1
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Michielsen S, Vercelli GT, Cordero OX, Bachmann H. Spatially structured microbial consortia and their role in food fermentations. Curr Opin Biotechnol 2024; 87:103102. [PMID: 38461750 DOI: 10.1016/j.copbio.2024.103102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Microbial consortia are important for the fermentation of foods. They bring combined functionalities to the fermented product, but stability and product consistency of fermentations with complex consortia can be hard to control. Some of these consortia, such as water- and milk-kefir and kombucha, grow as multispecies aggregates or biofilms, in which micro-organisms taking part in a fermentation cascade are spatially organized. The spatial organization of micro-organisms in these aggregates can impact what metabolic interactions are realized in the consortia, ultimately affecting the growth dynamics and evolution of microbes. A better understanding of such spatially structured communities is of interest from the perspective of microbial ecology and biotechnology, as multispecies aggregates can be used to valorize energy-rich substrates, such as plant-based substrates or side streams from the food industry.
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Affiliation(s)
- Sabine Michielsen
- Systems Biology Lab, A-LIFE/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands
| | - Gabriel T Vercelli
- Department of Civil and Environmental Engineering, 15 Vassar St, Cambridge, MA 02139, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, 15 Vassar St, Cambridge, MA 02139, USA
| | - Herwig Bachmann
- Systems Biology Lab, A-LIFE/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands; Microbiology Department, NIZO Food Research, Ede, the Netherlands.
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2
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D’Souza G, Schwartzman J, Keegstra J, Schreier JE, Daniels M, Cordero OX, Stocker R, Ackermann M. Interspecies interactions determine growth dynamics of biopolymer-degrading populations in microbial communities. Proc Natl Acad Sci U S A 2023; 120:e2305198120. [PMID: 37878716 PMCID: PMC10622921 DOI: 10.1073/pnas.2305198120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 10/27/2023] Open
Abstract
Microbial communities perform essential ecosystem functions such as the remineralization of organic carbon that exists as biopolymers. The first step in mineralization is performed by biopolymer degraders, which harbor enzymes that can break down polymers into constituent oligo- or monomeric forms. The released nutrients not only allow degraders to grow, but also promote growth of cells that either consume the degradation products, i.e., exploiters, or consume metabolites released by the degraders or exploiters, i.e., scavengers. It is currently not clear how such remineralizing communities assemble at the microscale-how interactions between the different guilds influence their growth and spatial distribution, and hence the development and dynamics of the community. Here, we address this knowledge gap by studying marine microbial communities that grow on the abundant marine biopolymer alginate. We used batch growth assays and microfluidics coupled to time-lapse microscopy to quantitatively investigate growth and spatial distribution of single cells. We found that the presence of exploiters or scavengers alters the spatial distribution of degrader cells. In general, exploiters and scavengers-which we collectively refer to as cross-feeder cells-slowed down the growth of degrader cells. In addition, coexistence with cross-feeders altered the production of the extracellular enzymes that break down polymers by degrader cells. Our findings reveal that ecological interactions by nondegrading community members have a profound impact on the functions of microbial communities that remineralize carbon biopolymers in nature.
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Affiliation(s)
- Glen D’Souza
- Microbial Systems Ecology Group, Department of Environmental Systems Sciences, Institute of Biogeochemistry and Pollutant Dynamics, ETH-Zurich, Zurich8006, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Sciences, Duebendorf8600, Switzerland
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Johannes Keegstra
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich8093, Switzerland
| | | | - Michael Daniels
- Microbial Systems Ecology Group, Department of Environmental Systems Sciences, Institute of Biogeochemistry and Pollutant Dynamics, ETH-Zurich, Zurich8006, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Sciences, Duebendorf8600, Switzerland
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich8093, Switzerland
| | - Martin Ackermann
- Microbial Systems Ecology Group, Department of Environmental Systems Sciences, Institute of Biogeochemistry and Pollutant Dynamics, ETH-Zurich, Zurich8006, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Sciences, Duebendorf8600, Switzerland
- Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École polytechnique fédérale de Lausanne, CH-1015Lausanne, Switzerland
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3
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Gralka M, Pollak S, Cordero OX. Genome content predicts the carbon catabolic preferences of heterotrophic bacteria. Nat Microbiol 2023; 8:1799-1808. [PMID: 37653010 DOI: 10.1038/s41564-023-01458-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
Heterotrophic bacteria-bacteria that utilize organic carbon sources-are taxonomically and functionally diverse across environments. It is challenging to map metabolic interactions and niches within microbial communities due to the large number of metabolites that could serve as potential carbon and energy sources for heterotrophs. Whether their metabolic niches can be understood using general principles, such as a small number of simplified metabolic categories, is unclear. Here we perform high-throughput metabolic profiling of 186 marine heterotrophic bacterial strains cultured in media containing one of 135 carbon substrates to determine growth rates, lag times and yields. We show that, despite high variability at all levels of taxonomy, the catabolic niches of heterotrophic bacteria can be understood in terms of their preference for either glycolytic (sugars) or gluconeogenic (amino and organic acids) carbon sources. This preference is encoded by the total number of genes found in pathways that feed into the two modes of carbon utilization and can be predicted using a simple linear model based on gene counts. This allows for coarse-grained descriptions of microbial communities in terms of prevalent modes of carbon catabolism. The sugar-acid preference is also associated with genomic GC content and thus with the carbon-nitrogen requirements of their encoded proteome. Our work reveals how the evolution of bacterial genomes is structured by fundamental constraints rooted in metabolism.
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Affiliation(s)
- Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Systems Biology Group, Amsterdam Institute for Life and Environment (A-LIFE) and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Shaul Pollak
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Amarnath K, Narla AV, Pontrelli S, Dong J, Reddan J, Taylor BR, Caglar T, Schwartzman J, Sauer U, Cordero OX, Hwa T. Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance. Nat Commun 2023; 14:3165. [PMID: 37258505 DOI: 10.1038/s41467-023-38913-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving the extensive cross-feeding needed to support the coexistence of free-living microbes are poorly understood. Here we characterize bacterial physiology under self-acidification and establish that extensive excretion of key metabolites following growth arrest provides a collaborative, inter-species mechanism of stress resistance. This collaboration occurs not only between species isolated from the same community, but also between unrelated species with complementary (glycolytic vs. gluconeogenic) modes of metabolism. Cultures of such communities progress through distinct phases of growth-dilution cycles, comprising of exponential growth, acidification-triggered growth arrest, collaborative deacidification, and growth recovery, with each phase involving different combinations of physiological states of individual species. Our findings challenge the steady-state view of ecosystems commonly portrayed in ecological models, offering an alternative dynamical view based on growth advantages of complementary species in different phases.
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Affiliation(s)
- Kapil Amarnath
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Avaneesh V Narla
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Sammy Pontrelli
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Jiajia Dong
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
- Department of Physics and Astronomy, Bucknell University, Lewisburg, PA, 17837, USA
| | - Jack Reddan
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA
| | - Brian R Taylor
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Tolga Caglar
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Uwe Sauer
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Terence Hwa
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA.
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA.
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5
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Capovilla G, Braakman R, Fournier GP, Hackl T, Schwartzman J, Lu X, Yelton A, Longnecker K, Soule MCK, Thomas E, Swarr G, Mongera A, Payette JG, Castro KG, Waldbauer JR, Kujawinski EB, Cordero OX, Chisholm SW. Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle. Proc Natl Acad Sci U S A 2023; 120:e2213271120. [PMID: 37159478 DOI: 10.1073/pnas.2213271120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Marine picocyanobacteria Prochlorococcus and Synechococcus, the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of picocyanobacteria to supplement photosynthetic carbon fixation with the use of exogenous organic carbon, we found the widespread occurrence of genes for breaking down chitin, an abundant source of organic carbon that exists primarily as particles. We show that cells that encode a chitin degradation pathway display chitin degradation activity, attach to chitin particles, and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated soluble form of chitin. Marine chitin is largely derived from arthropods, which underwent major diversifications 520 to 535 Mya, close to when marine picocyanobacteria are inferred to have appeared in the ocean. Phylogenetic analyses confirm that the chitin utilization trait was acquired at the root of marine picocyanobacteria. Together this leads us to postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Subsequently, transitioning to a constitutive planktonic life without chitin associations led to cellular and genomic streamlining along a major early branch within Prochlorococcus. Our work highlights how the emergence of associations between organisms from different trophic levels, and their coevolution, creates opportunities for colonizing new environments. In this view, the rise of ecological complexity and the expansion of the biosphere are deeply intertwined processes.
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Affiliation(s)
- Giovanna Capovilla
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Rogier Braakman
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9747 Groningen, Netherlands
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Xinda Lu
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Alexis Yelton
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Krista Longnecker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 02543 Woods Hole, MA
| | - Melissa C Kido Soule
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 02543 Woods Hole, MA
| | - Elaina Thomas
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Gretchen Swarr
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 02543 Woods Hole, MA
| | - Alessandro Mongera
- Department of Pathology, Brigham and Women's Hospital, 02115 Boston, MA
- Department of Genetics, Harvard Medical School, 02115 Boston, MA
| | - Jack G Payette
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Kurt G Castro
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, 60637 Chicago, IL
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 02543 Woods Hole, MA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139 Cambridge, MA
- Department of Biology, Massachusetts Institute of Technology, 02139 Cambridge, MA
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6
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Shan X, Szabo RE, Cordero OX. Mutation-induced infections of phage-plasmids. Nat Commun 2023; 14:2049. [PMID: 37041135 PMCID: PMC10090143 DOI: 10.1038/s41467-023-37512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/17/2023] [Indexed: 04/13/2023] Open
Abstract
Phage-plasmids are extra-chromosomal elements that act both as plasmids and as phages, whose eco-evolutionary dynamics remain poorly constrained. Here, we show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in a population of marine Roseobacter. Recurrent loss-of-function mutations in the phage repressor that controls prophage induction leads to constitutively lytic phage-plasmids that spread rapidly throughout the population. The entire phage-plasmid genome is packaged into virions, which were horizontally transferred by re-infecting lysogenized cells, leading to an increase in phage-plasmid copy number and to heterozygosity in a phage repressor locus in re-infected cells. However, the uneven distribution of phage-plasmids after cell division (i.e., segregational drift) leads to the production of offspring carrying only the constitutively lytic phage-plasmid, thus restarting the lysis-reinfection-segregation life cycle. Mathematical models and experiments show that these dynamics lead to a continuous productive infection of the bacterial population, in which lytic and lysogenic phage-plasmids coexist. Furthermore, analyses of marine bacterial genome sequences indicate that the plasmid backbone here can carry different phages and disseminates trans-continentally. Our study highlights how the interplay between phage infection and plasmid genetics provides a unique eco-evolutionary strategy for phage-plasmids.
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Affiliation(s)
- Xiaoyu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachel E Szabo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Shan X, Goyal A, Gregor R, Cordero OX. Annotation-free discovery of functional groups in microbial communities. Nat Ecol Evol 2023; 7:716-724. [PMID: 36997739 DOI: 10.1038/s41559-023-02021-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/16/2023] [Indexed: 04/01/2023]
Abstract
Recent studies have shown that microbial communities are composed of groups of functionally cohesive taxa whose abundance is more stable and better-associated with metabolic fluxes than that of any individual taxon. However, identifying these functional groups in a manner that is independent of error-prone functional gene annotations remains a major open problem. Here we tackle this structure-function problem by developing a novel unsupervised approach that coarse-grains taxa into functional groups, solely on the basis of the patterns of statistical variation in species abundances and functional read-outs. We demonstrate the power of this approach on three distinct datasets. On data of replicate microcosms with heterotrophic soil bacteria, our unsupervised algorithm recovered experimentally validated functional groups that divide metabolic labour and remain stable despite large variation in species composition. When leveraged against the ocean microbiome data, our approach discovered a functional group that combines aerobic and anaerobic ammonia oxidizers whose summed abundance tracks closely with nitrate concentrations in the water column. Finally, we show that our framework can enable the detection of species groups that are probably responsible for the production or consumption of metabolites abundant in animal gut microbiomes, serving as a hypothesis-generating tool for mechanistic studies. Overall, this work advances our understanding of structure-function relationships in complex microbiomes and provides a powerful approach to discover functional groups in an objective and systematic manner.
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Affiliation(s)
- Xiaoyu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshit Goyal
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Vincent F, Gralka M, Schleyer G, Schatz D, Cabrera-Brufau M, Kuhlisch C, Sichert A, Vidal-Melgosa S, Mayers K, Barak-Gavish N, Flores JM, Masdeu-Navarro M, Egge JK, Larsen A, Hehemann JH, Marrasé C, Simó R, Cordero OX, Vardi A. Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms. Nat Commun 2023; 14:510. [PMID: 36720878 PMCID: PMC9889395 DOI: 10.1038/s41467-023-36049-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023] Open
Abstract
Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.
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Affiliation(s)
- Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Developmental Biology Unit, European Molecular Biological Laboratory, 69117, Heidelberg, Germany
| | - Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Systems Biology Lab, Amsterdam Institute for Life and Environment (A-Life)/Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081, Amsterdam, The Netherlands
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Andreas Sichert
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Kyle Mayers
- NORCE Norwegian Research Centre, 5008, Bergen, Norway
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - J Michel Flores
- Department of Earth and Planetary Science, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Jorun Karin Egge
- Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Aud Larsen
- NORCE Norwegian Research Centre, 5008, Bergen, Norway.,Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Celia Marrasé
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Rafel Simó
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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9
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Schwartzman JA, Ebrahimi A, Chadwick G, Sato Y, Roller BRK, Orphan VJ, Cordero OX. Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles. Curr Biol 2022; 32:3059-3069.e7. [PMID: 35777363 PMCID: PMC9496226 DOI: 10.1016/j.cub.2022.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/03/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023]
Abstract
Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.
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Affiliation(s)
- Julia A Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ali Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuya Sato
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Benjamin R K Roller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Center for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria; Department of Environmental Systems Sciences, ETH Zürich, Universitätsstrasse 16, Zürich 8092, Switzerland; Department of Environmental Microbiology, Eawag, Ueberlandstrasse 133, Dübendorf 8600, Switzerland
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Pascual-García A, Schwartzman J, Enke TN, Iffland-Stettner A, Cordero OX, Bonhoeffer S. Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles. Front Microbiol 2022; 13:812116. [PMID: 35814698 PMCID: PMC9260654 DOI: 10.3389/fmicb.2022.812116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
Particulate organic matter (POM) in the ocean sustains diverse communities of bacteria that mediate the remineralization of organic complex matter. However, the variability of these particles and of the environmental conditions surrounding them present a challenge to the study of the ecological processes shaping particle-associated communities and their function. In this work, we utilize data from experiments in which coastal water communities are grown on synthetic particles to ask which are the most important ecological drivers of their assembly and associated traits. Combining 16S rRNA amplicon sequencing with shotgun metagenomics, together with an analysis of the full genomes of a subset of isolated strains, we were able to identify two-to-three distinct community classes, corresponding to early vs. late colonizers. We show that these classes are shaped by environmental selection (early colonizers) and facilitation (late colonizers) and find distinctive traits associated with each class. While early colonizers have a larger proportion of genes related to the uptake of nutrients, motility, and environmental sensing with few pathways enriched for metabolism, late colonizers devote a higher proportion of genes for metabolism, comprising a wide array of different pathways including the metabolism of carbohydrates, amino acids, and xenobiotics. Analysis of selected pathways suggests the existence of a trophic-chain topology connecting both classes for nitrogen metabolism, potential exchange of branched chain amino acids for late colonizers, and differences in bacterial doubling times throughout the succession. The interpretation of these traits suggests a distinction between early and late colonizers analogous to other classifications found in the literature, and we discuss connections with the classical distinction between r- and K-strategists.
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Affiliation(s)
- Alberto Pascual-García
- Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH)-Zürich, Zurich, Switzerland
- *Correspondence: Alberto Pascual-García
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tim N. Enke
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Institute of Biogeochemistry and Pollutant Dynamics, Eidgenössische Technische Hochschule (ETH)-Zürich, Zurich, Switzerland
| | - Arion Iffland-Stettner
- Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH)-Zürich, Zurich, Switzerland
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH)-Zürich, Zurich, Switzerland
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11
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Nguyen TTH, Zakem EJ, Ebrahimi A, Schwartzman J, Caglar T, Amarnath K, Alcolombri U, Peaudecerf FJ, Hwa T, Stocker R, Cordero OX, Levine NM. Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates. Nat Commun 2022; 13:1657. [PMID: 35351873 PMCID: PMC8964765 DOI: 10.1038/s41467-022-29297-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
Sinking particulate organic carbon out of the surface ocean sequesters carbon on decadal to millennial timescales. Predicting the particulate carbon flux is therefore critical for understanding both global carbon cycling and the future climate. Microbes play a crucial role in particulate organic carbon degradation, but the impact of depth-dependent microbial dynamics on ocean-scale particulate carbon fluxes is poorly understood. Here we scale-up essential features of particle-associated microbial dynamics to understand the large-scale vertical carbon flux in the ocean. Our model provides mechanistic insight into the microbial contribution to the particulate organic carbon flux profile. We show that the enhanced transfer of carbon to depth can result from populations struggling to establish colonies on sinking particles due to diffusive nutrient loss, cell detachment, and mortality. These dynamics are controlled by the interaction between multiple biotic and abiotic factors. Accurately capturing particle-microbe interactions is essential for predicting variability in large-scale carbon cycling. Micro-scale microbial community dynamics can substantially alter the fate of sinking particulates in the ocean thus playing a key role in setting the vertical flux of particulate carbon in the ocean.
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12
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Ebrahimi A, Goyal A, Cordero OX. Particle foraging strategies promote microbial diversity in marine environments. eLife 2022; 11:73948. [PMID: 35289269 PMCID: PMC8956285 DOI: 10.7554/elife.73948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Microbial foraging in patchy environments, where resources are fragmented into particles or pockets embedded in a large matrix, plays a key role in natural environments. In the oceans and freshwater systems, particle-associated bacteria can interact with particle surfaces in different ways: some colonize only during short transients, while others form long-lived, stable colonies. We do not yet understand the ecological mechanisms by which both short- and long-term colonizers can coexist. Here, we address this problem with a mathematical model that explains how marine populations with different detachment rates from particles can stably coexist. In our model, populations grow only while on particles, but also face the increased risk of mortality by predation and sinking. Key to coexistence is the idea that detachment from particles modulates both net growth and mortality, but in opposite directions, creating a trade-off between them. While slow-detaching populations show the highest growth return (i.e., produce more net offspring), they are more susceptible to suffer higher rates of mortality than fast-detaching populations. Surprisingly, fluctuating environments, manifesting as blooms of particles (favoring growth) and predators (favoring mortality) significantly expand the likelihood that populations with different detachment rates can coexist. Our study shows how the spatial ecology of microbes in the ocean can lead to a predictable diversification of foraging strategies and the coexistence of multiple taxa on a single growth-limiting resource.
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Affiliation(s)
- Ali Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Akshit Goyal
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
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13
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Pontrelli S, Szabo R, Pollak S, Schwartzman J, Ledezma-Tejeida D, Cordero OX, Sauer U. Metabolic cross-feeding structures the assembly of polysaccharide degrading communities. Sci Adv 2022; 8:eabk3076. [PMID: 35196097 PMCID: PMC8865766 DOI: 10.1126/sciadv.abk3076] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/27/2021] [Indexed: 06/01/2023]
Abstract
Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders structure the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical cross-feeding structure that allows biopolymer degraders to shape the dynamics of community assembly.
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Affiliation(s)
- Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zürich, Zurich 8093, Switzerland
| | - Rachel Szabo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shaul Pollak
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zurich 8093, Switzerland
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14
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Abstract
Microbes commonly exist in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filter as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters communities revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intrapopulation sequence diversity, although possible clonal expansion was detected in a few abundant local comammox populations. Nitrospira species showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected for genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interaction and evolution in complex microbial communities and sheds light on the environmental dependency of evolutionary processes. IMPORTANCE Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems. In this study, these limitations are circumvented by examining the microbial communities found in stable and well-described groundwater-fed sand filters. Combining metagenomics and strain-level analyses, we identified the microbial interactions and evolutionary processes affecting comammox Nitrospira, a recently discovered bacterial type capable of performing the whole nitrification process. We found that abundant and co-occurrent Nitrospira populations in groundwater-fed sand filters are characterized by low recombination and strong purifying selection. In addition, by comparing these observations with those obtained from Nitrospira species inhabiting other environments, we revealed that evolutionary processes are more affected by habitat type than by species identity.
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Affiliation(s)
- Alejandro Palomo
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Otto X. Cordero
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Barth F. Smets
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
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15
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Abstract
Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.
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16
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Abstract
Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found in animal guts, oceans, or soils, it is still unclear whether there are generalizable biological or ecological processes that control their dynamics and function. Here, we review experimental and theoretical advances to argue that networks of trophic interactions, in which the metabolic excretions of one species are the primary resource for another, constitute the central drivers of microbial community assembly. Trophic interactions emerge from the deconstruction of complex forms of organic matter into a wealth of smaller metabolic intermediates, some of which are released to the environment and serve as a nutritional buffet for the community. The structure of the emergent trophic network and the rate at which primary resources are supplied control many features of microbial community assembly, including the relative contributions of competition and cooperation and the emergence of alternative community states. Viewing microbial community assembly through the lens of trophic interactions also has important implications for the spatial dynamics of communities as well as the functional redundancy of taxonomic groups. Given the ubiquity of trophic interactions across environments, they impart a common logic that can enable the development of a more quantitative and predictive microbial community ecology.
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Affiliation(s)
- Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel Szabo
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich 8093, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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17
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Pollak S, Gralka M, Sato Y, Schwartzman J, Lu L, Cordero OX. Public good exploitation in natural bacterioplankton communities. Sci Adv 2021; 7:7/31/eabi4717. [PMID: 34321201 PMCID: PMC8318375 DOI: 10.1126/sciadv.abi4717] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/10/2021] [Indexed: 05/19/2023]
Abstract
Bacteria often interact with their environment through extracellular molecules that increase access to limiting resources. These secretions can act as public goods, creating incentives for exploiters to invade and "steal" public goods away from producers. This phenomenon has been studied extensively in vitro, but little is known about the occurrence and impact of public good exploiters in the environment. Here, we develop a genomic approach to systematically identify bacteria that can exploit public goods produced during the degradation of polysaccharides. Focusing on chitin, a highly abundant marine biopolymer, we show that public good exploiters are active in natural chitin degrading microbial communities, invading early during colonization, and potentially hindering degradation. In contrast to in vitro studies, we find that exploiters and degraders belong to distant lineages, facilitating their coexistence. Our approach opens novel avenues to use the wealth of genomic data available to infer ecological roles and interactions among microbes.
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Affiliation(s)
- Shaul Pollak
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuya Sato
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lu Lu
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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18
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Polz MF, Cordero OX. The genetic law of the minimum. Science 2020; 370:655-656. [PMID: 33154123 DOI: 10.1126/science.abf2588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Martin F Polz
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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19
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Affiliation(s)
- Shaul Pollak
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Furman O, Shenhav L, Sasson G, Kokou F, Honig H, Jacoby S, Hertz T, Cordero OX, Halperin E, Mizrahi I. Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics. Nat Commun 2020; 11:1904. [PMID: 32312972 PMCID: PMC7170844 DOI: 10.1038/s41467-020-15652-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 03/09/2020] [Indexed: 02/06/2023] Open
Abstract
How complex communities assemble through the animal's life, and how predictable the process is remains unexplored. Here, we investigate the forces that drive the assembly of rumen microbiomes throughout a cow's life, with emphasis on the balance between stochastic and deterministic processes. We analyse the development of the rumen microbiome from birth to adulthood using 16S-rRNA amplicon sequencing data and find that the animals shared a group of core successional species that invaded early on and persisted until adulthood. Along with deterministic factors, such as age and diet, early arriving species exerted strong priority effects, whereby dynamics of late successional taxa were strongly dependent on microbiome composition at early life stages. Priority effects also manifest as dramatic changes in microbiome development dynamics between animals delivered by C-section vs. natural birth, with the former undergoing much more rapid species invasion and accelerated microbiome development. Overall, our findings show that together with strong deterministic constrains imposed by diet and age, stochastic colonization in early life has long-lasting impacts on the development of animal microbiomes.
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Affiliation(s)
- Ori Furman
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Beer-Sheva, Israel
| | - Liat Shenhav
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Goor Sasson
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Beer-Sheva, Israel
| | - Fotini Kokou
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Beer-Sheva, Israel
| | - Hen Honig
- Institute of Animal Sciences, Agricultural Research Organization, Rishon Letziyon, Israel
| | - Shamay Jacoby
- Institute of Animal Sciences, Agricultural Research Organization, Rishon Letziyon, Israel
| | - Tomer Hertz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Beer-Sheva, Israel
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eran Halperin
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Beer-Sheva, Israel.
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21
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Mahmoudi N, Enke TN, Beaupré SR, Teske AP, Cordero OX, Pearson A. Illuminating microbial species‐specific effects on organic matter remineralization in marine sediments. Environ Microbiol 2019; 22:1734-1747. [DOI: 10.1111/1462-2920.14871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences McGill University Montreal QC H3A 0E8
| | - Tim N. Enke
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology (MIT) Cambridge Massachusetts 02139
| | - Steven R. Beaupré
- School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York 11794
| | - Andreas P. Teske
- Department of Marine Sciences University of North Carolina Chapel Hill North Carolina 27599
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology (MIT) Cambridge Massachusetts 02139
| | - Ann Pearson
- Department of Earth and Planetary Sciences Harvard University Cambridge Massachusetts 02138
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22
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Abstract
Oligosaccharides produced from the extracellular hydrolysis of biological materials can act as common goods that promote cooperative growth in microbial populations, whereby cell–cell aggregation increases both the per capita availability of resources and the per-cell growth rate. However, aggregation can also have detrimental consequences for growth, as gradients form within aggregates limiting the resource accessibility. We built a computational model, which predicts cooperation is restricted in dense cell aggregates larger than 10 µm because of the emergence of polymer and oligomer counter gradients. We compared these predictions to experiments performed with two well-studied alginate-degrading strains of Vibrio splendidus, which varied in their ability to secrete alginate lyase. We observed that both strains can form large aggregates (less than 50 µm), overcoming diffusion limitation by rearranging their internal structure. The stronger enzyme producer grew non-cooperatively and formed aggregates with internal channels that allowed exchange between the bulk environment and the aggregate, whereas the weak enzyme producer showed strongly cooperative growth and formed dense aggregates in which cells near the core mixed by active swimming. Our simulations suggest that the mixing and channelling reduce diffusion limitation and allow cells to uniformly grow in aggregates. Together, these data demonstrate that bacterial behaviour can help overcome competition imposed by resource gradients within cell aggregates. This article is part of a discussion meeting issue ‘Single cell ecology’.
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Affiliation(s)
- Ali Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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23
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Abstract
In the natural environment, insoluble biomatter provides a preeminent source of carbon for bacteria. Its degradation by microbial communities thus plays a major role in the global carbon-cycle. The prediction of degradation processes and their sensitivity to changes in environmental conditions can therefore provide critical insights into globally occurring environmental adaptations. To elucidate and quantify this macro-scale phenomenon, we conduct micro-scale experiments that examine the degradation of isolated biopolymer particles and observe highly nonlinear degradation kinetics. Since conventional scaling arguments fail to explain these observations, it is inferred that the coupled influence of both the physical and biochemical processes must be considered. Hence, we develop a theoretical model that accounts for the bio-chemo-mechanically coupled kinetics of polymer degradation, by considering the production of bio-degraders and their ability to both dissociate the material from its external boundaries and to penetrate it to degrade its internal mechanical properties. This change in mechanical properties combined with the intake of solvent or moisture from the environment leads to chemo-mechanically coupled swelling of the material and, in-turn, influences the degradation kinetics. We show that the model quantitatively captures our experimental results and reveals distinct signatures of different bacteria that are independent of the specific experimental conditions (i.e. particle volume and initial concentrations). Finally, after validating our model against the experimental data we extend our predictions for degradation processes across various length and time scales that are inaccessible in a laboratory setting.
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Affiliation(s)
- Rami Abi-Akl
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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24
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Enke TN, Datta MS, Schwartzman J, Cermak N, Schmitz D, Barrere J, Pascual-García A, Cordero OX. Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities. Curr Biol 2019; 29:1528-1535.e6. [PMID: 31031118 DOI: 10.1016/j.cub.2019.03.047] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 03/21/2019] [Indexed: 02/05/2023]
Abstract
Understanding the principles that govern the assembly of microbial communities across earth's biomes is a major challenge in modern microbial ecology. This pursuit is complicated by the difficulties of mapping functional roles and interactions onto communities with immense taxonomic diversity and of identifying the scale at which microbes interact [1]. To address this challenge, here, we focused on the bacterial communities that colonize and degrade particulate organic matter in the ocean [2-4]. We show that the assembly of these communities can be simplified as a linear combination of functional modules. Using synthetic polysaccharide particles immersed in natural bacterioplankton assemblages [1, 5], we showed that successional particle colonization dynamics are driven by the interaction of two types of modules: a first type made of narrowly specialized primary degraders, whose dynamics are controlled by particle polysaccharide composition, and a second type containing substrate-independent taxa whose dynamics are controlled by interspecific interactions-in particular, cross-feeding via organic acids, amino acids, and other metabolic byproducts. We show that, as a consequence of this trophic structure, communities can assemble modularly-i.e., by a simple sum of substrate-specific primary degrader modules, one for each complex polysaccharide in the particle, connected to a single broad-niche range consumer module. Consistent with this model, a linear combination of the communities on single-polysaccharide particles accurately predicts community composition on mixed-polysaccharide particles. Our results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineer heterotrophic microbiomes.
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Affiliation(s)
- Tim N Enke
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Environmental Systems Science, ETH Zurich, 8093 Zurich, Switzerland
| | - Manoshi S Datta
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nathan Cermak
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Désirée Schmitz
- Department of Environmental Systems Science, ETH Zurich, 8093 Zurich, Switzerland
| | - Julien Barrere
- Department of Environmental Systems Science, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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25
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Leventhal GE, Boix C, Kuechler U, Enke TN, Sliwerska E, Holliger C, Cordero OX. Strain-level diversity drives alternative community types in millimetre-scale granular biofilms. Nat Microbiol 2018; 3:1295-1303. [DOI: 10.1038/s41564-018-0242-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 08/07/2018] [Indexed: 01/12/2023]
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26
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Abstract
A recent genomic analysis of Synechococcus cyanophages sampled for over 15 years reveals a remarkable pattern of stable phage population structure, highly reminiscent of the ecotype structure observed in bacteria and archaeal ecotypes. In this highlight I discuss the importance of this finding and the questions and opportunities it opens to learn more about the nature of phage-bacterial coevolution in the environment.
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Affiliation(s)
- Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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27
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Affiliation(s)
- Otto X Cordero
- Department of Civil and Environmental Engineering, Cambridge, MIT, MA, 02139, USA
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, 8093, Switzerland
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28
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Bongrand C, Koch EJ, Moriano-Gutierrez S, Cordero OX, McFall-Ngai M, Polz MF, Ruby EG. A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior. ISME J 2016; 10:2907-2917. [PMID: 27128997 PMCID: PMC5148191 DOI: 10.1038/ismej.2016.69] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/14/2016] [Accepted: 03/22/2016] [Indexed: 11/09/2022]
Abstract
Newly hatched Euprymna scolopes squid obtain their specific light-organ symbionts from an array of Vibrio (Allivibrio) fischeri strains present in their environment. Two genetically distinct populations of this squid species have been identified, one in Kaneohe Bay (KB), and another in Maunaloa Bay (MB), Oahu. We asked whether symbionts isolated from squid in each of these populations outcompete isolates from the other population in mixed-infection experiments. No relationship was found between a strain's host source (KB or MB) and its ability to competitively colonize KB or MB juveniles in a mixed inoculum. Instead, two colonization behaviors were identified among the 11 KB and MB strains tested: a 'dominant' outcome, in which one strain outcompetes the other for colonization, and a 'sharing' outcome, in which two strains co-colonize the squid. A genome-level comparison of these and other V. fischeri strains suggested that the core genomic structure of this species is both syntenous and highly conserved over time and geographical distance. We also identified ~250 Kb of sequence, encoding 194 dispersed orfs, that was specific to those strains that expressed the dominant colonization behavior. Taken together, the results indicate a link between the genome content of V. fischeri strains and their colonization behavior when initiating a light-organ symbiosis.
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Affiliation(s)
- Clotilde Bongrand
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Eric J Koch
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Silvia Moriano-Gutierrez
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret McFall-Ngai
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Edward G Ruby
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
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29
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30
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Cordero OX, Datta MS. Microbial interactions and community assembly at microscales. Curr Opin Microbiol 2016; 31:227-234. [PMID: 27232202 DOI: 10.1016/j.mib.2016.03.015] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 11/16/2022]
Abstract
In most environments, microbial interactions take place within microscale cell aggregates. At the scale of these aggregates (∼100μm), interactions are likely to be the dominant driver of population structure and dynamics. In particular, organisms that exploit interspecific interactions to increase ecological performance often co-aggregate. Conversely, organisms that antagonize each other will tend to spatially segregate, creating distinct micro-communities and increased diversity at larger length scales. We argue that, in order to understand the role that biological interactions play in microbial community function, it is necessary to study microscale spatial organization with enough throughput to measure statistical associations between taxa and possible alternative community states. We conclude by proposing strategies to tackle this challenge.
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Affiliation(s)
- Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Manoshi S Datta
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H, Soyer OS. Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME J 2016; 10:2557-2568. [PMID: 27022995 PMCID: PMC5113837 DOI: 10.1038/ismej.2016.45] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/12/2016] [Accepted: 02/22/2016] [Indexed: 12/21/2022]
Abstract
The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.
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Affiliation(s)
- Stefanie Widder
- CUBE, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Rosalind J Allen
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Thomas Pfeiffer
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Thomas P Curtis
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - William T Sloan
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, UK
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sam P Brown
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Babak Momeni
- Department of Biology, Boston College, Chestnut Hill, MA, USA.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wenying Shou
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Helen Kettle
- Biomathematics and Statistics Scotland, Edinburgh, UK
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Andreas F Haas
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Béatrice Laroche
- Département de Mathématiques Informatiques Appliquées, INRA, Jouy-en-Josas, France
| | | | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Kim Milferstedt
- INRA, UR0050, Laboratoire de Biotechnologie de l'Environnement, Narbonne, France
| | - Jan R van der Meer
- Department of Fundamental Microbiology, Université de Lausanne, Lausanne, Switzerland
| | - Tobias Groβkopf
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Jef Huisman
- Department of Aquatic Microbiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrew Free
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Science, University of Edinburgh, Edinburgh, UK
| | - Cristian Picioreanu
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Isaac Klapper
- Department of Mathematics, Temple University, Philadelphia, PA, USA
| | - Simon Labarthe
- Département de Mathématiques Informatiques Appliquées, INRA, Jouy-en-Josas, France
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Harris Wang
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, UK
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32
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Takeuchi N, Cordero OX, Koonin EV, Kaneko K. Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection. BMC Biol 2015; 13:20. [PMID: 25928466 PMCID: PMC4410459 DOI: 10.1186/s12915-015-0131-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 03/13/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Fixation of beneficial genes in bacteria and archaea (collectively, prokaryotes) is often believed to erase pre-existing genomic diversity through the hitchhiking effect, a phenomenon known as genome-wide selective sweep. Recent studies, however, indicate that beneficial genes spread through a prokaryotic population via recombination without causing genome-wide selective sweeps. These gene-specific selective sweeps seem to be at odds with the existing estimates of recombination rates in prokaryotes, which appear far too low to explain such phenomena. RESULTS We use mathematical modeling to investigate potential solutions to this apparent paradox. Most microbes in nature evolve in heterogeneous, dynamic communities, in which ecological interactions can substantially impact evolution. Here, we focus on the effect of negative frequency-dependent selection (NFDS) such as caused by viral predation (kill-the-winner dynamics). The NFDS maintains multiple genotypes within a population, so that a gene beneficial to every individual would have to spread via recombination, hence a gene-specific selective sweep. However, gene loci affected by NFDS often are located in variable regions of microbial genomes that contain genes involved in the mobility of selfish genetic elements, such as integrases or transposases. Thus, the NFDS-affected loci are likely to experience elevated rates of recombination compared with the other loci. Consequently, these loci might be effectively unlinked from the rest of the genome, so that NFDS would be unable to prevent genome-wide selective sweeps. To address this problem, we analyzed population genetic models of selective sweeps in prokaryotes under NFDS. The results indicate that NFDS can cause gene-specific selective sweeps despite the effect of locally elevated recombination rates, provided NFDS affects more than one locus and the basal rate of recombination is sufficiently low. Although these conditions might seem to contradict the intuition that gene-specific selective sweeps require high recombination rates, they actually decrease the effective rate of recombination at loci affected by NFDS relative to the per-locus basal level, so that NFDS can cause gene-specific selective sweeps. CONCLUSION Because many free-living prokaryotes are likely to evolve under NFDS caused by ubiquitous viruses, gene-specific selective sweeps driven by NFDS are expected to be a major, general phenomenon in prokaryotic populations.
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Affiliation(s)
- Nobuto Takeuchi
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.
| | - Otto X Cordero
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
| | - Eugene V Koonin
- National Institutes of Health, National Library of Medicine, National Center for Biotechnology Information, Bethesda, USA.
| | - Kunihiko Kaneko
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.
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Abstract
Comparisons of closely related microorganisms have shown that individual genomes can be highly diverse in terms of gene content. In this Review, we discuss several studies showing that much of this variation is associated with social and ecological interactions, which have an important role in the population biology of wild populations of bacteria and archaea. These interactions create frequency-dependent selective pressures that can either stabilize gene frequencies at intermediate levels in populations or promote fast gene turnover, which presents as low gene frequencies in genome surveys. Thus, interpretation of gene-content diversity requires the delineation of populations according to cohesive gene flow and ecology, as micro-evolutionary changes arise in response to local selection pressures and population dynamics.
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Affiliation(s)
- Otto X Cordero
- Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich (ETH-Zürich), CH-8092 Zürich, Switzerland
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139-4307, USA
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Sharma AK, Becker JW, Ottesen EA, Bryant JA, Duhamel S, Karl DM, Cordero OX, Repeta DJ, DeLong EF. Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations ofProchlorococcus,Pelagibacterand the OM60 clade. Environ Microbiol 2013; 16:2815-30. [DOI: 10.1111/1462-2920.12254] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/26/2013] [Accepted: 08/15/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Adrian K. Sharma
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Jamie W. Becker
- Department of Marine Chemistry and Geochemistry; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Elizabeth A. Ottesen
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Department of Microbiology; University of Georgia; Athens GA 30602 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Jessica A. Bryant
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Solange Duhamel
- Department of Marine Chemistry and Geochemistry; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
- Lamont Doherty Earth Observatory; Columbia University; Palisades NY 10964 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - David M. Karl
- Department of Oceanography; School of Ocean and Earth Science and Technology (SOEST); University of Hawaii; Honolulu HI 96822 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Otto X. Cordero
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
| | - Edward F. DeLong
- Departments of Civil and Environmental Engineering and Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Center for Microbial Oceanography: Research and Education (C-MORE); 1950 East-West Road Honolulu HI 96822 USA
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Cordero OX, Wildschutte H, Kirkup B, Proehl S, Ngo L, Hussain F, Le Roux F, Mincer T, Polz MF. Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance. Science 2012; 337:1228-31. [PMID: 22955834 DOI: 10.1126/science.1219385] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In animals and plants, social structure can reduce conflict within populations and bias aggression toward competing populations; however, for bacteria in the wild it remains unknown whether such population-level organization exists. Here, we show that environmental bacteria are organized into socially cohesive units in which antagonism occurs between rather than within ecologically defined populations. By screening approximately 35,000 possible mutual interactions among Vibrionaceae isolates from the ocean, we show that genotypic clusters known to have cohesive habitat association also act as units in terms of antibiotic production and resistance. Genetic analyses show that within populations, broad-range antibiotics are produced by few genotypes, whereas all others are resistant, suggesting cooperation between conspecifics. Natural antibiotics may thus mediate competition between populations rather than solely increase the success of individuals.
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Affiliation(s)
- Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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36
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Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ. Population genomics of early events in the ecological differentiation of bacteria. Science 2012; 336:48-51. [PMID: 22491847 PMCID: PMC3337212 DOI: 10.1126/science.1218198] [Citation(s) in RCA: 335] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.
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Affiliation(s)
- B. Jesse Shapiro
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Jonathan Friedman
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah P. Preheim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sonia C. Timberlake
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gitta Szabó
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric J. Alm
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute, Cambridge, MA 02142, USA
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Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 2011; 480:241-4. [PMID: 22037308 DOI: 10.1038/nature10571] [Citation(s) in RCA: 572] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 09/19/2011] [Indexed: 12/13/2022]
Abstract
Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99% nucleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 × 10(-270)). We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.
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Affiliation(s)
- Chris S Smillie
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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38
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Wang L, Chen S, Vergin KL, Giovannoni SJ, Chan SW, DeMott MS, Taghizadeh K, Cordero OX, Cutler M, Timberlake S, Alm EJ, Polz MF, Pinhassi J, Deng Z, Dedon PC. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci U S A 2011; 108:2963-8. [PMID: 21285367 PMCID: PMC3041111 DOI: 10.1073/pnas.1017261108] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.
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Affiliation(s)
- Lianrong Wang
- Department of Biological Engineering
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Shi Chen
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Kevin L. Vergin
- Department of Microbiology, Oregon State University, Corvallis, OR 97331; and
| | | | | | | | | | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael Cutler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Eric J. Alm
- Department of Biological Engineering
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jarone Pinhassi
- Marine Microbiology, School of Natural Sciences, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Zixin Deng
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Peter C. Dedon
- Department of Biological Engineering
- Center for Environmental Health Sciences, and
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39
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Abstract
Given the dramatic variation in guanine-cytosine (GC) content observed in prokaryotes, from approximately 20% to approximately 75% GC, one wonders if these extreme biases in base pair composition affect the evolution of transcription factor-binding sites (BS). This letter shows that, along the wide range of GC content variation in bacteria, bacterial BS keep a high frequency of AT bases, roughly independently of the background (BG) base pair composition of intergenic regions. As a result, the equilibrium base pair frequencies of BS depart the most from those of BS DNA in GC-rich genomes. This not only implies a higher specificity but also a higher coding barrier for BS in GC-rich genomes. In accordance, we observe that the average percentage of divergently transcribed regions increases with the GC content of the genome, suggesting the use of a more efficient coding strategy.
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40
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Cordero OX, Hogeweg P. Regulome size in Prokaryotes: universality and lineage-specific variations. Trends Genet 2009; 25:285-6. [PMID: 19540614 DOI: 10.1016/j.tig.2009.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/19/2022]
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41
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Abstract
We study gene family coevolution on a tree of life based on a large-scale ancestral gene content reconstruction, which includes gene duplication and deletion events. The insights obtained from this study are threefold: (1) Global properties, such as the distribution of coevolution partners and the formation of disconnected clusters of coevolving families, can be an inevitable consequence of evolution along a tree. (2) Concerted family expansion (gene duplication) and contraction (gene deletion) reflect functional constraints and therefore lead to better function prediction. (3) "Long-range" coevolutionary relationships, caused mostly by large family expansions or contractions, reveal high-level evolutionary organization of cellular processes in prokaryotes.
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Affiliation(s)
- Otto X Cordero
- Theoretical Biology and Bioinformatics, University of Utrecht, 3584 CH Utrecht, The Netherlands.
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Cordero OX, Hogeweg P. Large changes in regulome size herald the main prokaryotic lineages. Trends Genet 2007; 23:488-93. [PMID: 17692992 DOI: 10.1016/j.tig.2007.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 04/17/2007] [Accepted: 07/30/2007] [Indexed: 11/16/2022]
Abstract
Using a large-scale reconstruction of ancestral gene content, we show that radical changes in regulome size occur at the origins of major prokaryotic lineages. Subsequently, the duplication and deletion of regulators slows down in most lineages, except proteobacteria, significantly reducing the scaling of regulators and keeping their average proportion lineage-specific. Our results also suggest that major transitions in prokaryote evolution are related to changes in regulatory capacity rather than proteome innovations.
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Affiliation(s)
- Otto X Cordero
- Department of Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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43
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Abstract
In this article, we establish a connection between the mechanics of genome evolution and the topology of gene regulation networks, focusing in particular on the evolution of the feed-forward loop (FFL) circuits. For this, we design a model of stochastic duplications, deletions, and mutations of binding sites and genes and compare our results with yeast network data. We show that the mechanics of genome evolution may provide a mechanism of FFL circuit generation. Our simulations result in overrepresentation of FFL circuits as well as in their clustering around few regulator pairs, in concordance with data from transcription networks. The mechanism here proposed and the analysis of the yeast data show that regulator duplication could have played an important role in FFL evolution.
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Affiliation(s)
- Otto X Cordero
- Department of Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands.
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