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Henriquez T, Santoro F, Medaglini D, Pallecchi L, Clemente I, Bonechi C, Magnani A, Paccagnini E, Gentile M, Lupetti P, Marvasi M, Pini A, Bracci L, Falciani C. Analysis of the utility of a rapid vesicle isolation method for clinical strains of Pseudomonas aeruginosa. Microbiol Spectr 2024:e0064924. [PMID: 39248554 DOI: 10.1128/spectrum.00649-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/29/2024] [Indexed: 09/10/2024] Open
Abstract
Pseudomonas aeruginosa, a pathogen capable of causing diseases ranging from mild to life-threatening, has a large arsenal of virulence factors. Notably, extracellular vesicles have emerged as significant players in the pathogenesis of this organism. However, the full range of their functions is still being studied, and difficulties related to vesicle purification (long protocols, low yields, and specialized instruments) have become a major obstacle for their characterization. In this context, the utility of rapid new methods of vesicle isolation from clinical strains is still unknown. Here, we analyze the utility of the ExoBacteria OMV isolation kit for a collection of clinical strains of P. aeruginosa. We first phenotypically characterized 15 P. aeruginosa strains to ensure that our samples were heterogeneous. We then determined the best conditions for purifying vesicles from P. aeruginosa PAO1 reference strain by the rapid method and used them to isolate vesicles from clinical strains. Our results indicated that M9 minimal medium is the best for obtaining high purity with the rapid isolation kit. Although we were able to isolate vesicles from at least four strains, the low yield and the large number of strains with unpurifiable vesicles showed that the kit was not practical or convenient for clinical strains. Our findings suggest that although fast procedures for vesicle purification can be of great utility for Escherichia coli, the more complex phenotypes of clinical isolates of P. aeruginosa are a challenge for these protocols and new alternatives/optimizations need to be developed.IMPORTANCEPseudomonas aeruginosa is recognized as an opportunistic pathogen in humans and animals. It can effectively colonize various environments thanks to a large set of virulence factors that include extracellular vesicles. Different methods were recently developed to reduce the time and effort associated with vesicle purification. However, the utility of rapid vesicle isolation methods for clinical strains of P. aeruginosa (which are recognized as being highly diverse) is not yet known. In this context, we analyzed the utility of the ExoBacteria OMV Isolation kit for vesicle purification in P. aeruginosa clinical strains. Our findings showed that the kit does not seem to be convenient for research on clinical strains due to low vesicle recovery. Our results underscore the importance of developing new rapid vesicle purification protocols/techniques for specific clinical phenotypes.
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Affiliation(s)
- Tania Henriquez
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Santoro
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Donata Medaglini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Lucia Pallecchi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ilaria Clemente
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Claudia Bonechi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Agnese Magnani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | | | - Pietro Lupetti
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Alessandro Pini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Luisa Bracci
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Falciani
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Hesse E, Luján AM, O'Brien S, Newbury A, McAvoy T, Soria Pascual J, Bayer F, Hodgson DJ, Buckling A. Parallel ecological and evolutionary responses to selection in a natural bacterial community. Proc Natl Acad Sci U S A 2024; 121:e2403577121. [PMID: 39190353 DOI: 10.1073/pnas.2403577121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024] Open
Abstract
Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes from in vitro studies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within- and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic nonferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same-intermediate siderophore levels were favored-and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members.
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Affiliation(s)
- Elze Hesse
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Adela M Luján
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas, Consejo Nacional de Investigaciones Científicas y Técnicas/Universidad Católica de Córdoba, Córdoba X5016DHK, Argentina
- Facultad de Ciencias de la Salud, Universidad Católica de Córdoba (UCC), Córdoba X5004ASK, Argentina
| | - Siobhan O'Brien
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Arthur Newbury
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Terence McAvoy
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Jesica Soria Pascual
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Florian Bayer
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - David J Hodgson
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Angus Buckling
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
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3
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Jeong GJ, Khan F, Tabassum N, Jo DM, Jung WK, Kim YM. Roles of Pseudomonas aeruginosa siderophores in interaction with prokaryotic and eukaryotic organisms. Res Microbiol 2024; 175:104211. [PMID: 38734157 DOI: 10.1016/j.resmic.2024.104211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that produces two types of siderophores, pyoverdine and pyochelin, that play pivotal roles in iron scavenging from the environment and host cells. P. aeruginosa siderophores can serve as virulence factors and perform various functions. Several bacterial and fungal species are likely to interact with P. aeruginosa due to its ubiquity in soil and water as well as its potential to cause infections in plants, animals, and humans. Siderophores produced by P. aeruginosa play critical roles in iron scavenging for prokaryotic species (bacteria) and eukaryotic hosts (fungi, animals, insects, invertebrates, and plants) as well. This review provides a comprehensive discussion of the role of P. aeruginosa siderophores in interaction with prokaryotes and eukaryotes as well as their underlying mechanisms of action. The evolutionary relationship between P. aeruginosa siderophore recognition receptors, such as FpvA, FpvB, and FptA, and those of other bacterial species has also been investigated.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea; Institute of Fisheries Science, Pukyong National University. Busan 48513, Republic of Korea; International Graduate Program of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Du-Min Jo
- National Marine Biodiversity Institute of Korea, Seochun, Chungcheongnam-do, 33662, Republic of Korea
| | - Won-Kyo Jung
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea; Major of Biomedical Engineering, Division of Smart Healthcare, College of Information Technology and Convergence and New-senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
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4
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Shao Z, Gu S, Zhang X, Xue J, Yan T, Guo S, Pommier T, Jousset A, Yang T, Xu Y, Shen Q, Wei Z. Siderophore interactions drive the ability of Pseudomonas spp . consortia to protect tomato against Ralstonia solanacearum. HORTICULTURE RESEARCH 2024; 11:uhae186. [PMID: 39247881 PMCID: PMC11377186 DOI: 10.1093/hr/uhae186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 07/01/2024] [Indexed: 09/10/2024]
Abstract
The soil-borne bacterial pathogen Ralstonia solanacearum causes significant losses in Solanaceae crop production worldwide, including tomato, potato, and eggplant. To efficiently prevent outbreaks, it is essential to understand the complex interactions between pathogens and the microbiome. One promising mechanism for enhancing microbiome functionality is siderophore-mediated competition, which is shaped by the low iron availability in the rhizosphere. This study explores the critical role of iron competition in determining microbiome functionality and its potential for designing high-performance microbiome engineering strategies. We investigated the impact of siderophore-mediated interactions on the efficacy of Pseudomonas spp. consortia in suppressing R. solanacearum , both in vitro and in vivo. Our findings show that siderophore production significantly enhances the inhibitory effects of Pseudomonas strains on pathogen growth, while other metabolites are less effective under iron-limited conditions. Moreover, siderophores play a crucial role in shaping interactions within the consortia, ultimately determining the level of protection against bacterial wilt disease. This study highlights the key role of siderophores in mediating consortium interactions and their impact on tomato health. Our results also emphasize the limited efficacy of other secondary metabolites in iron-limited environments, underscoring the importance of siderophore-mediated competition in maintaining tomato health and suppressing disease.
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Affiliation(s)
- Zhengying Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaohua Gu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaoni Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiao Xue
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Saisai Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Thomas Pommier
- Setec Energie Environnement, 97/101 bvd Vivier Merle, Lyon 69003, France
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianjie Yang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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5
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Gray J, Torres VVL, Goodall E, McKeand SA, Scales D, Collins C, Wetherall L, Lian ZJ, Bryant JA, Milner MT, Dunne KA, Icke C, Rooke JL, Schneiders T, Lund PA, Cunningham AF, Cole JA, Henderson IR. Transposon mutagenesis screen in Klebsiella pneumoniae identifies genetic determinants required for growth in human urine and serum. eLife 2024; 12:RP88971. [PMID: 39189918 PMCID: PMC11349299 DOI: 10.7554/elife.88971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024] Open
Abstract
Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multidrug-resistant clones both alarmingly associated with high mortality. The molecular mechanisms underpinning these recalcitrant K. pneumoniae infection, and how virulence is coupled with the emergence of lineages resistant to nearly all present-day clinically important antimicrobials, are unclear. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani [LB] medium), human urine, and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. These studies not only provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections.
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Affiliation(s)
- Jessica Gray
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Von Vergel L Torres
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Emily Goodall
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Samantha A McKeand
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Danielle Scales
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Christy Collins
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Laura Wetherall
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Zheng Jie Lian
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Matthew T Milner
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Karl A Dunne
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Christopher Icke
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Jessica L Rooke
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Thamarai Schneiders
- Division of Infection Medicine, University of EdinburghEdinburghUnited Kingdom
| | - Peter A Lund
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of BirminghamBirminghamUnited Kingdom
| | - Jeff A Cole
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Ian R Henderson
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
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6
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Graña-Miraglia L, Geney Higuita JL, Salazar JC, Guaya Iñiguez D, Alcolado León C, García-Angulo VA. Total substitution and partial modification of the set of non-ribosomal peptide synthetases clusters lead to pyoverdine diversity in the Pseudomonas fluorescens complex. Front Microbiol 2024; 15:1421749. [PMID: 39224222 PMCID: PMC11366639 DOI: 10.3389/fmicb.2024.1421749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
Pyoverdines are high affinity siderophores produced by most Pseudomonas with a wide role in microbial interspecies interactions. They are primarily composed of a conserved chromophore moiety, an acyl side chain and a peptide backbone which may be highly variable among strains. Upon ferric iron sequestration, pyoverdines are internalized through specialized receptors. The peptide precursor of pyoverdine, termed ferribactin, is synthesized by a set of non-ribosomal peptide synthetase (NRPS) enzymes and further modified by tailoring enzymes. While PvdL, the NRPS responsible for the synthesis of the peptide moiety that derives into the chromophore is conserved, the NRPSs for the peptide backbone are different across fluorescent Pseudomonas. Although the variation of pyoverdine is a widely recognized characteristic within the genus, the evolutionary events associated with the diversity and distribution of this trait remain mostly unknown. This study analyzed the NRPSs clusters for the biosynthesis of the peptide backbone of ferribactin in the genomes of a representative subset of strains of the Pseudomonas fluorescens complex. Bioinformatic analysis of the specificity of adenylation domains of the NRPSs allowed the prediction of 30 different pyoverdine variants. Phylogenetic reconstruction and mapping of the NRPS clusters pinpointed two different general levels of modifications. In the first level, a complete replacement of the set of NRPRs by horizontal transfer occurs. In the second level, the original set of NRPSs is modified through different mechanisms, including partial substitution of the NRPS genes by horizontal transfer, adenylation domain specificity change or NRPS accessory domain gain/loss.
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Affiliation(s)
- Lucía Graña-Miraglia
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Jorge Luis Geney Higuita
- Bacterial Metabolism Laboratory, Instituto de Ciencias Biomédicas, Microbiology and Mycology Program, University of Chile, Santiago, Chile
| | - Juan Carlos Salazar
- Laboratory of Enteropathogens, Instituto de Ciencias Biomédicas, Microbiology and Mycology Program, University of Chile, Santiago, Chile
| | - Diana Guaya Iñiguez
- Bacterial Metabolism Laboratory, Instituto de Ciencias Biomédicas, Microbiology and Mycology Program, University of Chile, Santiago, Chile
| | - Carlos Alcolado León
- Bacterial Metabolism Laboratory, Instituto de Ciencias Biomédicas, Microbiology and Mycology Program, University of Chile, Santiago, Chile
| | - Víctor A. García-Angulo
- Bacterial Metabolism Laboratory, Instituto de Ciencias Biomédicas, Microbiology and Mycology Program, University of Chile, Santiago, Chile
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7
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Yu G, Ge X, Li W, Ji L, Yang S. Interspecific cross-talk: The catalyst driving microbial biosynthesis of secondary metabolites. Biotechnol Adv 2024; 76:108420. [PMID: 39128577 DOI: 10.1016/j.biotechadv.2024.108420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/07/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Microorganisms co-exist and co-evolve in nature, forming intricate ecological communities. The interspecies cross-talk within these communities creates and sustains their great biosynthetic potential, making them an important source of natural medicines and high-value-added chemicals. However, conventional investigations into microbial metabolites are typically carried out in pure cultures, resulting in the absence of specific activating factors and consequently causing a substantial number of biosynthetic gene clusters to remain silent. This, in turn, hampers the in-depth exploration of microbial biosynthetic potential and frequently presents researchers with the challenge of rediscovering compounds. In response to this challenge, the coculture strategy has emerged to explore microbial biosynthetic capabilities and has shed light on the study of cross-talk mechanisms. These elucidated mechanisms will contribute to a better understanding of complex biosynthetic regulations and offer valuable insights to guide the mining of secondary metabolites. This review summarizes the research advances in microbial cross-talk mechanisms, with a particular focus on the mechanisms that activate the biosynthesis of secondary metabolites. Additionally, the instructive value of these mechanisms for developing strategies to activate biosynthetic pathways is discussed. Moreover, challenges and recommendations for conducting in-depth studies on the cross-talk mechanisms are presented.
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Affiliation(s)
- Guihong Yu
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China.
| | - Xiaoxuan Ge
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Wanting Li
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Linwei Ji
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China.
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8
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Zytnick AM, Gutenthaler-Tietze SM, Aron AT, Reitz ZL, Phi MT, Good NM, Petras D, Daumann LJ, Martinez-Gomez NC. Identification and characterization of a small-molecule metallophore involved in lanthanide metabolism. Proc Natl Acad Sci U S A 2024; 121:e2322096121. [PMID: 39078674 PMCID: PMC11317620 DOI: 10.1073/pnas.2322096121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 06/14/2024] [Indexed: 07/31/2024] Open
Abstract
Many bacteria secrete metallophores, low-molecular-weight organic compounds that bind ions with high selectivity and affinity, in order to access essential metals from the environment. Previous work has elucidated the structures and biosynthetic machinery of metallophores specific for iron, zinc, nickel, molybdenum, and copper. No physiologically relevant lanthanide-binding metallophore has been discovered despite the knowledge that lanthanide metals (Ln) have been revealed to be essential cofactors for certain alcohol dehydrogenases across a diverse range of phyla. Here, we report the biosynthetic machinery, the structure, and the physiological relevance of a lanthanophore, methylolanthanin. The structure of methylolanthanin exhibits a unique 4-hydroxybenzoate moiety which has not previously been described in other metallophores. We find that production of methylolanthanin is required for normal levels of Ln accumulation in the methylotrophic bacterium Methylobacterium extorquens AM1, while overexpression of the molecule greatly increases bioaccumulation and adsorption. Our results provide a clearer understanding of how Ln-utilizing bacteria sense, scavenge, and store Ln; essential processes in the environment where Ln are poorly bioavailable. More broadly, the identification of this lanthanophore opens doors for study of how biosynthetic gene clusters are repurposed for additional functions and the complex relationship between metal homeostasis and fitness.
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Affiliation(s)
- Alexa M. Zytnick
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA94720
| | - Sophie M. Gutenthaler-Tietze
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf40225, Germany
| | - Allegra T. Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO80210
| | - Zachary L. Reitz
- Bioinformatics Group, Wageningen University, Wageningen6708PB, The Netherlands
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93117
| | - Manh Tri Phi
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA94720
| | - Daniel Petras
- Interfaculty Institute of Microbiology and Medicine, Universität Tübingen, Tübingen72074, Germany
| | - Lena J. Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf40225, Germany
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9
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Philippot L, Chenu C, Kappler A, Rillig MC, Fierer N. The interplay between microbial communities and soil properties. Nat Rev Microbiol 2024; 22:226-239. [PMID: 37863969 DOI: 10.1038/s41579-023-00980-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/22/2023]
Abstract
In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.
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Affiliation(s)
- Laurent Philippot
- Université de Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Department of Agroecology, Dijon, France.
| | - Claire Chenu
- University of Paris-Saclay, INRAE, AgroParisTech, Palaiseau, France
| | - Andreas Kappler
- Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, USA
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10
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Bingham A, Sur A, Shaw LB, Murphy HA. The effect of cooperator recognition on competition among clones in spatially structured microbial communities. PLoS One 2024; 19:e0299546. [PMID: 38547104 PMCID: PMC10977701 DOI: 10.1371/journal.pone.0299546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/12/2024] [Indexed: 04/02/2024] Open
Abstract
In spatially structured microbial communities, clonal growth of stationary cells passively generates clusters of related individuals. This can lead to stable cooperation without the need for recognition mechanisms. However, recent research suggests that some biofilm-forming microbes may have mechanisms of kin recognition. To explore this unexpected observation, we studied the effects of different types of cooperation in a microbial colony using spatially explicit, agent-based simulations of two interacting strains. We found scenarios that favor a form of kin recognition in spatially structured microbial communities. In the presence of a "cheater" strain, a strain with greenbeard cooperation was able to increase in frequency more than a strain with obligate cooperation. This effect was most noticeable in high density colonies and when the cooperators were not as abundant as the cheaters. We also studied whether a polychromatic greenbeard, in which cells only cooperate with their own type, could provide a numerical benefit beyond a simple, binary greenbeard. We found the greatest benefit to a polychromatic greenbeard when cooperation is highly effective. These results suggest that in some ecological scenarios, recognition mechanisms may be beneficial even in spatially structured communities.
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Affiliation(s)
- Adrienna Bingham
- Department of Applied Science, William & Mary, Williamsburg, VA, United States of America
| | - Aparajita Sur
- Department of Mathematics, William & Mary, Williamsburg, VA, United States of America
| | - Leah B. Shaw
- Department of Mathematics, William & Mary, Williamsburg, VA, United States of America
| | - Helen A. Murphy
- Department of Biology, William & Mary, Williamsburg, VA, United States of America
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11
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Fulte S, Atto B, McCarty A, Horn KJ, Redzic JS, Eisenmesser E, Yang M, Marsh RL, Tristram S, Clark SE. Heme sequestration by hemophilin from Haemophilus haemolyticus reduces respiratory tract colonization and infection with non-typeable Haemophilus influenzae. mSphere 2024; 9:e0000624. [PMID: 38380941 PMCID: PMC10964412 DOI: 10.1128/msphere.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
Iron acquisition is a key feature dictating the success of pathogen colonization and infection. Pathogens scavenging iron from the host must contend with other members of the microbiome similarly competing for the limited pool of bioavailable iron, often in the form of heme. In this study, we identify a beneficial role for the heme-binding protein hemophilin (Hpl) produced by the non-pathogenic bacterium Haemophilus haemolyticus against its close relative, the opportunistic respiratory tract pathogen non-typeable Haemophilus influenzae (NTHi). Using a mouse model, we found that pre-exposure to H. haemolyticus significantly reduced NTHi colonization of the upper airway and impaired NTHi infection of the lungs in an Hpl-dependent manner. Further, treatment with recombinant Hpl was sufficient to decrease airway burdens of NTHi without exacerbating lung immunopathology or systemic inflammation. Instead, mucosal production of the neutrophil chemokine CXCL2, lung myeloperoxidase, and serum pro-inflammatory cytokines IL-6 and TNFα were lower in Hpl-treated mice. Mechanistically, H. haemolyticus suppressed NTHi growth and adherence to human respiratory tract epithelial cells through the expression of Hpl, and recombinant Hpl could recapitulate these effects. Together, these findings indicate that heme sequestration by non-pathogenic, Hpl-producing H. haemolyticus is protective against NTHi colonization and infection. IMPORTANCE The microbiome provides a critical layer of protection against infection with bacterial pathogens. This protection is accomplished through a variety of mechanisms, including interference with pathogen growth and adherence to host cells. In terms of immune defense, another way to prevent pathogens from establishing infections is by limiting the availability of nutrients, referred to as nutritional immunity. Restricting pathogen access to iron is a central component of this approach. Here, we uncovered an example where these two strategies intersect to impede infection with the respiratory tract bacterial pathogen Haemophilus influenzae. Specifically, we find that a non-pathogenic (commensal) bacterium closely related to H. influenzae called Haemophilus haemolyticus improves protection against H. influenzae by limiting the ability of this pathogen to access iron. These findings suggest that beneficial members of the microbiome improve protection against pathogen infection by effectively contributing to host nutritional immunity.
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Affiliation(s)
- Sam Fulte
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Arianna McCarty
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kadi J. Horn
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, USA
| | - Elan Eisenmesser
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, USA
| | - Michael Yang
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Robyn L. Marsh
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Stephen Tristram
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Sarah E. Clark
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado, USA
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12
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Su L, Souaibou Y, Hôtel L, Paris C, Weissman KJ, Aigle B. Biosynthesis of novel desferrioxamine derivatives requires unprecedented crosstalk between separate NRPS-independent siderophore pathways. Appl Environ Microbiol 2024; 90:e0211523. [PMID: 38323847 PMCID: PMC10952394 DOI: 10.1128/aem.02115-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 02/08/2024] Open
Abstract
Iron is essential to many biological processes but its poor solubility in aerobic environments restricts its bioavailability. To overcome this limitation, bacteria have evolved a variety of strategies, including the production and secretion of iron-chelating siderophores. Here, we describe the discovery of four series of siderophores from Streptomyces ambofaciens ATCC23877, three of which are unprecedented. MS/MS-based molecular networking revealed that one of these series corresponds to acylated desferrioxamines (acyl-DFOs) recently identified from S. coelicolor. The remaining sets include tetra- and penta-hydroxamate acyl-DFO derivatives, all of which incorporate a previously undescribed building block. Stable isotope labeling and gene deletion experiments provide evidence that biosynthesis of the acyl-DFO congeners requires unprecedented crosstalk between two separate non-ribosomal peptide synthetase (NRPS)-independent siderophore (NIS) pathways in the producing organism. Although the biological role(s) of these new derivatives remain to be elucidated, they may confer advantages in terms of metal chelation in the competitive soil environment due to the additional bidentate hydroxamic functional groups. The metabolites may also find application in various fields including biotechnology, bioremediation, and immuno-PET imaging.IMPORTANCEIron-chelating siderophores play important roles for their bacterial producers in the environment, but they have also found application in human medicine both in iron chelation therapy to prevent iron overload and in diagnostic imaging, as well as in biotechnology, including as agents for biocontrol of pathogens and bioremediation. In this study, we report the discovery of three novel series of related siderophores, whose biosynthesis depends on the interplay between two NRPS-independent (NIS) pathways in the producing organism S. ambofaciens-the first example to our knowledge of such functional cross-talk. We further reveal that two of these series correspond to acyl-desferrioxamines which incorporate four or five hydroxamate units. Although the biological importance of these novel derivatives is unknown, the increased chelating capacity of these metabolites may find utility in diagnostic imaging (for instance, 89Zr-based immuno-PET imaging) and other applications of metal chelators.
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Affiliation(s)
- Li Su
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Yaouba Souaibou
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
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13
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Raj N, Saini S. Increased privatization of a public resource leads to spread of cooperation in a microbial population. Microbiol Spectr 2024; 12:e0235823. [PMID: 38206031 PMCID: PMC10846273 DOI: 10.1128/spectrum.02358-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
The phenomenon of cooperation is prevalent at all levels of life. In one such manifestation of cooperation in microbial communities, some cells produce costly extracellular resources that are freely available to others. These resources are referred to as public goods. Saccharomyces cerevisiae secretes invertase (public good) in the periplasm to hydrolyze sucrose into glucose and fructose, which are then imported by the cells. After hydrolysis of sucrose, a cooperator retains only 1% of the monosaccharides, while 99% of the monosaccharides diffuse into the environment and can be utilized by any cell. The non-producers of invertase (cheaters) exploit the invertase-producing cells (cooperators) by utilizing the monosaccharides and not paying the metabolic cost of producing the invertase. In this work, we investigate the evolutionary dynamics of this cheater-cooperator system. In a co-culture, if cheaters are selected for their higher fitness, the population will collapse. On the other hand, for cooperators to survive in the population, a strategy to increase fitness would likely be required. To understand the adaptation of cooperators in sucrose, we performed a coevolution experiment in sucrose. Our results show that cooperators increase in fitness as the experiment progresses. This phenomenon was not observed in environments which involved a non-public good system. Genome sequencing reveals duplication of several HXT transporters in the evolved cooperators. Based on these results, we hypothesize that increased privatization of the monosaccharides is the most likely explanation of spread of cooperators in the population.IMPORTANCEHow is cooperation, as a trait, maintained in a population? In order to answer this question, we perform a coevolution experiment between two strains of yeast-one which produces a public good to release glucose and fructose in the media, thus generating a public resource, and the other which does not produce public resource and merely benefits from the presence of the cooperator strain. What is the outcome of this coevolution experiment? We demonstrate that after ~200 generations of coevolution, cooperators increase in frequency in the co-culture. Remarkably, in all parallel lines of our experiment, this is obtained via duplication of regions which likely allow greater privatization of glucose and fructose. Thus, increased privatization, which is intuitively thought to be a strategy against cooperation, enables spread of cooperation.
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Affiliation(s)
- Namratha Raj
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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14
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Song L, Xu L, Wu T, Shi Z, Kareem HA, Wang Z, Dai Q, Guo C, Pan J, Yang M, Wei X, Wang Y, Wei G, Shen X. Trojan horselike T6SS effector TepC mediates both interference competition and exploitative competition. THE ISME JOURNAL 2024; 18:wrad028. [PMID: 38365238 PMCID: PMC10833071 DOI: 10.1093/ismejo/wrad028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 02/18/2024]
Abstract
The type VI secretion system (T6SS) is a bacterial weapon capable of delivering antibacterial effectors to kill competing cells for interference competition, as well as secreting metal ion scavenging effectors to acquire essential micronutrients for exploitation competition. However, no T6SS effectors that can mediate both interference competition and exploitation competition have been reported. In this study, we identified a unique T6SS-1 effector in Yersinia pseudotuberculosis named TepC, which plays versatile roles in microbial communities. First, secreted TepC acts as a proteinaceous siderophore that binds to iron and mediates exploitative competition. Additionally, we discovered that TepC has DNase activity, which gives it both contact-dependent and contact-independent interference competition abilities. In conditions where iron is limited, the iron-loaded TepC is taken up by target cells expressing the outer membrane receptor TdsR. For kin cells encoding the cognate immunity protein TipC, TepC facilitates iron acquisition, and its toxic effects are neutralized. On the other hand, nonkin cells lacking TipC are enticed to uptake TepC and are killed by its DNase activity. Therefore, we have uncovered a T6SS effector, TepC, that functions like a "Trojan horse" by binding to iron ions to provide a valuable resource to kin cells, whereas punishing cheaters that do not produce public goods. This lure-to-kill mechanism, mediated by a bifunctional T6SS effector, may offer new insights into the molecular mechanisms that maintain stability in microbial communities.
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Affiliation(s)
- Li Song
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Xu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tong Wu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenkun Shi
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hafiz Abdul Kareem
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuo Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingyun Dai
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chenghao Guo
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junfeng Pan
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaomeng Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xihui Shen
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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15
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Filloux A. Bacterial type VI secretion system helps prevent cheating in microbial communities. THE ISME JOURNAL 2024; 18:wrae003. [PMID: 38365258 PMCID: PMC10839747 DOI: 10.1093/ismejo/wrae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/26/2023] [Accepted: 01/04/2024] [Indexed: 02/18/2024]
Affiliation(s)
- Alain Filloux
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
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16
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Zhao Y, Bitzer A, Power JJ, Belikova D, Torres Salazar BO, Adolf LA, Gerlach D, Krismer B, Heilbronner S. Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability. THE ISME JOURNAL 2024; 18:wrae123. [PMID: 38987933 PMCID: PMC11296517 DOI: 10.1093/ismejo/wrae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/19/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
The human microbiome is critically associated with human health and disease. One aspect of this is that antibiotic-resistant opportunistic bacterial pathogens, such as methicillin-resistant Staphylococcus aureus, can reside within the nasal microbiota, which increases the risk of infection. Epidemiological studies of the nasal microbiome have revealed positive and negative correlations between non-pathogenic species and S. aureus, but the underlying molecular mechanisms remain poorly understood. The nasal cavity is iron-limited, and bacteria are known to produce iron-scavenging siderophores to proliferate in such environments. Siderophores are public goods that can be consumed by all members of a bacterial community. Accordingly, siderophores are known to mediate bacterial competition and collaboration, but their role in the nasal microbiome is unknown. Here, we show that siderophore acquisition is crucial for S. aureus nasal colonization in vivo. We screened 94 nasal bacterial strains from seven genera for their capacity to produce siderophores as well as to consume the siderophores produced by S. aureus. We found that 80% of the strains engaged in siderophore-mediated interactions with S. aureus. Non-pathogenic corynebacterial species were found to be prominent consumers of S. aureus siderophores. In co-culture experiments, consumption of siderophores by competitors reduced S. aureus growth in an iron-dependent fashion. Our data show a wide network of siderophore-mediated interactions between the species of the human nasal microbiome and provide mechanistic evidence for inter-species competition and collaboration impacting pathogen proliferation. This opens avenues for designing nasal probiotics to displace S. aureus from the nasal cavity of humans.
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Affiliation(s)
- Yanfeng Zhao
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Laboratory Medicine Center, The Second Affiliated Hospital, Nanjing Medical University, 210011 Nanjing, P. R. China
| | - Alina Bitzer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Jeffrey John Power
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Darya Belikova
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany
| | - Benjamin Orlando Torres Salazar
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Lea Antje Adolf
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany
| | - David Gerlach
- Ludwig-Maximilians-Universität München, Faculty of Biology, Microbiology, 82152 Martinsried, Germany
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Simon Heilbronner
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany
- Ludwig-Maximilians-Universität München, Faculty of Biology, Microbiology, 82152 Martinsried, Germany
- German Center for Infection Research “DZIF” partnersite Tübingen, Germany
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17
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Smith P, Schuster M. The fitness benefit of pyoverdine cross-feeding by Pseudomonas protegens Pf-5. Environ Microbiol 2024; 26:e16554. [PMID: 38097191 DOI: 10.1111/1462-2920.16554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
Under iron-limiting conditions, fluorescent pseudomonads acquire iron from the environment by secreting strain-specific, iron-chelating siderophores termed pyoverdines (PVD). The rhizosphere bacterium Pseudomonas protegens Pf-5 produces its own PVD but also can cross-feed on PVDs produced by other species. Previous work has found that Pf-5 continues to produce its own PVD when allowed to cross-feed, raising questions about the benefit of heterologous PVD utilisation. Here, we investigate this question using a defined, unidirectional P. protegens Pf-5/Pseudomonas aeruginosa PAO1 cross-feeding model. Quantifying the production of PVD in the presence of heterologous PVD produced by PAO1, we show that cross-feeding Pf-5 strains reduce the production of their own PVD, while non-cross-feeding Pf-5 strains increase the production of PVD. Measuring the fitness of cross-feeding and non-cross-feeding Pf-5 strains in triple coculture with PAO1, we find that cross-feeding provides a fitness benefit to Pf-5 when the availability of heterologous PVD is high. We conclude that cross-feeding can reduce the costs of self-PVD production and may thus aid in the colonisation of iron-limited environments that contain compatible siderophores produced by other resident microbes. Taken together, these results expand our understanding of the mechanisms of interspecific competition for iron in microbial communities.
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Affiliation(s)
- Parker Smith
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
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18
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Jafra S, Jabłońska M, Maciąg T, Matuszewska M, Borowicz M, Prusiński M, Żmudzińska W, Thiel M, Czaplewska P, Krzyżanowska DM, Czajkowski R. An iron fist in a velvet glove: The cooperation of a novel pyoverdine from Pseudomonas donghuensis P482 with 7-hydroxytropolone is pivotal for its antibacterial activity. Environ Microbiol 2024; 26:e16559. [PMID: 38151794 DOI: 10.1111/1462-2920.16559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Pseudomonas donghuensis P482 exhibits broad antimicrobial activity against phytopathogens, including the soft rot bacteria of the Dickeya genus. Here, we report that under limited nutrient availability, the antibacterial activity of P. donghuensis P482 against Dickeya solani requires the reciprocal action of two iron scavengers: 7-hydroxytropolone (7-HT) and a newly characterized pyoverdine (PVDP482 ) and is quenched in the iron-augmented environment. Further, we show that the biosynthesis of pyoverdine and 7-HT is metabolically coordinated, and the functional BV82_4709 gene involved in 7-HT synthesis is pivotal for expressing the BV82_3755 gene, essential for pyoverdine biosynthesis and vice versa. The synthesis of both scavengers is under the control of Gac/Rsm, but only PVD is controlled by Fur. The isoelectric focusing profile of the P482 siderophore differs from that of the other Pseudomonas spp. tested. This finding led to the unveiling of the chemical structure of the new pyoverdine PVDP482 . To summarize, the antibacterial activity of P. donghuensis P482 is attributed to 7-HT and PVDP482 varies depending on the nutrient and iron availability, highlighting the importance of these factors in the competition between P482 and D. solani.
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Affiliation(s)
- Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Magdalena Jabłońska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Tomasz Maciąg
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Marta Matuszewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Marcin Borowicz
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Michał Prusiński
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Wioletta Żmudzińska
- Laboratory of Biopolymers Structure, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Marcel Thiel
- Laboratory of Biopolymers Structure, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Dorota M Krzyżanowska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, University of Gdansk, Gdansk, Poland
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19
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Calderón Celis F, González-Álvarez I, Fabjanowicz M, Godin S, Ouerdane L, Lauga B, Łobiński R. Unveiling the Pool of Metallophores in Native Environments and Correlation with Their Potential Producers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17302-17311. [PMID: 37921623 DOI: 10.1021/acs.est.3c04582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
For many organisms, metallophores are essential biogenic ligands that ensure metal scavenging and acquisition from their environment. Their identification is challenging in highly organic matter rich environments like peatlands due to low solubilization and metal scarcity and high matrix complexity. In contrast to common approaches based on sample modification by spiking of metal isotope tags, we have developed a two-dimensional (2D) Solid-phase extraction-Liquid chromatography-mass spectrometry (SPE-LC-MS) approach for the highly sensitive (LOD 40 fmol per g of soil), high-resolution direct detection and identification of metallophores in both their noncomplexed (apo) and metal-complexed forms in native environments. The characterization of peat collected in the Bernadouze (France) peatland resulted in the identification of 53 metallophores by a database mass-based search, 36 among which are bacterial. Furthermore, the detection of the characteristic (natural) metal isotope patterns in MS resulted in the detection of both Fe and Cu potential complexes. A taxonomic-based inference method was implemented based on literature and public database (antiSMASH database version 3.0) searches, enabling to associate over 40% of the identified bacterial metallophores with potential producers. In some cases, low completeness with the MIBiG reference BCG might be indicative of alternative producers in the ecosystem. Thus, coupling of metallophore detection and producers' inference could pave a new way to investigate poorly documented environment searching for new metallophores and their producers yet unknown.
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Affiliation(s)
| | | | - Magdalena Fabjanowicz
- Faculty of Chemistry, Department of Analytical Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Simon Godin
- E2S UPPA, CNRS, IPREM, Universite de Pau et des Pays de l'Adour, 64000 Pau, France
| | - Laurent Ouerdane
- E2S UPPA, CNRS, IPREM, Universite de Pau et des Pays de l'Adour, 64000 Pau, France
| | - Béatrice Lauga
- E2S UPPA, CNRS, IPREM, Universite de Pau et des Pays de l'Adour, 64000 Pau, France
| | - Ryszard Łobiński
- E2S UPPA, CNRS, IPREM, Universite de Pau et des Pays de l'Adour, 64000 Pau, France
- Chair of Analytical Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
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20
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Belcher LJ, Dewar AE, Hao C, Ghoul M, West SA. Signatures of kin selection in a natural population of the bacteria Bacillus subtilis. Evol Lett 2023; 7:315-330. [PMID: 37829498 PMCID: PMC10565896 DOI: 10.1093/evlett/qrad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 10/14/2023] Open
Abstract
Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.
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Affiliation(s)
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
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21
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Shao J, Rong N, Wu Z, Gu S, Liu B, Shen N, Li Z. Siderophore-mediated iron partition promotes dynamical coexistence between cooperators and cheaters. iScience 2023; 26:107396. [PMID: 37701813 PMCID: PMC10494312 DOI: 10.1016/j.isci.2023.107396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/26/2023] [Accepted: 07/11/2023] [Indexed: 09/14/2023] Open
Abstract
Microbes shape their habitats by consuming resources and producing a diverse array of chemicals that can serve as public goods. Despite the risk of exploitation by cheaters, genes encoding sharable molecules like siderophores are widely found in nature, prompting investigations into the mechanisms that allow producers to resist invasion by cheaters. In this work, we presented the chemostat-typed "resource partition model" to demonstrate that dividing the iron resource between private and public siderophores can promote stable or dynamic coexistence between producers and cheaters in a well-mixed environment. Moreover, our analysis shows that when microbes not only consume but also produce resources, chemical innovation leads to stability criteria that differ from those of classical consumer resource models, resulting in more complex dynamics. Our work sheds light on the role of chemical innovations in microbial communities and the potential for resource partition to facilitate dynamical coexistence between cooperative and cheating organisms.
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Affiliation(s)
- Jiqi Shao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhenchao Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Beibei Liu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Ning Shen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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22
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O'Brien S, Culbert CT, Barraclough TG. Community composition drives siderophore dynamics in multispecies bacterial communities. BMC Ecol Evol 2023; 23:45. [PMID: 37658316 PMCID: PMC10472669 DOI: 10.1186/s12862-023-02152-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 08/17/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Intraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e., interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence drive intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacterium Pseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2 to 15 species. RESULTS We find, contrary to our prediction, that siderophore production is favoured at higher levels of community species richness, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains of P. fluorescens. CONCLUSIONS Our results suggest that maintaining a diverse soil microbiota could partly contribute to the maintenance of siderophore production in natural communities.
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Affiliation(s)
- Siobhán O'Brien
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Christopher T Culbert
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
| | - Timothy G Barraclough
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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23
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Volke DC, Gurdo N, Milanesi R, Nikel PI. Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida. Metab Eng 2023; 79:159-172. [PMID: 37454792 DOI: 10.1016/j.ymben.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Pseudomonas putida, a microbial host widely adopted for metabolic engineering, processes glucose through convergent peripheral pathways that ultimately yield 6-phosphogluconate. The periplasmic gluconate shunt (PGS), composed by glucose and gluconate dehydrogenases, sequentially transforms glucose into gluconate and 2-ketogluconate. Although the secretion of these organic acids by P. putida has been extensively recognized, the mechanism and spatiotemporal regulation of the PGS remained elusive thus far. To address this challenge, we adopted a dynamic 13C- and 2H-metabolic flux analysis strategy, termed D-fluxomics. D-fluxomics demonstrated that the PGS underscores a highly dynamic metabolic architecture in glucose-dependent batch cultures of P. putida, characterized by hierarchical carbon uptake by the PGS throughout the cultivation. Additionally, we show that gluconate and 2-ketogluconate accumulation and consumption can be solely explained as a result of the interplay between growth rate-coupled and decoupled metabolic fluxes. As a consequence, the formation of these acids in the PGS is inversely correlated to the bacterial growth rate-unlike the widely studied overflow metabolism of Escherichia coli and yeast. Our findings, which underline survival strategies of soil bacteria thriving in their natural environments, open new avenues for engineering P. putida towards efficient, sugar-based bioprocesses.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - Nicolas Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Riccardo Milanesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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24
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Lewis JP, Gui Q. Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation. Microbiol Spectr 2023; 11:e0473322. [PMID: 37314331 PMCID: PMC10434189 DOI: 10.1128/spectrum.04733-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/05/2023] [Indexed: 06/15/2023] Open
Abstract
Bacteria have to persist under low iron conditions in order to adapt to the nutritional immunity of a host. Since the knowledge of iron stimulon of Bacteroidetes is sparse, we examined oral (Porphyromonas gingivalis and Prevotella intermedia) and gut (Bacteroides thataiotaomicron) representatives for their ability to adapt to iron deplete and iron replete conditions. Our transcriptomics and comparative genomics analysis show that many iron-regulated mechanisms are conserved within the phylum. They include genes upregulated in low iron, as follows: fldA (flavodoxin), hmu (hemin uptake operon), and loci encoding ABC transporters. Downregulated genes were frd (ferredoxin), rbr (rubrerythrin), sdh (succinate dehydrogenase/fumarate reductase), vor (oxoglutarate oxidoreductase/dehydrogenase), and pfor (pyruvate:ferredoxin/flavodoxin oxidoreductase). Some genus-specific mechanisms, such as the sus of B. thetaiotaomicron coding for carbohydrate metabolism and the xusABC coding for xenosiderophore utilization were also identified. While all bacteria tested in our study had the nrfAH operon coding for nitrite reduction and were able to reduce nitrite levels present in culture media, the expression of the operon was iron dependent only in B. thetaiotaomicron. It is noteworthy that we identified a significant overlap between regulated genes found in our study and the B. thetaiotaomicron colitis study (W. Zhu, M. G. Winter, L. Spiga, E. R. Hughes et al., Cell Host Microbe 27:376-388, 2020, http://dx.doi.org/10.1016/j.chom.2020.01.010). Many of those commonly regulated genes were also iron regulated in the oral bacterial genera. Overall, this work points to iron being the master regulator enabling bacterial persistence in the host and paves the way for a more generalized investigation of the molecular mechanisms of iron homeostasis in Bacteroidetes. IMPORTANCE Bacteroidetes are an important group of anaerobic bacteria abundant both in the oral and gut microbiomes. Although iron is a required nutrient for most living organisms, the molecular mechanisms of adaptation to the changing levels of iron are not well known in this group of bacteria. We defined the iron stimulon of Bacteroidetes by examination of the transcriptomic response of Porphyromonas gingivalis and Prevotella intermedia (both belong to the oral microbiome) and Bacteroidetes thetaiotaomicron (belongs to the gut microbiome). Our results indicate that many of the iron-regulated operons are shared among the three genera. Furthermore, using bioinformatics analysis, we identified a significant overlap between our in vitro studies and transcriptomic data derived from a colitis study, thus underscoring the biological significance of our work. Defining the iron-dependent stimulon of Bacteroidetes can help to identify the molecular mechanisms of iron-dependent regulation as well as better understand the persistence of the anaerobes in the human host.
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Affiliation(s)
- Janina P. Lewis
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Biochemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qin Gui
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, USA
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25
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Bonhomme L, Dubard L, Riha M, Rodrigues A, Aussel L. [Metallophores: The metal rush]. Med Sci (Paris) 2023; 39:676-680. [PMID: 37695159 DOI: 10.1051/medsci/2023104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Affiliation(s)
- Laura Bonhomme
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille université, Marseille, France
| | - Ludovic Dubard
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille université, Marseille, France
| | - Melvin Riha
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille université, Marseille, France
| | - Anthony Rodrigues
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille université, Marseille, France
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26
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Shen Y, Zhao J, Zou X, Shi Z, Liao Y, He Y, Wang H, Chen Q, Yang P, Li M. Differential Responses of Bacterial and Fungal Communities to Siderophore Supplementation in Soil Affected by Tobacco Bacterial Wilt ( Ralstonia solanacearum). Microorganisms 2023; 11:1535. [PMID: 37375037 DOI: 10.3390/microorganisms11061535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Siderophores secreted by microorganisms can promote ecological efficiency and could be used to regulate the unbalanced microbial community structure. The influence of the siderophore activity of Trichoderma yunnanense strain 2-14F2 and Beauveria pseudobassiana strain (2-8F2) on the physiological/biochemical functions and community structure of soil microbes affected by tobacco bacterial wilt (TBW) was studied. DNS Colorimetry and Biolog-eco plates were used to quantify the impacts of strain siderophores on soil enzyme activities and microbial metabolism. Based on Illumina MiSeq high-throughput sequencing, the soil 16S rDNA and ITS sequences were amplified to dissect the response characteristics of alpha/beta diversity and the structure/composition of a soil microbial community toward siderophores. The KEGG database was used to perform the PICRUSt functional prediction of the microbial community. We found that siderophores of 2-14F2 and 2-8F2, at certain concentrations, significantly increased the activities of sucrase (S-SC) and urease (S-UE) in the TBW soil and enhanced the average well color development (AWCD, carbon source utilization capacity) of the microbial community. The metabolic capacity of the diseased soil to amino acids, carbohydrates, polymers, aromatics, and carboxylic acids also increased significantly. The response of the bacterial community to siderophore active metabolites was more significant in alpha diversity, while the beta diversity of the fungal community responded more positively to siderophores. The relative abundance of Actinobacteria, Chloroflexi, and Acidobacteria increased and was accompanied by reductions in Proteobacteria and Firmicutes. LEfSe analysis showed that Pseudonocardiaceae, Gemmatimonas, Castellaniella, Chloridiumand and Acrophialophora altered the most under different concentrations of siderophore active metabolites. The PICRUSt functional prediction results showed that siderophore increased the abundance of the redox-related enzymes of the microbial community in TBW soil. The BugBase phenotypic prediction results showed that the siderophore activity could decrease the abundance of pathogenic bacteria. The study concludes that siderophore activity could decrease the abundance of pathogenic bacteria and regulate the composition of the microbial community in TBW soil. The activities of sucrase (S-SC) and urease (S-UE) in TBW soil were significantly increased. Overall, the siderophore regulation of community structures is a sustainable management strategy for soil ecosystems.
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Affiliation(s)
- Yunxin Shen
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Jiangyuan Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650106, China
| | - Xuefeng Zou
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Zhufeng Shi
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Yongqin Liao
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Yonghong He
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
| | - Hang Wang
- National Plateau Wetlands Research Center, Wetlands College, Southwest Forestry University, Kunming 650233, China
| | - Qibin Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming 655508, China
| | - Peiweng Yang
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Minggang Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650106, China
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27
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Chepsergon J, Moleleki LN. Rhizosphere bacterial interactions and impact on plant health. Curr Opin Microbiol 2023; 73:102297. [PMID: 37002974 DOI: 10.1016/j.mib.2023.102297] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/30/2023] [Accepted: 02/24/2023] [Indexed: 04/01/2023]
Abstract
The rhizosphere is a chemically complex environment that harbors a strikingly diverse microbial community. The past few decades have seen a rapid growth in the body of literature on plant-microbe-microbe interactions and plant health. Thus, the aim of this paper is to review current knowledge on plant-microbe-microbe (specifically bacteria) interactions in the rhizosphere and how these influence rhizosphere microbiomes and impact plant health. This article discusses (i) how the plant recruits beneficial rhizosphere bacteria and ii) how competition between rhizosphere bacteria and mechanisms/weapons employed in bacteria-bacteria competition shapes rhizosphere microbiome and in turn affects plant heath. The discussion mainly focuses on interference competition, characterized by production of specialized metabolites (antibacterial compounds) and exploitative competition where a bacterial strain restricts the competitor's access to nutrients such as through secretion of siderophores that could allude to cooperation. Understanding mechanisms employed in bacteria-bacteria and plant-bacteria interactions could provide insights into how to manipulate microbiomes for improved agricultural outcomes.
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28
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Charron-Lamoureux V, Haroune L, Pomerleau M, Hall L, Orban F, Leroux J, Rizzi A, Bourassa JS, Fontaine N, d'Astous ÉV, Dauphin-Ducharme P, Legault CY, Bellenger JP, Beauregard PB. Pulcherriminic acid modulates iron availability and protects against oxidative stress during microbial interactions. Nat Commun 2023; 14:2536. [PMID: 37137890 PMCID: PMC10156857 DOI: 10.1038/s41467-023-38222-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
Siderophores are soluble or membrane-embedded molecules that bind the oxidized form of iron, Fe(III), and play roles in iron acquisition by microorganisms. Fe(III)-bound siderophores bind to specific receptors that allow microbes to acquire iron. However, certain soil microbes release a compound (pulcherriminic acid, PA) that, upon binding to Fe(III), forms a precipitate (pulcherrimin) that apparently functions by reducing iron availability rather than contributing to iron acquisition. Here, we use Bacillus subtilis (PA producer) and Pseudomonas protegens as a competition model to show that PA is involved in a peculiar iron-managing system. The presence of the competitor induces PA production, leading to precipitation of Fe(III) as pulcherrimin, which prevents oxidative stress in B. subtilis by restricting the Fenton reaction and deleterious ROS formation. In addition, B. subtilis uses its known siderophore bacillibactin to retrieve Fe(III) from pulcherrimin. Our findings indicate that PA plays multiple roles by modulating iron availability and conferring protection against oxidative stress during inter-species competition.
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Affiliation(s)
| | - Lounès Haroune
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Institut de pharmacologie de Sherbrooke, Faculté de médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Maude Pomerleau
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Léo Hall
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Frédéric Orban
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Julie Leroux
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Adrien Rizzi
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Sébastien Bourassa
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nicolas Fontaine
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Élodie V d'Astous
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Claude Y Legault
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Philippe Bellenger
- Département de chimie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pascale B Beauregard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.
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29
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Farr AD, Pesce D, Das SG, Zwart MP, de Visser JAGM. The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations. mBio 2023:e0009823. [PMID: 37129484 DOI: 10.1128/mbio.00098-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Adaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit and together make up the fitness landscape, which maps genotype space onto fitness under specified conditions. Experimentally derived fitness landscapes have demonstrated a predictability to evolution by identifying limited "mutational routes" that evolution by natural selection may take between low and high-fitness genotypes. However, such studies often utilize indirect measures to determine fitness. We estimated the competitive fitness of mutants relative to all single-mutation neighbors to describe the fitness landscape of three mutations in a β-lactamase enzyme. Fitness assays were performed at sublethal concentrations of the antibiotic cefotaxime in a structured and unstructured environment. In the unstructured environment, the antibiotic selected for higher-resistance types-but with an equivalent fitness for a subset of mutants, despite substantial variation in resistance-resulting in a stratified fitness landscape. In contrast, in a structured environment with a low antibiotic concentration, antibiotic-susceptible genotypes had a relative fitness advantage, which was associated with antibiotic-induced filamentation. These results cast doubt that highly resistant genotypes have a unique selective advantage in environments with subinhibitory concentrations of antibiotics and demonstrate that direct fitness measures are required for meaningful predictions of the accessibility of evolutionary routes. IMPORTANCE The evolution of antibiotic-resistant bacterial populations underpins the ongoing antibiotic resistance crisis. We aim to understand how antibiotic-degrading enzymes can evolve to cause increased resistance, how this process is constrained, and whether it can be predictable. To this end, competition experiments were performed with a combinatorially complete set of mutants of a β-lactamase gene subject to subinhibitory concentrations of the antibiotic cefotaxime. While some mutations confer on their hosts high resistance to cefotaxime, in competition these mutations do not always confer a selective advantage. Specifically, high-resistance mutants had equivalent fitnesses despite different resistance levels and even had selective disadvantages under conditions involving spatial structure. Together, our findings suggest that the relationship between resistance level and fitness at subinhibitory concentrations is complex; predicting the evolution of antibiotic resistance requires knowledge of the conditions that select for resistant genotypes and the selective advantage evolved types have over their predecessors.
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Affiliation(s)
- Andrew D Farr
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diego Pesce
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Suman G Das
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Mark P Zwart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - J Arjan G M de Visser
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
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Barton LL, Duarte AG, Staicu LC. Genomic insight into iron acquisition by sulfate-reducing bacteria in microaerophilic environments. Biometals 2023; 36:339-350. [PMID: 35767096 DOI: 10.1007/s10534-022-00410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
Historically, sulfate-reducing bacteria (SRB) have been considered to be strict anaerobes, but reports in the past couple of decades indicate that SRB tolerate exposure to O2 and can even grow in aerophilic environments. With the transition from anaerobic to microaerophilic conditions, the uptake of Fe(III) from the environment by SRB would become important. In evaluating the metabolic capability for the uptake of iron, the genomes of 26 SRB, representing eight families, were examined. All SRB reviewed carry genes (feoA and feoB) for the ferrous uptake system to transport Fe(II) across the plasma membrane into the cytoplasm. In addition, all of the SRB genomes examined have putative genes for a canonical ABC transporter that may transport ferric siderophore or ferric chelated species from the environment. Gram-negative SRB have additional machinery to import ferric siderophores and ferric chelated species since they have the TonB system that can work alongside any of the outer membrane porins annotated in the genome. Included in this review is the discussion that SRB may use the putative siderophore uptake system to import metals other than iron.
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Affiliation(s)
- Larry L Barton
- Department of Biology, University of New Mexico, MSCO3 2020, Albuquerque, NM, 87131, USA
| | - Americo G Duarte
- Instituto de Tecnologia Química E Biológica António Xavier/Universidade NOVA de Lisboa, Av. República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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Kint N, Dubois T, Viollier PH. Stereoisomer-specific reprogramming of a bacterial flagellin sialyltransferase. EMBO J 2023; 42:e112880. [PMID: 36636824 PMCID: PMC9975948 DOI: 10.15252/embj.2022112880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/02/2022] [Accepted: 12/16/2022] [Indexed: 01/14/2023] Open
Abstract
Glycosylation of surface structures diversifies cells chemically and physically. Nucleotide-activated sialic acids commonly serve as glycosyl donors, particularly pseudaminic acid (Pse) and its stereoisomer legionaminic acid (Leg), which decorate eubacterial and archaeal surface layers or protein appendages. FlmG, a recently identified protein sialyltransferase, O-glycosylates flagellins, the subunits of the flagellar filament. We show that flagellin glycosylation and motility in Caulobacter crescentus and Brevundimonas subvibrioides is conferred by functionally insulated Pse and Leg biosynthesis pathways, respectively, and by specialized FlmG orthologs. We established a genetic glyco-profiling platform for the classification of Pse or Leg biosynthesis pathways, discovered a signature determinant of eubacterial and archaeal Leg biosynthesis, and validated it by reconstitution experiments in a heterologous host. Finally, by rewiring FlmG glycosylation using chimeras, we defined two modular determinants that govern flagellin glycosyltransferase specificity: a glycosyltransferase domain that either donates Leg or Pse and a specialized flagellin-binding domain that identifies the acceptor.
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Affiliation(s)
- Nicolas Kint
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of MedicineUniversity of GenevaGenèveSwitzerland
| | - Thomas Dubois
- University of Lille, CNRS, INRAE, Centrale Lille, UMR 8207‐UMET‐Unité Matériaux et TransformationsLilleFrance
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of MedicineUniversity of GenevaGenèveSwitzerland
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Rattray JB, Brown SP. Beyond Thresholds: Quorum‐Sensing as Quantitatively Varying Reaction Norms to Multiple Environmental Dimensions. Isr J Chem 2023. [DOI: 10.1002/ijch.202200109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
| | - Sam P. Brown
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
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Narh Mensah DL, Wingfield BD, Coetzee MPA. Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae. Curr Genet 2023; 69:7-24. [PMID: 36369495 DOI: 10.1007/s00294-022-01256-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022]
Abstract
Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)3(TC)2. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Council for Scientific and Industrial Research-Food Research Institute (CSIR-FRI), P. O. Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
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LeBlanc N. Green Manures Alter Taxonomic and Functional Characteristics of Soil Bacterial Communities. MICROBIAL ECOLOGY 2023; 85:684-697. [PMID: 35112152 DOI: 10.1007/s00248-022-01975-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Incorporation of plant biomass into soil as green manures can reduce soilborne diseases and improve crop and soil health in agricultural ecosystems. Soil microbial communities can mediate beneficial effects of these amendments, but their response to different types of green manures is poorly understood. This study tested the effect of green manures from broccoli, marigold, and sudangrass on taxonomic and functional characteristics of soil bacterial communities. Green manures were amended to field soil and maintained in microcosms artificially infested with the soilborne plant pathogen Verticillium dahliae. Lettuce seedlings were transplanted into green manure amended and fallow soil and maintained under growth chamber conditions for 12 weeks. Bacterial communities in bulk and rhizosphere soils were characterized using nanopore sequencing of 16S rRNA and shotgun metagenome libraries. Under microcosm conditions, all green manures reduced the abundance of the soilborne plant pathogen V. dahliae and altered the taxonomic composition of bacterial communities. Twelve weeks following amendment, green manures had differential effects on lettuce yield as well as the taxonomic diversity and composition of soil bacterial communities. In addition, multiple green manures increased the abundance of bacterial functional traits in rhizosphere soil related to iron and polysaccharide acquisition and decreased the abundance of functional traits related to bacterial protein secretion systems. This study demonstrates green manures alter the taxonomic composition and functional traits in soil bacterial communities suggesting these changes may impact beneficial effects of green manures on plant and soil health.
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Affiliation(s)
- Nicholas LeBlanc
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St., Salinas, CA, 93905, USA.
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Shepherdson EM, Baglio CR, Elliot MA. Streptomyces behavior and competition in the natural environment. Curr Opin Microbiol 2023; 71:102257. [PMID: 36565538 DOI: 10.1016/j.mib.2022.102257] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
Streptomyces are ubiquitous terrestrial bacteria that are renowned for their robust metabolic capabilities and their behavioral flexibility. In competing for environmental niches, these bacteria can employ novel growth and dispersal behaviors. They also wield their diverse metabolic repertoire for everything from maximizing nutrient uptake, to preventing phage replication or inhibiting bacterial and fungal growth. Increasingly, they are found to live in association with plants and insects, often conferring protective benefits to their host courtesy of their ability to produce pathogen-inhibitory antimicrobial compounds. Here, we highlight recent advances in understanding the competitive and cooperative interactions between Streptomyces and phage, microbes, and higher organisms in their environment.
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Affiliation(s)
- Evan Mf Shepherdson
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada
| | - Christine R Baglio
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada
| | - Marie A Elliot
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada.
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Rehm K, Vollenweider V, Kümmerli R, Bigler L. Rapid identification of pyoverdines of fluorescent Pseudomonas spp. by UHPLC-IM-MS. Biometals 2023; 36:19-34. [PMID: 36261676 PMCID: PMC9925543 DOI: 10.1007/s10534-022-00454-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/26/2022] [Indexed: 11/02/2022]
Abstract
Siderophores are iron-chelating molecules produced by bacteria and other microbes. They are involved with virulence in infections and play key roles in bacterial community assembly and as plant protectants due to their pathogen control properties. Although assays exist to screen whether newly isolated bacteria can produce siderophores, the chemical structures of many of these bio-active molecules remain unidentified due to the lack of rapid analytical procedures. An important group of siderophores are pyoverdines. They consist of a structurally diverse group of chromopeptides, whose amino acid sequence is characteristic for the fluorescent Pseudomonas species that secrets them. Although over 60 pyoverdine structures have been described so far, their characterization is cumbersome and several methods (isoelectrofocusing, iron uptake measurement, mass determination) are typically combined as ambiguous results are often achieved by a single method. Those additional experiments consume valuable time and resources and prevent high-throughput analysis. In this work, we present a new pyoverdine characterisation option by recording their collision cross sections (CCS) using trapped ion mobility spectrometry. This can be done simultaneously in combination with UHPLC and high-resolution MS resulting in a rapid identification of pyoverdines. The high specificity of CCS values is presented for 17 pyoverdines secreted by different Pseudomonas strains. The pyoverdine mass determination by full scan MS was supported by fragments obtained from broadband collision induced dissociation (bbCID). As iron contaminations in laboratories are not uncommon, CCS values of ferripyoverdines were also evaluated. Thereby, unusual and highly characteristic ion mobility patterns were obtained that are suitable as an alternative identification marker.
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Affiliation(s)
- Karoline Rehm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Vera Vollenweider
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
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37
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Martín-Rodríguez AJ. Respiration-induced biofilm formation as a driver for bacterial niche colonization. Trends Microbiol 2023; 31:120-134. [PMID: 36075785 DOI: 10.1016/j.tim.2022.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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Villar-Moreno R, Tienda S, Gutiérrez-Barranquero JA, Carrión VJ, de Vicente A, Cazorla FM, Arrebola E. Interplay between rhizospheric Pseudomonas chlororaphis strains lays the basis for beneficial bacterial consortia. FRONTIERS IN PLANT SCIENCE 2022; 13:1063182. [PMID: 36589057 PMCID: PMC9797978 DOI: 10.3389/fpls.2022.1063182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Pseudomonas chlororaphis (Pc) representatives are found as part of the rhizosphere-associated microbiome, and different rhizospheric Pc strains frequently perform beneficial activities for the plant. In this study we described the interactions between the rhizospheric Pc strains PCL1601, PCL1606 and PCL1607 with a focus on their effects on root performance. Differences among the three rhizospheric Pc strains selected were first observed in phylogenetic studies and confirmed by genome analysis, which showed variation in the presence of genes related to antifungal compounds or siderophore production, among others. Observation of the interactions among these strains under lab conditions revealed that PCL1606 has a better adaptation to environments rich in nutrients, and forms biofilms. Interaction experiments on plant roots confirmed the role of the different phenotypes in their lifestyle. The PCL1606 strain was the best adapted to the habitat of avocado roots, and PCL1607 was the least, and disappeared from the plant root scenario after a few days of interaction. These results confirm that 2 out 3 rhizospheric Pc strains were fully compatible (PCL1601 and PCL1606), efficiently colonizing avocado roots and showing biocontrol activity against the fungal pathogen Rosellinia necatrix. The third strain (PCL1607) has colonizing abilities when it is alone on the root but displayed difficulties under the competition scenario, and did not cause deleterious effects on the other Pc competitors when they were present. These results suggest that strains PCL1601 and PCL1606 are very well adapted to the avocado root environment and could constitute a basis for constructing a more complex beneficial microbial synthetic community associated with avocado plant roots.
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Affiliation(s)
- Rafael Villar-Moreno
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Sandra Tienda
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Jose A. Gutiérrez-Barranquero
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Víctor J. Carrión
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Antonio de Vicente
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Francisco M. Cazorla
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Eva Arrebola
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
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Schaal KA, Yu YTN, Vasse M, Velicer GJ. Allopatric divergence of cooperators confers cheating resistance and limits effects of a defector mutation. BMC Ecol Evol 2022; 22:141. [PMID: 36510120 PMCID: PMC9746145 DOI: 10.1186/s12862-022-02094-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Social defectors may meet diverse cooperators. Genotype-by-genotype interactions may constrain the ranges of cooperators upon which particular defectors can cheat, limiting cheater spread. Upon starvation, the soil bacterium Myxococcus xanthus cooperatively develops into spore-bearing fruiting bodies, using a complex regulatory network and several intercellular signals. Some strains (cheaters) are unable to sporulate effectively in pure culture due to mutations that reduce signal production but can exploit and outcompete cooperators within mixed groups. RESULTS In this study, interactions between a cheater disrupted at the signaling gene csgA and allopatrically diversified cooperators reveal a very small cheating range. Expectedly, the cheater failed to cheat on all natural-isolate cooperators owing to non-cheater-specific antagonisms. Surprisingly, some lab-evolved cooperators had already exited the csgA mutant's cheating range after accumulating fewer than 20 mutations and without experiencing cheating during evolution. Cooperators might also diversify in the potential for a mutation to reduce expression of a cooperative trait or generate a cheating phenotype. A new csgA mutation constructed in several highly diverged cooperators generated diverse sporulation phenotypes, ranging from a complete defect to no defect, indicating that genetic backgrounds can limit the set of genomes in which a mutation creates a defector. CONCLUSIONS Our results demonstrate that natural populations may feature geographic mosaics of cooperators that have diversified in their susceptibility to particular cheaters, limiting defectors' cheating ranges and preventing them from spreading. This diversification may also lead to variation in the phenotypes generated by any given cooperation-gene mutation, further decreasing the chance of a cheater emerging which threatens the persistence of cooperation in the system.
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Affiliation(s)
- Kaitlin A. Schaal
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
| | - Marie Vasse
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland ,grid.121334.60000 0001 2097 0141Institute MIVEGEC (UMR 5290 CNRS, IRD, UM), 34394 Montpellier, France
| | - Gregory J. Velicer
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
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Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals 2022:10.1007/s10534-022-00480-8. [PMID: 36508064 PMCID: PMC10393863 DOI: 10.1007/s10534-022-00480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
AbstractIron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.
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Lerch BA, Smith DA, Koffel T, Bagby SC, Abbott KC. How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods. PLoS Comput Biol 2022; 18:e1010666. [PMID: 36318525 PMCID: PMC9651594 DOI: 10.1371/journal.pcbi.1010666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/11/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
The production of costly public goods (as distinct from metabolic byproducts) has largely been understood through the realization that spatial structure can minimize losses to non-producing "cheaters" by allowing for the positive assortment of producers. In well-mixed systems, where positive assortment is not possible, the stable production of public goods has been proposed to depend on lineages that become indispensable as the sole producers of those goods while their neighbors lose production capacity through genome streamlining (the Black Queen Hypothesis). Here, we develop consumer-resource models motivated by nitrogen-fixing, siderophore-producing bacteria that consider the role of colimitation in shaping eco-evolutionary dynamics. Our models demonstrate that in well-mixed environments, single "public goods" can only be ecologically and evolutionarily stable if they are partially privatized (i.e., if producers reserve a portion of the product pool for private use). Colimitation introduces the possibility of subsidy: strains producing a fully public good can exclude non-producing strains so long as the producing strain derives sufficient benefit from the production of a second partially private good. We derive a lower bound for the degree of privatization necessary for production to be advantageous, which depends on external resource concentrations. Highly privatized, low-investment goods, in environments where the good is limiting, are especially likely to be stably produced. Coexistence emerges more rarely in our mechanistic model of the external environment than in past phenomenological approaches. Broadly, we show that the viability of production depends critically on the environmental context (i.e., external resource concentrations), with production of shared resources favored in environments where a partially-privatized resource is scarce.
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Affiliation(s)
- Brian A. Lerch
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Derek A. Smith
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas Koffel
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
| | - Sarah C. Bagby
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Karen C. Abbott
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
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Classifying Interactions in a Synthetic Bacterial Community Is Hindered by Inhibitory Growth Medium. mSystems 2022; 7:e0023922. [PMID: 36197097 PMCID: PMC9600862 DOI: 10.1128/msystems.00239-22] [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] [Indexed: 12/24/2022] Open
Abstract
Predicting the fate of a microbial community and its member species relies on understanding the nature of their interactions. However, designing simple assays that distinguish between interaction types can be challenging. Here, we performed spent medium assays based on the predictions of a mathematical model to decipher the interactions among four bacterial species: Agrobacterium tumefaciens, Comamonas testosteroni, Microbacterium saperdae, and Ochrobactrum anthropi. While most experimental results matched model predictions, the behavior of C. testosteroni did not: its lag phase was reduced in the pure spent media of A. tumefaciens and M. saperdae but prolonged again when we replenished our growth medium. Further experiments showed that the growth medium actually delayed the growth of C. testosteroni, leading us to suspect that A. tumefaciens and M. saperdae could alleviate this inhibitory effect. There was, however, no evidence supporting such "cross-detoxification," and instead, we identified metabolites secreted by A. tumefaciens and M. saperdae that were then consumed or "cross-fed" by C. testosteroni, shortening its lag phase. Our results highlight that even simple, defined growth media can have inhibitory effects on some species and that such negative effects need to be included in our models. Based on this, we present new guidelines to correctly distinguish between different interaction types such as cross-detoxification and cross-feeding. IMPORTANCE Communities of microbes colonize virtually every place on earth. Ultimately, we strive to predict and control how these communities behave, for example, if they reside in our guts and make us sick. But precise control is impossible unless we can identify exactly how their member species interact with one another. To find a systematic way to measure interactions, we started very simply with a small community of four bacterial species and carefully designed experiments based on a mathematical model. This first attempt accurately mapped out interactions for all species except one. By digging deeper, we understood that our method failed for that species as it was suffering in the growth medium that we chose. A revised model that considered that growth media can be harmful could then make more accurate predictions. What we have learned with these four species can now be applied to decipher interactions in larger communities.
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Liu M, West SA, Wild G. The evolution of manipulative cheating. eLife 2022; 11:e80611. [PMID: 36193888 PMCID: PMC9633066 DOI: 10.7554/elife.80611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/03/2022] [Indexed: 01/07/2023] Open
Abstract
A social cheat is typically assumed to be an individual that does not perform a cooperative behaviour, or performs less of it, but can still exploit the cooperative behaviour of others. However, empirical data suggests that cheating can be more subtle, involving evolutionary arms races over the ability to both exploit and resist exploitation. These complications have not been captured by evolutionary theory, which lags behind empirical studies in this area. We bridge this gap with a mixture of game-theoretical models and individual-based simulations, examining what conditions favour more elaborate patterns of cheating. We found that as well as adjusting their own behaviour, individuals can be selected to manipulate the behaviour of others, which we term 'manipulative cheating'. Further, we found that manipulative cheating can lead to dynamic oscillations (arms races), between selfishness, manipulation, and suppression of manipulation. Our results can help explain both variation in the level of cheating, and genetic variation in the extent to which individuals can be exploited by cheats.
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Affiliation(s)
- Ming Liu
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | | | - Geoff Wild
- Department of Mathematics, The University of Western OntarioLondonCanada
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Dell’Anno F, Vitale GA, Buonocore C, Vitale L, Palma Esposito F, Coppola D, Della Sala G, Tedesco P, de Pascale D. Novel Insights on Pyoverdine: From Biosynthesis to Biotechnological Application. Int J Mol Sci 2022; 23:ijms231911507. [PMID: 36232800 PMCID: PMC9569983 DOI: 10.3390/ijms231911507] [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: 09/09/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Pyoverdines (PVDs) are a class of siderophores produced mostly by members of the genus Pseudomonas. Their primary function is to accumulate, mobilize, and transport iron necessary for cell metabolism. Moreover, PVDs also play a crucial role in microbes’ survival by mediating biofilm formation and virulence. In this review, we reorganize the information produced in recent years regarding PVDs biosynthesis and pathogenic mechanisms, since PVDs are extremely valuable compounds. Additionally, we summarize the therapeutic applications deriving from the PVDs’ use and focus on their role as therapeutic target themselves. We assess the current biotechnological applications of different sectors and evaluate the state-of-the-art technology relating to the use of synthetic biology tools for pathway engineering. Finally, we review the most recent methods and techniques capable of identifying such molecules in complex matrices for drug-discovery purposes.
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Hu J, Shuai W, Sumner JT, Moghadam AA, Hartmann EM. Clinically relevant pathogens on surfaces display differences in survival and transcriptomic response in relation to probiotic and traditional cleaning strategies. NPJ Biofilms Microbiomes 2022; 8:72. [PMID: 36123373 PMCID: PMC9485146 DOI: 10.1038/s41522-022-00335-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/02/2022] [Indexed: 02/05/2023] Open
Abstract
Indoor surfaces are paradoxically presumed to be both colonized by pathogens, necessitating disinfection, and "microbial wastelands." In these resource-poor, dry environments, competition and decay are thought to be important drivers of microbial community composition. However, the relative contributions of these two processes have not been specifically evaluated. To bridge this knowledge gap, we used microcosms to evaluate whether interspecies interactions occur on surfaces. We combined transcriptomics and traditional microbiology techniques to investigate whether competition occurred between two clinically important pathogens, Acinetobacter baumannii and Klebsiella pneumoniae, and a probiotic cleaner containing a consortium of Bacillus species. Probiotic cleaning seeks to take advantage of ecological principles such as competitive exclusion, thus using benign microorganisms to inhibit viable pathogens, but there is limited evidence that competitive exclusion in fact occurs in environments of interest (i.e., indoor surfaces). Our results indicate that competition in this setting has a negligible impact on community composition but may influence the functions expressed by active organisms. Although Bacillus spp. remained viable on surfaces for an extended period of time after application, viable colony forming units (CFUs) of A. baumannii recovered following exposure to a chemical-based detergent with and without Bacillus spp. showed no statistical difference. Similarly, for K. pneumoniae, there were small statistical differences in CFUs between cleaning scenarios with or without Bacillus spp. in the chemical-based detergent. The transcriptome of A. baumannii with and without Bacillus spp. exposure shared a high degree of similarity in overall gene expression, but the transcriptome of K. pneumoniae differed in overall gene expression, including reduced response in genes related to antimicrobial resistance. Together, these results highlight the need to fully understand the underlying biological and ecological mechanisms for community assembly and function on indoor surfaces, as well as having practical implications for cleaning and disinfection strategies for infection prevention.
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Affiliation(s)
- Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Weitao Shuai
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Jack T Sumner
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Anahid A Moghadam
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
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Finn DR, App M, Hertzog L, Tebbe CC. Reconciling concepts of black queen and tragedy of the commons in simulated bulk soil and rhizosphere prokaryote communities. Front Microbiol 2022; 13:969784. [PMID: 36187971 PMCID: PMC9520196 DOI: 10.3389/fmicb.2022.969784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
The Black Queen hypothesis describes the evolutionary strategy to lose costly functions in favour of improving growth efficiency. This results in mutants (cheaters) becoming obligately dependent upon a provider (black queen) to produce a necessary resource. Previous analyses demonstrate black queens and cheaters reach a state of equilibrium in pair-wise systems. However, in complex communities, accumulation of cheaters likely poses a serious burden on shared resources. This should result in a Tragedy of the Commons (ToC), whereby over-utilisation of public resources risks making them growth-limiting. With a collection of differential equations, microbial communities composed of twenty prokaryote ‘species’ either from rhizosphere, characterised by abundant carbon and energy sources, or bulk soil, with limited carbon and energy supply, were simulated. Functional trait groups differed based on combinations of cellulase and amino acid production, growth and resource uptake. Randomly generated communities were thus composed of species that acted as cellulolytic prototrophic black queens, groups that were either cellulolytic or prototrophic, or non-cellulolytic auxotrophic cheaters. Groups could evolve to lose functions over time. Biomass production and biodiversity were tracked in 8,000 Monte Carlo simulations over 500 generations. Bulk soil favoured oligotrophic co-operative communities where biodiversity was positively associated with growth. Rhizosphere favoured copiotrophic cheaters. The most successful functional group across both environments was neither black queens nor cheaters, but those that balanced providing an essential growth-limiting function at a relatively low maintenance cost. Accumulation of loss of function mutants in bulk soil risked resulting in loss of cumulative growth by ToC, while cumulative growth increased in the rhizosphere. In the bulk soil, oligotrophic adaptations assisted species in avoiding extinction. This demonstrated that loss of function by mutation is a successful evolutionary strategy in host-associated and/or resource-rich environments, but poses a risk to communities that must co-operate with each other for mutual co-existence. It was concluded that microbial communities must follow different evolutionary and community assembly strategies in bulk soil versus rhizosphere, with bulk soil communities more dependent on traits that promote co-operative interactions between microbial species.
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Abstract
All organisms rely on complex metabolites such as amino acids, nucleotides, and cofactors for essential metabolic processes. Some microbes synthesize these fundamental ingredients of life de novo, while others rely on uptake to fulfill their metabolic needs. Although certain metabolic processes are inherently "leaky," the mechanisms enabling stable metabolite provisioning among microbes in the absence of a host remain largely unclear. In particular, how can metabolite provisioning among free-living bacteria be maintained under the evolutionary pressure to economize resources? Salvaging, the process of "recycling and reusing," can be a metabolically efficient route to obtain access to required resources. Here, we show experimentally how precursor salvaging in engineered Escherichia coli populations can lead to stable, long-term metabolite provisioning. We find that salvaged cobamides (vitamin B12 and related enzyme cofactors) are readily made available to nonproducing population members, yet salvagers are strongly protected from overexploitation. We also describe a previously unnoted benefit of precursor salvaging, namely, the removal of the nonfunctional, proliferation-inhibiting precursor. As long as compatible precursors are present, any microbe possessing the terminal steps of a biosynthetic process can, in principle, forgo de novo biosynthesis in favor of salvaging. Consequently, precursor salvaging likely represents a potent, yet overlooked, alternative to de novo biosynthesis for the acquisition and provisioning of metabolites in free-living bacterial populations. IMPORTANCE Recycling gives new life to old things. Bacteria have the ability to recycle and reuse complex molecules they encounter in their environment to fulfill their basic metabolic needs in a resource-efficient way. By studying the salvaging (recycling and reusing) of vitamin B12 precursors, we found that metabolite salvaging can benefit others and provide stability to a bacterial community at the same time. Salvagers of vitamin B12 precursors freely share the result of their labor yet cannot be outcompeted by freeloaders, likely because salvagers retain preferential access to the salvaging products. Thus, salvaging may represent an effective, yet overlooked, mechanism of acquiring and provisioning nutrients in microbial populations.
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Brault A, Mbuya B, Labbé S. Sib1, Sib2, and Sib3 proteins are required for ferrichrome-mediated cross-feeding interaction between Schizosaccharomyces pombe and Saccharomyces cerevisiae. Front Microbiol 2022; 13:962853. [PMID: 35928155 PMCID: PMC9344042 DOI: 10.3389/fmicb.2022.962853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
Although Saccharomyces cerevisiae is unable to produce siderophores, this fungal organism can assimilate iron bound to the hydroxamate-type siderophore ferrichrome (Fc) produced and secreted by other microbes. Fc can enter S. cerevisiae cells via Arn1. Unlike S. cerevisiae, Schizosaccharomyces pombe synthesizes and secretes Fc. The sib1+ and sib2+ genes encode, respectively, a Fc synthetase and an ornithine-N5-oxygenase, which are required for Fc production. When both genes were expressed in S. pombe, cross-feeding experiments revealed that S. cerevisiae fet3Δ arn1-4Δ cells expressing Arn1 could grow in the vicinity of S. pombe under low-iron conditions. In contrast, deletion of sib1+ and sib2+ produced a defect in the ability of S. pombe to keep S. cerevisiae cells alive when Fc is used as the sole source of iron. Further analysis identified a gene designated sib3+ that encodes an N5-transacetylase required for Fc production in S. pombe. The sib3Δ mutant strain exhibited a severe growth defect in iron-poor media, and it was unable to promote Fc-dependent growth of S. cerevisiae cells. Microscopic analyses of S. pombe cells expressing a functional Sib3-GFP protein revealed that Sib3 was localized throughout the cells, with a proportion of Sib3 being colocalized with Sib1 and Sib2 within the cytosol. Collectively, these results describe the first example of a one-way cross-feeding interaction, with S. pombe providing Fc that enables S. cerevisiae to grow when Fc is used as the sole source of iron.
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Pita-Grisanti V, Chasser K, Sobol T, Cruz-Monserrate Z. Understanding the Potential and Risk of Bacterial Siderophores in Cancer. Front Oncol 2022; 12:867271. [PMID: 35785195 PMCID: PMC9248441 DOI: 10.3389/fonc.2022.867271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/06/2022] [Indexed: 01/19/2023] Open
Abstract
Siderophores are iron chelating molecules produced by nearly all organisms, most notably by bacteria, to efficiently sequester the limited iron that is available in the environment. Siderophores are an essential component of mammalian iron homeostasis and the ongoing interspecies competition for iron. Bacteria produce a broad repertoire of siderophores with a canonical role in iron chelation and the capacity to perform versatile functions such as interacting with other microbes and the host immune system. Siderophores are a vast area of untapped potential in the field of cancer research because cancer cells demand increased iron concentrations to sustain rapid proliferation. Studies investigating siderophores as therapeutics in cancer generally focused on the role of a few siderophores as iron chelators; however, these studies are limited and some show conflicting results. Moreover, siderophores are biologically conserved, structurally diverse molecules that perform additional functions related to iron chelation. Siderophores also have a role in inflammation due to their iron acquisition and chelation properties. These diverse functions may contribute to both risks and benefits as therapeutic agents in cancer. The potential of siderophore-mediated iron and bacterial modulation to be used in the treatment of cancer warrants further investigation. This review discusses the wide range of bacterial siderophore functions and their utilization in cancer treatment to further expand their functional relevance in cancer detection and treatment.
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Affiliation(s)
- Valentina Pita-Grisanti
- The Ohio State University Interdisciplinary Nutrition Program, The Ohio State University, Columbus, OH, United States
- Division of Gastroenterology, Hepatology, and Nutrition, Division of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- The Comprehensive Cancer Center–Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, United States
| | - Kaylin Chasser
- Division of Gastroenterology, Hepatology, and Nutrition, Division of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- The Comprehensive Cancer Center–Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, United States
| | - Trevor Sobol
- Division of Gastroenterology, Hepatology, and Nutrition, Division of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- The Comprehensive Cancer Center–Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, United States
| | - Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology, and Nutrition, Division of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- The Comprehensive Cancer Center–Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, United States
- *Correspondence: Zobeida Cruz-Monserrate,
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