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Ni Y, Chu T, Yan S, Wang Y. Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae. J Gen Virol 2024; 105. [PMID: 38446011 DOI: 10.1099/jgv.0.001967] [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: 03/07/2024] Open
Abstract
Twenty complete genomes (29-63 kb) and 29 genomes with an estimated completeness of over 90 % (30-90 kb) were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered viruses contribute to the expansion of viral taxonomy by introducing 46 potential new families. Except for one virus, all others belong to the class Caudoviricetes. The exception is a novel member of the recently characterized viral group known as Gossevirus. Fifteen viruses were predicted to be temperate. The predicted hosts for the viruses appear to be involved in various aspects of the nitrogen cycle, including nitrogen fixation, oxidation and denitrification. Two viruses were identified to have a host of Flavobacterium and Tepidimonas fonticaldi, respectively, by matching CRISPR spacers with viral protospacers. Our findings provide an overview for characterizing and identifying specific viruses from Yangshan Harbor. The Gossevirus-like virus uncovered emphasizes the need for further comprehensive isolation and investigation of polinton-like viruses.
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Affiliation(s)
- Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Ting Chu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Shuling Yan
- Entwicklungsgenetik und Zellbiologie der Tiere, Philipps-Universität Marburg, Marburg, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, PR China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, PR China
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2
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Murúa P, Garvetto A, Egan S, Gachon CMM. The Reemergence of Phycopathology: When Algal Biology Meets Ecology and Biosecurity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:231-255. [PMID: 37253694 DOI: 10.1146/annurev-phyto-020620-120425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.
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Affiliation(s)
- Pedro Murúa
- Instituto de Acuicultura, Universidad Austral de Chile-Sede Puerto Montt, Los Lagos, Chile;
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Andrea Garvetto
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Tyrol, Austria
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Claire M M Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Muséum National d'Histoire Naturelle, CNRS, Paris, France
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3
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Moreno-García DM, Salas-Rojas M, Fernández-Martínez E, López-Cuellar MDR, Sosa-Gutierrez CG, Peláez-Acero A, Rivero-Perez N, Zaragoza-Bastida A, Ojeda-Ramírez D. Sea urchins: an update on their pharmacological properties. PeerJ 2022; 10:e13606. [PMID: 35811815 PMCID: PMC9261939 DOI: 10.7717/peerj.13606] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
Sea urchins are a group of benthic invertebrates characterized by having rigid globose bodies, covered in spines, and have an innate immune system that has allowed them to survive in the environment and defend against many pathogens that affect them. They are consumed for their unique flavor, but also for possessing a rich source of bioactive compounds which make them a source for a wide array of medicinal properties. Thus, these may be used to discover and develop new drugs such as anti-bacterials, anti-carcinogenics and anti-virals. Precisely for those reasons, this revision is centered on the known biological activities in various sea urchin species. Recently, the potential pharmacological benefits of nine sea urchin species [Diadema antillarum (Philippi 1845), Echinometra mathaei (de Blainville), Evechinus chloroticus (Valenciennes), Mesocentrotus nudus (Agassiz, 1863), Paracentrotus lividus (Lamarck, 1816), Scaphechinus mirabilis (Agazzis, 1863), Stomopneustes variolaris (Lamarck, 1816), Tripneustes depressus (Agassiz, 1863), and Tripneustes ventricosus (Lamarck, 1816)] have been evaluated. Our work includes a comprehensive review of the anti-fungal, anti-parasitic, anti-inflammatory, hepatoprotective, anti-viral, anti-diabetic, anti-lipidemic, gastro-protective and anti-cardiotoxic effects. Furthermore, we revised the compounds responsible of these pharmacological effects. This work was intended for a broad readership in the fields of pharmacology, drugs and devices, marine biology and aquaculture, fisheries and fish science. Our results suggest that organic extracts, as well as pure compounds obtained from several parts of sea urchin bodies are effective in vitro and in vivo pharmacological models. As such, these properties manifest the potential use of sea urchins to develop emergent active ingredients.
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Affiliation(s)
- Dulce María Moreno-García
- Área Académica de Medicina Veterinaria y Zootecnia. Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo de Bravo, Hidalgo, México
| | - Monica Salas-Rojas
- Unidad de Investigación Médica en Inmunología, Unidad Medica de Alta Especialidad, Hospital de Pediatría, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Eduardo Fernández-Martínez
- Área Académica de Medicina, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca, Hidalgo, Mexico
| | - Ma del Rocío López-Cuellar
- Área Académica de Ingeniería en Alimentos e Ingeniería Agroindustrial. Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, México
| | - Carolina G. Sosa-Gutierrez
- Área Académica de Medicina Veterinaria y Zootecnia. Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo de Bravo, Hidalgo, México
| | - Armando Peláez-Acero
- Área Académica de Medicina Veterinaria y Zootecnia. Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo de Bravo, Hidalgo, México
| | - Nallely Rivero-Perez
- Área Académica de Medicina Veterinaria y Zootecnia. Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo de Bravo, Hidalgo, México
| | - Adrian Zaragoza-Bastida
- Área Académica de Medicina Veterinaria y Zootecnia. Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo de Bravo, Hidalgo, México
| | - Deyanira Ojeda-Ramírez
- Área Académica de Medicina Veterinaria y Zootecnia. Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo de Bravo, Hidalgo, México
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4
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Gao Y, Lu Y, Dungait JAJ, Liu J, Lin S, Jia J, Yu G. The "Regulator" Function of Viruses on Ecosystem Carbon Cycling in the Anthropocene. Front Public Health 2022; 10:858615. [PMID: 35425734 PMCID: PMC9001988 DOI: 10.3389/fpubh.2022.858615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
Viruses act as "regulators" of the global carbon cycle because they impact the material cycles and energy flows of food webs and the microbial loop. The average contribution of viruses to the Earth ecosystem carbon cycle is 8.6‰, of which its contribution to marine ecosystems (1.4‰) is less than its contribution to terrestrial (6.7‰) and freshwater (17.8‰) ecosystems. Over the past 2,000 years, anthropogenic activities and climate change have gradually altered the regulatory role of viruses in ecosystem carbon cycling processes. This has been particularly conspicuous over the past 200 years due to rapid industrialization and attendant population growth. The progressive acceleration of the spread and reproduction of viruses may subsequently accelerate the global C cycle.
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Affiliation(s)
- Yang Gao
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yao Lu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jennifer A J Dungait
- Geography, College of Life and Environmental Science, University of Exeter, Exeter, United Kingdom.,Carbon Management Centre, SRUC-Scotland's Rural College, Edinburgh, United Kingdom
| | - Jianbao Liu
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shunhe Lin
- Department of Obstetrics and Gynecology, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Junjie Jia
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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5
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Grzybowski A, Żaczek M, Górski A, Weber-Dąbrowska B, Międzybrodzki R. Bronisława Fejgin (1883-1943): Forgotten Important Contributor to International Microbiology and Phage Therapy. Antibiotics (Basel) 2021; 10:1353. [PMID: 34827291 PMCID: PMC8614871 DOI: 10.3390/antibiotics10111353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Bronisława Brandla Fejgin was a Polish-born Jewish female physician. Among Fejgin's numerous articles in the field of microbiology, her later work was almost entirely devoted to phage research. Although not equally famous as the phage pioneers from Western Europe, F.W. Twort and F. d'Herelle, Fejgin's contribution to phage research deserves proper recognition. Her studies on phages resulted in the publication of numerous original scientific reports. These articles, published mostly in French, constitute an important source of information and expertise on early attempts towards therapeutic use of phages in humans. The interwar period marks the most intense years in Bronisława Fejgin's research activity, brutally interrupted by her death in the Warsaw Ghetto in 1943. Her microbiology contributions have not been analyzed so far. Thus, the aim of this article is to fill the existing gap in the history of microbiology and phage therapy.
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Affiliation(s)
- Andrzej Grzybowski
- Institute for Research in Ophthalmology, 60-836 Poznań, Poland;
- Department of Ophthalmology, University of Warmia and Mazury, 10-561 Olsztyn, Poland
| | - Maciej Żaczek
- Bacteriophage Laboratory, Department of Phage Therapy, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (A.G.); (B.W.-D.); (R.M.)
| | - Andrzej Górski
- Bacteriophage Laboratory, Department of Phage Therapy, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (A.G.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Teaching Hospital, Medical University of Warsaw, 02-005 Warsaw, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Department of Phage Therapy, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (A.G.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Department of Phage Therapy, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (A.G.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, 02-006 Warsaw, Poland
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6
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Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia JM, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A. Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. mSystems 2021; 6:e0053721. [PMID: 34184913 PMCID: PMC8269241 DOI: 10.1128/msystems.00537-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 05/26/2021] [Indexed: 01/21/2023] Open
Abstract
Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes; however, little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes (the entire plasmid content of an environment) and identified 200 viral sequences, which clustered into 41 genus-level viral clusters (approximately equivalent to viral genera) including 9 known and 32 putative new genera. We used publicly available bacterial whole-genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria. The publicly available WGS enabled mapping bacterial hosts to several viral sequences. The WGS of groundwater isolates increased the depth of host prediction by allowing host identification at the strain level. The latter included 4 viruses that were almost entirely (>99% query coverage, >99% identity) identified as integrated in the genomes of Pseudomonas, Acidovorax, and Castellaniella strains, resulting in high-confidence host assignments. Lastly, 21 of these viruses carried putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they are key players in microbial adaption to environmental stress. IMPORTANCE To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detected several novel phage genera along with those previously established. Our approach of using the whole-genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage genes suggest that they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their life cycles, and their effects on groundwater microbiome and biogeochemistry.
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Affiliation(s)
- Ankita Kothari
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hanqiao Zhang
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Anatori Prieto
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Drishti Soneja
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sarah Spencer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sara Altenburg
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Matthew W. Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, USA
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Energy Biosciences Institute, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Eric J. Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of MIT Cambridge, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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7
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Viral footprints across Gulfs of Kathiawar Peninsula and Arabian Sea: Unraveled from pelagic sediment metagenomic data. Virus Res 2021; 302:198485. [PMID: 34146609 DOI: 10.1016/j.virusres.2021.198485] [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: 11/19/2020] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 11/21/2022]
Abstract
Marine biosphere is one of the largest, diverse and dynamic system hosting numerous of microorganisms. Viruses being the most abundant under explored lifeforms in ocean, represent a reservoir of great genetic diversity. We report the metagenomic insights on the viral communities in the deep sediments of the two Gulfs of Gujarat i.e. Gulf of Khambhat and Gulf of Kutch, with one sample from Arabian Sea, treated as open sea control. The viral reads were filtered from the whole dataset, assembled and studied for viral diversity, which was visualized by Pavian. The sequences were checked for the viral abundance, diversity and functionality. The resulting viral taxonomic classification contained 6 orders, 8 families and 47 genera. The results revealed that the phages infecting Cyanobacterium, Bacillus and Vibrio dominated the sediments. Further, it was observed that majority of viral sequences belonged to double-stranded DNA phages. The present study attempts to provide a primary insight of the viral signals and potential genetic content in the Gulfs of Kathiawar.
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8
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Boilard A, Dubé CE, Gruet C, Mercière A, Hernandez-Agreda A, Derome N. Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont. Microorganisms 2020; 8:microorganisms8111682. [PMID: 33138319 PMCID: PMC7692791 DOI: 10.3390/microorganisms8111682] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Coral microbiomes are critical to holobiont health and functioning, but the stability of host–microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, “bleaching”), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont’s diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.
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Affiliation(s)
- Aurélie Boilard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
| | - Caroline E. Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA;
- Correspondence: (C.E.D.); (N.D.)
| | - Cécile Gruet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
| | - Alexandre Mercière
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan CEDEX, France;
- Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea, French Polynesia
| | | | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Correspondence: (C.E.D.); (N.D.)
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9
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Colombet J, Fuster M, Billard H, Sime-Ngando T. Femtoplankton: What's New? Viruses 2020; 12:E881. [PMID: 32806713 PMCID: PMC7472349 DOI: 10.3390/v12080881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 01/01/2023] Open
Abstract
Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010-2020) of high abundances of biomimetic mineral-organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities.
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Affiliation(s)
- Jonathan Colombet
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (M.F.); (H.B.); (T.S.-N.)
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10
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Tang BL, Yang J, Chen XL, Wang P, Zhao HL, Su HN, Li CY, Yu Y, Zhong S, Wang L, Lidbury I, Ding H, Wang M, McMinn A, Zhang XY, Chen Y, Zhang YZ. A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria. Nat Commun 2020; 11:285. [PMID: 31941905 PMCID: PMC6962226 DOI: 10.1038/s41467-019-14133-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/13/2019] [Indexed: 12/23/2022] Open
Abstract
Predator-prey interactions play important roles in the cycling of marine organic matter. Here we show that a Gram-negative bacterium isolated from marine sediments (Pseudoalteromonas sp. strain CF6-2) can kill Gram-positive bacteria of diverse peptidoglycan (PG) chemotypes by secreting the metalloprotease pseudoalterin. Secretion of the enzyme requires a Type II secretion system. Pseudoalterin binds to the glycan strands of Gram positive bacterial PG and degrades the PG peptide chains, leading to cell death. The released nutrients, including PG-derived D-amino acids, can then be utilized by strain CF6-2 for growth. Pseudoalterin synthesis is induced by PG degradation products such as glycine and glycine-rich oligopeptides. Genes encoding putative pseudoalterin-like proteins are found in many other marine bacteria. This study reveals a new microbial interaction in the ocean. Predator-prey interactions play important roles in the cycling of marine organic matter. Here the authors show that a Gram-negative bacterium isolated from marine sediments can kill and feed on Gram-positive bacteria by secreting a peptidoglycan-degrading enzyme.
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Affiliation(s)
- Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Jie Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Hui-Lin Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yang Yu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Shuai Zhong
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Lei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Haitao Ding
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yin Chen
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China. .,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China.
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11
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Howard-Varona C, Lindback MM, Bastien GE, Solonenko N, Zayed AA, Jang H, Andreopoulos B, Brewer HM, Glavina Del Rio T, Adkins JN, Paul S, Sullivan MB, Duhaime MB. Phage-specific metabolic reprogramming of virocells. ISME JOURNAL 2020; 14:881-895. [PMID: 31896786 PMCID: PMC7082346 DOI: 10.1038/s41396-019-0580-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/25/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022]
Abstract
Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. Here we investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. We independently infected the marine Pseudoalteromonas bacterium with siphovirus PSA-HS2 and podovirus PSA-HP1. Time-resolved multi-omics unveiled drastically different metabolic reprogramming and resource requirements by each virocell, which were related to phage–host genomic complementarity and viral fitness. Namely, HS2 was more complementary to the host in nucleotides and amino acids, and fitter during infection than HP1. Functionally, HS2 virocells hardly differed from uninfected cells, with minimal host metabolism impacts. HS2 virocells repressed energy-consuming metabolisms, including motility and translation. Contrastingly, HP1 virocells substantially differed from uninfected cells. They repressed host transcription, responded to infection continuously, and drastically reprogrammed resource acquisition, central carbon and energy metabolisms. Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. Finally, we relate phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA
| | - G Eric Bastien
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - HoBin Jang
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Bill Andreopoulos
- US Department of Energy Joint Genome Institute, 1800 Mitchell Dr #100, Walnut Creek, CA, 94598, USA
| | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), 902 Battelle Blvd, Richland, WA, 99354, USA
| | - Tijana Glavina Del Rio
- US Department of Energy Joint Genome Institute, 1800 Mitchell Dr #100, Walnut Creek, CA, 94598, USA
| | - Joshua N Adkins
- Biological Science Division, PNNL, 902 Battelle Blvd, Richland, WA, 99354, USA
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH, 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA. .,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH, 43210, USA. .,Center for RNA Biology, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, USA.
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA.
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12
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Shapshak P. Astrovirology, Astrobiology, Artificial Intelligence: Extra-Solar System Investigations. GLOBAL VIROLOGY III: VIROLOGY IN THE 21ST CENTURY 2019. [PMCID: PMC7120930 DOI: 10.1007/978-3-030-29022-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This chapter attempts to encompass and tackle a large problem in Astrovirology and Astrobiology. There is a huge anthropomorphic prejudice that although life is unlikely, the just-right Goldilocks terrestrial conditions mean that the just-right balance of minerals and basic small molecules inevitably result in life as we know it throughout our solar system, galaxy, and the rest of the universe. Moreover, when such conditions on planets such as ours may not be quite right for the origin of life, it is popularly opined that asteroids and comets magically produce life or at the very least, the important, if not crucial components of terrestrial life so that life then blooms, when their fragments cruise the solar system, stars, and galaxies, and plummet onto appropriately bedecked planets and moons. It is no longer extraordinary to detect extraterrestrial solar systems. Moreover, since extra-solar system space exploration has commenced, this provides the problem of detecting life with enhanced achievability. Small organisms, which replicate outside of a living cell or host, would not be catalogued as viruses. How about viruses that cohabit with life? On the Earth, viruses are a major, if underestimated, condition of life – will that be the case elsewhere? Detection of extra-solar system viruses, if they exist, requires finding life, since viruses necessitate life to replicate. (It should be noted, though, that viruses could be detected through various types of portable ultra-microscopes, including Electron Microscopes (EM) (scanning and transmission) as well as Atomic Force Microscopes (AFM).) However, extra-solar system detection of life does not oblige that viruses exist ubiquitously. Viruses are important potential components of biospheres because of their multiple interactions and influence on evolution, although viruses are small and obligatory parasitic. In addition, nanotechnology – living or replicating nano-synthetic machine organisms might also be present out there, and require consideration as well. An imposing caveat is that, if found, could some extraterrestrial viruses and synthetic nanotechnological microorganisms infect humans? Possibly, intelligence and cognition may at times be contemporaneous with life. Concomitantly, life and viruses that may be detected, could well be impacted upon by intelligences existing on such exoplanets (and vice versa). Coming to an understanding of the plurality of extraterrestrial intelligence is an optimal objective, in order to avoid causing harm on exoplanets, as well as avoiding conflict and possible human devastation. This is especially the case if we encounter greatly advanced galactic-level civilizations, compared to terrestrial civilizations. Their machine and bionic technologies on the Dyson engineering civilization scale may be prominently superior to ours; their biological expertise may be similarly critically radical. For example, they may use viruses for purposes for which we are barely aware, and which could be utterly deadly for humans. A series of steps is being taken in space exploration. Scientists hypothesize and claim that types of life may be near the Earth, in the solar system, and outside the solar system, similar to ours in the sense that only such conditions, Goldilocks conditions, are key sine qua non requirements, based on our terrestrial chemistry and biochemistry. If detected within the solar system, will life or its remnants resemble terrestrial life? Outside the solar system a similar chauvinism exists, although the likelihood for life, in any event, remains probably low, according to more cautious approaches to the problem. The study of our solar system includes planets, asteroids, comets, and other planetesimals that have been in overall contiguity during several billion years; anthropomorphisms claims life consequently has been developing along terrestrial-type mechanisms. However, a non-anthropomorphic view would surmise, probably not, especially for extra-solar system locales. The prime warning and admonition in all these deliberations is the contamination and damage, which current and past practice and procedures has caused and continues, due to insufficient biocontainment concepts and technology to date. Advances in the development of robotics, artificial intelligence (AI), and high capacity ultrafast quantum computers (QC) greatly enhance the sophisticated control and logical development of extra-solar system studies. Consequently, future long-range manned space exploration seems unwarranted. Clearly, reduced dangers to human health and safety, will result from the use of intelligent machine-based investigations and besides, with increased cost-effectiveness. Space exploration comes at great cost to humanity as a whole and utilizes global resources. Consequently, appropriate organizational measures and planning/cooperation need to be in place. Moreover, the bottom line is that despite all the slogans and claims, there have been next to no financial benefits to our planet as a whole. Such financial and heedless difficulties need to be addressed, the sooner the better. In addition, prior to exposure to exoplanetary life, deep understanding of the problems of infectious diseases and immune dysfunction risks are needed. In addition, global efforts should avoid serendipity and stochasticity as this work should be directed with long-term organization, commitment, scientific, and technological methodology. This chapter briefly reviews such questions assuming a new paradigm for oversight of extrasolar system viral investigations including intelligence and life. Finances are included as an essential adjunct.
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