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Vostinar AE, Skocelas KG, Lalejini A, Zaman L. Symbiosis in Digital Evolution: Past, Present, and Future. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.739047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Symbiosis, the living together of unlike organisms as symbionts, is ubiquitous in the natural world. Symbioses occur within and across all scales of life, from microbial to macro-faunal systems. Further, the interactions between symbionts are multimodal in both strength and type, can span from parasitic to mutualistic within one partnership, and persist over generations. Studying the ecological and evolutionary dynamics of symbiosis in natural or laboratory systems poses a wide range of challenges, including the long time scales at which symbioses evolve de novo, the limited capacity to experimentally control symbiotic interactions, the weak resolution at which we can quantify interactions, and the idiosyncrasies of current model systems. These issues are especially challenging when seeking to understand the ecological effects and evolutionary pressures on and of a symbiosis, such as how a symbiosis may shift between parasitic and mutualistic modes and how that shift impacts the dynamics of the partner population. In digital evolution, populations of computational organisms compete, mutate, and evolve in a virtual environment. Digital evolution features perfect data tracking and allows for experimental manipulations that are impractical or impossible in natural systems. Furthermore, modern computational power allows experimenters to observe thousands of generations of evolution in minutes (as opposed to several months or years), which greatly expands the range of possible studies. As such, digital evolution is poised to become a keystone technique in our methodological repertoire for studying the ecological and evolutionary dynamics of symbioses. Here, we review how digital evolution has been used to study symbiosis, and we propose a series of open questions that digital evolution is well-positioned to answer.
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Yu GH, Kuzyakov Y, Luo Y, Goodman BA, Kappler A, Liu FF, Sun FS. Molybdenum Bioavailability and Asymbiotic Nitrogen Fixation in Soils are Raised by Iron (Oxyhydr)oxide-Mediated Free Radical Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14979-14989. [PMID: 34677955 DOI: 10.1021/acs.est.1c04240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nitrogen (N) fixation in soils is closely linked to microbially mediated molybdenum (Mo) cycling. Therefore, elucidating the mechanisms and factors that affect Mo bioavailability is crucial for understanding N fixation. Here, we demonstrate that long-term (26 years) manure fertilization increased microbial diversity and content of short-range ordered iron (oxyhydr)oxides that raised Mo bioavailability (by 2.8 times) and storage (by ∼30%) and increased the abundance of nifH genes (by ∼14%) and nitrogenase activity (by ∼60%). Nanosized iron (oxyhydr)oxides (ferrihydrite, goethite, and hematite nanoparticles) play a dual role in soil Mo cycling: (i) in concert with microorganisms, they raise Mo bioavailability by catalyzing hydroxyl radical (HO•) production via the Fenton reactions and (ii) they increase Mo retention by association with the nanosized iron (oxyhydr)oxides. In summary, long-term manure fertilization raised the stock and bioavailability of Mo (and probably also of other micronutrients) by increasing iron (oxyhydr)oxide reactivity and intensified asymbiotic N fixation through an increased abundance of nifH genes and nitrogenase activity. This work provides a strategy for increasing biological N fixation in agricultural ecosystems.
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Affiliation(s)
- Guang-Hui Yu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37073, Germany
- Agro-Technological Institute, RUDN University, Moscow 117198, Russia
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Bernard A Goodman
- College of Physical Science and Technology, Guangxi University, Nanning 530004, China
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infections, Tübingen 72076, Germany
| | - Fei-Fei Liu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fu-Sheng Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
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Hill BM, Bisht K, Atkins GR, Gomez AA, Rumbaugh KP, Wakeman CA, Brown AMV. Lysis-Hi-C as a method to study polymicrobial communities and eDNA. Mol Ecol Resour 2021; 22:1029-1042. [PMID: 34669257 PMCID: PMC9215119 DOI: 10.1111/1755-0998.13535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]
Abstract
Microbes interact in natural communities in a spatially structured manner, particularly in biofilms and polymicrobial infections. While next generation sequencing approaches provide powerful insights into diversity, metabolic capacity, and mutational profiles of these communities, they generally fail to recover in situ spatial proximity between distinct genotypes in the interactome. Hi‐C is a promising method that has assisted in analysing complex microbiomes, by creating chromatin cross‐links in cells, that aid in identifying adjacent DNA, to improve de novo assembly. This study explored a modified Hi‐C approach involving an initial lysis phase prior to DNA cross‐linking, to test whether adjacent cell chromatin can be cross‐linked, anticipating that this could provide a new avenue for study of spatial‐mutational dynamics in structured microbial communities. An artificial polymicrobial mixture of Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli was lysed for 1–18 h, then prepared for Hi‐C. A murine biofilm infection model was treated with sonication, mechanical lysis, or chemical lysis before Hi‐C. Bioinformatic analyses of resulting Hi‐C interspecies chromatin links showed that while microbial species differed from one another, generally lysis significantly increased links between species and increased the distance of Hi‐C links within species, while also increasing novel plasmid‐chromosome links. The success of this modified lysis‐Hi‐C protocol in creating extracellular DNA links is a promising first step toward a new lysis‐Hi‐C based method to recover genotypic microgeography in polymicrobial communities, with potential future applications in diseases with localized resistance, such as cystic fibrosis lung infections and chronic diabetic ulcers.
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Affiliation(s)
- Bravada M Hill
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Karishma Bisht
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Georgia Rae Atkins
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Amy A Gomez
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Kendra P Rumbaugh
- Department of Surgery, School of Medicine, Texas Tech Health Sciences Center, Lubbock, Texas, USA
| | - Catherine A Wakeman
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
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Abstract
Bioremediation is a sustainable remediation technology as it utilizes microorganisms to convert hazardous compounds into their less toxic or non-toxic constituent elements. This technology has achieved some success in the past decades; however, factors involving microbial consortia, such as microbial assembly, functional interactions, and the role of member species, hinder its development. Microbial consortia may be engineered to reconfigure metabolic pathways and reprogram social interactions to get the desired function, thereby providing solutions to its inherent problems. The engineering of microbial consortia is commonly applied for the commercial production of biomolecules. However, in the field of bioremediation, the engineering of microbial consortia needs to be emphasized. In this review, we will discuss the molecular and ecological mechanisms of engineering microbial consortia with a particular focus on metabolic cross-feeding within species and the transfer of metabolites. We also discuss the advantages and limitations of top-down and bottom-up approaches of engineering microbial consortia and their applications in bioremediation.
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Guilhot R, Rombaut A, Xuéreb A, Howell K, Fellous S. Influence of bacteria on the maintenance of a yeast during Drosophila melanogaster metamorphosis. Anim Microbiome 2021; 3:68. [PMID: 34602098 PMCID: PMC8489055 DOI: 10.1186/s42523-021-00133-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022] Open
Abstract
Interactions between microorganisms associated with metazoan hosts are emerging as key features of symbiotic systems. Little is known about the role of such interactions on the maintenance of host-microorganism association throughout the host’s life cycle. We studied the influence of extracellular bacteria on the maintenance of a wild isolate of the yeast Saccharomyces cerevisiae through metamorphosis of the fly Drosophila melanogaster reared in fruit. Yeasts maintained through metamorphosis only when larvae were associated with extracellular bacteria isolated from D. melanogaster faeces. One of these isolates, an Enterobacteriaceae, favoured yeast maintenance during metamorphosis. Such bacterial influence on host-yeast association may have consequences for the ecology and evolution of insect-yeast-bacteria symbioses in the wild.
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Affiliation(s)
- Robin Guilhot
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
| | - Antoine Rombaut
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Anne Xuéreb
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Kate Howell
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Simon Fellous
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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Henriques GJB, van Vliet S, Doebeli M. Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities. PLoS Comput Biol 2021; 17:e1008896. [PMID: 34516543 PMCID: PMC8460008 DOI: 10.1371/journal.pcbi.1008896] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/23/2021] [Accepted: 08/27/2021] [Indexed: 02/02/2023] Open
Abstract
Reproduction is one of the requirements for evolution and a defining feature of life. Yet, across the tree of life, organisms reproduce in many different ways. Groups of cells (e.g., multicellular organisms, colonial microbes, or multispecies biofilms) divide by releasing propagules that can be single-celled or multicellular. What conditions determine the number and size of reproductive propagules? In multicellular organisms, existing theory suggests that single-cell propagules prevent the accumulation of deleterious mutations (e.g., cheaters). However, groups of cells, such as biofilms, sometimes contain multiple metabolically interdependent species. This creates a reproductive dilemma: small daughter groups, which prevent the accumulation of cheaters, are also unlikely to contain the species diversity that is required for ecological success. Here, we developed an individual-based, multilevel selection model to investigate how such multi-species groups can resolve this dilemma. By tracking the dynamics of groups of cells that reproduce by fragmenting into smaller groups, we identified fragmentation modes that can maintain cooperative interactions. We systematically varied the fragmentation mode and calculated the maximum mutation rate that communities can withstand before being driven to extinction by the accumulation of cheaters. We find that for groups consisting of a single species, the optimal fragmentation mode consists of releasing single-cell propagules. For multi-species groups we find various optimal strategies. With migration between groups, single-cell propagules are favored. Without migration, larger propagules sizes are optimal; in this case, group-size dependent fissioning rates can prevent the accumulation of cheaters. Our work shows that multi-species groups can evolve reproductive strategies that allow them to maintain cooperative interactions.
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Affiliation(s)
| | - Simon van Vliet
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Biozentrum, University of Basel, Basel, Switzerland
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Mathematics, University of British Columbia, Vancouver, Canada
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King WL, Kaestli M, Siboni N, Padovan A, Christian K, Mills D, Seymour J, Gibb K. Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues. Front Microbiol 2021; 12:723649. [PMID: 34434182 PMCID: PMC8381468 DOI: 10.3389/fmicb.2021.723649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/21/2021] [Indexed: 12/25/2022] Open
Abstract
Diseases of bivalves of aquacultural importance, including the valuable Australian silver-lipped pearl oyster (Pinctada maxima), have been increasing in frequency and severity. The bivalve microbiome is linked to health and disease dynamics, particularly in oysters, with putative pathogens within the Vibrio genus commonly implicated in oyster diseases. Previous studies have been biased toward the Pacific oyster because of its global dominance in oyster aquaculture, while much less is known about the microbiome of P. maxima. We sought to address this knowledge gap by characterizing the P. maxima bacterial community, and we hypothesized that bacterial community composition, and specifically the occurrence of Vibrio, will vary according to the sampled microenvironment. We also predicted that the inside shell swab bacterial composition could represent a source of microbial spillover biofilm into the solid pearl oyster tissues, thus providing a useful predictive sampling environment. We found that there was significant heterogeneity in bacterial composition between different pearl oyster tissues, which is consistent with patterns reported in other bivalve species and supports the hypothesis that each tissue type represents a unique microenvironment for bacterial colonization. We suggest that, based on the strong effect of tissue-type on the pearl oyster bacterial community, future studies should apply caution when attempting to compare microbial patterns from different locations, and when searching for disease agents. The lack of association with water at each farm also supported the unique nature of the microbial communities in oyster tissues. In contrast to the whole bacterial community, there was no significant difference in the Vibrio community among tissue types nor location. These results suggest that Vibrio species are shared among different pearl oyster tissues. In particular, the similarity between the haemolymph, inside shell and solid tissues, suggests that the haemolymph and inside shell environment is a source of microbial spillover into the oyster tissues, and a potentially useful tool for non-destructive routine disease testing and early warning surveillance. These data provide important foundational information for future studies identifying the factors that drive microbial assembly in a valuable aquaculture species.
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Affiliation(s)
- William L King
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Anna Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Keith Christian
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - David Mills
- Genecology Research Centre, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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Detman A, Laubitz D, Chojnacka A, Kiela PR, Salamon A, Barberán A, Chen Y, Yang F, Błaszczyk MK, Sikora A. Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production. MICROBIOME 2021; 9:158. [PMID: 34261525 PMCID: PMC8281708 DOI: 10.1186/s40168-021-01105-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/28/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacteria (LAB). Previously, we have confirmed that DF microbial communities (MCs) that fed on molasses are able to convert lactate and acetate to butyrate. The aims of the study were to recognize the biodiversity of DF-MCs able and unable to convert lactate and acetate to butyrate and to define the conditions for the transformation. RESULTS MCs sampled from a DF bioreactor were grown anaerobically in mesophilic conditions on different media containing molasses or sucrose and/or lactate and acetate in five independent static batch experiments. The taxonomic composition (based on 16S_rRNA profiling) of each experimental MC was analysed in reference to its metabolites and pH of the digestive liquids. In the samples where the fermented media contained carbohydrates, the two main tendencies were observed: (i) a low pH (pH ≤ 4), lactate and ethanol as the main fermentation products, MCs dominated with Lactobacillus, Bifidobacterium, Leuconostoc and Fructobacillus was characterized by low biodiversity; (ii) pH in the range 5.0-6.0, butyrate dominated among the fermentation products, the MCs composed mainly of Clostridium (especially Clostridium_sensu_stricto_12), Lactobacillus, Bifidobacterium and Prevotella. The biodiversity increased with the ability to convert acetate and lactate to butyrate. The MC processing exclusively lactate and acetate showed the highest biodiversity and was dominated by Clostridium (especially Clostridium_sensu_stricto_12). LAB were reduced; other genera such as Terrisporobacter, Lachnoclostridium, Paraclostridium or Sutterella were found. Butyrate was the main metabolite and pH was 7. Shotgun metagenomic analysis of the selected butyrate-producing MCs independently on the substrate revealed C.tyrobutyricum as the dominant Clostridium species. Functional analysis confirmed the presence of genes encoding key enzymes of the fermentation routes. CONCLUSIONS Batch tests revealed the dynamics of metabolic activity and composition of DF-MCs dependent on fermentation conditions. The balance between LAB and the butyrate producers and the pH values were shown to be the most relevant for the process of lactate and acetate conversion to butyrate. To close the knowledge gaps is to find signalling factors responsible for the metabolic shift of the DF-MCs towards lactate fermentation. Video Abstract.
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Affiliation(s)
- Anna Detman
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Daniel Laubitz
- Department of Pediatrics at Steel Children’s Research Center College of Medicine, University of Arizona, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, Arizona 85724-5073 USA
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Pawel R. Kiela
- Department of Pediatrics at Steel Children’s Research Center College of Medicine, University of Arizona, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, Arizona 85724-5073 USA
| | - Agnieszka Salamon
- Institute of Agricultural and Food Biotechnology, Rakowiecka 36, 02-532 Warsaw, Poland
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Fei Yang
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Mieczysław K. Błaszczyk
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Anna Sikora
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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Law KP, He W, Tao J, Zhang C. Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:658781. [PMID: 34276593 PMCID: PMC8281238 DOI: 10.3389/fmicb.2021.658781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Marine Thaumarchaeota (formerly known as the marine group I archaea) have received much research interest in recent years since these chemolithoautotrophic organisms are abundant in the subsurface ocean and oxidize ammonium to nitrite, which makes them a major contributor to the marine carbon and nitrogen cycles. However, few studies have investigated the chemical composition of their exometabolome and their contributions to the pool of dissolved organic matter (DOM) in seawater. This study exploits the recent advances in ion mobility mass spectrometry (IM-MS) and integrates this instrumental capability with bioinformatics to reassess the exometabolome of a model ammonia-oxidizing archaeon, Nitrosopumilus maritimus strain SCM1. Our method has several advantages over the conventional approach using an Orbitrap or ion cyclotron resonance mass analyzer and allows assignments or annotations of spectral features to known metabolites confidently and indiscriminately, as well as distinction of biological molecules from background organics. Consistent with the results of a previous report, the SPE-extracted exometabolome of N. maritimus is dominated by biologically active nitrogen-containing metabolites, in addition to peptides secreted extracellularly. Cobalamin and associated intermediates, including α-ribazole and α-ribazole 5'-phosphate, are major components of the SPE-extracted exometabolome of N. maritimus. This supports the proposition that Thaumarchaeota have the capacity of de novo biosynthesizing cobalamin. Other biologically significant metabolites, such as agmatidine and medicagenate, predicted by genome screening are also detected, which indicates that Thaumarchaeota have remarkable metabolic potentials, underlining their importance in driving elemental cycles critical to biological processes in the ocean.
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Affiliation(s)
- Kai P. Law
- SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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Manriquez B, Muller D, Prigent-Combaret C. Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities. Front Microbiol 2021; 12:619122. [PMID: 34025595 PMCID: PMC8137971 DOI: 10.3389/fmicb.2021.619122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of microbial communities to new (and often complex) environments can be tackled with a combination of experimental evolution and next generation sequencing. This combination allows to analyse the real-time evolution of microbial populations in response to imposed environmental factors or during the interaction with a host, by screening for phenotypic and genotypic changes over a multitude of identical experimental cycles. Experimental evolution (EE) coupled with comparative genomics has indeed facilitated the monitoring of bacterial genetic evolution and the understanding of adaptive evolution processes. Basically, EE studies had long been done on single strains, allowing to reveal the dynamics and genetic targets of natural selection and to uncover the correlation between genetic and phenotypic adaptive changes. However, species are always evolving in relation with other species and have to adapt not only to the environment itself but also to the biotic environment dynamically shaped by the other species. Nowadays, there is a growing interest to apply EE on microbial communities evolving under natural environments. In this paper, we provide a non-exhaustive review of microbial EE studies done with systems of increasing complexity (from single species, to synthetic communities and natural communities) and with a particular focus on studies between plants and plant-associated microorganisms. We highlight some of the mechanisms controlling the functioning of microbial species and their adaptive responses to environment changes and emphasize the importance of considering bacterial communities and complex environments in EE studies.
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Affiliation(s)
| | | | - Claire Prigent-Combaret
- UMR 5557 Ecologie Microbienne, VetAgro Sup, CNRS, INRAE, University of Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
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61
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Rojas CA, De Santiago Torio A, Park S, Bosak T, Klepac-Ceraj V. Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake. Front Microbiol 2021; 12:620424. [PMID: 33967973 PMCID: PMC8103211 DOI: 10.3389/fmicb.2021.620424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin's index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.
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Affiliation(s)
- Connie A. Rojas
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
- Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, United States
| | - Ana De Santiago Torio
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Serry Park
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
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Fernandez-Julia PJ, Munoz-Munoz J, van Sinderen D. A comprehensive review on the impact of β-glucan metabolism by Bacteroides and Bifidobacterium species as members of the gut microbiota. Int J Biol Macromol 2021; 181:877-889. [PMID: 33864864 DOI: 10.1016/j.ijbiomac.2021.04.069] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/01/2021] [Accepted: 04/10/2021] [Indexed: 12/16/2022]
Abstract
β-glucans are polysaccharides which can be obtained from different sources, and which have been described as potential prebiotics. The beneficial effects associated with β-glucan intake are that they reduce energy intake, lower cholesterol levels and support the immune system. Nevertheless, the mechanism(s) of action underpinning these health effects related to β-glucans are still unclear, and the precise impact of β-glucans on the gut microbiota has been subject to debate and revision. In this review, we summarize the most recent advances involving structurally different types of β-glucans as fermentable substrates for Bacteroidetes (mainly Bacteroides) and Bifidobacterium species as glycan degraders. Bacteroides is one of the most abundant bacterial components of the human gut microbiota, while bifidobacteria are widely employed as a probiotic ingredient. Both are generalist glycan degraders capable of using a wide range of substrates: Bacteroides spp. are specialized as primary degraders in the metabolism of complex carbohydrates, whereas Bifidobacterium spp. more commonly metabolize smaller glycans, in particular oligosaccharides, sometimes through syntrophic interactions with Bacteroides spp., in which they act as secondary degraders.
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Affiliation(s)
- Pedro J Fernandez-Julia
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, Tyne & Wear, England, United Kingdom
| | - Jose Munoz-Munoz
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, Tyne & Wear, England, United Kingdom.
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland.
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Martín-Garcia A, Riu-Aumatell M, López-Tamames E. Influence of Process Parameters on Sourdough Microbiota, Physical Properties and Sensory Profile. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1906698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Alba Martín-Garcia
- Departament of Nutrition, Food Sciences and Gastronomy, Campus Torribera, Universitat de Barcelona (UB), Institut de Recerca En Nutrició I Seguretat Alimentària (INSA-UB), XaRTA, Santa Coloma De Gramenet, España
| | - Montserrat Riu-Aumatell
- Departament of Nutrition, Food Sciences and Gastronomy, Campus Torribera, Universitat de Barcelona (UB), Institut de Recerca En Nutrició I Seguretat Alimentària (INSA-UB), XaRTA, Santa Coloma De Gramenet, España
| | - Elvira López-Tamames
- Departament of Nutrition, Food Sciences and Gastronomy, Campus Torribera, Universitat de Barcelona (UB), Institut de Recerca En Nutrició I Seguretat Alimentària (INSA-UB), XaRTA, Santa Coloma De Gramenet, España
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65
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Murphy TR, Xiao R, Hamilton-Brehm SD. Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13 T. BMC Genomics 2021; 22:209. [PMID: 33757423 PMCID: PMC7988955 DOI: 10.1186/s12864-021-07535-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life endures in the extreme oligotrophic subsurface environments is greatly hindered. Using a de novo hybrid assembly of Illumina and Oxford Nanopore sequences we produced a circular genome with corresponding methylome profile of the recently characterized thermophilic, anaerobic, and fumarate-respiring subsurface bacterium, Thermanaerosceptrum fracticalcis, strain DRI-13T to understand how this microorganism survives the deep subsurface. RESULTS The hybrid assembly produced a single circular genome of 3.8 Mb in length with an overall GC content of 45%. Out of the total 4022 annotated genes, 3884 are protein coding, 87 are RNA encoding genes, and the remaining 51 genes were associated with regulatory features of the genome including riboswitches and T-box leader sequences. Approximately 24% of the protein coding genes were hypothetical. Analysis of strain DRI-13T genome revealed: 1) energy conservation by bifurcation hydrogenase when growing on fumarate, 2) four novel bacterial prophages, 3) methylation profile including 76.4% N6-methyladenine and 3.81% 5-methylcytosine corresponding to novel DNA methyltransferase motifs. As well a cluster of 45 genes of unknown protein families that have enriched DNA mCpG proximal to the transcription start sites, and 4) discovery of a putative core of bacteriophage exclusion (BREX) genes surrounded by hypothetical proteins, with predicted functions as helicases, nucleases, and exonucleases. CONCLUSIONS The de novo hybrid assembly of strain DRI-13T genome has provided a more contiguous and accurate view of the subsurface bacterium T. fracticalcis, strain DRI-13T. This genome analysis reveals a physiological focus supporting syntrophy, non-homologous double stranded DNA repair, mobility/adherence/chemotaxis, unique methylome profile/recognized motifs, and a BREX defense system. The key to microbial subsurface survival may not rest on genetic diversity, but rather through specific syntrophy niches and novel methylation strategies.
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Affiliation(s)
- Trevor R Murphy
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Rui Xiao
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Scott D Hamilton-Brehm
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA.
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66
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Targeting the Gut Microbiome to Mitigate Immunotherapy-Induced Colitis in Cancer. Trends Cancer 2021; 7:583-593. [PMID: 33741313 DOI: 10.1016/j.trecan.2021.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022]
Abstract
Immune checkpoint inhibitors (ICIs) have been a transformational advance in cancer therapy in the past decade. However, ICIs can produce immune-related adverse effects (irAEs), which can lead to both morbidity and premature termination of therapy. Recent studies suggest that the gut microbiota and its metabolites affect ICI efficacy and toxicity. Herein, we review such evidence in the context of ICI-induced colitis. In particular, the short-chain fatty acid butyrate, a microbial metabolite, has known protective effects on the intestine. We discuss how the use of dietary prebiotics, which can be metabolized by bacteria to produce butyrate, can be an intriguing new investigational approach to prevent ICI-associated colitis and lead to improved patient outcomes.
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67
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Larsen T, Jefferson C, Bartley A, Strassmann JE, Queller DC. Inference of symbiotic adaptations in nature using experimental evolution. Evolution 2021; 75:945-955. [PMID: 33590884 DOI: 10.1111/evo.14193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/30/2021] [Indexed: 11/27/2022]
Abstract
Microbes must adapt to the presence of other species, but it can be difficult to recreate the natural context for these interactions in the laboratory. We describe a method for inferring the existence of symbiotic adaptations by experimentally evolving microbes that would normally interact in an artificial environment without access to other species. By looking for changes in the fitness effects microbes adapted to isolation have on their partners, we can infer the existence of ancestral adaptations that were lost during experimental evolution. The direction and magnitude of trait changes can offer useful insight as to whether the microbes have historically been selected to help or harm one another in nature. We apply our method to the complex symbiosis between the social amoeba Dictyostelium discoideum and two intracellular bacterial endosymbionts, Paraburkholderia agricolaris and Paraburkholderia hayleyella. Our results suggest P. hayleyella-but not P. agricolaris-has generally been selected to attenuate its virulence in nature, and that D. discoideum has evolved to antagonistically limit the growth of Paraburkholderia. The approach demonstrated here can be a powerful tool for studying adaptations in microbes, particularly when the specific natural context in which the adaptations evolved is unknown or hard to reproduce.
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Affiliation(s)
- Tyler Larsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Cara Jefferson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Anthony Bartley
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Joan E Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - David C Queller
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
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Fritts RK, McCully AL, McKinlay JB. Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:e00135-20. [PMID: 33441489 PMCID: PMC7849352 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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Affiliation(s)
- Ryan K Fritts
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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69
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Cocco N, Llabrés M, Reyes-Prieto M, Simeoni M. MetNet: A two-level approach to reconstructing and comparing metabolic networks. PLoS One 2021; 16:e0246962. [PMID: 33577575 PMCID: PMC7880445 DOI: 10.1371/journal.pone.0246962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/28/2021] [Indexed: 11/28/2022] Open
Abstract
Metabolic pathway comparison and interaction between different species can detect important information for drug engineering and medical science. In the literature, proposals for reconstructing and comparing metabolic networks present two main problems: network reconstruction requires usually human intervention to integrate information from different sources and, in metabolic comparison, the size of the networks leads to a challenging computational problem. We propose to automatically reconstruct a metabolic network on the basis of KEGG database information. Our proposal relies on a two-level representation of the huge metabolic network: the first level is graph-based and depicts pathways as nodes and relations between pathways as edges; the second level represents each metabolic pathway in terms of its reactions content. The two-level representation complies with the KEGG database, which decomposes the metabolism of all the different organisms into “reference” pathways in a standardised way. On the basis of this two-level representation, we introduce some similarity measures for both levels. They allow for both a local comparison, pathway by pathway, and a global comparison of the entire metabolism. We developed a tool, MetNet, that implements the proposed methodology. MetNet makes it possible to automatically reconstruct the metabolic network of two organisms selected in KEGG and to compare their two networks both quantitatively and visually. We validate our methodology by presenting some experiments performed with MetNet.
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Affiliation(s)
- Nicoletta Cocco
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Venice, Italy
| | - Mercè Llabrés
- Mathematics and Computer Science Department, University of the Balearic Islands, Palma, Spain
| | - Mariana Reyes-Prieto
- Evolutionary Systems Biology of Symbionts, Institute for Integrative Systems Biology (I 2 SysBio), Universitat de Valencia, Paterna, Valencia, Spain
- Sequencing and Bioinformatics Service, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region (FISABIO), València, Spain
| | - Marta Simeoni
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Venice, Italy
- European Centre for Living Technology (ECLT), Venice, Italy
- * E-mail:
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70
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A Novel Enterococcus faecalis Heme Transport Regulator (FhtR) Senses Host Heme To Control Its Intracellular Homeostasis. mBio 2021; 12:mBio.03392-20. [PMID: 33531389 PMCID: PMC7858072 DOI: 10.1128/mbio.03392-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecalis, a normal and harmless colonizer of the human intestinal flora can cause severe infectious diseases in immunocompromised patients, particularly those that have been heavily treated with antibiotics. Therefore, it is important to understand the factors that promote its resistance and its virulence. E. faecalis, which cannot synthesize heme, an essential but toxic metabolite, needs to scavenge this molecule from the host to respire and fight stress generated by oxidants. Enterococcus faecalis is a commensal Gram-positive pathogen found in the intestines of mammals and is also a leading cause of severe infections occurring mainly among antibiotic-treated dysbiotic hospitalized patients. Like most intestinal bacteria, E. faecalis does not synthesize heme (in this report, heme refers to iron protoporphyrin IX regardless of the iron redox state). Nevertheless, environmental heme can improve E. faecalis fitness by activating respiration metabolism and a catalase that limits hydrogen peroxide stress. Since free heme also generates toxicity, its intracellular levels need to be strictly controlled. Here, we describe a unique transcriptional regulator, FhtR (named FhtR for faecalis heme transport regulator), which manages heme homeostasis by controlling an HrtBA-like efflux pump (named HrtBAEf for the HrtBA from E. faecalis). We show that FhtR, by managing intracellular heme concentration, regulates the functional expression of the heme-dependent catalase A (KatA), thus participating in heme detoxification. The biochemical features of FhtR binding to DNA, and its interaction with heme that induces efflux, are characterized. The FhtR-HrtBAEf system is shown to be relevant in a mouse intestinal model. We further show that FhtR senses heme from blood and hemoglobin but also from crossfeeding by Escherichia coli. These findings bring to light the central role of heme sensing by FhtR in response to heme fluctuations within the gastrointestinal tract, which allow this pathogen to limit heme toxicity while ensuring expression of an oxidative defense system.
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71
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van Dongen KCW, van der Zande M, Bruyneel B, Vervoort JJM, Rietjens IMCM, Belzer C, Beekmann K. An in vitro model for microbial fructoselysine degradation shows substantial interindividual differences in metabolic capacities of human fecal slurries. Toxicol In Vitro 2021; 72:105078. [PMID: 33429044 DOI: 10.1016/j.tiv.2021.105078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Fructoselysine is formed upon heating during processing of food products, and being a key intermediate in advanced glycation end product formation considered to be potentially hazardous to human health. Human gut microbes can degrade fructoselysine to yield the short chain fatty acid butyrate. However, quantitative information on these biochemical reactions is lacking, and interindividual differences therein are not well established. Anaerobic incubations with pooled and individual human fecal slurries were optimized and applied to derive quantitative kinetic information for these biochemical reactions. Of 16 individuals tested, 11 were fructoselysine metabolizers, with Vmax, Km and kcat-values varying up to 14.6-fold, 9.5-fold, and 4.4-fold, respectively. Following fructoselysine exposure, 10 of these 11 metabolizers produced significantly increased butyrate concentrations, varying up to 8.6-fold. Bacterial taxonomic profiling of the fecal samples revealed differential abundant taxa for these reactions (e.g. families Ruminococcaceae, Christenellaceae), and Ruminococcus_1 showed the strongest correlation with fructoselysine degradation and butyrate production (ρ ≥ 0.8). This study highlights substantial interindividual differences in gut microbial degradation of fructoselysine. The presented method allows for quantification of gut microbial degradation kinetics for foodborne xenobiotics, and interindividual differences therein, which can be used to refine prediction of internal exposure.
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Affiliation(s)
- Katja C W van Dongen
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands.
| | - Meike van der Zande
- Wageningen Food Safety Research (WFSR), part of Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, the Netherlands
| | - Ben Bruyneel
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands
| | - Jacques J M Vervoort
- Laboratory of Biochemistry, Wageningen University and Research, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH Wageningen, the Netherlands
| | - Karsten Beekmann
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands; Wageningen Food Safety Research (WFSR), part of Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, the Netherlands
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72
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Domingo-Sananes MR, McInerney JO. Mechanisms That Shape Microbial Pangenomes. Trends Microbiol 2021; 29:493-503. [PMID: 33423895 DOI: 10.1016/j.tim.2020.12.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/02/2023]
Abstract
Analyses of multiple whole-genome sequences from the same species have revealed that differences in gene content can be substantial, particularly in prokaryotes. Such variation has led to the recognition of pangenomes, the complete set of genes present in a species - consisting of core genes, present in all individuals, and accessory genes whose presence is variable. Questions now arise about how pangenomes originate and evolve. We describe how gene content variation can arise as a result of the combination of several processes, including random drift, selection, gain/loss balance, and the influence of ecological and epistatic interactions. We believe that identifying the contributions of these processes to pangenomes will need novel theoretical approaches and empirical data.
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Affiliation(s)
- Maria Rosa Domingo-Sananes
- School of Life Sciences, University of Nottingham, Nottingham, UK; School of Science and Technology, Nottingham Trent University, Nottingham, UK.
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73
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Dulay H, Tabares M, Kashefi K, Reguera G. Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Front Microbiol 2020; 11:600463. [PMID: 33324382 PMCID: PMC7726332 DOI: 10.3389/fmicb.2020.600463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
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Affiliation(s)
- Hunter Dulay
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Marcela Tabares
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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Sousa JAB, Bolgár A, Christel S, Dopson M, Bijmans MFM, Stams AJM, Plugge CM. Immobilization of sulfate and thiosulfate-reducing biomass on sand under haloalkaline conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:141017. [PMID: 32736107 DOI: 10.1016/j.scitotenv.2020.141017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Biological sulfate and thiosulfate reduction under haloalkaline conditions can be applied to treat waste streams from biodesulfurization systems. However, the lack of microbial aggregation under haloalkaline conditions limits the volumetric rates of sulfate and thiosulfate reducing bioreactors. As biomass retention in haloalkaline bioreactors has not been studied before, sand was chosen as a biomass carrier material to increase cell retention and consequently raise the volumetric rates. The results showed that ~10 fold higher biomass concentrations could be achieved with sand, compared to previous studies without carrier addition. The volumetric rates of sulfate/thiosulfate reduction increased approximately 4.5 times. Biomass attachment to the sand was restricted to cavities within the sand particles. Acetate produced by acetogenic bacteria from H2 and CO2 was used as carbon source for biomass growth, while formate that was also produced from H2 and CO2 enhanced sulfate reduction. The microbial community composition was analyzed by 16S rRNA gene amplicon sequencing, and Tindallia related bacteria were probably responsible for formate formation from hydrogen. The community attached to the sand particles was similar to the suspended fraction, but the relative abundance of sequences most closely related to Desulfohalobiaceae was much higher in the attached fraction compared to the suspended fraction (30% and 13%, respectively). The results indicated that even though the biomass attachment to sand was poor, it still increased the biomass concentration and consequently the sulfate and thiosulfate reduction volumetric rates.
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Affiliation(s)
- João A B Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Andrea Bolgár
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Martijn F M Bijmans
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands.
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75
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Guilhot R, Fellous S, Cohen JE. Yeast facilitates the multiplication of Drosophila bacterial symbionts but has no effect on the form or parameters of Taylor's law. PLoS One 2020; 15:e0242692. [PMID: 33227009 PMCID: PMC7682849 DOI: 10.1371/journal.pone.0242692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/08/2020] [Indexed: 11/19/2022] Open
Abstract
Interactions between microbial symbionts influence their demography and that of their hosts. Taylor’s power law (TL)–a well-established relationship between population size mean and variance across space and time–may help to unveil the factors and processes that determine symbiont multiplications. Recent studies suggest pervasive interactions between symbionts in Drosophila melanogaster. We used this system to investigate theoretical predictions regarding the effects of interspecific interactions on TL parameters. We assayed twenty natural strains of bacteria in the presence and absence of a strain of yeast using an ecologically realistic set-up with D. melanogaster larvae reared in natural fruit. Yeast presence led to a small increase in bacterial cell numbers; bacterial strain identity largely affected yeast multiplication. The spatial version of TL held among bacterial and yeast populations with slopes of 2. However, contrary to theoretical prediction, the facilitation of bacterial symbionts by yeast had no detectable effect on TL’s parameters. These results shed new light on the nature of D. melanogaster’s symbiosis with yeast and bacteria. They further reveal the complexity of investigating TL with microorganisms.
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Affiliation(s)
- Robin Guilhot
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Simon Fellous
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Joel E Cohen
- Laboratory of Populations, Rockefeller University, New York, New York, United States of America
- Earth Institute and Department of Statistics, Columbia University, New York, New York, United States of America
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
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76
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Zhou YY, Shao WL, Liu YD, Li X, Shan XY, Jin XB, Gao J, Li W. Genome-based analysis to understanding rapid resuscitation of cryopreserved anammox consortia via sequential supernatant addition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140785. [PMID: 32707413 DOI: 10.1016/j.scitotenv.2020.140785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/23/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Simple cryopreservation of anaerobic ammonium-oxidation (anammox) consortia has become a promising preservation technology for the fast start-up of the anammox process. Here, we use genome-resolved metagenomics and metatranscriptomics to understand of the microbial interaction in a simple and effective resuscitation process for long-term cryopreserved anammox consortia by sequential addition of anammox SBR supernatant. Performance results showed that sequential addition of anammox supernatant significantly reduced the resuscitation time of the granule-based anammox process from 40 to 20 days. Genome-centric metagenomics were used to recover 19 high-quality draft genomes of anammox and heterotrophic bacteria. Comparative metatranscriptomic analysis was conducted to examine the gene expression of Candidatus Kuenenia stuttgartiensis, the dominant anammox bacterium, and heterotrophic bacteria to better understand their potential interactions. Proteobacteria-affiliated bacteria found in the supernatant were highly active in producing the secondary metabolites molybdopterin cofactor and folate which are needed for growth of the auxotrophic anammox bacteria. In addition, the significantly higher expression levels of hzsA and CO2-fixtion genes in the Candidatus Kuenenia genome indicated the anammox bacteria were likely more active and growing faster after sequential anammox supernatant addition during the resuscitation process. The resuscitation treatment pulse assays confirmed that sequential addition of supernatant was an effective way for the rapid resuscitation of anammox consortia. Our findings offer the first evidence of cross-feeding during the rapid resuscitation of cryopreserved anammox consortia.
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Affiliation(s)
- Yuan-Yuan Zhou
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Wen-Li Shao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Yong-di Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Xiang Li
- Suzhou University of Science and Technology, Suzhou, China
| | - Xiao-Yu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Xin-Bai Jin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Jie Gao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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77
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Madi N, Vos M, Murall CL, Legendre P, Shapiro BJ. Does diversity beget diversity in microbiomes? eLife 2020; 9:e58999. [PMID: 33215610 PMCID: PMC7755399 DOI: 10.7554/elife.58999] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. 'Ecological Controls' (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, 'Diversity Begets Diversity' (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favouring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).
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Affiliation(s)
- Naïma Madi
- Département de sciences biologiques, Université de MontréalMontrealCanada
| | - Michiel Vos
- European Centre for Environment and Human Health, University of ExeterPenrynUnited Kingdom
| | - Carmen Lia Murall
- Département de sciences biologiques, Université de MontréalMontrealCanada
| | - Pierre Legendre
- Département de sciences biologiques, Université de MontréalMontrealCanada
| | - B Jesse Shapiro
- Département de sciences biologiques, Université de MontréalMontrealCanada
- Department of Microbiology and Immunology, McGill UniversityMontrealCanada
- McGill Genome Centre, McGill UniversityMontrealCanada
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78
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Chia LW, Mank M, Blijenberg B, Bongers RS, van Limpt K, Wopereis H, Tims S, Stahl B, Belzer C, Knol J. Cross-feeding between Bifidobacterium infantis and Anaerostipes caccae on lactose and human milk oligosaccharides. Benef Microbes 2020; 12:69-83. [PMID: 33191780 DOI: 10.3920/bm2020.0005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The establishment of the gut microbiota immediately after birth is a dynamic process that may impact lifelong health. At this important developmental stage in early life, human milk oligosaccharides (HMOs) serve as specific substrates to shape the gut microbiota of the nursling. The well-orchestrated transition is important as an aberrant microbial composition and bacterial-derived metabolites are associated with colicky symptoms and atopic diseases in infants. Here, we study the trophic interactions between an HMO-degrader, Bifidobacterium infantis and the butyrogenic Anaerostipes caccae using carbohydrate substrates that are relevant in the early life period including lactose and total human milk carbohydrates. Mono- and co-cultures of these bacterial species were grown at pH 6.5 in anaerobic bioreactors supplemented with lactose or total human milk carbohydrates. A. caccae was not able to grow on these substrates except when grown in co-culture with B. infantis, leading to growth and concomitant butyrate production. Two levels of cross-feeding were observed, in which A. caccae utilised the liberated monosaccharides as well as lactate and acetate produced by B. infantis. This microbial cross-feeding points towards the key ecological role of bifidobacteria in providing substrates for other important species that will colonise the infant gut. The progressive shift of the gut microbiota composition that contributes to the gradual production of butyrate could be important for host-microbial crosstalk and gut maturation.
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Affiliation(s)
- L W Chia
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - M Mank
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - B Blijenberg
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - R S Bongers
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - K van Limpt
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - H Wopereis
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - S Tims
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
| | - B Stahl
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands.,Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - C Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - J Knol
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.,Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, the Netherlands
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79
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Johnson WM, Alexander H, Bier RL, Miller DR, Muscarella ME, Pitz KJ, Smith H. Auxotrophic interactions: a stabilizing attribute of aquatic microbial communities? FEMS Microbiol Ecol 2020; 96:fiaa115. [PMID: 32520336 PMCID: PMC7609354 DOI: 10.1093/femsec/fiaa115] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/09/2020] [Indexed: 11/14/2022] Open
Abstract
Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
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Affiliation(s)
- Winifred M Johnson
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Sciences and Engineering, Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543, USA
| | - Raven L Bier
- Stroud Water Research Center, 970 Spencer Rd., Avondale, PA 19311, USA
| | - Dan R Miller
- PureMagic LTD, Rambam 67, Yad Rambam 9979300, Israel
| | - Mario E Muscarella
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Kathleen J Pitz
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Heidi Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
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80
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Abdul Aziz FA, Suzuki K, Honjo M, Amano K, Mohd Din ARJB, Tashiro Y, Futamata H. Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture. J Biosci Bioeng 2020; 131:77-83. [PMID: 33268319 DOI: 10.1016/j.jbiosc.2020.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/24/2022]
Abstract
The coexisting mechanism of a synthetic bacterial community (SBC) was investigated to better understand how to manage microbial communities. The SBC was constructed with three kinds of phenol-utilizing bacteria, Pseudomonas sp. LAB-08, Comamonas testosteroni R2, and Cupriavidus sp. P-10, under chemostat conditions supplied with phenol as a sole carbon and energy source. Population densities of all strains were monitored by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase. Although the supply of phenol was stopped to allow perturbation in the SBC, all of the strains coexisted and the degradation of phenol was maintained for more than 800 days. The qPCR analyses showed that strains LAB-08 and R2 became dominant simultaneously, whereas strain P-10 was a minor population. This phenomenon was observed before and after the phenol-supply stoppage. The kinetic parameters for phenol of the SBC changed before and after the phenol-supply stoppage, which suggests a change in functional roles of strains in the SBC. Transcriptional levels of phenol hydroxylase and catechol dioxygenases of three strains were monitored by reverse-transcription qPCR (RT-qPCR). The RT-qPCR analyses revealed that all strains shared phenol and survived independently before the phenol-supply stoppage. After the stoppage, strain P-10 would incur the cost for degradation of phenol and catechol, whereas strains LAB-08 and R2 seemed to be cheaters using metabolites, indicating the development of the metabolic network. These results indicated that it is important for the management and redesign of microbial communities to understand the metabolism of bacterial communities.
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Affiliation(s)
- Fatma Azwani Abdul Aziz
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Kenshi Suzuki
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Masahiro Honjo
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Koki Amano
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan
| | | | - Yosuke Tashiro
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan; Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan; Research Institution of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan.
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81
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Sela R, Hammer BK, Halpern M. Quorum-sensing signaling by chironomid egg masses' microbiota, affects haemagglutinin/protease (HAP) production by Vibrio cholerae. Mol Ecol 2020; 30:1736-1746. [PMID: 33001525 DOI: 10.1111/mec.15662] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 01/01/2023]
Abstract
Vibrio cholerae, the causative agent of cholera, is commonly isolated, along with other bacterial species, from chironomid insects (Diptera: Chironomidae). Nevertheless, its prevalence in the chironomid egg masses' microbiota is less than 0.5%. V. cholerae secretes haemagglutinin/protease (HAP) that degrades the gelatinous matrix of chironomid egg masses and prevents hatching. Quorum sensing (QS) activates HAP production in response to accumulation of bacterial autoinducers (AIs). Our aim was to define the impact of chironomid microbiota on HAP production by V. cholerae. To study QS signaling, we used V. cholerae bioluminescence reporter strains (QS-proficient O1 El-Tor wild-type and QS-deficient mutants) and different bacterial species that we isolated from chironomid egg masses. These egg mass isolates, as well as a synthetic AI-2, caused an enhancement in lux expression by a V. cholerae QS-deficient mutant. The addition of the egg mass bacterial isolate supernatant to the QS-deficient mutant also enhanced HAP production and egg mass degradation activities. Moreover, the V. cholerae wild-type strain was able to proliferate using egg masses as their sole carbon source, while the QS-deficient was not. The results demonstrate that members of the chironomid bacterial consortium produce external chemical cues that, like AI-2, induce expression of the hapA gene in V. cholerae. Understanding the interactions between V. cholerae and the insects' microbiota may help uncover the interactions between this pathogen and the human gut microbiota.
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Affiliation(s)
- Rotem Sela
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Brian K Hammer
- School of Biological Science, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.,Department of Biology and Environment, University of Haifa at Oranim, Tivon, Israel
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82
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Baum C, Menezes RC, Svatoš A, Schubert T. Cobamide remodeling in the freshwater microalga Chlamydomonas reinhardtii. FEMS Microbiol Lett 2020; 367:5932200. [DOI: 10.1093/femsle/fnaa171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/16/2020] [Indexed: 11/13/2022] Open
Abstract
ABSTRACTMicroalgae are not able to produce cobamides (Cbas, B12 vitamers) de novo. Hence, the production of catalytically active Cba-containing methionine synthase (MetH), which is present in selected representatives, is dependent on the availability of exogenous B12 vitamers. Preferences in the utilization of exogenous Cbas equipped with either adenine or 5,6-dimethylbenzimidazole as lower base have been reported for some microalgae. Here, we investigated the utilization of norcobamides (NorCbas) for growth by the Cba-dependent Chlamydomonas reinhardtii mutant strain (ΔmetE). The growth yields in the presence of NorCbas were lower in comparison to those achieved with Cbas. NorCbas lack a methyl group in the linker moiety of the nucleotide loop. C. reinhardtii was also tested for the remodeling of NorCbas (e.g. adeninyl-norcobamide) in the presence of different benzimidazoles. Extraction of the NorCbas from C. reinhardtii, their purification, and identification confirmed the exchange of the lower base of the vitamers. However, the linker moiety of the NorCbas nucleotide loop was not exchanged. This observation strongly indicates the presence of an alternative mode of Cba deconstruction in C. reinhardtii that differs from the amidohydrolase (CbiZ)-dependent pathway described in Cba-remodeling bacteria and archaea.
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Affiliation(s)
- Christoph Baum
- Research Group Anaerobic Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Riya C Menezes
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Torsten Schubert
- Research Group Anaerobic Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
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83
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Huo T, Zhao Y, Tang X, Zhao H, Ni S, Gao Q, Liu S. Metabolic acclimation of anammox consortia to decreased temperature. ENVIRONMENT INTERNATIONAL 2020; 143:105915. [PMID: 32652345 DOI: 10.1016/j.envint.2020.105915] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Widespread application of anammox process has been primarily limited to the high sensitivity of anammox consortia to fluctuations of temperature. However, the metabolic acclimation of anammox consortia to decreased temperature remains unclear, which is the core of developing potential strategies for improving their low-temperature resistance. Here, we operated anammox reactors at 25 °C and 35 °C to explore the acclimation mechanism of anammox consortia in terms of metabolic responses and cross-feedings. Accordingly, we found that the adaptation of anammox consortia to ambient temperature (25 °C) was significantly linked to energy conservation strategy, resulting in decreased extracellular polymeric substance secretion, accumulation of ATP and amino acids. The expression patterns of cold shock proteins and core enzymes caused the apparent metabolic advantage of Candidatus Brocadia fulgida for acclimation to ambient temperature compared to other anammox species. Importantly, strengthened cross-feedings of amino acids, nitrite and glycine betaine benefited adaptation of anammox consortia to ambient temperature. Our work not only uncovers the temperature-adaptive mechanisms of anammox consortia, but also emphasizes the important role of metabolic cross-feeding in the temperature adaptation of microbial community.
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Affiliation(s)
- Tangran Huo
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yunpeng Zhao
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xi Tang
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Huazhang Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Shouqing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
| | - Sitong Liu
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
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84
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Abstract
While there has been much study of bacterial gene dispensability, there is a lack of comprehensive genome-scale examinations of the impact of gene deletion on growth in different carbon sources. In this context, a lot can be learned from such experiments in the model microbe Escherichia coli where much is already understood and there are existing tools for the investigation of carbon metabolism and physiology (1). Gene deletion studies have practical potential in the field of antibiotic drug discovery where there is emerging interest in bacterial central metabolism as a target for new antibiotics (2). Furthermore, some carbon utilization pathways have been shown to be critical for initiating and maintaining infection for certain pathogens and sites of infection (3–5). Here, with the use of high-throughput solid medium phenotyping methods, we have generated kinetic growth measurements for 3,796 genes under 30 different carbon source conditions. This data set provides a foundation for research that will improve our understanding of genes with unknown function, aid in predicting potential antibiotic targets, validate and advance metabolic models, and help to develop our understanding of E. coli metabolism. Central metabolism is a topic that has been studied for decades, and yet, this process is still not fully understood in Escherichia coli, perhaps the most amenable and well-studied model organism in biology. To further our understanding, we used a high-throughput method to measure the growth kinetics of each of 3,796 E. coli single-gene deletion mutants in 30 different carbon sources. In total, there were 342 genes (9.01%) encompassing a breadth of biological functions that showed a growth phenotype on at least 1 carbon source, demonstrating that carbon metabolism is closely linked to a large number of processes in the cell. We identified 74 genes that showed low growth in 90% of conditions, defining a set of genes which are essential in nutrient-limited media, regardless of the carbon source. The data are compiled into a Web application, Carbon Phenotype Explorer (CarPE), to facilitate easy visualization of growth curves for each mutant strain in each carbon source. Our experimental data matched closely with the predictions from the EcoCyc metabolic model which uses flux balance analysis to predict growth phenotypes. From our comparisons to the model, we found that, unexpectedly, phosphoenolpyruvate carboxylase (ppc) was required for robust growth in most carbon sources other than most trichloroacetic acid (TCA) cycle intermediates. We also identified 51 poorly annotated genes that showed a low growth phenotype in at least 1 carbon source, which allowed us to form hypotheses about the functions of these genes. From this list, we further characterized the ydhC gene and demonstrated its role in adenosine efflux.
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85
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Canon F, Nidelet T, Guédon E, Thierry A, Gagnaire V. Understanding the Mechanisms of Positive Microbial Interactions That Benefit Lactic Acid Bacteria Co-cultures. Front Microbiol 2020; 11:2088. [PMID: 33013761 PMCID: PMC7500094 DOI: 10.3389/fmicb.2020.02088] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/07/2020] [Indexed: 12/20/2022] Open
Abstract
Microorganisms grow in concert, both in natural communities and in artificial or synthetic co-cultures. Positive interactions between associated microbes are paramount to achieve improved substrate conversion and process performance in biotransformation and fermented food production. The mechanisms underlying such positive interactions have been the focus of numerous studies in recent decades and are now starting to be well characterized. Lactic acid bacteria (LAB) contribute to the final organoleptic, nutritional, and health properties of fermented food products. However, interactions in LAB co-cultures have been little studied, apart from the well-characterized LAB co-culture used for yogurt manufacture. LAB are, however, multifunctional microorganisms that display considerable potential to create positive interactions between them. This review describes why LAB co-cultures are of such interest, particularly in foods, and how their extensive nutritional requirements can be used to favor positive interactions. In that respect, our review highlights the benefits of co-cultures in different areas of application, details the mechanisms underlying positive interactions and aims to show how mechanisms based on nutritional interactions can be exploited to create efficient LAB co-cultures.
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Affiliation(s)
| | - Thibault Nidelet
- SPO, INRAE, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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86
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Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community. ISME JOURNAL 2020; 14:2816-2828. [PMID: 32788711 DOI: 10.1038/s41396-020-00737-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 01/12/2023]
Abstract
Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes essential carbon as fermentation products to R. palustris. Here, we sought to determine whether a reciprocal cross-feeding relationship would evolve spontaneously in cocultures with wild-type R. palustris, which is not known to excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ transporter. This activity likely allowed E. coli to subsist on the small amount of leaked NH4+ and better reciprocate through elevated excretion of fermentation products from a larger E. coli population. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge.
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87
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Frerejacques M, Rousselle C, Gauthier L, Cottet-Emard S, Derobert L, Roynette A, Lerch TZ, Changey F. Human Skin Bacterial Community Response to Probiotic ( Lactobacillus reuteri DSM 17938) Introduction. Microorganisms 2020; 8:microorganisms8081223. [PMID: 32796763 PMCID: PMC7465198 DOI: 10.3390/microorganisms8081223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
The introduction of a strain or consortium has often been considered as a potential solution to restore microbial ecosystems. Extensive research on the skin microbiota has led to the development of probiotic products (with live bacterial strains) that are likely to treat dysbiosis. However, the effects of such introductions on the indigenous microbiota have not yet been investigated. Here, through a daily application of Lactobacillus reuteri DSM 17938 on volunteers’ forearm skin, we studied in vivo the impact of a probiotic on the indigenous skin bacterial community diversity using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) for 3 weeks. The results demonstrate that Lactobacillus reuteri DSM 17938 inoculum had a transient effect on the indigenous community, as the resilience phenomenon was observed within the skin microbiota. Moreover, Lactobacillus reuteri DSM 17938 monitoring showed that, despite a high level of detection after 2 weeks of application, thereafter the colonization rate drops drastically. The probiotic colonization rate was correlated significantly to the effect on the indigenous microbial community structure. These preliminary results suggest that the success of probiotic use and the potential health benefits resides in the interactions with the human microbiota.
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Affiliation(s)
- Marie Frerejacques
- EBInnov, School of Industrial Biology—EBI, 49 Avenue des Genottes, 95800 Cergy, France; (M.F.); (C.R.); (L.G.); (S.C.-E.); (L.D.); (A.R.)
| | - Camille Rousselle
- EBInnov, School of Industrial Biology—EBI, 49 Avenue des Genottes, 95800 Cergy, France; (M.F.); (C.R.); (L.G.); (S.C.-E.); (L.D.); (A.R.)
| | - Loüen Gauthier
- EBInnov, School of Industrial Biology—EBI, 49 Avenue des Genottes, 95800 Cergy, France; (M.F.); (C.R.); (L.G.); (S.C.-E.); (L.D.); (A.R.)
| | - Salomé Cottet-Emard
- EBInnov, School of Industrial Biology—EBI, 49 Avenue des Genottes, 95800 Cergy, France; (M.F.); (C.R.); (L.G.); (S.C.-E.); (L.D.); (A.R.)
| | - Léa Derobert
- EBInnov, School of Industrial Biology—EBI, 49 Avenue des Genottes, 95800 Cergy, France; (M.F.); (C.R.); (L.G.); (S.C.-E.); (L.D.); (A.R.)
| | - Anne Roynette
- EBInnov, School of Industrial Biology—EBI, 49 Avenue des Genottes, 95800 Cergy, France; (M.F.); (C.R.); (L.G.); (S.C.-E.); (L.D.); (A.R.)
| | - Thomas Z. Lerch
- IEES-Paris, UMR 7618 (Sorbonne Université, IRD, CNRS, INRA, UPEC, Université de Paris), 61 Avenue du Général de Gaulle, 94010 Créteil, France;
| | - Frédérique Changey
- EBInnov, School of Industrial Biology—EBI, 49 Avenue des Genottes, 95800 Cergy, France; (M.F.); (C.R.); (L.G.); (S.C.-E.); (L.D.); (A.R.)
- Correspondence: ; Tel.: +33-01-85-76-66-90
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88
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Mathur Y, Sreyas S, Datar PM, Sathian MB, Hazra AB. CobT and BzaC catalyze the regiospecific activation and methylation of the 5-hydroxybenzimidazole lower ligand in anaerobic cobamide biosynthesis. J Biol Chem 2020; 295:10522-10534. [PMID: 32503839 PMCID: PMC7397103 DOI: 10.1074/jbc.ra120.014197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/01/2020] [Indexed: 11/06/2022] Open
Abstract
Vitamin B12 and other cobamides are essential cofactors required by many organisms and are synthesized by a subset of prokaryotes via distinct aerobic and anaerobic routes. The anaerobic biosynthesis of 5,6-dimethylbenzimidazole (DMB), the lower ligand of vitamin B12, involves five reactions catalyzed by the bza operon gene products, namely the hydroxybenzimidazole synthase BzaAB/BzaF, phosphoribosyltransferase CobT, and three methyltransferases, BzaC, BzaD, and BzaE, that conduct three distinct methylation steps. Of these, the methyltransferases that contribute to benzimidazole lower ligand diversity in cobamides remain to be characterized, and the precise role of the bza operon protein CobT is unclear. In this study, we used the bza operon from the anaerobic bacterium Moorella thermoacetica (comprising bzaA-bzaB-cobT-bzaC) to examine the role of CobT and investigate the activity of the first methyltransferase, BzaC. We studied the phosphoribosylation catalyzed by MtCobT and found that it regiospecifically activates 5-hydroxybenzimidazole (5-OHBza) to form the 5-OHBza-ribotide (5-OHBza-RP) isomer as the sole product. Next, we characterized the domains of MtBzaC and reconstituted its methyltransferase activity with the predicted substrate 5-OHBza and with two alternative substrates, the MtCobT product 5-OHBza-RP and its riboside derivative 5-OHBza-R. Unexpectedly, we found that 5-OHBza-R is the most favored MtBzaC substrate. Our results collectively explain the long-standing observation that the attachment of the lower ligand in anaerobic cobamide biosynthesis is regiospecific. In conclusion, we validate MtBzaC as a SAM:hydroxybenzimidazole-riboside methyltransferase (HBIR-OMT). Finally, we propose a new pathway for the synthesis and activation of the benzimidazolyl lower ligand in anaerobic cobamide biosynthesis.
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Affiliation(s)
- Yamini Mathur
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Sheryl Sreyas
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Prathamesh M Datar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Manjima B Sathian
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
| | - Amrita B Hazra
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
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89
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Preussger D, Giri S, Muhsal LK, Oña L, Kost C. Reciprocal Fitness Feedbacks Promote the Evolution of Mutualistic Cooperation. Curr Biol 2020; 30:3580-3590.e7. [PMID: 32707067 DOI: 10.1016/j.cub.2020.06.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/29/2020] [Accepted: 06/29/2020] [Indexed: 10/23/2022]
Abstract
Mutually beneficial interactions are ubiquitous in nature and have played a pivotal role for the evolution of life on earth. However, the factors facilitating their emergence remain poorly understood. Here, we address this issue both experimentally and by mathematical modeling using cocultures of auxotrophic strains of Escherichia coli, whose growth depends on a reciprocal exchange of amino acids. Coevolving auxotrophic pairs in a spatially heterogeneous environment for less than 150 generations transformed the initial interaction that was merely based on an exchange of metabolic byproducts into a costly metabolic cooperation, in which both partners increased the amounts of metabolites they produced to benefit their corresponding partner. The observed changes were afforded by the formation of multicellular clusters, within which increased cooperative investments were favored by positive fitness feedbacks among interacting genotypes. Under these conditions, non-cooperative individuals were less fit than cooperative mutants. Together, our results highlight the ease with which mutualistic cooperation can evolve, suggesting similar mechanisms likely operate in natural communities. VIDEO ABSTRACT.
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Affiliation(s)
- Daniel Preussger
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll Str. 8, Jena 07745, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Samir Giri
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll Str. 8, Jena 07745, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Linéa K Muhsal
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll Str. 8, Jena 07745, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany.
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90
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Adamowicz EM, Muza M, Chacón JM, Harcombe WR. Cross-feeding modulates the rate and mechanism of antibiotic resistance evolution in a model microbial community of Escherichia coli and Salmonella enterica. PLoS Pathog 2020; 16:e1008700. [PMID: 32687537 PMCID: PMC7392344 DOI: 10.1371/journal.ppat.1008700] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/30/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022] Open
Abstract
With antibiotic resistance rates on the rise, it is critical to understand how microbial species interactions influence the evolution of resistance. In obligate mutualisms, the survival of any one species (regardless of its intrinsic resistance) is contingent on the resistance of its cross-feeding partners. This sets the community antibiotic sensitivity at that of the 'weakest link' species. In this study, we tested the hypothesis that weakest link dynamics in an obligate cross-feeding relationship would limit the extent and mechanisms of antibiotic resistance evolution. We experimentally evolved an obligate co-culture and monoculture controls along gradients of two different antibiotics. We measured the rate at which each treatment increased antibiotic resistance, and sequenced terminal populations to question whether mutations differed between mono- and co-cultures. In both rifampicin and ampicillin treatments, we observed that resistance evolved more slowly in obligate co-cultures of E. coli and S. enterica than in monocultures. While we observed similar mechanisms of resistance arising under rifampicin selection, under ampicillin selection different resistance mechanisms arose in co-cultures and monocultures. In particular, mutations in an essential cell division protein, ftsI, arose in S. enterica only in co-culture. A simple mathematical model demonstrated that reliance on a partner is sufficient to slow the rate of adaptation, and can change the distribution of adaptive mutations that are acquired. Our results demonstrate that cooperative metabolic interactions can be an important modulator of resistance evolution in microbial communities.
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Affiliation(s)
- Elizabeth M. Adamowicz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michaela Muza
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jeremy M. Chacón
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - William R. Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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91
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Sokolovskaya OM, Shelton AN, Taga ME. Sharing vitamins: Cobamides unveil microbial interactions. Science 2020; 369:369/6499/eaba0165. [PMID: 32631870 DOI: 10.1126/science.aba0165] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda N Shelton
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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92
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Kißling L, Schneider C, Seibel K, Dorjjugder N, Busche T, Kalinowski J, Mack M. The roseoflavin producer
Streptomyces davaonensis
has a high catalytic capacity and specific genetic adaptations with regard to the biosynthesis of riboflavin. Environ Microbiol 2020; 22:3248-3265. [DOI: 10.1111/1462-2920.15066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/06/2020] [Accepted: 05/10/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Lena Kißling
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Carmen Schneider
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Katharina Seibel
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Nasanjargal Dorjjugder
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Tobias Busche
- Center for Biotechnology Bielefeld University Bielefeld 33594 Germany
| | - Jörn Kalinowski
- Center for Biotechnology Bielefeld University Bielefeld 33594 Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
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93
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LaSarre B, Deutschbauer AM, Love CE, McKinlay JB. Covert Cross-Feeding Revealed by Genome-Wide Analysis of Fitness Determinants in a Synthetic Bacterial Mutualism. Appl Environ Microbiol 2020; 86:e00543-20. [PMID: 32332139 PMCID: PMC7301861 DOI: 10.1128/aem.00543-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N2 gas and provides nitrogen to E. coli in the form of NH4+ The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. In addition, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a prioriIMPORTANCE Microbial communities impact life on Earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodopseudomonas palustris Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.
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Affiliation(s)
- Breah LaSarre
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Crystal E Love
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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94
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Abstract
PURPOSE OF REVIEW The human body plays host to bacterial biofilms across diverse anatomical sites. The treatment of pathogenic biofilm infection is confounded by their high rate of antibiotic resistance. Therefore, it is critical to understand the interplay between these biofilms and the host immune system to develop new tactics to combat these infections. RECENT FINDINGS Bacterial biofilms and the components they produce affect and are affected by the host immune system. Host anatomical sites represent distinct niches in which defined bacterial biofilms are able to form and interact with the host immune system. For persistent colonization to occur, the bacteria must either avoid or suppress the host immune system, or induce an immune response that facilitates their perpetuation. SUMMARY Commensal bacterial biofilms form a protective barrier against colonization by pathogens. Using similar mechanisms, bacteria modulate the immune system to orchestrate persistence and sometimes disease. Clinicians must balance the need to avoid disturbing beneficial commensal biofilms with the difficulty in preventing or treating pathogenic bacterial biofilms such as those that develop on medical implants and open wounds.
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Affiliation(s)
- Christina N Morra
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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95
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Chen F, Wegner SV. Blue-Light-Switchable Bacterial Cell-Cell Adhesions Enable the Control of Multicellular Bacterial Communities. ACS Synth Biol 2020; 9:1169-1180. [PMID: 32243746 DOI: 10.1021/acssynbio.0c00054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the fundamental importance and biotechnological potential of multibacterial communities, also called biofilms, are well-known, our ability to control them is limited. We present a new way of dynamically controlling bacteria-bacteria adhesions by using blue light and how these photoswitchable adhesions can be used to regulate multicellularity and associated bacterial behavior. To achieve this, the photoswitchable proteins nMagHigh and pMagHigh were expressed on bacterial surfaces as adhesins to allow multicellular clusters to assemble under blue light and reversibly disassemble in the dark. Regulation of the bacterial cell-cell adhesions with visible light provides unique advantages including high spatiotemporal control, tunability, and noninvasive remote regulation. Moreover, these photoswitchable adhesions make it possible to regulate collective bacterial functions including aggregation, quorum sensing, biofilm formation, and metabolic cross-feeding between auxotrophic bacteria with light. Overall, the photoregulation of bacteria-bacteria adhesions provides a new way of studying bacterial cell biology and will enable the design of biofilms for biotechnological applications.
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Affiliation(s)
- Fei Chen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
| | - Seraphine V. Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
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96
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Welp AL, Bomberger JM. Bacterial Community Interactions During Chronic Respiratory Disease. Front Cell Infect Microbiol 2020; 10:213. [PMID: 32477966 PMCID: PMC7240048 DOI: 10.3389/fcimb.2020.00213] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic respiratory diseases including chronic rhinosinusitis, otitis media, asthma, cystic fibrosis, non-CF bronchiectasis, and chronic obstructive pulmonary disease are a major public health burden. Patients suffering from chronic respiratory disease are prone to persistent, debilitating respiratory infections due to the decreased ability to clear pathogens from the respiratory tract. Such infections often develop into chronic, life-long complications that are difficult to treat with antibiotics due to the formation of recalcitrant biofilms. The microbial communities present in the upper and lower respiratory tracts change as these respiratory diseases progress, often becoming less diverse and dysbiotic, correlating with worsening patient morbidity. Those with chronic respiratory disease are commonly infected with a shared group of respiratory pathogens including Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis, among others. In order to understand the microbial landscape of the respiratory tract during chronic disease, we review the known inter-species interactions among these organisms and other common respiratory flora. We consider both the balance between cooperative and competitive interactions in relation to microbial community structure. By reviewing the major causes of chronic respiratory disease, we identify common features across disease states and signals that might contribute to community shifts. As microbiome shifts have been associated with respiratory disease progression, worsening morbidity, and increased mortality, these underlying community interactions likely have an impact on respiratory disease state.
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Affiliation(s)
- Allison L. Welp
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
- Graduate Program in Microbiology and Immunology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
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97
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Pacciani-Mori L, Giometto A, Suweis S, Maritan A. Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities. PLoS Comput Biol 2020; 16:e1007896. [PMID: 32379752 PMCID: PMC7244184 DOI: 10.1371/journal.pcbi.1007896] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/22/2020] [Accepted: 04/21/2020] [Indexed: 01/19/2023] Open
Abstract
Microbes are capable of physiologically adapting to diverse environmental conditions by differentially varying the rates at which they uptake different nutrients. In particular, microbes can switch hierarchically between different energy sources, consuming first those that ensure the highest growth rate. Experimentally, this can result in biphasic growth curves called "diauxic shifts" that typically arise when microbes are grown in media containing several nutrients. Despite these observations are well known in microbiology and molecular biology, the mathematical models generally used to describe the population dynamics of microbial communities do not account for dynamic metabolic adaptation, thus implicitly assuming that microbes cannot switch dynamically from one resource to another. Here, we introduce dynamic metabolic adaptation in the framework of consumer-resource models, which are commonly used to describe competitive microbial communities, allowing each species to temporally change its preferred energy source to maximize its own relative fitness. We show that dynamic metabolic adaptation enables the community to self-organize, allowing several species to coexist even in the presence of few resources, and to respond optimally to a time-dependent environment, thus showing that dynamic metabolic adaptation could be an important mechanism for maintaining high levels of diversity even in environments with few energy sources. We show that introducing dynamic metabolic strategies in consumer-resource models is necessary for reproducing experimental growth curves of the baker's yeast Saccharomyces cerevisiae growing in the presence of two carbon sources. Even though diauxic shifts emerge naturally from the model when two resources are qualitatively very different, the model predicts that the existence of such shifts is not a prerequisite for species coexistence in competitive communities.
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Affiliation(s)
- Leonardo Pacciani-Mori
- Department of Physics and Astronomy “Galileo Galilei”, University of Padua, Padua, Italy
| | - Andrea Giometto
- Department of Physics and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Samir Suweis
- Department of Physics and Astronomy “Galileo Galilei”, University of Padua, Padua, Italy
| | - Amos Maritan
- Department of Physics and Astronomy “Galileo Galilei”, University of Padua, Padua, Italy
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98
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Microbial Co-Occurrence in Floral Nectar Affects Metabolites and Attractiveness to a Generalist Pollinator. J Chem Ecol 2020; 46:659-667. [PMID: 32246258 DOI: 10.1007/s10886-020-01169-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/27/2020] [Accepted: 03/06/2020] [Indexed: 12/25/2022]
Abstract
Microbial metabolism can shape cues important for animal attraction in service-resource mutualisms. Resources are frequently colonized by microbial communities, but experimental assessment of animal-microbial interactions often focus on microbial monocultures. Such an approach likely fails to predict effects of microbial assemblages, as microbe-microbe interactions may affect in a non-additive manner microbial metabolism and resulting chemosensory cues. Here, we compared effects of microbial mono- and cocultures on growth of constituent microbes, volatile metabolite production, sugar catabolism, and effects on pollinator foraging across two nectar environments that differed in sugar concentration. Growth in co-culture decreased the abundance of the yeast Metschnikowia reukaufii, but not the bacterium Asaia astilbes. Volatile emissions differed significantly between microbial treatments and with nectar concentration, while sugar concentration was relatively similar among mono- and cocultures. Coculture volatile emission closely resembled an additive combination of monoculture volatiles. Despite differences in microbial growth and chemosensory cues, honey bee feeding did not differ between microbial monocultures and assemblages. Taken together, our results suggest that in some cases, chemical and ecological effects of microbial assemblages are largely predictable from those of component species, but caution that more work is necessary to predict under what circumstances non-additive effects are important.
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Baumgartner M, Bayer F, Pfrunder-Cardozo KR, Buckling A, Hall AR. Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples. PLoS Biol 2020; 18:e3000465. [PMID: 32310938 PMCID: PMC7192512 DOI: 10.1371/journal.pbio.3000465] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/30/2020] [Accepted: 04/02/2020] [Indexed: 01/05/2023] Open
Abstract
Countering the rise of antibiotic-resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g., via resource competition) but could also potentially accelerate resistance evolution via horizontal transfer of resistance genes. It remains unclear how these different effects balance out, partly because it is difficult to observe them directly. Here, we used a gut microcosm approach to quantify the effect of three human gut microbiome communities on growth and resistance evolution of a focal strain of Escherichia coli. We found the resident microbial communities not only suppressed growth and colonisation by focal E. coli but also prevented it from evolving antibiotic resistance upon exposure to a beta-lactam antibiotic. With samples from all three human donors, our focal E. coli strain only evolved antibiotic resistance in the absence of the resident microbial community, even though we found resistance genes, including a highly effective resistance plasmid, in resident microbial communities. We identified physical constraints on plasmid transfer that can explain why our focal strain failed to acquire some of these beneficial resistance genes, and we found some chromosomal resistance mutations were only beneficial in the absence of the resident microbiota. This suggests, depending on in situ gene transfer dynamics, interactions with resident microbiota can inhibit antibiotic-resistance evolution of individual species.
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Affiliation(s)
- Michael Baumgartner
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Florian Bayer
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Katia R. Pfrunder-Cardozo
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Alex R. Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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Yang DD, Alexander A, Kinnersley M, Cook E, Caudy A, Rosebrock A, Rosenzweig F. Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment. Appl Environ Microbiol 2020; 86:e00051-20. [PMID: 32060029 PMCID: PMC7117940 DOI: 10.1128/aem.00051-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/05/2020] [Indexed: 12/11/2022] Open
Abstract
The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new "species." We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation.IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.
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Affiliation(s)
- Dong-Dong Yang
- Division Biological Sciences, University of Montana, Missoula, Montana, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ashley Alexander
- Division Biological Sciences, University of Montana, Missoula, Montana, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Margie Kinnersley
- Division Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Emily Cook
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amy Caudy
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Adam Rosebrock
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Frank Rosenzweig
- Division Biological Sciences, University of Montana, Missoula, Montana, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
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