1
|
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.
Collapse
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
| |
Collapse
|
2
|
Darvishi F, Rafatiyan S, Abbaspour Motlagh Moghaddam MH, Atkinson E, Ledesma-Amaro R. Applications of synthetic yeast consortia for the production of native and non-native chemicals. Crit Rev Biotechnol 2024; 44:15-30. [PMID: 36130800 DOI: 10.1080/07388551.2022.2118569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/03/2022] [Accepted: 08/19/2022] [Indexed: 11/03/2022]
Abstract
The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.
Collapse
Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran
| | - Sajad Rafatiyan
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Eliza Atkinson
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| |
Collapse
|
3
|
Hosoda K, Seno S, Murakami N, Matsuda H, Osada Y, Kamiura R, Kondoh M. Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach. Biosystems 2024; 235:105087. [PMID: 37989470 DOI: 10.1016/j.biosystems.2023.105087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/23/2023]
Abstract
Simultaneous understanding of both population and ecosystem dynamics is crucial in an era marked by the degradation of ecosystem services. Experimental ecosystems are a powerful tool for understanding these dynamics; however, they often face technical challenges, typically falling into two categories: "complex but with limited replicability microcosms" and "highly replicable but overly simplistic microcosms." Herein, we present a high-throughput synthetic microcosm system comprising 12 functionally and phylogenetically diverse microbial species. These species are axenically culturable, cryopreservable, and can be measured noninvasively via microscopy, aided by machine learning. This system includes prokaryotic and eukaryotic producers and decomposers, and eukaryotic consumers to ensure functional redundancy. Our model system exhibited key features of a complex ecosystem: (i) various positive and negative interspecific interactions, (ii) higher-order interactions beyond two-species dynamics, (iii) probabilistic dynamics leading to divergent outcomes, and (iv) stable nonlinear transitions. We identified several conditions under which at least one species from each of the three functional groups-producers, consumers, and decomposers-and one functionally redundant species, persisted for over six months. These conditions set the stage for detailed investigations in the future. Given its designability and experimental replicability, our model ecosystem offers a promising platform for deeper insights integrating both population and ecosystem dynamics.
Collapse
Affiliation(s)
- Kazufumi Hosoda
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan; Center for Information and Neural Networks (CiNet), National Institute of Information and Communications Technology (NICT), Osaka, Japan; Institute for Transdisciplinary Graduate Degree Programs, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan; Life and Medical Sciences Area, Health Sciences Discipline, Kobe University, Tomogaoka 7-10-2, Suma-ku, Kobe, Hyogo, 654-0142, Japan.
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naomi Murakami
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yutaka Osada
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Rikuto Kamiura
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
| |
Collapse
|
4
|
Ramoneda J, Jensen TBN, Price MN, Casamayor EO, Fierer N. Taxonomic and environmental distribution of bacterial amino acid auxotrophies. Nat Commun 2023; 14:7608. [PMID: 37993466 PMCID: PMC10665431 DOI: 10.1038/s41467-023-43435-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
Many microorganisms are auxotrophic-unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of 'streamlined' life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.
Collapse
Affiliation(s)
- Josep Ramoneda
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, CO, USA.
| | - Thomas B N Jensen
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, CO, USA
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morgan N Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emilio O Casamayor
- Spanish Research Council (CSIC), Center for Advanced Studies of Blanes (CEAB), Blanes, Spain
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, CO, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| |
Collapse
|
5
|
Chen J, Siliceo SL, Ni Y, Nielsen HB, Xu A, Panagiotou G. Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions. MICROBIOME 2023; 11:178. [PMID: 37553697 PMCID: PMC10408196 DOI: 10.1186/s40168-023-01604-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 06/19/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND A growing body of evidence suggests that the gut microbiota is strongly linked to general human health. Microbiome-directed interventions, such as diet and exercise, are acknowledged as a viable and achievable strategy for preventing disorders and improving human health. However, due to the significant inter-individual diversity of the gut microbiota between subjects, lifestyle recommendations are expected to have distinct and highly variable impacts to the microbiome structure. RESULTS Here, through a large-scale meta-analysis including 1448 shotgun metagenomics samples obtained longitudinally from 396 individuals during lifestyle studies, we revealed Bacteroides stercoris, Prevotella copri, and Bacteroides vulgatus as biomarkers of microbiota's resistance to structural changes, and aromatic and non-aromatic amino acid biosynthesis as important regulator of microbiome dynamics. We established criteria for distinguishing between significant compositional changes from normal microbiota fluctuation and classified individuals based on their level of response. We further developed a machine learning model for predicting "responders" and "non-responders" independently of the type of intervention with an area under the curve of up to 0.86 in external validation cohorts of different ethnicities. CONCLUSIONS We propose here that microbiome-based stratification is possible for identifying individuals with highly plastic or highly resistant microbial structures. Identifying subjects that will not respond to generalized lifestyle therapeutic interventions targeting the restructuring of gut microbiota is important to ensure that primary end-points of clinical studies are reached. Video Abstract.
Collapse
Affiliation(s)
- Jiarui Chen
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute -Microbiome Dynamics, Jena, Germany
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Sara Leal Siliceo
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute -Microbiome Dynamics, Jena, Germany
| | - Yueqiong Ni
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute -Microbiome Dynamics, Jena, Germany
| | - Henrik B Nielsen
- Clinical Microbiomics, Fruebjergvej 3, 2100, Copenhagen, Denmark
| | - Aimin Xu
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong S.A.R., China
| | - Gianni Panagiotou
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute -Microbiome Dynamics, Jena, Germany.
- Department of Medicine, The University of Hong Kong, Hong Kong S.A.R., China.
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
| |
Collapse
|
6
|
Jo C, Bernstein DB, Vaisman N, Frydman HM, Segrè D. Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions. mSystems 2023; 8:e0001721. [PMID: 36802169 PMCID: PMC10134821 DOI: 10.1128/msystems.00017-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 01/24/2023] [Indexed: 02/23/2023] Open
Abstract
The dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microorganisms. Quantitative measurements of these interactions are important for understanding and engineering ecosystem structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment. We first applied BioMe to recapitulate recently characterized, natural symbiotic interactions between bacteria isolated from the Drosophila melanogaster gut microbiome. Specifically, the BioMe plate allowed us to observe the benefit provided by two Lactobacillus strains to an Acetobacter strain. We next explored the use of BioMe to gain quantitative insight into the engineered obligate syntrophic interaction between a pair of Escherichia coli amino acid auxotrophs. We integrated experimental observations with a mechanistic computational model to quantify key parameters associated with this syntrophic interaction, including metabolite secretion and diffusion rates. This model also allowed us to explain the slow growth observed for auxotrophs growing in adjacent wells by demonstrating that, under the relevant range of parameters, local exchange between auxotrophs is essential for efficient growth. The BioMe plate provides a scalable and flexible approach for the study of dynamic microbial interactions. IMPORTANCE Microbial communities participate in many essential processes from biogeochemical cycles to the maintenance of human health. The structure and functions of these communities are dynamic properties that depend on poorly understood interactions among different species. Unraveling these interactions is therefore a crucial step toward understanding natural microbiota and engineering artificial ones. Microbial interactions have been difficult to measure directly, largely due to limitations of existing methods to disentangle the contribution of different organisms in mixed cocultures. To overcome these limitations, we developed the BioMe plate, a custom microplate-based device that enables direct measurement of microbial interactions, by detecting the abundance of segregated populations of microbes that can exchange small molecules through a membrane. We demonstrated the possible application of the BioMe plate for studying both natural and artificial consortia. BioMe is a scalable and accessible platform that can be used to broadly characterize microbial interactions mediated by diffusible molecules.
Collapse
Affiliation(s)
- Charles Jo
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - David B. Bernstein
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Natalie Vaisman
- Department of Biology, Boston University, Boston, Massachusetts, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | | | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
7
|
Abstract
Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.
Collapse
Affiliation(s)
- Elizabeth J Culp
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
8
|
Du H, Pan J, Zou D, Huang Y, Liu Y, Li M. Microbial active functional modules derived from network analysis and metabolic interactions decipher the complex microbiome assembly in mangrove sediments. MICROBIOME 2022; 10:224. [PMID: 36510268 PMCID: PMC9746113 DOI: 10.1186/s40168-022-01421-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/09/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND The metabolic interactions of microbes significantly affect the assembly of microbial communities that play important roles in biogeochemical processes. However, most interspecies interactions between microorganisms in natural communities remain unknown, leading to a poor understanding of community assembly mechanisms. RESULTS Here, we used a genome-scale metabolic modeling-based approach to explore the potential interactions among bacteria and archaea in mangrove sediments. More than half of the assembled microbial species ([Formula: see text]) combined about 3000 pairwise metabolic interaction relationship with high potential. The examples of predicted interactions are consistent with the implications of studies based on microbial enrichment/culture, indicating the feasibility of our strategy for extracting diverse potential interactions from complex interspecies networks. Moreover, a substantial number of previously unknown microbial metabolic interactions were also predicted. We proposed a concept of microbial active functional module (mAFM), defined as a consortium constituted by a group of microbes possessing relatively high metabolic interactions via which they can actively realize certain dominant functions in element transformations. Based on the metabolic interactions and the transcript distribution of microorganisms, five mAFMs distributed in different layers of the sediments were identified. The whole group of mAFMs covered most of the principal pathways in the cycle of carbon, nitrogen, and sulfur, while each module possessed divergently dominant functions. According to thinctiis diston, we inferred that the mAFMs participated in the element cycles via their intra-cycle and the inter-exchange among them and the sediments. CONCLUSIONS The results of this study greatly expanded interaction potential of microbes in mangrove sediments, which could provide supports for prospective mutualistic system construction and microbial enrichment culture. Furthermore, the mAFMs can help to extract valuable microbial metabolic interactions from the whole community and to profile the functioning of the microbial community that promote biogeochemical cycling in mangrove sediments. Video Abstract.
Collapse
Affiliation(s)
- Huan Du
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yuhan Huang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| |
Collapse
|
9
|
Martinez JA, Delvenne M, Henrion L, Moreno F, Telek S, Dusny C, Delvigne F. Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages. PLoS Comput Biol 2022; 18:e1010674. [PMID: 36315576 PMCID: PMC9648842 DOI: 10.1371/journal.pcbi.1010674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/10/2022] [Accepted: 10/22/2022] [Indexed: 11/12/2022] Open
Abstract
Microbial consortia are an exciting alternative for increasing the performances of bioprocesses for the production of complex metabolic products. However, the functional properties of microbial communities remain challenging to control, considering the complex interaction mechanisms occurring between co-cultured microbial species. Indeed, microbial communities are highly dynamic and can adapt to changing environmental conditions through complex mechanisms, such as phenotypic diversification. We focused on stabilizing a co-culture of Saccharomyces cerevisiae and Escherichia coli in continuous cultures. Our preliminary data pointed out that transient diauxic shifts could lead to stable co-culture by providing periodic fitness advantages to the yeast. Based on a computational toolbox called MONCKS (for MONod-type Co-culture Kinetic Simulation), we were able to predict the dynamics of diauxic shift for both species based on a cybernetic approach. This toolbox was further used to predict the frequency of diauxic shift to be applied to reach co-culture stability. These simulations were successfully reproduced experimentally in continuous bioreactors with glucose pulsing. Finally, based on a bet-hedging reporter, we observed that the yeast population exhibited an increased phenotypic diversification process in co-culture compared with mono-culture, suggesting that this mechanism could be the basis of the metabolic fitness of the yeast. Being able to manipulate the dynamics of microbial co-cultures is a technical challenge that need to be addressed in order to get a deeper insight about how microbial communities are evolving in their ecological context, as well as for exploiting the potential offered by such communities in an applied context e.g., for setting up more robust bioprocesses relying on the use of several microbial species. In this study, we used continuous cultures of bacteria (E. coli) and yeast (S. cerevisiae) in order to demonstrate that a simple nutrient pulsing strategy can be used for adjusting the composition of the community with time. As expected, during growth on glucose, E. coli quickly outcompeted S. cerevisiae. However, when glucose is pulsed into the culture, increased metabolic fitness of the yeast was observed upon reconsumption of the main side metabolites i.e., acetate and ethanol, leading to a robust oscillating growth profile for both species. The optimal pulsing frequency was predicted based on a cybernetic version of a Monod growth model taking into account the main metabolic routes involved in the process. Considering the limited number of metabolic details needed, this cybernetic approach could be generalized to other communities.
Collapse
Affiliation(s)
- J. Andres Martinez
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Matheo Delvenne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Lucas Henrion
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Fabian Moreno
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Samuel Telek
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Christian Dusny
- Microscale Analysis and Engineering, Department of Solar Materials, Helmholtz-Centre for Environmental Research- UFZ Leipzig, Leipzig, Germany
| | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
- * E-mail:
| |
Collapse
|
10
|
Miao CH, Wang XF, Qiao B, Xu QM, Cao CY, Cheng JS. Artificial consortia of Bacillus amyloliquefaciens HM618 and Bacillus subtilis for utilizing food waste to synthetize iturin A. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:72628-72638. [PMID: 35612705 DOI: 10.1007/s11356-022-21029-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Food waste is a cheap and abundant organic resource that can be used as a substrate for the production of the broad-spectrum antifungal compound iturin A. To increase the efficiency of food waste biotransformation, different artificial consortia incorporating the iturin A producer Bacillus amyloliquefaciens HM618 together with engineered Bacillus subtilis WB800N producing lipase or amylase were constructed. The results showed that recombinant B. subtilis WB-A13 had the highest amylase activity of 23406.4 U/mL, and that the lipase activity of recombinant B. subtilis WB-L01 was 57.5 U/mL. When strain HM618 was co-cultured with strain WB-A14, the higher yield of iturin A reached to 7.66 mg/L, representing a 32.9% increase compared to the pure culture of strain HM618. In the three-strain consortium comprising strains HM618, WB-L02, and WB-A14 with initial OD600 values of 0.2, 0.15, and 0.15, respectively, the yield of iturin A reached 8.12 mg/L, which was 38.6% higher than the control. Taken together, artificial consortia of B. amyloliquefaciens and recombinant B. subtilis can produce an increased yield of iturin A, which provides a new strategy for the valorization of food waste.
Collapse
Affiliation(s)
- Chang-Hao Miao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Xiao-Feng Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin, 300387, People's Republic of China
| | - Chun-Yang Cao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China.
| |
Collapse
|
11
|
Vasileiadis S, Perruchon C, Scheer B, Adrian L, Steinbach N, Trevisan M, Plaza-Bolaños P, Agüera A, Chatzinotas A, Karpouzas DG. Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole. Environ Microbiol 2022; 24:5105-5122. [PMID: 35799498 DOI: 10.1111/1462-2920.16116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on 13 C-labelled versus 12 C-TBZ showed that 66% of the 13 C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.
Collapse
Affiliation(s)
- Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Chiara Perruchon
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Benjamin Scheer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Nicole Steinbach
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Marco Trevisan
- Department of Sustainable Food Process, Universitá Cattolica del Sacro Cuore, Piacenza, Italy
| | - Patricia Plaza-Bolaños
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Ana Agüera
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| |
Collapse
|
12
|
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
Collapse
|
13
|
Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
Collapse
Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| |
Collapse
|
14
|
Espinosa-Ortiz EJ, Rene ER, Gerlach R. Potential use of fungal-bacterial co-cultures for the removal of organic pollutants. Crit Rev Biotechnol 2021; 42:361-383. [PMID: 34325585 DOI: 10.1080/07388551.2021.1940831] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.
Collapse
Affiliation(s)
- Erika J Espinosa-Ortiz
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Eldon R Rene
- Department of Water Supply, Sanitary and Environmental Engineering, IHE Delft Institute for Water Education, 2601DA Delft, The Netherlands
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| |
Collapse
|
15
|
Grandel NE, Reyes Gamas K, Bennett MR. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol 2021; 29:1095-1105. [PMID: 33966922 DOI: 10.1016/j.tim.2021.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
While synthetic microbial systems are becoming increasingly complicated, single-strain systems cannot match the complexity of their multicellular counterparts. Such complexity, however, is much more difficult to control. Recent advances have increased our ability to control temporal, spatial, and community compositional organization, including modular adhesive systems, strain growth relationships, and asymmetric cell division. While these systems generally work independently, combining them into unified systems has proven difficult. Once such unification is proven successful we will unlock a new frontier of synthetic biology and open the door to the creation of synthetic biological systems with true multicellularity.
Collapse
Affiliation(s)
- Nicolas E Grandel
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Kiara Reyes Gamas
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA.
| |
Collapse
|
16
|
Johnson WM, Alexander H, Bier RL, Miller DR, Muscarella ME, Pitz KJ, Smith H. Auxotrophic interactions: a stabilizing attribute of aquatic microbial communities? FEMS Microbiol Ecol 2021; 96:5855490. [PMID: 32520336 PMCID: PMC7609354 DOI: 10.1093/femsec/fiaa115] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/09/2020] [Indexed: 11/14/2022] Open
Abstract
Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
Collapse
Affiliation(s)
- Winifred M Johnson
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Sciences and Engineering, Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543, USA
| | - Raven L Bier
- Stroud Water Research Center, 970 Spencer Rd., Avondale, PA 19311, USA
| | - Dan R Miller
- PureMagic LTD, Rambam 67, Yad Rambam 9979300, Israel
| | - Mario E Muscarella
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Kathleen J Pitz
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Heidi Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| |
Collapse
|
17
|
Qian Y, Xu M, Deng T, Hu W, He Z, Yang X, Wang B, Song D, Chen L, Huang Y, Sun G. Synergistic interactions of Desulfovibrio and Petrimonas for sulfate-reduction coupling polycyclic aromatic hydrocarbon degradation. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124385. [PMID: 33229269 DOI: 10.1016/j.jhazmat.2020.124385] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
Microbial sulfate-reduction coupling polycyclic aromatic hydrocarbon (PAH) degradation is an important process for the remediation of contaminated sediments. However, little is known about core players and their mechanisms in this process due to the complexity of PAH degradation and the large number of microorganisms involved. Here we analyzed potential core players in a black-odorous sediment using gradient-dilution culturing, isolation and genomic/metagenomic approaches. Along the dilution gradient, microbial PAH degradation and sulfate consumption were not decreased, and even a significant (p = 0.003) increase was observed in the degradation of phenanthrene although the microbial diversity declined. Two species, affiliated with Desulfovibrio and Petrimonas, were commonly present in all of the gradients as keystone taxa and showed as the dominant microorganisms in the single colony (SB8) isolated from the highest dilution culture with 93.49% and 4.73% of the microbial community, respectively. Desulfovibrio sp. SB8 and Petrimonas sp. SB8 could serve together as core players for sulfate-reduction coupling PAH degradation, in which Desulfovibrio sp. SB8 could degrade PAHs to hexahydro-2-naphthoyl through the carboxylation pathway while Petrimonas sp. SB8 might degrade intermediate metabolites of PAHs. This study provides new insights into the microbial sulfate-reduction coupling PAH degradation in black-odorous sediments.
Collapse
Affiliation(s)
- Youfen Qian
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Tongchu Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Wenzhe Hu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhili He
- Environmental Microbiomics Research Center and School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Da Song
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Letian Chen
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| |
Collapse
|
18
|
Frenemies: Interactions between Rhizospheric Bacteria and Fungi from Metalliferous Soils. Life (Basel) 2021; 11:life11040273. [PMID: 33806067 PMCID: PMC8064463 DOI: 10.3390/life11040273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 11/17/2022] Open
Abstract
Is it possible to improve the efficiency of bioremediation technologies? The use of mixed cultures of bacteria and fungi inoculated at the rhizosphere level could promote the growth of the associated hyperaccumulating plant species and increase the absorption of metals in polluted soils, broadening new horizons on bioremediation purposes. This work investigates interactions between Ni-tolerant plant growth-promoting bacteria and fungi (BF) isolated from the rhizosphere of a hyperaccumulating plant. The aim is to select microbial consortia with synergistic activity to be used in integrated bioremediation protocols. Pseudomonas fluorescens (Pf), Streptomyces vinaceus (Sv) Penicillium ochrochloron (Po), and Trichoderma harzianum group (Th) were tested in mixes (Po-Sv, Po-Pf, Th-Pf, and Th-Sv). These strains were submitted to tests (agar overlay, agar plug, and distance growth co-growth tests), tailored for this aim, on Czapek yeast agar (CYA) and tryptic soy agar (TSA) media and incubated at 26 ± 1 °C for 10 days. BF growth, shape of colonies, area covered on plate, and inhibition capacity were evaluated. Most BF strains still exhibit their typical characters and the colonies separately persisted without inhibition (as Po-Sv) or with reciprocal confinement (as Th-Sv and Th-Pf). Even if apparently inhibited, the Po-Pf mix really merged, thus obtaining morphological traits representing a synergic co-growth, where both strains reached together the maturation phase and developed a sort of mixed biofilm. Indeed, bacterial colonies surround the mature fungal structures adhering to them without any growth inhibition. First data from in vivo experimentation with Po and Pf inocula in pot with metalliferous soils and hyperaccumulator plants showed their beneficial effect on plant growth. However, there is a lack of information regarding the effective co-growth between bacteria and fungi. Indeed, several studies, which directly apply the co-inoculum, do not consider suitable microorganisms consortia. Synergic rhizosphere BFs open new scenarios for plant growth promotion and soil bioremediation.
Collapse
|
19
|
Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:85/1/e00135-20. [PMID: 33441489 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
Collapse
|
20
|
Espeso DR, Martínez-García E, de Lorenzo V. Quantitative assessment of morphological traits of planktonic bacterial aggregates. WATER RESEARCH 2021; 188:116468. [PMID: 33038714 DOI: 10.1016/j.watres.2020.116468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/12/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
The efficiency of multi-strain planktonic flocs of bacteria as biocatalytic agents in aqueous media depends to a considerable extent on their three-dimensional aggregation patterns. Yet, numerical methodologies for full characterization of such heterogeneous biomass structures are largely missing. In this work we present a descriptive methodology for quantitatively portraying and identifying suspended cell clumps formed by planktonic bacteria. In order to benchmark the procedure, we tackled the behavior of cells of the environmental and biotechnologically robust species Pseudomonas putida whose surfaces were decorated with genetically encoded adhesins. Upon induction, such adhesins promoted specific inter-bacterial attachment leading to controllable and tractable floc formation in suspension. Microscopy and flow cytometry data were then gathered and further analyzed by means of a distinct metric set. Applying these parameters permitted creating comparable clumping footprints for every sample at both single-cell and population level. The hereby described approach provides a rigorous frame for following the assembly and organization of complex microbial communities as planktonic flocs.
Collapse
Affiliation(s)
- David R Espeso
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Esteban Martínez-García
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| |
Collapse
|
21
|
Sophorolipid Production Using Lignocellulosic Biomass by Co-culture of Several Recombinant Strains of Starmerella bombicola with Different Heterologous Cellulase Genes from Penicillum oxalicum. Appl Biochem Biotechnol 2020; 193:377-388. [PMID: 33006017 DOI: 10.1007/s12010-020-03433-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
One of the reasons hindering large-scale application of sophorolipids (SLs) is high production cost. In this study, six recombinant strains of Starmerella bombicola, sbEG1, sbEG2, sbCBH1, sbCBH1-2, sbBGL1, and sbCBH2 expressing cellulase genes eg1, eg2, cbh, cbh1-2, bgl1, and cbh2 from Penicillium oxalicum were respectively constructed. Four strains showed cellulase activities and were co-cultivated in fermentation media containing 2% glucose, 1% Regenerated Amorphous Cellulose (RAC), 2% glucose, and 1% RAC, respectively. After 7 days' cultivation, concentration of SLs in medium with 1% RAC (g/L) reached 1.879 g/L. When 2% glucose and 1% of RAC were both contained, the titer of SLs increased by 39.5% than that of control strain and increased by 68.8% than that in the medium with only 2% glucose. Results demonstrated that cellulase genes from filamentous fungi in S. bombicola can function to degrade lignocellulosic cellulose to produce SLs.
Collapse
|
22
|
Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H, Huang J. Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation. Front Cell Infect Microbiol 2020; 10:434. [PMID: 33102244 PMCID: PMC7546801 DOI: 10.3389/fcimb.2020.00434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Many studies have explored changes in the gut microbiome associated with HIV infection, but the consistent pattern of changes has not been clarified. Men who have sex with men (MSM) are very likely to be an independent influencing factor of the gut microbiome, but relevant research is still lacking. Methods: We conducted a meta-analysis by screening 12 published studies of 16S rRNA gene amplicon sequencing of gut microbiomes related to HIV/AIDS (six of these studies contain data that is relevant and available to MSM) from NCBI and EBI databases. The analysis of gut microbiomes related to HIV infection status and MSM status included 1,288 samples (HIV-positive (HIV+) individuals, n = 744; HIV-negative (HIV–) individuals, n = 544) and 632 samples (MSM, n = 328; non-MSM, n = 304), respectively. The alpha diversity indexes, beta diversity indexes, differentially enriched genera, differentially enriched species, and differentially enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways related to gut microbiomes were calculated. Finally, the overall trend of the above indicators was evaluated. Results: Our results indicate that HIV+ status is associated with decreased alpha diversity of the gut microbiome. MSM status is an important factor that affects the study of HIV-related gut microbiomes; that is, MSM are associated with alpha diversity changes in the gut microbiome regardless of HIV infection, and the changes in the gut microbiome composition of MSM are more significant than those of HIV+ individuals. A consistent change in Bacteroides caccae, Bacteroides ovatus, Bacteroides uniformis, and Prevotella stercorea was found in HIV+ individuals and MSM. The differential expression of the gut microbiome may be accompanied by changes in functional pathways of carbohydrate metabolism, amino acid metabolism, and lipid Metabolism. Conclusions: This study shows that the changes in the gut microbiome are related to HIV and MSM status. Importantly, MSM status may have a far greater impact on the gut microbiome than HIV status.
Collapse
Affiliation(s)
- Jie Zhou
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Yu Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Lijia Luo
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Hui Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| | - Chuanyi Ning
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Li Tian
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaodan Zhong
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Guangxi Medical University, Nanning, China.,School of Public Health, Guangxi Medical University, Nanning, China
| |
Collapse
|
23
|
Circadian clock-controlled gene expression in co-cultured, mat-forming cyanobacteria. Sci Rep 2020; 10:14095. [PMID: 32839512 PMCID: PMC7445270 DOI: 10.1038/s41598-020-69294-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 05/11/2020] [Indexed: 11/08/2022] Open
Abstract
Natural coastal microbial mat communities are multi-species assemblages that experience fluctuating environmental conditions and are shaped by resource competition as well as by cooperation. Laboratory studies rarely address the natural complexity of microbial communities but are usually limited to homogeneous mono-cultures of key species grown in liquid media. The mat-forming filamentous cyanobacteria Lyngbya aestuarii and Coleofasciculus chthonoplastes were cultured under different conditions to investigate the expression of circadian clock genes and genes that are under their control. The cyanobacteria were grown in liquid medium or on a solid substrate (glass beads) as mono- or as co-cultures under a light-dark regime and subsequently transferred to continuous light. TaqMan-probe based qPCR assays were used to quantify the expression of the circadian clock genes kaiA, kaiB, and kaiC, and of four genes that are under control of the circadian clock: psbA, nifH, ftsZ, and prx. Expression of kaiABC was influenced by co-culturing the cyanobacteria and whether grown in liquid media or on a solid substrate. Free-running (i.e. under continuous light) expression cycle of the circadian clock genes was observed in L. aestuarii but not in C. chthonoplastes. In the former organism, maximum expression of psbA and nifH occurred temporally separated and independent of the light regime, although the peak shifted in time when the culture was transferred to continuous illumination. Although functionally similar, both species of cyanobacteria displayed different 24-h transcriptional patterns in response to the experimental treatments, suggesting that their circadian clocks have adapted to different life strategies adopted by these mat-forming cyanobacteria.
Collapse
|
24
|
Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community. ISME JOURNAL 2020; 14:2816-2828. [PMID: 32788711 DOI: 10.1038/s41396-020-00737-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 01/12/2023]
Abstract
Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes essential carbon as fermentation products to R. palustris. Here, we sought to determine whether a reciprocal cross-feeding relationship would evolve spontaneously in cocultures with wild-type R. palustris, which is not known to excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ transporter. This activity likely allowed E. coli to subsist on the small amount of leaked NH4+ and better reciprocate through elevated excretion of fermentation products from a larger E. coli population. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge.
Collapse
|
25
|
Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment. Appl Environ Microbiol 2020; 86:AEM.00051-20. [PMID: 32060029 PMCID: PMC7117940 DOI: 10.1128/aem.00051-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/05/2020] [Indexed: 12/11/2022] Open
Abstract
Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections. The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new “species.” We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation. IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.
Collapse
|
26
|
Seif Y, Choudhary KS, Hefner Y, Anand A, Yang L, Palsson BO. Metabolic and genetic basis for auxotrophies in Gram-negative species. Proc Natl Acad Sci U S A 2020; 117:6264-6273. [PMID: 32132208 PMCID: PMC7084086 DOI: 10.1073/pnas.1910499117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Auxotrophies constrain the interactions of bacteria with their environment, but are often difficult to identify. Here, we develop an algorithm (AuxoFind) using genome-scale metabolic reconstruction to predict auxotrophies and apply it to a series of available genome sequences of over 1,300 Gram-negative strains. We identify 54 auxotrophs, along with the corresponding metabolic and genetic basis, using a pangenome approach, and highlight auxotrophies conferring a fitness advantage in vivo. We show that the metabolic basis of auxotrophy is species-dependent and varies with 1) pathway structure, 2) enzyme promiscuity, and 3) network redundancy. Various levels of complexity constitute the genetic basis, including 1) deleterious single-nucleotide polymorphisms (SNPs), in-frame indels, and deletions; 2) single/multigene deletion; and 3) movement of mobile genetic elements (including prophages) combined with genomic rearrangements. Fourteen out of 19 predictions agree with experimental evidence, with the remaining cases highlighting shortcomings of sequencing, assembly, annotation, and reconstruction that prevent predictions of auxotrophies. We thus develop a framework to identify the metabolic and genetic basis for auxotrophies in Gram-negatives.
Collapse
Affiliation(s)
- Yara Seif
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Kumari Sonal Choudhary
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Ying Hefner
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Amitesh Anand
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
| | - Laurence Yang
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122
- Department of Chemical Engineering, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Bernhard O Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122;
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| |
Collapse
|
27
|
Conde-Pueyo N, Vidiella B, Sardanyés J, Berdugo M, Maestre FT, de Lorenzo V, Solé R. Synthetic Biology for Terraformation Lessons from Mars, Earth, and the Microbiome. Life (Basel) 2020; 10:E14. [PMID: 32050455 PMCID: PMC7175242 DOI: 10.3390/life10020014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022] Open
Abstract
What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems capable of persisting in closed environments? Can synthetic communities be created to thrive on planets different from ours? These and other questions pervade major future developments within synthetic biology. The goal of engineering ecosystems is plagued with all kinds of technological, scientific and ethic problems. In this paper, we consider the requirements for terraformation, i.e., for changing a given environment to make it hospitable to some given class of life forms. Although the standard use of this term involved strategies for planetary terraformation, it has been recently suggested that this approach could be applied to a very different context: ecological communities within our own planet. As discussed here, this includes multiple scales, from the gut microbiome to the entire biosphere.
Collapse
Affiliation(s)
- Nuria Conde-Pueyo
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
| | - Blai Vidiella
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
| | - Josep Sardanyés
- Centre de Recerca Matemàtica, Campus UAB Edifici C, 08193 Bellaterra, Barcelona, Spain;
- Barcelona Graduate School of Mathematics (BGSMath), Campus UAB Edifici C, 08193 Bellaterra, Barcelona, Spain
| | - Miguel Berdugo
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio “Ramon Margalef”, Universidad de Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain;
| | - Fernando T. Maestre
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio “Ramon Margalef”, Universidad de Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain;
| | - Victor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| |
Collapse
|
28
|
Bayer B, Hansman RL, Bittner MJ, Noriega-Ortega BE, Niggemann J, Dittmar T, Herndl GJ. Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean. Environ Microbiol 2019; 21:4062-4075. [PMID: 31336026 PMCID: PMC6899801 DOI: 10.1111/1462-2920.14755] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/25/2023]
Abstract
Ammonia‐oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%–40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen‐containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%–1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.
Collapse
Affiliation(s)
- Barbara Bayer
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria
| | - Roberta L Hansman
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria.,International Atomic Energy Agency - Environment Laboratories, Radioecology Laboratory, 98000, Monaco, Monaco
| | - Meriel J Bittner
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria
| | - Beatriz E Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Jutta Niggemann
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Gerhard J Herndl
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, 1790, AB Den Burg, Texel, The Netherlands
| |
Collapse
|
29
|
Eng A, Borenstein E. Microbial community design: methods, applications, and opportunities. Curr Opin Biotechnol 2019; 58:117-128. [PMID: 30952088 PMCID: PMC6710113 DOI: 10.1016/j.copbio.2019.03.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/13/2019] [Accepted: 03/01/2019] [Indexed: 12/20/2022]
Abstract
Microbial communities can perform a variety of behaviors that are useful in both therapeutic and industrial settings. Engineered communities that differ in composition from naturally occurring communities offer a unique opportunity for improving upon existing community functions and expanding the range of microbial community applications. This has prompted recent advances in various community design approaches including artificial selection procedures, reduction from existing communities, combinatorial evaluation of potential microbial combinations, and model-based in silico community optimization. Computational methods in particular offer a likely avenue toward improved synthetic community development going forward. This review introduces each class of design approach and surveys their recent applications and notable innovations, closing with a discussion of existing design challenges and potential opportunities for advancement.
Collapse
Affiliation(s)
- Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Santa Fe Institute, Santa Fe, NM 87501, USA.
| |
Collapse
|
30
|
|
31
|
Stump SM, Johnson EC, Klausmeier CA. Local interactions and self-organized spatial patterns stabilize microbial cross-feeding against cheaters. J R Soc Interface 2019; 15:rsif.2017.0822. [PMID: 29563243 DOI: 10.1098/rsif.2017.0822] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/27/2018] [Indexed: 12/13/2022] Open
Abstract
Mutualisms are ubiquitous, but models predict they should be susceptible to cheating. Resolving this paradox has become relevant to synthetic ecology: cooperative cross-feeding, a nutrient-exchange mutualism, has been proposed to stabilize microbial consortia. Previous attempts to understand how cross-feeders remain robust to non-producing cheaters have relied on complex behaviour (e.g. cheater punishment) or group selection. Using a stochastic spatial model, we demonstrate two novel mechanisms that can allow cross-feeders to outcompete cheaters, rather than just escape from them. Both mechanisms work through the spatial segregation of the resources, which prevents individual cheaters from acquiring the resources they need to reproduce. First, if microbe dispersal is low but resources are shared widely, then the cross-feeders self-organize into stable spatial patterns. Here the cross-feeders can build up where the resource they need is abundant, and send their resource to where their partner is, separating resources at regular intervals in space. Second, if dispersal is high but resource sharing is local, then random variation in population density creates small-scale variation in resource density, separating the resources from each other by chance. These results suggest that cross-feeding may be more robust than previously expected and offer strategies to engineer stable consortia.
Collapse
Affiliation(s)
- Simon Maccracken Stump
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA .,School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT 06511, USA
| | - Evan Curtis Johnson
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Population Biology Graduate Group, University of California, Davis 2320 Storer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Christopher A Klausmeier
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Department of Plant BiologyBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA
| |
Collapse
|
32
|
Bernstein DB, Dewhirst FE, Segrè D. Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. eLife 2019; 8:39733. [PMID: 31194675 PMCID: PMC6609349 DOI: 10.7554/elife.39733] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.
Collapse
Affiliation(s)
- David B Bernstein
- Department of Biomedical Engineering, Boston University, Boston, United States.,Biological Design Center, Boston University, Boston, United States
| | - Floyd E Dewhirst
- The Forsyth Institute, Cambridge, United States.,Harvard School of Dental Medicine, Boston, United States
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, United States.,Biological Design Center, Boston University, Boston, United States.,Bioinformatics Program, Boston University, Boston, United States.,Department of Biology, Boston University, Boston, United States.,Department of Physics, Boston University, Boston, United States
| |
Collapse
|
33
|
Uribe‐Alvarez C, Chiquete‐Félix N, Morales‐García L, Bohórquez‐Hernández A, Delgado‐Buenrostro NL, Vaca L, Peña A, Uribe‐Carvajal S. Wolbachia pipientis grows in Saccharomyces cerevisiae evoking early death of the host and deregulation of mitochondrial metabolism. Microbiologyopen 2019; 8:e00675. [PMID: 29897678 PMCID: PMC6460262 DOI: 10.1002/mbo3.675] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 12/12/2022] Open
Abstract
Wolbachia sp. has colonized over 70% of insect species, successfully manipulating host fertility, protein expression, lifespan, and metabolism. Understanding and engineering the biochemistry and physiology of Wolbachia holds great promise for insect vector-borne disease eradication. Wolbachia is cultured in cell lines, which have long duplication times and are difficult to manipulate and study. The yeast strain Saccharomyces cerevisiae W303 was used successfully as an artificial host for Wolbachia wAlbB. As compared to controls, infected yeast lost viability early, probably as a result of an abnormally high mitochondrial oxidative phosphorylation activity observed at late stages of growth. No respiratory chain proteins from Wolbachia were detected, while several Wolbachia F1 F0 -ATPase subunits were revealed. After 5 days outside the cell, Wolbachia remained fully infective against insect cells.
Collapse
Affiliation(s)
- Cristina Uribe‐Alvarez
- Depto. de Genética MolecularInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Natalia Chiquete‐Félix
- Depto. de Genética MolecularInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Lilia Morales‐García
- Depto. de Genética MolecularInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Arlette Bohórquez‐Hernández
- Depto. de Biología Celular y del DesarrolloInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Norma Laura Delgado‐Buenrostro
- Unidad de Biomedicina UBIMEDFacultad de Estudios Superiores IztacalaUniversidad Nacional Autónoma de MéxicoTlanepantlaEdo. de MéxicoMéxico
| | - Luis Vaca
- Depto. de Biología Celular y del DesarrolloInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Antonio Peña
- Depto. de Genética MolecularInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Salvador Uribe‐Carvajal
- Depto. de Genética MolecularInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| |
Collapse
|
34
|
McCarty NS, Ledesma-Amaro R. Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology. Trends Biotechnol 2019; 37:181-197. [PMID: 30497870 PMCID: PMC6340809 DOI: 10.1016/j.tibtech.2018.11.002] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial consortia for diverse applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. An improved understanding of natural microbial ecosystems, and the development of new tools to construct synthetic consortia and program their behaviors, will vastly expand the functions that can be performed by communities of interacting microorganisms. Here, we review recent advancements in synthetic biology tools and approaches to engineer synthetic microbial consortia, discuss ongoing and emerging efforts to apply consortia for various biotechnological applications, and suggest future applications.
Collapse
Affiliation(s)
- Nicholas S. McCarty
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
35
|
Wu F, Lopatkin AJ, Needs DA, Lee CT, Mukherjee S, You L. A unifying framework for interpreting and predicting mutualistic systems. Nat Commun 2019; 10:242. [PMID: 30651549 PMCID: PMC6335432 DOI: 10.1038/s41467-018-08188-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/18/2018] [Indexed: 11/09/2022] Open
Abstract
Coarse-grained rules are widely used in chemistry, physics and engineering. In biology, however, such rules are less common and under-appreciated. This gap can be attributed to the difficulty in establishing general rules to encompass the immense diversity and complexity of biological systems. Furthermore, even when a rule is established, it is often challenging to map it to mechanistic details and to quantify these details. Here we report a framework that addresses these challenges for mutualistic systems. We first deduce a general rule that predicts the various outcomes of mutualistic systems, including coexistence and productivity. We further develop a standardized machine-learning-based calibration procedure to use the rule without the need to fully elucidate or characterize their mechanistic underpinnings. Our approach consistently provides explanatory and predictive power with various simulated and experimental mutualistic systems. Our strategy can pave the way for establishing and implementing other simple rules for biological systems.
Collapse
Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Allison J Lopatkin
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Daniel A Needs
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Charlotte T Lee
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Sayan Mukherjee
- Departments of Statistical Science, Mathematics, Computer Science, and Bioinformatics & Biostatistics, Duke University, Durham, NC, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
| |
Collapse
|
36
|
Campbell K, Correia-Melo C, Ralser M. Self-Establishing Communities: A Yeast Model to Study the Physiological Impact of Metabolic Cooperation in Eukaryotic Cells. Methods Mol Biol 2019; 2049:263-282. [PMID: 31602617 DOI: 10.1007/978-1-4939-9736-7_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
All biosynthetically active cells are able to export and import metabolites, the small molecule intermediaries of metabolism. In dense cell populations, this hallmark of cells results in the intercellular exchange of a wide spectrum of metabolites. Such metabolite exchange enables metabolic specialization of individual cells, leading to far reaching biological implications, as a consequence of the intrinsic connection between metabolism and cell physiology. In this chapter, we discuss methods on how to study metabolite exchange interactions by using self-establishing metabolically cooperating communities (SeMeCos) in the budding yeast Saccharomyces cerevisiae. SeMeCos exploit the stochastic segregation of episomes to progressively increase the number of essential metabolic interdependencies in a community that grows out from an initially prototrophic cell. By coupling genotype to metabotype, SeMeCos allow for the tracking of cells while they specialize metabolically and hence the opportunity to study their progressive change in physiology.
Collapse
Affiliation(s)
- Kate Campbell
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Clara Correia-Melo
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK. .,Institute of Biochemistry, Charité University Medicine, Berlin, Germany.
| |
Collapse
|
37
|
Haruta S, Yamamoto K. Model Microbial Consortia as Tools for Understanding Complex Microbial Communities. Curr Genomics 2018; 19:723-733. [PMID: 30532651 PMCID: PMC6225455 DOI: 10.2174/1389202919666180911131206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/19/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023] Open
Abstract
A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.
Collapse
Affiliation(s)
- Shin Haruta
- Address correspondence to this author at the Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; Tel: +81-42-677-2580; Fax: +81-42-677-2559; E-mail:
| | | |
Collapse
|
38
|
Stump SM, Johnson EC, Klausmeier CA. How leaking and overproducing resources affect the evolutionary robustness of cooperative cross-feeding. J Theor Biol 2018; 454:278-291. [DOI: 10.1016/j.jtbi.2018.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/11/2018] [Accepted: 06/12/2018] [Indexed: 11/30/2022]
|
39
|
Kan A, Del Valle I, Rudge T, Federici F, Haseloff J. Intercellular adhesion promotes clonal mixing in growing bacterial populations. J R Soc Interface 2018; 15:rsif.2018.0406. [PMID: 30232243 PMCID: PMC6170782 DOI: 10.1098/rsif.2018.0406] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/28/2018] [Indexed: 12/22/2022] Open
Abstract
Dense bacterial communities, known as biofilms, can have functional spatial organization driven by self-organizing chemical and physical interactions between cells, and their environment. In this work, we investigated intercellular adhesion, a pervasive property of bacteria in biofilms, to identify effects on the internal structure of bacterial colonies. We expressed the self-recognizing ag43 adhesin protein in Escherichia coli to generate adhesion between cells, which caused aggregation in liquid culture and altered microcolony morphology on solid media. We combined the adhesive phenotype with an artificial colony patterning system based on plasmid segregation, which marked clonal lineage domains in colonies grown from single cells. Engineered E. coli were grown to colonies containing domains with varying adhesive properties, and investigated with microscopy, image processing and computational modelling techniques. We found that intercellular adhesion elongated the fractal-like boundary between cell lineages only when both domains within the colony were adhesive, by increasing the rotational motion during colony growth. Our work demonstrates that adhesive intercellular interactions can have significant effects on the spatial organization of bacterial populations, which can be exploited for biofilm engineering. Furthermore, our approach provides a robust platform to study the influence of intercellular interactions on spatial structure in bacterial populations.
Collapse
Affiliation(s)
- Anton Kan
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Ilenne Del Valle
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tim Rudge
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Santiago, Chile
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| |
Collapse
|
40
|
Hynes WF, Chacón J, Segrè D, Marx CJ, Cady NC, Harcombe WR. Bioprinting microbial communities to examine interspecies interactions in time and space. Biomed Phys Eng Express 2018. [DOI: 10.1088/2057-1976/aad544] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
41
|
Puentes-Téllez PE, Falcao Salles J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. MICROBIAL ECOLOGY 2018; 76:419-429. [PMID: 29392382 PMCID: PMC6061470 DOI: 10.1007/s00248-017-1141-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/29/2017] [Indexed: 06/02/2023]
Abstract
Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.
Collapse
Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
42
|
Conrad JC, Poling-Skutvik R. Confined Flow: Consequences and Implications for Bacteria and Biofilms. Annu Rev Chem Biomol Eng 2018; 9:175-200. [DOI: 10.1146/annurev-chembioeng-060817-084006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria overwhelmingly live in geometrically confined habitats that feature small pores or cavities, narrow channels, or nearby interfaces. Fluid flows through these confined habitats are ubiquitous in both natural and artificial environments colonized by bacteria. Moreover, these flows occur on time and length scales comparable to those associated with motility of bacteria and with the formation and growth of biofilms, which are surface-associated communities that house the vast majority of bacteria to protect them from host and environmental stresses. This review describes the emerging understanding of how flow near surfaces and within channels and pores alters physical processes that control how bacteria disperse, attach to surfaces, and form biofilms. This understanding will inform the development and deployment of technologies for drug delivery, water treatment, and antifouling coatings and guide the structuring of bacterial consortia for production of chemicals and pharmaceuticals.
Collapse
Affiliation(s)
- Jacinta C. Conrad
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
| | - Ryan Poling-Skutvik
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
| |
Collapse
|
43
|
Jiang X, Zerfaß C, Feng S, Eichmann R, Asally M, Schäfer P, Soyer OS. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. THE ISME JOURNAL 2018; 12:1443-1456. [PMID: 29572468 PMCID: PMC5955953 DOI: 10.1038/s41396-018-0095-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 01/21/2023]
Abstract
A key prerequisite to achieve a deeper understanding of microbial communities and to engineer synthetic ones is to identify the individual metabolic interactions among key species and how these interactions are affected by different environmental factors. Deciphering the physiological basis of species-species and species-environment interactions in spatially organized environments requires reductionist approaches using ecologically and functionally relevant species. To this end, we focus here on a defined system to study the metabolic interactions in a spatial context among the plant-beneficial endophytic fungus Serendipita indica, and the soil-dwelling model bacterium Bacillus subtilis. Focusing on the growth dynamics of S. indica under defined conditions, we identified an auxotrophy in this organism for thiamine, which is a key co-factor for essential reactions in the central carbon metabolism. We found that S. indica growth is restored in thiamine-free media, when co-cultured with B. subtilis. The success of this auxotrophic interaction, however, was dependent on the spatial and temporal organization of the system; the beneficial impact of B. subtilis was only visible when its inoculation was separated from that of S. indica either in time or space. These findings describe a key auxotrophic interaction in the soil among organisms that are shown to be important for plant ecosystem functioning, and point to the potential importance of spatial and temporal organization for the success of auxotrophic interactions. These points can be particularly important for engineering of minimal functional synthetic communities as plant seed treatments and for vertical farming under defined conditions.
Collapse
Affiliation(s)
- Xue Jiang
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Christian Zerfaß
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK
| | - Song Feng
- Los Alamos National Laboratory, Theoretical Division (T-6), Center for Nonlinear Studies, Los Alamos, NM, 87545, USA
| | - Ruth Eichmann
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Munehiro Asally
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK.
| | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK.
| |
Collapse
|
44
|
Zengler K, Zaramela LS. The social network of microorganisms - how auxotrophies shape complex communities. Nat Rev Microbiol 2018; 16:383-390. [PMID: 29599459 PMCID: PMC6059367 DOI: 10.1038/s41579-018-0004-5] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microorganisms engage in complex interactions with other organisms and their environment. Recent studies have shown that these interactions are not limited to the exchange of electron donors. Most microorganisms are auxotrophs, thus relying on external nutrients for growth, including the exchange of amino acids and vitamins. Currently, we lack a deeper understanding of auxotrophies in microorganisms and how nutrient requirements differ between different strains and different environments. In this Opinion article, we describe how the study of auxotrophies and nutrient requirements among members of complex communities will enable new insights into community composition and assembly. Understanding this complex network over space and time is crucial for developing strategies to interrogate and shape microbial communities.
Collapse
Affiliation(s)
- Karsten Zengler
- Department of Pediatrics, Division of Host-Microbe Systems & Therapeutics, University of California, San Diego, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, CA, USA.
| | - Livia S Zaramela
- Department of Pediatrics, Division of Host-Microbe Systems & Therapeutics, University of California, San Diego, CA, USA
| |
Collapse
|
45
|
Biofilm Lithography enables high-resolution cell patterning via optogenetic adhesin expression. Proc Natl Acad Sci U S A 2018; 115:3698-3703. [PMID: 29555779 PMCID: PMC5889658 DOI: 10.1073/pnas.1720676115] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacteria live in surface-attached communities known as biofilms, where spatial structure is tightly linked to community function. We have developed a genetically encoded biofilm patterning tool (“Biofilm Lithography”) by engineering bacteria such that the expression of membrane adhesion proteins responsible for surface attachment is optically regulated. Accordingly, these bacteria only form biofilm on illuminated surface regions. With this tool, we are able to use blue light to pattern Escherichia coli biofilms with 25 μm spatial resolution. We present an accompanying biophysical model to understand the mechanism behind light-regulated biofilm formation and to provide insight on related natural biofilm processes. Overall, this biofilm patterning tool can be applied to study natural microbial communities as well as to engineer living biomaterials. Bacterial biofilms represent a promising opportunity for engineering of microbial communities. However, our ability to control spatial structure in biofilms remains limited. Here we engineer Escherichia coli with a light-activated transcriptional promoter (pDawn) to optically regulate expression of an adhesin gene (Ag43). When illuminated with patterned blue light, long-term viable biofilms with spatial resolution down to 25 μm can be formed on a variety of substrates and inside enclosed culture chambers without the need for surface pretreatment. A biophysical model suggests that the patterning mechanism involves stimulation of transiently surface-adsorbed cells, lending evidence to a previously proposed role of adhesin expression during natural biofilm maturation. Overall, this tool—termed “Biofilm Lithography”—has distinct advantages over existing cell-depositing/patterning methods and provides the ability to grow structured biofilms, with applications toward an improved understanding of natural biofilm communities, as well as the engineering of living biomaterials and bottom–up approaches to microbial consortia design.
Collapse
|
46
|
Stump SM, Johnson EC, Sun Z, Klausmeier CA. How spatial structure and neighbor uncertainty promote mutualists and weaken black queen effects. J Theor Biol 2018; 446:33-60. [PMID: 29499252 DOI: 10.1016/j.jtbi.2018.02.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 02/17/2018] [Accepted: 02/26/2018] [Indexed: 10/17/2022]
Abstract
The ubiquity of cooperative cross-feeding (a resource-exchange mutualism) raises two related questions: Why is cross-feeding favored over self-sufficiency, and how are cross-feeders protected from non-producing cheaters? The Black Queen Hypothesis suggests that if leaky resources are costly, then there should be selection for either gene loss or self-sufficiency, but selection against mutualistic inter-dependency. Localized interactions have been shown to protect mutualists against cheaters, though their effects in the presence of self-sufficient organisms are not well understood. Here we develop a stochastic spatial model to examine how spatial effects alter the predictions of the Black Queen Hypothesis. Microbes need two essential resources to reproduce, which they can produce themselves (at a cost) or take up from neighbors. Additionally, microbes need empty sites to give birth into. Under well mixed mean-field conditions, the cross-feeders will always be displaced by a non-producer and a self-sufficient microbe. However, localized interactions have two effects that favor production. First, a microbe that interacts with a small number of neighbors will not always receive the essential resources it needs; this effect slightly harms cross-feeders but greatly harms non-producers. Second, microbes tend to displace other microbes that produce resources they need; this effect also slightly harms cross-feeders but greatly harms non-producers. Our work therefore suggests localized interactions produce an accelerating cost of non-production. Thus, the right trade-off between the cost of producing resources and the cost of sometimes being resource-limited can favor mutualistic inter-dependence over both self-sufficiency and non-production.
Collapse
Affiliation(s)
- Simon Maccracken Stump
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.
| | - Evan Curtis Johnson
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA; Population Biology Graduate Group, University of California, Davis, 2320 Storer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Zepeng Sun
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA
| | - Christopher A Klausmeier
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA; Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824-1312, USA; Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI 48824-1312, USA
| |
Collapse
|
47
|
Dolinšek J, Goldschmidt F, Johnson DR. Synthetic microbial ecology and the dynamic interplay between microbial genotypes. FEMS Microbiol Rev 2018; 40:961-979. [PMID: 28201744 DOI: 10.1093/femsre/fuw024] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/27/2016] [Accepted: 07/04/2016] [Indexed: 01/27/2023] Open
Abstract
Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.
Collapse
Affiliation(s)
- Jan Dolinšek
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Felix Goldschmidt
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| |
Collapse
|
48
|
Rubbens P, Props R, Garcia-Timermans C, Boon N, Waegeman W. Stripping flow cytometry: How many detectors do we need for bacterial identification? Cytometry A 2017; 91:1184-1191. [DOI: 10.1002/cyto.a.23284] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/10/2017] [Accepted: 10/25/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Peter Rubbens
- KERMIT, Department of Mathematical Modelling; Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Ruben Props
- Center for Microbial Technology and Ecology (CMET); Ghent University; Ghent, Belgium
| | | | - Nico Boon
- Center for Microbial Technology and Ecology (CMET); Ghent University; Ghent, Belgium
| | - Willem Waegeman
- KERMIT, Department of Mathematical Modelling; Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| |
Collapse
|
49
|
Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists. Processes (Basel) 2017. [DOI: 10.3390/pr5040053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
With our growing understanding of the impact of microbial communities, understanding how such communities function has become a priority. The influence of microbial communities is widespread. Human-associated microbiota impacts health, environmental microbes determine ecosystem sustainability, and microbe-driven industrial processes are expanding. This broad range of applications has led to a wide range of approaches to analyze and describe microbial communities. In particular, theoretical work based on mathematical modeling has been a steady source of inspiration for explaining and predicting microbial community processes. Here, we survey some of the modeling approaches used in different contexts. We promote classifying different approaches using a unified platform, and encourage cataloging the findings in a database. We believe that the synergy emerging from a coherent collection facilitates a better understanding of important processes that determine microbial community functions. We emphasize the importance of close collaboration between theoreticians and experimentalists in formulating, classifying, and improving models of microbial communities.
Collapse
|
50
|
Ding MZ, Song H, Wang EX, Liu Y, Yuan YJ. Design and construction of synthetic microbial consortia in China. Synth Syst Biotechnol 2016; 1:230-235. [PMID: 29062948 PMCID: PMC5625796 DOI: 10.1016/j.synbio.2016.08.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 11/25/2022] Open
Abstract
The rapid development of synthetic biology enables the design, construction and optimization of synthetic microbial consortia to achieve specific functions. In China, the "973" project-"Design and Construction of Microbial Consortia" was funded by the National Basic Research Program of China in January 2014. It was proposed to address the fundamental challenges in engineering natural microbial consortia and reconstructing microbial consortia to meet industrial demands. In this review, we will introduce this "973" project, including the significance of microbial consortia, the fundamental scientific issues, the recent research progresses, and some case studies about synthetic microbial consortia in the past two and a half years.
Collapse
Affiliation(s)
- Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Hao Song
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - En-Xu Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Yue Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| |
Collapse
|