN RESEARCH 2022. [DOI: 10.1080/13235818.2022.2107503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Christian Drerup
- Marine Behavioural Ecology Group, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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Abstract
During colonization of the Hawaiian bobtail squid (Euprymna scolopes), Vibrio fischeri bacteria undergo a lifestyle transition from a planktonic motile state in the environment to a biofilm state in host mucus. Cyclic diguanylate (c-di-GMP) is a cytoplasmic signaling molecule that is important for regulating motility-biofilm transitions in many bacterial species. V. fischeri encodes 50 proteins predicted to synthesize and/or degrade c-di-GMP, but a role for c-di-GMP regulation during host colonization has not been investigated. We examined strains exhibiting either low or high levels of c-di-GMP during squid colonization and found that while a low-c-di-GMP strain had no colonization defect, a high c-di-GMP strain was severely impaired. Expression of a heterologous c-di-GMP phosphodiesterase restored colonization, demonstrating that the effect is due to high c-di-GMP levels. In the constitutive high-c-di-GMP state, colonizing V. fischeri exhibited reduced motility, altered biofilm aggregate morphology, and a regulatory interaction where transcription of one polysaccharide locus is inhibited by the presence of the other polysaccharide. Our results highlight the importance of proper c-di-GMP regulation during beneficial animal colonization, illustrate multiple pathways regulated by c-di-GMP in the host, and uncover an interplay of multiple exopolysaccharide systems in host-associated aggregates.
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Impact of transit time on the reproductive capacity of Euprymna scolopes as a laboratory animal. Lab Anim Res 2022; 38:25. [PMID: 35908064 PMCID: PMC9338615 DOI: 10.1186/s42826-022-00135-2] [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: 04/06/2022] [Accepted: 07/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Hawaiian bobtail squid Euprymna scolopes hosts various marine bacterial symbionts, and these symbioses have served as models for the animal-microbe relationships that are important for host health. Within a light organ, E. scolopes harbors populations of the bacterium Vibrio fischeri, which produce low levels of bioluminescence that the squid uses for camouflage. The symbiosis is initially established after a juvenile squid hatches from its egg and acquires bacterial symbionts from the ambient marine environment. The relative ease with which a cohort of wild-caught E. scolopes can be maintained in a mariculture facility has facilitated over 3 decades of research involving juvenile squid. However, because E. scolopes is native to the Hawaiian archipelago, their transport from Hawaii to research facilities often represents a stress that has the potential to impact their physiology. RESULTS Here, we describe animal survival and reproductive capacity associated with a cohort of squid assembled from two shipments with markedly different transit times. We found that the lower juvenile squid counts generated by animals with the longer transit time were not due to the discrepancy in shipment but instead to fewer female squid that produced egg clutches at an elevated rate, which we term hyper-reproductivity. We find that hyper-reproductive females were responsible for 58% of the egg clutches laid. CONCLUSIONS The significance of these findings for E. scolopes biology and husbandry is discussed, thereby providing a platform for future investigation and further development of this cephalopod as a valuable lab animal for microbiology research.
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Mutational Analysis of Vibrio fischeri c-di-GMP-Modulating Genes Reveals Complex Regulation of Motility. J Bacteriol 2022; 204:e0010922. [PMID: 35758751 PMCID: PMC9295575 DOI: 10.1128/jb.00109-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The symbiont Vibrio fischeri uses motility to colonize its host. In numerous bacterial species, motility is negatively controlled by cyclic-di-GMP (c-di-GMP), which is produced by diguanylate cyclases (DGCs) with GGDEF domains and degraded by phosphodiesterases with either EAL or HD-GYP domains. To begin to decode the functions of the 50 Vibrio fischeri genes with GGDEF, EAL, and/or HD-GYP domains, we deleted each gene and assessed each mutant's migration through tryptone broth salt (TBS) soft agar medium containing or lacking magnesium (Mg) and calcium (Ca), which are known to influence V. fischeri motility. We identified 6, 13, and 16 mutants with altered migration in TBS-Mg, TBS, and TBS-Ca soft agar, respectively, a result that underscores the importance of medium conditions in assessing gene function. A biosensor-based assay revealed that Mg and Ca affected c-di-GMP levels negatively and positively, respectively; the severe decrease in c-di-GMP caused by Mg addition correlates with its strong positive impact on bacterial migration. A mutant defective for VF_0494, a homolog of V. cholerae rocS, exhibited a severe defect in migration across all conditions. Motility of a VF_1603 VF_2480 double mutant was also severely defective and could be restored by expression of "c-di-GMP-blind" alleles of master flagellar regulator flrA. Together, this work sheds light on the genes and conditions that influence c-di-GMP-mediated control over motility in V. fischeri and provides a foundation for (i) assessing roles of putative c-di-GMP-binding proteins, (ii) evaluating other c-di-GMP-dependent phenotypes in V. fischeri, (iii) uncovering potential redundancy, and (iv) deciphering signal transduction mechanisms. IMPORTANCE Critical bacterial processes, including motility, are influenced by c-di-GMP, which is controlled by environment-responsive synthetic and degradative enzymes. Because bacteria such as Vibrio fischeri use motility to colonize their hosts, understanding the roles of c-di-GMP-modulating enzymes in controlling motility has the potential to inform on microbe-host interactions. We leveraged recent advances in genetic manipulation to generate 50 mutants defective for putative c-di-GMP synthetic and degradative enzymes. We then assessed the consequences on motility, manipulating levels of magnesium and calcium, which inversely influenced motility and levels of c-di-GMP. Distinct subsets of the 50 genes were required under the different conditions. Our data thus provide needed insight into the functions of these enzymes and environmental factors that influence them.
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Gundlach KA, Briegel A. Zooming in on host-symbiont interactions: advances in cryo-EM sample processing methods and future application to symbiotic tissues. Symbiosis 2022. [DOI: 10.1007/s13199-022-00859-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractAnimals, plants, and fungi live in a microbe-dominated world. Investigating the interactions and processes at the host-microbe interface offers insight to how bacteria influence the development, health, and disease of the host. Optimization of existing imaging technologies and development of novel instrumentation will provide the tools needed to fully understand the dynamic relationship that occurs at the host-microbe interface throughout the lifetime of the host. In this review, we describe the current methods used in cryo-electron microscopy (cryo-EM) including cryo-fixation, sample processing, FIB-SEM, and cryotomography. Further, we highlight the new advances associated with these methods that open the cryo-EM discipline to large, complex multicellular samples, like symbiotic tissues. We describe the advantages and challenges associated with correlative imaging techniques and sample thinning methods like lift-out. By highlighting recent pioneering studies in the large-volume or symbiotic sample workflows, we provide insight into how symbiotic model systems will benefit from cryo-EM methods to provide artefact-free, near-native, macromolecular-scale resolution imaging at the host-microbe interface throughout the development and maintenance of symbiosis. Cryo-EM methods have brought a deep fundamental understanding of prokaryotic biology since its conception. We propose the application of existing and novel cryo-EM techniques to symbiotic systems is the logical next step that will bring an even greater understanding how microbes interact with their host tissues.
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Abstract
Animal development is an inherently complex process that is regulated by highly conserved genomic networks, and the resulting phenotype may remain plastic in response to environmental signals. Despite development having been studied in a more natural setting for the past few decades, this framework often precludes the role of microbial prokaryotes in these processes. Here, we address how microbial symbioses impact animal development from the onset of gametogenesis through adulthood. We then provide a first assessment of which developmental processes may or may not be influenced by microbial symbioses and, in doing so, provide a holistic view of the budding discipline of developmental symbiosis.
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Affiliation(s)
- Tyler J Carrier
- GEOMAR Helmholtz Centre for Ocean Research, Kiel 24105, Germany.,Zoological Institute, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Thomas C G Bosch
- Zoological Institute, Christian-Albrechts University of Kiel, Kiel 24118, Germany
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Fronk DC, Sachs JL. Symbiotic organs: the nexus of host-microbe evolution. Trends Ecol Evol 2022; 37:599-610. [PMID: 35393155 DOI: 10.1016/j.tree.2022.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
Abstract
Diverse plants and animals have evolved specialized structures to filter and house beneficial microbes. These symbiotic organs form crucial points of exchange between host and symbiont, are often shaped by both partners, and exhibit features that facilitate a suite of microbial services. While symbiotic organs exhibit varied function, morphology, and developmental plasticity, they share core features linked to the evolutionary maintenance of beneficial symbiosis. Moreover, these organs can have a significant role in altering the demographic forces that shape microbial genomes, driving population bottlenecks and horizontal gene transfer (HGT). To advance our understanding of these 'joint phenotypes' across varied systems, future research must consider the emergent forces that can shape symbiotic organs, including fitness feedbacks and conflicts between interacting genomes.
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Affiliation(s)
- David C Fronk
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA; Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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James EB, Pan X, Schwartz O, Wilson ACC. SymbiQuant: A Machine Learning Object Detection Tool for Polyploid Independent Estimates of Endosymbiont Population Size. Front Microbiol 2022; 13:816608. [PMID: 35663891 PMCID: PMC9160162 DOI: 10.3389/fmicb.2022.816608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Quantifying the size of endosymbiont populations is challenging because endosymbionts are typically difficult or impossible to culture and commonly polyploid. Current approaches to estimating endosymbiont population sizes include quantitative PCR (qPCR) targeting endosymbiont genomic DNA and flow-cytometry. While qPCR captures genome copy number data, it does not capture the number of bacterial cells in polyploid endosymbiont populations. In contrast, flow cytometry can capture accurate estimates of whole host-level endosymbiont population size, but it is not readily able to capture data at the level of endosymbiotic host cells. To complement these existing approaches for estimating endosymbiont population size, we designed and implemented an object detection/segmentation tool for counting the number of endosymbiont cells in micrographs of host tissues. The tool, called SymbiQuant, which makes use of recent advances in deep neural networks includes a graphic user interface that allows for human curation of tool output. We trained SymbiQuant for use in the model aphid/Buchnera endosymbiosis and studied Buchnera population dynamics and phenotype over aphid postembryonic development. We show that SymbiQuant returns accurate counts of endosymbionts, and readily captures Buchnera phenotype. By replacing our training data with data composed of annotated microscopy images from other models of endosymbiosis, SymbiQuant has the potential for broad application. Our tool, which is available on GitHub, adds to the repertoire of methods researchers can use to study endosymbiosis at the organismal, genome, and now endosymbiotic host tissue or cell levels.
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Affiliation(s)
- Edward B. James
- Department of Biology, University of Miami, Coral Gables, FL, United States
- *Correspondence: Edward B. James,
| | - Xu Pan
- Computational Neuroscience Lab, Department of Computer Science, University of Miami, Coral Gables, FL, United States
| | - Odelia Schwartz
- Computational Neuroscience Lab, Department of Computer Science, University of Miami, Coral Gables, FL, United States
| | - Alex C. C. Wilson
- Department of Biology, University of Miami, Coral Gables, FL, United States
- Alex C. C. Wilson,
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