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Browne RK, Luo Q, Wang P, Mansour N, Kaurova SA, Gakhova EN, Shishova NV, Uteshev VK, Kramarova LI, Venu G, Vaissi S, Taheri-Khas Z, Heshmatzad P, Bagaturov MF, Janzen P, Naranjo RE, Swegen A, Strand J, McGinnity D, Dunce I. Ecological Civilisation and Amphibian Sustainability through Reproduction Biotechnologies, Biobanking, and Conservation Breeding Programs (RBCs). Animals (Basel) 2024; 14:1455. [PMID: 38791672 PMCID: PMC11117272 DOI: 10.3390/ani14101455] [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: 03/05/2024] [Revised: 04/23/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Intergenerational justice entitles the maximum retention of Earth's biodiversity. The 2022 United Nations COP 15, "Ecological Civilisation: Building a Shared Future for All Life on Earth", is committed to protecting 30% of Earth's terrestrial environments and, through COP 28, to mitigate the effects of the climate catastrophe on the biosphere. We focused this review on three core themes: the need and potential of reproduction biotechnologies, biobanks, and conservation breeding programs (RBCs) to satisfy sustainability goals; the technical state and current application of RBCs; and how to achieve the future potentials of RBCs in a rapidly evolving environmental and cultural landscape. RBCs include the hormonal stimulation of reproduction, the collection and storage of sperm and oocytes, and artificial fertilisation. Emerging technologies promise the perpetuation of species solely from biobanked biomaterials stored for perpetuity. Despite significant global declines and extinctions of amphibians, and predictions of a disastrous future for most biodiversity, practical support for amphibian RBCs remains limited mainly to a few limited projects in wealthy Western countries. We discuss the potential of amphibian RBCs to perpetuate amphibian diversity and prevent extinctions within multipolar geopolitical, cultural, and economic frameworks. We argue that a democratic, globally inclusive organisation is needed to focus RBCs on regions with the highest amphibian diversity. Prioritisation should include regional and international collaborations, community engagement, and support for RBC facilities ranging from zoos and other institutions to those of private carers. We tabulate a standard terminology for field programs associated with RBCs for publication and media consistency.
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Affiliation(s)
| | - Qinghua Luo
- School of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, China; (Q.L.); (P.W.)
- College of Biological and Chemical Engineering, Changsha University, Changsha 410022, China
| | - Pei Wang
- School of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, China; (Q.L.); (P.W.)
- College of Biological and Chemical Engineering, Changsha University, Changsha 410022, China
| | - Nabil Mansour
- Fujairah Research Centre (FRC), Al-Hilal Tower 3003, Fujairah P.O. Box 666, United Arab Emirates;
| | - Svetlana A. Kaurova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino 142290, Russia; (S.A.K.); (E.N.G.); (N.V.S.); (V.K.U.)
| | - Edith N. Gakhova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino 142290, Russia; (S.A.K.); (E.N.G.); (N.V.S.); (V.K.U.)
| | - Natalia V. Shishova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino 142290, Russia; (S.A.K.); (E.N.G.); (N.V.S.); (V.K.U.)
| | - Victor K. Uteshev
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino 142290, Russia; (S.A.K.); (E.N.G.); (N.V.S.); (V.K.U.)
| | - Ludmila I. Kramarova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Russia;
| | - Govindappa Venu
- Centre for Applied Genetics, Department of Zoology, Jnana Bharathi Campus, Bangalore University, Bengaluru 560056, India;
- Evolving Phylo Lab, Centre for Ecological Sciences, Indian Institute of Science, Bengaluru 560012, India
| | - Somaye Vaissi
- Department of Biology, Faculty of Science, Razi University, Kermanshah 57146, Iran; (S.V.); (Z.T.-K.)
| | - Zeynab Taheri-Khas
- Department of Biology, Faculty of Science, Razi University, Kermanshah 57146, Iran; (S.V.); (Z.T.-K.)
| | - Pouria Heshmatzad
- Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan 49138, Iran;
| | - Mikhail F. Bagaturov
- IUCN/SSC/Athens Institute for Education and Research/Zoological Institute RAS, St. Petersburg 199034, Russia;
| | - Peter Janzen
- Verband Deutscher Zoodirectoren/Justus-von-Liebig-Schule, 47166 Duisburg, Germany;
| | - Renato E. Naranjo
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, Giovanni, Farina 566 y Baltra, San Rafael, Quito 171102, Ecuador;
| | - Aleona Swegen
- School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan 2308, Australia;
| | - Julie Strand
- Department of Animal and Veterinary Science, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark;
| | - Dale McGinnity
- Ectotherm Department, Nashville Zoo at Grassmere, Nashville, TN 37211, USA;
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Çelekli A, Zariç ÖE. Breathing life into Mars: Terraforming and the pivotal role of algae in atmospheric genesis. LIFE SCIENCES IN SPACE RESEARCH 2024; 41:181-190. [PMID: 38670646 DOI: 10.1016/j.lssr.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024]
Abstract
The Martian environment, characterized by extreme aridity, frigid temperatures, and a lack of atmospheric oxygen, presents a formidable challenge for potential terraforming endeavors. This review article synthesizes current research on utilizing algae as biocatalysts in the proposed terraforming of Mars, assessing their capacity to facilitate Martian atmospheric conditions through photosynthetic bioengineering. We analyze the physiological and genetic traits of extremophile algae that equip them for survival in extreme habitats on Earth, which serve as analogs for Martian surface conditions. The potential for these organisms to mediate atmospheric change on Mars is evaluated, specifically their role in biogenic oxygen production and carbon dioxide sequestration. We discuss strategies for enhancing algal strains' resilience and metabolic efficiency, including genetic modification and the development of bioreactors for controlled growth in extraterrestrial environments. The integration of algal systems with existing mechanical and chemical terraforming proposals is also examined, proposing a synergistic approach for establishing a nascent Martian biosphere. Ethical and ecological considerations concerning introducing terrestrial life to extra-planetary bodies are critically appraised. This appraisal includes an examination of potential ecological feedback loops and inherent risks associated with biological terraforming. Biological terraforming is the theoretical process of deliberately altering a planet's atmosphere, temperature, and ecosystem to render it suitable for Earth-like life. The feasibility of a phased introduction of life, starting with microbial taxa and progressing to multicellular organisms, fosters a supportive atmosphere on Mars. By extending the frontier of biotechnological innovation into space, this work contributes to the foundational understanding necessary for one of humanity's most audacious goals-the terraforming of another planet.
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Affiliation(s)
- Abuzer Çelekli
- Gaziantep University, Faculty of Art and Science, Department of Biology, Gaziantep, Turkey; Gaziantep University, Environmental Research Center (GÜÇAMER), Gaziantep, Turkey.
| | - Özgür Eren Zariç
- Gaziantep University, Faculty of Art and Science, Department of Biology, Gaziantep, Turkey; Gaziantep University, Environmental Research Center (GÜÇAMER), Gaziantep, Turkey
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3
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Maull V, Pla Mauri J, Conde Pueyo N, Solé R. A synthetic microbial Daisyworld: planetary regulation in the test tube. J R Soc Interface 2024; 21:20230585. [PMID: 38321922 PMCID: PMC10847846 DOI: 10.1098/rsif.2023.0585] [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: 10/07/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
The idea that the Earth system self-regulates in a habitable state was proposed in the 1970s by James Lovelock, who conjectured that life plays a self-regulatory role on a planetary-level scale. A formal approach to such hypothesis was presented afterwards under a toy model known as the Daisyworld. The model showed how such life-geosphere homeostasis was an emergent property of the system, where two species with different properties adjusted their populations to the changing external environment. So far, this ideal world exists only as a mathematical or computational construct, but it would be desirable to have a real, biological implementation of Lovelock's picture beyond our one biosphere. Inspired by the exploration of synthetic ecosystems using genetic engineering and recent cell factory designs, here we propose a possible implementation for a microbial Daisyworld. This includes: (i) an explicit proposal for an engineered design of a two-strain consortia, using pH as the external, abiotic control parameter and (ii) several theoretical and computational case studies including two, three and multiple species assemblies. The special alternative implementations and their implications in other synthetic biology scenarios, including ecosystem engineering, are outlined.
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Affiliation(s)
- Victor Maull
- Institució Catalana de Recerca i Estudis Avançats, Psg Lluis Companys, Barcelona, Spain
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Jordi Pla Mauri
- Institució Catalana de Recerca i Estudis Avançats, Psg Lluis Companys, Barcelona, Spain
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Nuria Conde Pueyo
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona 08003, Spain
- EMBL Barcelona, European Molecular Biology Laboratory (EMBL), Barcelona 08003, Spain
| | - Ricard Solé
- Institució Catalana de Recerca i Estudis Avançats, Psg Lluis Companys, Barcelona, Spain
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona 08003, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Plante M. Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives. Front Bioeng Biotechnol 2023; 11:1266298. [PMID: 38053845 PMCID: PMC10694798 DOI: 10.3389/fbioe.2023.1266298] [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: 07/24/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.
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Affiliation(s)
- Mirco Plante
- Collège Montmorency, Laval, QC, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
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Coleine C, Delgado-Baquerizo M. Unearthing terrestrial extreme microbiomes for searching terrestrial-like life in the Solar System. Trends Microbiol 2022; 30:1101-1115. [PMID: 35568658 DOI: 10.1016/j.tim.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023]
Abstract
The possibility of life elsewhere in the universe has fascinated humankind for ages. To the best of our knowledge, life, as we know it, is limited to planet Earth; yet current investigation suggests that life might be more common than previously thought. In this review, we explore extreme terrestrial analogue environments in the search for some notable examples of extreme organisms, including overlooked microbial groups such as viruses, fungi, and protists, associated with limits of life on Earth. This knowledge is integral to provide the foundational principles needed to predict what sort of Earth-like organisms we might find in the Solar System and beyond, and to understand the future and origins of life on Earth.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain; Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, 41013 Sevilla, Spain.
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A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems. Nat Commun 2022; 13:5608. [PMID: 36153325 PMCID: PMC9509365 DOI: 10.1038/s41467-022-33358-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 09/14/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractMarine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.
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Maull V, Solé R. Network-level containment of single-species bioengineering. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210396. [PMID: 35757875 PMCID: PMC9234816 DOI: 10.1098/rstb.2021.0396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/09/2022] [Indexed: 01/03/2023] Open
Abstract
Ecological systems are facing major diversity losses in this century owing to Anthropogenic effects. Habitat loss, overexploitation of resources, invasion and pollution are rapidly jeopardizing the survival of whole communities. It has been recently suggested that a potential approach to flatten the curve of species extinction and prevent catastrophic shifts would involve the engineering of one selected species within one of these communities. Such possibility has started to become part of potential intervention scenarios to preserve biodiversity. Despite its potential, very little is known about the actual dynamic responses of complex ecological networks to the introduction of a synthetic strains derived from a resident species. In this paper, we address this problem by modelling the response of a community to the addition of a synthetic strain derived from a member of a stable ecosystem. We show that the community interaction matrix largely limits the spread of the engineered strain, thus suggesting that species diversity acts as an ecological firewall. The implications for future scenarios of ecosystem engineering are outlined. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.
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Affiliation(s)
- Victor Maull
- ICREA-Complex Systems Laboratory, UPF-PRBB, Dr Aiguader 80, Barcelona 08003, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, Barcelona 08003, Spain
| | - Ricard Solé
- ICREA-Complex Systems Laboratory, UPF-PRBB, Dr Aiguader 80, Barcelona 08003, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, Barcelona 08003, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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de Lorenzo V. Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210395. [PMID: 35757882 PMCID: PMC9234819 DOI: 10.1098/rstb.2021.0395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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Solé R, Levin S. Ecological complexity and the biosphere: the next 30 years. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210376. [PMID: 35757877 PMCID: PMC9234814 DOI: 10.1098/rstb.2021.0376] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Global warming, habitat loss and overexploitation of limited resources are leading to alarming biodiversity declines. Ecosystems are complex adaptive systems that display multiple alternative states and can shift from one to another in abrupt ways. Some of these tipping points have been identified and predicted by mathematical and computational models. Moreover, multiple scales are involved and potential mitigation or intervention scenarios are tied to particular levels of complexity, from cells to human–environment coupled systems. In dealing with a biosphere where humans are part of a complex, endangered ecological network, novel theoretical and engineering approaches need to be considered. At the centre of most research efforts is biodiversity, which is essential to maintain community resilience and ecosystem services. What can be done to mitigate, counterbalance or prevent tipping points? Using a 30-year window, we explore recent approaches to sense, preserve and restore ecosystem resilience as well as a number of proposed interventions (from afforestation to bioengineering) directed to mitigate or reverse ecosystem collapse. The year 2050 is taken as a representative future horizon that combines a time scale where deep ecological changes will occur and proposed solutions might be effective. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
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Affiliation(s)
- Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 80, Barcelona 08003, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, Barcelona 08003, Spain.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Simon Levin
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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10
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Ecological firewalls for synthetic biology. iScience 2022; 25:104658. [PMID: 35832885 PMCID: PMC9272386 DOI: 10.1016/j.isci.2022.104658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we present and discuss an alternative view grounded in the nonlinear attractor dynamics of some ecological network motifs. These ecological firewalls are designed to perform novel functionalities (such as plastic removal) while containment is achieved within the resident community. That could help provide a self-regulating biocontainment. In this way, engineered organisms have a limited spread while—when required—preventing their extinction. The basic synthetic designs and their dynamical behavior are presented, each one inspired in a given ecological class of interaction. Their possible applications are discussed and the broader connection with invasion ecology outlined. Population control of synthetic strains can be achieved by engineering ecological links We introduce ecological firewalls, inspired in four types of ecological interactions Our firewalls are shown to maintain diversity while performing designed functions Ecological firewalls will help to tackle future bioremediation strategies
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Zafeiropoulos H, Paragkamian S, Ninidakis S, Pavlopoulos GA, Jensen LJ, Pafilis E. PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. Microorganisms 2022; 10:microorganisms10020293. [PMID: 35208748 PMCID: PMC8879827 DOI: 10.3390/microorganisms10020293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.
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Affiliation(s)
- Haris Zafeiropoulos
- Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013 Heraklion, Crete, Greece; (H.Z.); (S.P.)
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece;
| | - Savvas Paragkamian
- Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013 Heraklion, Crete, Greece; (H.Z.); (S.P.)
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece;
| | - Stelios Ninidakis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece;
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece;
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece;
- Correspondence: or ; Tel.: +30-2810-337748
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Berdugo M, Vidiella B, Solé RV, Maestre FT. Ecological mechanisms underlying aridity thresholds in global drylands. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13962] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Miguel Berdugo
- ICREA‐Complex Systems Lab UPF‐PRBB Barcelona Spain
- Institut de Biologia Evolutiva CSIC‐UPF Barcelona Spain
- Institute of Integrative Biology Department of Environment Systems Science ETH Zürich Zürich Switzerland
| | - Blai Vidiella
- ICREA‐Complex Systems Lab UPF‐PRBB Barcelona Spain
- Institut de Biologia Evolutiva CSIC‐UPF Barcelona Spain
| | - Ricard V. Solé
- ICREA‐Complex Systems Lab UPF‐PRBB Barcelona Spain
- Institut de Biologia Evolutiva CSIC‐UPF Barcelona Spain
- Santa Fe Institute Santa Fe NM USA
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio “Ramon Margalef” Universidad de Alicante Alicante Spain
- Departamento de Ecología Universidad de Alicante Alicante Spain
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Ramos C, Calus M, Schokker D. Persistence of functional microbiota composition across generations. Sci Rep 2021; 11:19007. [PMID: 34561474 PMCID: PMC8463531 DOI: 10.1038/s41598-021-98097-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/30/2021] [Indexed: 12/11/2022] Open
Abstract
Holobionts are defined as a host and its microbiota, however, only a fraction of the bacteria are inherited vertically and thus coevolve with the host. The "it's the song, not the singer" theory proposes that functional traits, instead of taxonomical microbiota composition, could be preserved across generations if interspecies interaction patterns perpetuate themselves. We tested conservation of functional composition across generations using zooplankton, mosquito, and plant datasets. Then, we tested if there is a change of functional microbiota composition over time within a generation in human datasets. Finally, we simulated microbiota communities to investigate if (pairwise) interactions can lead to multiple stable community compositions. Our results suggest that the vertically transmitted microbiota starts a predictable change of functions performed by the microbiota over time, whose robustness depends on the arrival of diverse migrants. This succession culminates in a stable functional composition state. The results suggest that the host-microbiota interaction and higher order interactions in general have an important contribution to the robustness of the final community. If the proposed mechanism proves to be valid for a diverse array of host species, this would support the concept of holobionts being used as units of selection, including animal breeding, suggesting this has a wider applicability.
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Affiliation(s)
- Christian Ramos
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
- Carrera de Biología, Facultad de Ciencias Puras Y Naturales, Universidad Mayor de San Andrés, Casilla 10077-Correo Central, La Paz, Bolivia
| | - Mario Calus
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Dirkjan Schokker
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
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Vidiella B, Fontich E, Valverde S, Sardanyés J. Habitat loss causes long extinction transients in small trophic chains. THEOR ECOL-NETH 2021. [DOI: 10.1007/s12080-021-00509-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Timmis K, Ramos JL. The soil crisis: the need to treat as a global health problem and the pivotal role of microbes in prophylaxis and therapy. Microb Biotechnol 2021; 14:769-797. [PMID: 33751840 PMCID: PMC8085983 DOI: 10.1111/1751-7915.13771] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Soil provides a multitude of services that are essential to a healthily functioning biosphere and continuity of the human race, such as feeding the growing human population and the sequestration of carbon needed to counteract global warming. Healthy soil availability is the limiting parameter in the provision of a number of these services. As a result of anthropogenic abuses, and natural and global warming-promoted extreme weather events, Planet Earth is currently experiencing an unprecedented crisis of soil deterioration, desertification and erosive loss that increasingly prejudices the services it provides. Such services are pivotal to the Sustainability Development Goals formulated by the United Nations. Immediate and coordinated action on a global scale is urgently required to slow and ultimately reverse the loss of healthy soils. Despite the 'dirt-dust', non-vital appearance of soil, it is a highly dynamic living entity, whose life is overwhelmingly microbial. The soil microbiota, which constitutes the greatest reservoir and donor of microbial diversity on Earth, acts as a vast bioreactor, mediating a myriad of chemical reactions that turn the biogeochemical cycles, recycle wastes, purify water, and underpin the multitude of other services soil provides. Fuelling the belowground microbial bioreactor is the aboveground plant and photosynthetic surface microbial life which captures solar energy, fixes inorganic CO2 to organic carbon, and channels fixed carbon and energy into soil. In order to muster an effective response to the crisis, to avoid further deterioration, and to restore unhealthy soils, we need a new and coherent approach, namely to deal with soils worldwide as patients in need of health care and create (i) a public health system for development of effective policies for land use, conservation, restoration, recommendations of prophylactic measures, monitoring and identification of problems (epidemiology), organizing crisis responses, etc., and (ii) a healthcare system charged with soil care: the promotion of good practices, implementation of prophylaxis measures, and institution of therapies for treatment of unhealthy soils and restoration of drylands. These systems need to be national but there is also a desperate need for international coordination. To enable development of effective, evidence-based strategies that will underpin the efforts of soil healthcare systems, a substantial investment in wide-ranging interdisciplinary research on soil health and disease is mandatory. This must lead to a level of understanding of the soil:biota functionalities underlying key ecosystem services that enables formulation of effective diagnosis-prophylaxis-therapy pathways for sustainable use, protection and restoration of different types of soil resources in different climatic zones. These conservation-regenerative-restorative measures need to be complemented by an educative-political-economic-legislative framework that provides incentives encouraging soil care: knowledge, policy, economic and others, and laws which promote international adherence to the principles of restorative soil management. And: we must all be engaged in improving soil health; everyone has a duty of care (https://www.bbc.co.uk/ideas/videos/why-soil-is-one-of-the-most-amazing-things-on-eart/p090cf64). Creative application of microbes, microbiomes and microbial biotechnology will be central to the successful operation of the healthcare systems.
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Affiliation(s)
- Kenneth Timmis
- Institute of MicrobiologyTechnical University BraunschweigBraunschweigGermany
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16
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Schmidt M, Kubyshkin V. How To Quantify a Genetic Firewall? A Polarity-Based Metric for Genetic Code Engineering. Chembiochem 2021; 22:1268-1284. [PMID: 33231343 PMCID: PMC8049029 DOI: 10.1002/cbic.202000758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Indexed: 12/14/2022]
Abstract
Genetic code engineering aims to produce organisms that translate genetic information in a different way from that prescribed by the standard genetic code. This endeavor could eventually lead to genetic isolation, where an organism that operates under a different genetic code will not be able to transfer functional genes with other living species, thereby standing behind a genetic firewall. It is not clear however, how distinct the code should be, or how to measure the distance. We have developed a metric (Δcode ) where we assigned polarity indices (clog D7 ) to amino acids to calculate the distances between pairs of genetic codes. We then calculated the distance between a set of 204 genetic codes, including the 24 known distinct natural codes, 11 extreme-distance codes created computationally, nine theoretical special purpose codes from literature and 160 codes in which canonical amino acids were replaced by noncanonical chemical analogues. The metric can be used for building strategies towards creating semantically alienated organisms, and testing the strength of genetic firewalls. This metric provides the basis for a map of the genetic codes that could guide future efforts towards novel biochemical worlds, biosafety and deep barcoding applications.
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Affiliation(s)
| | - Vladimir Kubyshkin
- Department of ChemistryUniversity of ManitobaDysart Road 144WinnipegR3T 2N2Canada
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17
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Brooks SM, Alper HS. Applications, challenges, and needs for employing synthetic biology beyond the lab. Nat Commun 2021; 12:1390. [PMID: 33654085 PMCID: PMC7925609 DOI: 10.1038/s41467-021-21740-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Synthetic biology holds great promise for addressing global needs. However, most current developments are not immediately translatable to 'outside-the-lab' scenarios that differ from controlled laboratory settings. Challenges include enabling long-term storage stability as well as operating in resource-limited and off-the-grid scenarios using autonomous function. Here we analyze recent advances in developing synthetic biological platforms for outside-the-lab scenarios with a focus on three major application spaces: bioproduction, biosensing, and closed-loop therapeutic and probiotic delivery. Across the Perspective, we highlight recent advances, areas for further development, possibilities for future applications, and the needs for innovation at the interface of other disciplines.
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Affiliation(s)
- Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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18
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Morones-Ramírez JR. Reflections on the 2nd International Congress on NanoBioEngineering 2020. Front Bioeng Biotechnol 2021; 9:648634. [PMID: 33634091 PMCID: PMC7901877 DOI: 10.3389/fbioe.2021.648634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- José Rubén Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, UANL, San Nicolás de los Garza, Mexico.,Centro de Investigación en Biotecnología y Nanotecnología, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Mexico
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19
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Vidiella B, Sardanyés J, Solé RV. Synthetic soil crusts against green-desert transitions: a spatial model. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200161. [PMID: 32968506 PMCID: PMC7481726 DOI: 10.1098/rsos.200161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/22/2020] [Indexed: 05/07/2023]
Abstract
Semiarid ecosystems are threatened by global warming due to longer dehydration times and increasing soil degradation. Mounting evidence indicates that, given the current trends, drylands are likely to expand and possibly experience catastrophic shifts from vegetated to desert states. Here, we explore a recent suggestion based on the concept of ecosystem terraformation, where a synthetic organism is used to counterbalance some of the nonlinear effects causing the presence of such tipping points. Using an explicit spatial model incorporating facilitation and considering a simplification of states found in semiarid ecosystems including vegetation, fertile and desert soil, we investigate how engineered microorganisms can shape the fate of these ecosystems. Specifically, two different, but complementary, terraformation strategies are proposed: Cooperation-based: C-terraformation; and Dispersion-based: D-terraformation. The first strategy involves the use of soil synthetic microorganisms to introduce cooperative loops (facilitation) with the vegetation. The second one involves the introduction of engineered microorganisms improving their dispersal capacity, thus facilitating the transition from desert to fertile soil. We show that small modifications enhancing cooperative loops can effectively modify the aridity level of the critical transition found at increasing soil degradation rates, also identifying a stronger protection against soil degradation by using the D-terraformation strategy. The same results are found in a mean-field model providing insights into the transitions and dynamics tied to these terraformation strategies. The potential consequences and extensions of these models are discussed.
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Affiliation(s)
- Blai Vidiella
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva (CSIC-UPF), Psg. Maritim Barceloneta, 37, 08003 Barcelona, Spain
| | - Josep Sardanyés
- Centre de Recerca Matemàtica, Edifici C, Campus de Bellaterra, 08193 Cerdanyola del Vallès, Bellaterra, Barcelona, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Edifici C, Campus de Bellaterra, 08193 Cerdanyola del Vallès, Bellaterra, Barcelona, Spain
| | - Ricard V. Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva (CSIC-UPF), Psg. Maritim Barceloneta, 37, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA
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20
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Gorochowski TE, Hauert S, Kreft JU, Marucci L, Stillman NR, Tang TYD, Bandiera L, Bartoli V, Dixon DOR, Fedorec AJH, Fellermann H, Fletcher AG, Foster T, Giuggioli L, Matyjaszkiewicz A, McCormick S, Montes Olivas S, Naylor J, Rubio Denniss A, Ward D. Toward Engineering Biosystems With Emergent Collective Functions. Front Bioeng Biotechnol 2020; 8:705. [PMID: 32671054 PMCID: PMC7332988 DOI: 10.3389/fbioe.2020.00705] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/05/2020] [Indexed: 12/31/2022] Open
Abstract
Many complex behaviors in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is difficult because they arise as a consequence of complex multi-level feedback, which often spans many length-scales. Here, we present a perspective on how some of these challenges could be overcome by using multi-agent modeling as a design framework within synthetic biology. Using case studies covering the construction of synthetic ecologies to biological computation and synthetic cellularity, we show how multi-agent modeling can capture the core features of complex multi-scale systems and provide novel insights into the underlying mechanisms which guide emergent functionalities across scales. The ability to unravel design rules underpinning these behaviors offers a means to take synthetic biology beyond single molecules or cells and toward the creation of systems with functions that can only emerge from collectives at multiple scales.
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Affiliation(s)
| | - Sabine Hauert
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Jan-Ulrich Kreft
- School of Biosciences and Institute of Microbiology and Infection and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Namid R. Stillman
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - T.-Y. Dora Tang
- Max Plank Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Physics of Life, Cluster of Excellence, Technische Universität Dresden, Dresden, Germany
| | - Lucia Bandiera
- School of Engineering, University of Edinburgh, Edinburgh, United Kingdom
| | - Vittorio Bartoli
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | | | - Alex J. H. Fedorec
- Division of Biosciences, University College London, London, United Kingdom
| | - Harold Fellermann
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alexander G. Fletcher
- Bateson Centre and School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
| | - Tim Foster
- School of Biosciences and Institute of Microbiology and Infection and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | - Luca Giuggioli
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | | | - Scott McCormick
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Sandra Montes Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Jonathan Naylor
- School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ana Rubio Denniss
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Daniel Ward
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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