1
|
Boruta T, Englart G, Foryś M, Pawlikowska W. The repertoire and levels of secondary metabolites in microbial cocultures depend on the inoculation ratio: a case study involving Aspergillus terreus and Streptomyces rimosus. Biotechnol Lett 2024; 46:601-614. [PMID: 38844646 DOI: 10.1007/s10529-024-03500-4] [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: 03/26/2024] [Revised: 05/10/2024] [Accepted: 05/18/2024] [Indexed: 07/03/2024]
Abstract
OBJECTIVE The aim of this study was to determine the influence of the inoculation volume ratio on the production of secondary metabolites in submerged cocultures of Aspergillus terreus and Streptomyces rimosus. RESULTS The shake flask cocultures were initiated by using 23 inoculum variants that included different volumes of A. terreus and S. rimosus precultures. In addition, the axenic controls were propagated in parallel with the cocultures. UPLC‒MS analysis revealed the presence of 15 secondary metabolites, 12 of which were found both in the "A. terreus vs. S. rimosus" cocultures and axenic cultures of either A. terreus or S. rimosus. The production of the remaining 3 molecules was recorded solely in the cocultures. The repertoire and quantity of secondary metabolites were evidently dependent on the inoculation ratio. It was also noted that detecting filamentous structures resembling typical morphological forms of a given species was insufficient to predict the presence of a given metabolite. CONCLUSIONS The modification of the inoculation ratio is an effective strategy for awakening and enhancing the production of secondary metabolites that are not biosynthesized under axenic conditions.
Collapse
Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005, Lodz, Poland.
| | - Grzegorz Englart
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005, Lodz, Poland
| | - Martyna Foryś
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005, Lodz, Poland
| | - Weronika Pawlikowska
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005, Lodz, Poland
| |
Collapse
|
2
|
Kratzl F, Urban M, Pandhal J, Shi M, Meng C, Kleigrewe K, Kremling A, Pflüger-Grau K. Pseudomonas putida as saviour for troubled Synechococcus elongatus in a synthetic co-culture - interaction studies based on a multi-OMICs approach. Commun Biol 2024; 7:452. [PMID: 38609451 PMCID: PMC11014904 DOI: 10.1038/s42003-024-06098-5] [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: 08/20/2023] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
In their natural habitats, microbes rarely exist in isolation; instead, they thrive in consortia, where various interactions occur. In this study, a defined synthetic co-culture of the cyanobacterium S. elongatus cscB, which supplies sucrose to the heterotrophic P. putida cscRABY, is investigated to identify potential interactions. Initial experiments reveal a remarkable growth-promoting effect of the heterotrophic partner on the cyanobacterium, resulting in an up to 80% increase in the growth rate and enhanced photosynthetic capacity. Vice versa, the presence of the cyanobacterium has a neutral effect on P. putida cscRABY, highlighting the resilience of pseudomonads against stress and their potential as co-culture partners. Next, a suitable reference process reinforcing the growth-promoting effect is established in a parallel photobioreactor system, which sets the basis for the analysis of the co-culture at the transcriptome, proteome, and metabolome levels. In addition to several moderate changes, including alterations in the metabolism and stress response in both microbes, this comprehensive multi-OMICs approach strongly hints towards the exchange of further molecules beyond the unidirectional feeding with sucrose. Taken together, these findings provide valuable insights into the complex dynamics between both co-culture partners, indicating multi-level interactions, which can be employed for further streamlining of the co-cultivation system.
Collapse
Affiliation(s)
- Franziska Kratzl
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Marlene Urban
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Mengxun Shi
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas Kremling
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Katharina Pflüger-Grau
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany.
| |
Collapse
|
3
|
Chen MM, Kopittke PM, Zhao FJ, Wang P. Applications and opportunities of click chemistry in plant science. TRENDS IN PLANT SCIENCE 2024; 29:167-178. [PMID: 37612212 DOI: 10.1016/j.tplants.2023.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.
Collapse
Affiliation(s)
- Ming-Ming Chen
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
4
|
Odukoya JO, De Saeger S, De Boevre M, Adegoke GO, Devlieghere F, Croubels S, Antonissen G, Odukoya JO, Njobeh PB. Influence of traditional dehulling on mycotoxin reduction and GC-HRTOF-MS metabolites profile of fermented maize products. Heliyon 2024; 10:e23025. [PMID: 38205294 PMCID: PMC10776939 DOI: 10.1016/j.heliyon.2023.e23025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024] Open
Abstract
Contamination with mycotoxins has been a worldwide food safety concern for several decades, and food processing has been suggested as a potential method to mitigate their presence. In this study, the influence of traditional dehulling (TD) on the mycotoxin reduction and metabolites profile of fermented white maize products obtained via natural and three controlled fermentation methods (involving Lactobacillus fermentum, Lactobacillus plantarum, and their mixed cultures) was examined. Gas chromatography coupled with high resolution time-of-flight mass spectrometry (GC-HRTOF-MS) and ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) were employed. TD brought the levels of fumonisin B1 (FB1) and B2 (FB2) in the white maize below the regulatory limit set by the European Union (EU) for maize consumed by humans. While TD increased the concentration of several mycotoxins in the fermented maize products obtained from other studied fermentation methods, it primarily reduced aflatoxin B1 (AFB1), FB1, deoxynivalenol, and 15-acetyldeoxynivalenol in the L. plantarum-fermented products. By tempering the dehulled maize, a solid-state fermentation process began. This was used in TD to make it easier to remove the pericarp. GC-HR-TOF-MS metabolomics revealed that TD brought about the generation of 12 additional compounds in the dehulled maize though some metabolites in the whole maize were lost/biotransformed. The fermented dehulled maize products obtained from the four studied fermentation procedures contained fewer compounds than the fermented whole maize products. Overall, the analysis showed that all fermented maize (whole and dehulled) produced had varied nutritional metabolites and mycotoxin concentrations below the EU maximum level, except for fermented maize obtained from mixed strains (AFB1 + AFB2 > 4.0 g/kg).
Collapse
Affiliation(s)
- Julianah Olayemi Odukoya
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Gauteng, South Africa
- Centre of Excellence in Mycotoxicology & Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Department of Food Science and Technology, Kwara State University, Malete, PMB 1530, Ilorin, Kwara State, Nigeria
| | - Sarah De Saeger
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Gauteng, South Africa
- Centre of Excellence in Mycotoxicology & Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Marthe De Boevre
- Centre of Excellence in Mycotoxicology & Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Gabriel Olaniran Adegoke
- Department of Food Technology, Faculty of Technology, University of Ibadan, Ibadan, Nigeria
- Department of Biological Sciences, Dominion University, Ibadan, Nigeria
| | - Frank Devlieghere
- Research Unit Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Siska Croubels
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Gunther Antonissen
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Johnson Oluwaseun Odukoya
- Bader College, Queen's University (Canada), Herstmonceux Castle, Hailsham, East Sussex, United Kingdom
| | - Patrick Berka Njobeh
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Gauteng, South Africa
| |
Collapse
|
5
|
Li M, Raza M, Song S, Hou L, Zhang ZF, Gao M, Huang JE, Liu F, Cai L. Application of culturomics in fungal isolation from mangrove sediments. MICROBIOME 2023; 11:272. [PMID: 38082427 PMCID: PMC10712113 DOI: 10.1186/s40168-023-01708-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 10/19/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Fungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them remain unknown to science. The description rate of fungi is very low, mainly due to the inability of most fungi to grow in artificial media, which could not provide a sufficiently similar environment to their natural habitats. Moreover, many species in nature are in a state of low metabolic activity which cannot readily proliferate without proper resuscitation. Previously developed culturomics techniques are mostly designed and applicable for bacteria, with few attempts for fungal isolation because of their significantly larger cell size and hyphal growth properties. RESULTS This study attempted to isolate previously uncultured and rare fungi from mangrove sediments using newly developed fungal enrichment culture method (FECM) and fungal isolation chips (FiChips). Comparison of fungal community composition at different enrichment stages showed that FECM had great influence on fungal community composition, with rare taxa increased significantly, thus improving the isolation efficiency of previously uncultured fungi. Similarly, in situ cultivation using FiChips has a significant advantage in detecting and culturing rare fungi, as compared to the conventional dilution plate method (DPM). In addition, based on morphological comparisons and phylogenetic analyses, we described and proposed 38 new ascomycetous taxa, including three new families, eight new genera, 25 new species, and two new combinations (presented in additional file 1). CONCLUSIONS Our study demonstrated that mangrove sediments harbor a high diversity of fungi, and our new isolation approaches (FECM and FiChips) presented a high efficiency in isolating hitherto uncultured fungi, which is potentially usable for fungal isolation in other similar environments. Video Abstract.
Collapse
Affiliation(s)
- Meng Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mubashar Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Integrated Pest Management On Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Shuang Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingwei Hou
- Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Zhi-Feng Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-En Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
6
|
Santamaría RI, Martínez-Carrasco A, Tormo JR, Martín J, Genilloud O, Reyes F, Díaz M. Interactions of Different Streptomyces Species and Myxococcus xanthus Affect Myxococcus Development and Induce the Production of DK-Xanthenes. Int J Mol Sci 2023; 24:15659. [PMID: 37958645 PMCID: PMC10649082 DOI: 10.3390/ijms242115659] [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: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new signals and molecules produced by one species that affects other species' behavior. In this work, we have studied the effects of the interaction of nine Streptomyces species (S. albidoflavus, S. ambofaciens, S. argillaceus, S. griseus, S. lividans, S. olivaceus, S. parvulus, S. peucetius, and S. rochei) with the predator bacteria Myxococcus xanthus, five of which (S. albidoflavus, S. griseus, S. lividans, S. olivaceus, and S. argillaceus) induce mound formation of M. xanthus on complex media (Casitone Yeast extract (CYE) and Casitone tris (CTT); media on which M. xanthus does not form these aggregates under normal culture conditions. An in-depth study on S. griseus-M. xanthus interactions (the Streptomyces strain producing the strongest effect) has allowed the identification of two siderophores produced by S. griseus, demethylenenocardamine and nocardamine, responsible for this grouping effect over M. xanthus. Experiments using pure commercial nocardamine and different concentrations of FeSO4 show that iron depletion is responsible for the behavior of M. xanthus. Additionally, it was found that molecules, smaller than 3 kDa, produced by S. peucetius can induce the production of DK-xanthenes by M. xanthus.
Collapse
Affiliation(s)
- Ramón I. Santamaría
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| | - Ana Martínez-Carrasco
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| | - José R. Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| |
Collapse
|
7
|
Li X, Xu H, Li Y, Liao S, Liu Y. Exploring Diverse Bioactive Secondary Metabolites from Marine Microorganisms Using Co-Culture Strategy. Molecules 2023; 28:6371. [PMID: 37687200 PMCID: PMC10489945 DOI: 10.3390/molecules28176371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The isolation and identification of an increasing number of secondary metabolites featuring unique skeletons and possessing diverse bioactivities sourced from marine microorganisms have garnered the interest of numerous natural product chemists. There has been a growing emphasis on how to cultivate microorganisms to enhance the chemical diversity of metabolites and avoid the rediscovery of known ones. Given the significance of secondary metabolites as a means of communication among microorganisms, microbial co-culture has been introduced. By mimicking the growth patterns of microbial communities in their natural habitats, the co-culture strategy is anticipated to stimulate biosynthetic gene clusters that remain dormant under traditional laboratory culture conditions, thereby inducing the production of novel secondary metabolites. Different from previous reviews mainly focusing on fermentation conditions or metabolite diversities from marine-derived co-paired strains, this review covers the marine-derived co-culture microorganisms from 2012 to 2022, and turns to a particular discussion highlighting the selection of co-paired strains for marine-derived microorganisms, especially the fermentation methods for their co-cultural apparatus, and the screening approaches for the convenient and rapid detection of novel metabolites, as these are important in the co-culture. Finally, the structural and bioactivity diversities of molecules are also discussed. The challenges and prospects of co-culture are discussed on behave of the views of the authors.
Collapse
Affiliation(s)
- Xiaolin Li
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huayan Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yuyue Li
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengrong Liao
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghong Liu
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| |
Collapse
|
8
|
Boruta T. Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview. Comput Struct Biotechnol J 2023; 21:4021-4029. [PMID: 37649711 PMCID: PMC10462793 DOI: 10.1016/j.csbj.2023.08.011] [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: 05/14/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
Co-cultivation is an effective method of inducing the production of specialized metabolites (SMs) in microbial strains. By mimicking the ecological interactions that take place in natural environment, this approach enables to trigger the biosynthesis of molecules which are not formed under monoculture conditions. Importantly, microbial co-cultivation may lead to the discovery of novel chemical entities of pharmaceutical interest. The experimental efforts aimed at the induction of SMs are greatly facilitated by computational techniques. The aim of this overview is to highlight the relevance of computational methods for the investigation of SM induction via microbial co-cultivation. The concepts related to the induction of SMs in microbial co-cultures are briefly introduced by addressing four areas associated with the SM induction workflows, namely the detection of SMs formed exclusively under co-culture conditions, the annotation of induced SMs, the identification of SM producer strains, and the optimization of fermentation conditions. The computational infrastructure associated with these areas, including the tools of multivariate data analysis, molecular networking, genome mining and mathematical optimization, is discussed in relation to the experimental results described in recent literature. The perspective on the future developments in the field, mainly in relation to the microbiome-related research, is also provided.
Collapse
Affiliation(s)
- Tomasz Boruta
- Lodz University of Technology, Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, ul. Wólczańska 213, 93-005 Łódź, Poland
| |
Collapse
|
9
|
Luu GT, Little JC, Pierce EC, Morin M, Ertekin CA, Wolfe BE, Baars O, Dutton RJ, Sanchez LM. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms. Analyst 2023; 148:3002-3018. [PMID: 37259951 PMCID: PMC10330857 DOI: 10.1039/d3an00408b] [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] [Indexed: 06/02/2023]
Abstract
Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.
Collapse
Affiliation(s)
- Gordon T Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| | - Jessica C Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, 60612, USA
| | - Emily C Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
| | - Manon Morin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
| | - Celine A Ertekin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, USA
- Tufts University Sensory and Science Center, Medford, Massachusetts, 02155, USA
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27607, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, 92093, USA
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| |
Collapse
|
10
|
Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [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: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
Collapse
Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | | |
Collapse
|
11
|
Luu GT, Little JC, Pierce EC, Morin M, Ertekin CA, Wolfe BE, Baars O, Dutton RJ, Sanchez LM. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532449. [PMID: 36993360 PMCID: PMC10054941 DOI: 10.1101/2023.03.13.532449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecule mediated BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis spp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and their role in complex communities should continue to be a priority.
Collapse
Affiliation(s)
- Gordon T. Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| | - Jessica C. Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, 60612
| | - Emily C. Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
| | - Manon Morin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
| | - Celine A. Ertekin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, 02155
- Tufts University Sensory and Science Center, Medford Massachusetts, 02155
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27607
| | - Rachel J. Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, 92093
| | - Laura M. Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| |
Collapse
|
12
|
Microbiome engineering for bioremediation of emerging pollutants. Bioprocess Biosyst Eng 2023; 46:323-339. [PMID: 36029349 DOI: 10.1007/s00449-022-02777-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.
Collapse
|
13
|
Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
Collapse
|
14
|
Zhang S, Sun C, Liu X, Liang Y. Enriching the endophytic bacterial microbiota of Ginkgo roots. Front Microbiol 2023; 14:1163488. [PMID: 37138610 PMCID: PMC10150934 DOI: 10.3389/fmicb.2023.1163488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 05/05/2023] Open
Abstract
Bacterial endophytes of Ginkgo roots take part in the secondary metabolic processes of the fossil tree and contribute to plant growth, nutrient uptake, and systemic resistance. However, the diversity of bacterial endophytes in Ginkgo roots is highly underestimated due to the lack of successful isolates and enrichment collections. The resulting culture collection contains 455 unique bacterial isolates representing 8 classes, 20 orders, 42 families, and 67 genera from five phyla: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Deinococcus-Thermus, using simply modified media (a mixed medium without any additional carbon sources [MM)] and two other mixed media with separately added starch [GM] and supplemented glucose [MSM]). A series of plant growth-promoting endophytes had multiple representatives within the culture collection. Moreover, we investigated the impact of refilling carbon sources on enrichment outcomes. Approximately 77% of the natural community of root-associated endophytes were predicted to have successfully cultivated the possibility based on a comparison of the 16S rRNA gene sequences between the enrichment collections and the Ginkgo root endophyte community. The rare or recalcitrant taxa in the root endosphere were mainly associated with Actinobacteria, Alphaproteobacteria, Blastocatellia, and Ktedonobacteria. By contrast, more operational taxonomic units (OTUs) (0.6% in the root endosphere) became significantly enriched in MM than in GM and MSM. We further found that the bacterial taxa of the root endosphere had strong metabolisms with the representative of aerobic chemoheterotrophy, while the functions of the enrichment collections were represented by the sulfur metabolism. In addition, the co-occurrence network analysis suggested that the substrate supplement could significantly impact bacterial interactions within the enrichment collections. Our results support the fact that it is better to use the enrichment to assess the cultivable potential and the interspecies interaction as well as to increase the detection/isolation of certain bacterial taxa. Taken together, this study will deepen our knowledge of the indoor endophytic culture and provide important insights into the substrate-driven enrichment.
Collapse
Affiliation(s)
- Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Chongran Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
- *Correspondence: Yili Liang
| |
Collapse
|
15
|
Exploring Potential of Aspergillus sclerotiorum: Secondary Metabolites and Biotechnological Relevance. Mycol Prog 2023. [DOI: 10.1007/s11557-022-01856-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
16
|
Xia M, Zhang X, Xiao Y, Sheng Q, Tu L, Chen F, Yan Y, Zheng Y, Wang M. Interaction of acetic acid bacteria and lactic acid bacteria in multispecies solid-state fermentation of traditional Chinese cereal vinegar. Front Microbiol 2022; 13:964855. [PMID: 36246224 PMCID: PMC9557190 DOI: 10.3389/fmicb.2022.964855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The microbial community plays an important role on the solid-state fermentation (SSF) of Chinese cereal vinegar, where acetic acid bacteria (AAB) and lactic acid bacteria (LAB) are the dominant bacteria. In this study, the top-down (in situ) and bottom-up (in vitro) approaches were employed to reveal the interaction of AAB and LAB in SSF of Shanxi aged vinegar (SAV). The results of high-throughput sequencing indicates that Acetobacter pasteurianus and Lactobacillus helveticus are the predominant species of AAB and LAB, respectively, and they showed negative interrelationship during the fermentation. A. pasteurianus CGMCC 3089 and L. helveticus CGMCC 12062, both of which were isolated from fermentation of SAV, showed no nutritional competition when they were co-cultured in vitro. However, the growth and metabolism of L. helveticus CGMCC 12062 were inhibited during SSF due to the presence of A. pasteurianus CGMCC 3089, indicating an amensalism phenomenon between these two species. The transcriptomic results shows that there are 831 differentially expressed genes (|log2 (Fold Change)| > 1 and, p ≤ 0.05) in L. helveticus CGMCC 12062 under co-culture condition comparing to its mono-culture, which are mainly classified into Gene Ontology classification of molecular function, biological process, and cell composition. Of those 831 differentially expressed genes, 202 genes are up-regulated and 629 genes are down-regulated. The down-regulated genes were enriched in KEGG pathways of sugar, amino acid, purine, and pyrimidine metabolism. The transcriptomic results for A. pasteurianus CGMCC 3089 under co-culture condition reveals 529 differentially expressed genes with 393 up-regulated and 136 down-regulated, and the genes within KEGG pathways of sugar, amino acid, purine, and pyrimidine metabolism are up-regulated. Results indicate an amensalism relationship in co-culture of A. pasteurianus and L. helveticus. Therefore, this work gives a whole insight on the interaction between the predominant species in SSF of cereal vinegar from nutrient utilization, endogenous factors inhibition and the regulation of gene transcription.
Collapse
Affiliation(s)
- Menglei Xia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaofeng Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yun Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Qing Sheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Linna Tu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
| | - Yufeng Yan
- Shanxi Zilin Vinegar Industry Co., Ltd., Shanxi Province Key Laboratory of Vinegar Fermentation Science and Engineering, Taiyuan, China
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China,*Correspondence: Yu Zheng, Min Wang,
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China,*Correspondence: Yu Zheng, Min Wang,
| |
Collapse
|
17
|
Kuhn T, Buffi M, Bindschedler S, Chain PS, Gonzalez D, Stanley CE, Wick LY, Junier P, Richter XYL. Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces. BMC Biol 2022; 20:203. [PMID: 36104696 PMCID: PMC9476585 DOI: 10.1186/s12915-022-01406-z] [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: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/12/2022] Open
Abstract
Background To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements. Results We designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as “hitchhikers” when co-inoculated with motile cells. Conclusions The 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01406-z.
Collapse
|
18
|
Pope E, Cartmell C, Haltli B, Ahmadi A, Kerr RG. Microencapsulation and in situ incubation methodology for the cultivation of marine bacteria. Front Microbiol 2022; 13:958660. [PMID: 36071955 PMCID: PMC9441948 DOI: 10.3389/fmicb.2022.958660] [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: 05/31/2022] [Accepted: 08/05/2022] [Indexed: 11/28/2022] Open
Abstract
Environmental microorganisms are important sources of biotechnology innovations; however, the discovery process is hampered by the inability to culture the overwhelming majority of microbes. To drive the discovery of new biotechnology products from previously unculturable microbes, several methods such as modification of media composition, incubation conditions, single-cell isolation, and in situ incubation, have been employed to improve microbial recovery from environmental samples. To improve microbial recovery, we examined the effect of microencapsulation followed by in situ incubation on the abundance, viability, and diversity of bacteria recovered from marine sediment. Bacteria from marine sediment samples were resuspended or encapsulated in agarose and half of each sample was directly plated on agar and the other half inserted into modified Slyde-A-Lyzer™ dialysis cassettes. The cassettes were incubated in their natural environment (in situ) for a week, after which they were retrieved, and the contents plated. Colony counts indicated that bacterial abundance increased during in situ incubation and that cell density was significantly higher in cassettes containing non-encapsulated sediment bacteria. Assessment of viability indicated that a higher proportion of cells in encapsulated samples were viable at the end of the incubation period, suggesting that agarose encapsulation promoted higher cell viability during in situ incubation. One hundred and 46 isolates were purified from the study (32–38 from each treatment) to assess the effect of the four treatments on cultivable bacterial diversity. In total, 58 operational taxonomic units (OTUs) were identified using a 99% 16S rRNA gene sequence identity threshold. The results indicated that encapsulation recovered greater bacterial diversity from the sediment than simple resuspension (41 vs. 31 OTUs, respectively). While the cultivable bacterial diversity decreased by 43%–48% after in situ incubation, difficult-to-culture (Verrucomicrobia) and obligate marine (Pseudoalteromonas) taxa were only recovered after in situ incubation. These results suggest that agarose encapsulation coupled with in situ incubation in commercially available, low-cost, diffusion chambers facilitates the cultivation and improved recovery of bacteria from marine sediments. This study provides another tool that microbiologists can use to access microbial dark matter for environmental, biotechnology bioprospecting.
Collapse
Affiliation(s)
- Emily Pope
- Department of Biomedical Science, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Christopher Cartmell
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Bradley Haltli
- Department of Biomedical Science, University of Prince Edward Island, Charlottetown, PE, Canada
- Nautilus Biosciences Croda, Charlottetown, PE, Canada
| | - Ali Ahmadi
- Department of Biomedical Science, University of Prince Edward Island, Charlottetown, PE, Canada
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Charlottetown, PE, Canada
- Department of Mechanical Engineering, École de technologie supérieure (ÉTS), Montreal, QC, Canada
| | - Russell G. Kerr
- Department of Biomedical Science, University of Prince Edward Island, Charlottetown, PE, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
- Nautilus Biosciences Croda, Charlottetown, PE, Canada
- *Correspondence: Russell G. Kerr,
| |
Collapse
|
19
|
Knowles SL, Raja HA, Roberts CD, Oberlies NH. Fungal-fungal co-culture: a primer for generating chemical diversity. Nat Prod Rep 2022; 39:1557-1573. [PMID: 35137758 PMCID: PMC9384855 DOI: 10.1039/d1np00070e] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 01/25/2023]
Abstract
Covering: 2002 to 2020In their natural environment, fungi must compete for resources. It has been hypothesized that this competition likely induces the biosynthesis of secondary metabolites for defence. In a quest to discover new chemical diversity from fungal cultures, a growing trend has been to recapitulate this competitive environment in the laboratory, essentially growing fungi in co-culture. This review covers fungal-fungal co-culture studies beginning with the first literature report in 2002. Since then, there has been a growing number of new secondary metabolites reported as a result of fungal co-culture studies. Specifically, this review discusses and provides insights into (1) rationale for pairing fungal strains, (2) ways to grow fungi for co-culture, (3) different approaches to screening fungal co-cultures for chemical diversity, (4) determining the secondary metabolite-producing strain, and (5) final thoughts regarding the fungal-fungal co-culture approach. Our goal is to provide a set of practical strategies for fungal co-culture studies to generate unique chemical diversity that the natural products research community can utilize.
Collapse
Affiliation(s)
- Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Christopher D Roberts
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| |
Collapse
|
20
|
The relevance of hormesis at higher levels of biological organization: Hormesis in microorganisms. CURRENT OPINION IN TOXICOLOGY 2022. [DOI: 10.1016/j.cotox.2021.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
21
|
Hussain MH, Mohsin MZ, Zaman WQ, Yu J, Zhao X, Wei Y, Zhuang Y, Mohsin A, Guo M. Multiscale engineering of microbial cell factories: A step forward towards sustainable natural products industry. Synth Syst Biotechnol 2022; 7:586-601. [PMID: 35155840 PMCID: PMC8816652 DOI: 10.1016/j.synbio.2021.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 01/09/2023] Open
Abstract
Microbial cell factories (bacteria and fungi) are the leading producers of beneficial natural products such as lycopene, carotene, herbal medicine, and biodiesel etc. These microorganisms are considered efficient due to their effective bioprocessing strategy (monoculture- and consortial-based approach) under distinct processing conditions. Meanwhile, the advancement in genetic and process optimization techniques leads to enhanced biosynthesis of natural products that are known functional ingredients with numerous applications in the food, cosmetic and medical industries. Natural consortia and monoculture thrive in nature in a small proportion, such as wastewater, food products, and soils. In similitude to natural consortia, it is possible to engineer artificial microbial consortia and program their behaviours via synthetic biology tools. Therefore, this review summarizes the optimization of genetic and physicochemical parameters of the microbial system for improved production of natural products. Also, this review presents a brief history of natural consortium and describes the functional properties of monocultures. This review focuses on synthetic biology tools that enable new approaches to design synthetic consortia; and highlights the syntropic interactions that determine the performance and stability of synthetic consortia. In particular, the effect of processing conditions and advanced genetic techniques to improve the productibility of both monoculture and consortial based systems have been greatly emphasized. In this context, possible strategies are also discussed to give an insight into microbial engineering for improved production of natural products in the future. In summary, it is concluded that the coupling of genomic modifications with optimum physicochemical factors would be promising for producing a robust microbial cell factory that shall contribute to the increased production of natural products.
Collapse
Affiliation(s)
- Muhammad Hammad Hussain
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Muhammad Zubair Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Waqas Qamar Zaman
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Xueli Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yanlong Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, PR China.
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. P.O. box 329#, East China University of Science and Technology, 130 Meilong Rd., Shanghai, 200237, PR China.
| |
Collapse
|
22
|
A metanalysis approach to defining the culturable core of plant endophytic bacterial communities. Appl Environ Microbiol 2022; 88:e0253721. [PMID: 35138928 PMCID: PMC8939329 DOI: 10.1128/aem.02537-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in the last decades. On the other side, a synopsis of culturable plant endophytic bacteria is still lacking in the literature. However, culturability is necessary for biotechnology innovations related to sustainable agriculture, such as biofertilizer and biostimulant agents' development. In this review, 148 scientific papers were analyzed to establish a large dataset of cultured endophytic bacteria, reported at the genus level, inhabiting different compartments of wild and farmed plants, sampled around the world from different soil types and isolated using various growth media. To the best of our knowledge, this work provides the first overview of the current repertoire of cultured plant endophytic bacteria. Results indicate the presence of a recurrent set of culturable bacterial genera regardless of factors known to influence the plant bacterial community composition and the growth media used for the bacterial isolation. Moreover, a wide variety of bacterial genera that are currently rarely isolated from the plant endosphere was identified, demonstrating that culturomics can catch previously uncultured bacteria from the plant microbiome, widening the panorama of strains exploitable to support plant holobiont health and production.
Collapse
|
23
|
Sarkar S, Ward K, Kamke A, Ran Q, Feehan B, Richie T, Reese N, Lee STM. Perspective: Simple State Communities to Study Microbial Interactions: Examples and Future Directions. Front Microbiol 2022; 13:801864. [PMID: 35154052 PMCID: PMC8828649 DOI: 10.3389/fmicb.2022.801864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/04/2022] [Indexed: 01/04/2023] Open
Abstract
Microbial interactions in natural environments are intricately complex. High numbers and rich diversity of microorganisms, along with compositional heterogeneities complicate the cause. It is essential to simplify these complex communities to understand the microbial interactions. We proposed a concept of "simple state community," which represents a subset of microbes and/or microbial functions of the original population that is necessary to build a stable community. By combining microbial culturing and high-throughput sequencing, we can better understand microbe-microbe and microbe-host interactions. To support our proposed model, we used carbon-based and nitrogen-based media to capture the simple state communities. We used 16S rRNA amplicon sequencing and assigned taxonomic identity to the bacterial populations before and after simple state communities. We showed that simple state communities were a subset of the original microbial communities at both phyla and genera level. We further used shotgun metagenomics to gain insights into the functional potential of the assembled simple state communities. Our proposed model supported the goal of simplifying the complex communities across diverse systems to provide opportunity to facilitate comprehension of both the structure and function of the subset communities. Further applications of the concept include the high-throughput screening of simple state communities using the BIOLOG® system and continuous culturing (Chemostat). This concept has the potential to test diverse experimental hypotheses in simplified microbial communities, and further extend that knowledge to answer the overarching questions at a more holistic level.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, KS, United States
| |
Collapse
|
24
|
Extremophilic Fungi from Marine Environments: Underexplored Sources of Antitumor, Anti-Infective and Other Biologically Active Agents. Mar Drugs 2022; 20:md20010062. [PMID: 35049917 PMCID: PMC8781577 DOI: 10.3390/md20010062] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
Marine environments are underexplored terrains containing fungi that produce a diversity of natural products given unique environmental pressures and nutrients. While bacteria are commonly the most studied microorganism for natural products in the marine world, marine fungi are also abundant but remain an untapped source of bioactive metabolites. Given that their terrestrial counterparts have been a source of many blockbuster antitumor agents and anti-infectives, including camptothecin, the penicillins, and cyclosporin A, marine fungi also have the potential to produce new chemical scaffolds as leads to potential drugs. Fungi are more phylogenetically diverse than bacteria and have larger genomes that contain many silent biosynthetic gene clusters involved in making bioactive compounds. However, less than 5% of all known fungi have been cultivated under standard laboratory conditions. While the number of reported natural products from marine fungi is steadily increasing, their number is still significantly lower compared to those reported from their bacterial counterparts. Herein, we discuss many varied cytotoxic and anti-infective fungal metabolites isolated from extreme marine environments, including symbiotic associations as well as extreme pressures, temperatures, salinity, and light. We also discuss cultivation strategies that can be used to produce new bioactive metabolites or increase their production. This review presents a large number of reported structures though, at times, only a few of a large number of related structures are shown.
Collapse
|
25
|
Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
26
|
Quantitative Morphological Analysis of Filamentous Microorganisms in Cocultures and Monocultures: Aspergillus terreus and Streptomyces rimosus Warfare in Bioreactors. Biomolecules 2021; 11:biom11111740. [PMID: 34827738 PMCID: PMC8615777 DOI: 10.3390/biom11111740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to quantitatively characterize the morphology of the filamentous microorganisms Aspergillus terreus ATCC 20542 and Streptomyces rimosus ATCC 10970, cocultivated in stirred tank bioreactors, and to characterize their mutual influence with the use of quantitative image analysis. Three distinct coculture initiation strategies were applied: preculture versus preculture, spores versus spores and preculture versus preculture with time delay for one of the species. Bioreactor cocultures were accompanied by parallel monoculture controls. The results recorded for the mono- and cocultures were compared in order to investigate the effect of cocultivation on the morphological evolution of A. terreus and S. rimosus. Morphology-related observations were also confronted with the analysis of secondary metabolism. The morphology of the two studied filamentous species strictly depended on the applied coculture initiation strategy. In the cocultures initiated by the simultaneous inoculation, S. rimosus gained domination or advance over A. terreus. The latter microorganism dominated only in these experiments in which S. rimosus was introduced with a delay.
Collapse
|
27
|
Kehe J, Ortiz A, Kulesa A, Gore J, Blainey PC, Friedman J. Positive interactions are common among culturable bacteria. SCIENCE ADVANCES 2021; 7:eabi7159. [PMID: 34739314 PMCID: PMC8570599 DOI: 10.1126/sciadv.abi7159] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/16/2021] [Indexed: 05/19/2023]
Abstract
Interspecies interactions shape the structure and function of microbial communities. In particular, positive, growth-promoting interactions can substantially affect the diversity and productivity of natural and engineered communities. However, the prevalence of positive interactions and the conditions in which they occur are not well understood. To address this knowledge gap, we used kChip, an ultrahigh-throughput coculture platform, to measure 180,408 interactions among 20 soil bacteria across 40 carbon environments. We find that positive interactions, often described to be rare, occur commonly and primarily as parasitisms between strains that differ in their carbon consumption profiles. Notably, nongrowing strains are almost always promoted by strongly growing strains (85%), suggesting a simple positive interaction–mediated approach for cultivation, microbiome engineering, and microbial consortium design.
Collapse
Affiliation(s)
- Jared Kehe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anthony Ortiz
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anthony Kulesa
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul C. Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
28
|
Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways. Microbiol Spectr 2021; 9:e0089821. [PMID: 34523946 PMCID: PMC8557879 DOI: 10.1128/spectrum.00898-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Fungal secondary metabolites are widely used as therapeutics and are vital components of drug discovery programs. A major challenge hindering discovery of novel secondary metabolites is that the underlying pathways involved in their biosynthesis are transcriptionally silent under typical laboratory growth conditions, making it difficult to identify the transcriptional networks that they are embedded in. Furthermore, while the genes participating in secondary metabolic pathways are typically found in contiguous clusters on the genome, known as biosynthetic gene clusters (BGCs), this is not always the case, especially for global and pathway-specific regulators of pathways’ activities. To address these challenges, we used 283 genome-wide gene expression data sets of the ascomycete cell factory Aspergillus niger generated during growth under 155 different conditions to construct two gene coexpression networks based on Spearman’s correlation coefficients (SCCs) and on mutual rank-transformed Pearson’s correlation coefficients (MR-PCCs). By mining these networks, we predicted six transcription factors, named MjkA to MjkF, to regulate secondary metabolism in A. niger. Overexpression of each transcription factor using the Tet-On cassette modulated the production of multiple secondary metabolites. We found that the SCC and MR-PCC approaches complemented each other, enabling the delineation of putative global (SCC) and pathway-specific (MR-PCC) transcription factors. These results highlight the potential of coexpression network approaches to identify and activate fungal secondary metabolic pathways and their products. More broadly, we argue that drug discovery programs in fungi should move beyond the BGC paradigm and focus on understanding the global regulatory networks in which secondary metabolic pathways are embedded. IMPORTANCE There is an urgent need for novel bioactive molecules in both agriculture and medicine. The genomes of fungi are thought to contain vast numbers of metabolic pathways involved in the biosynthesis of secondary metabolites with diverse bioactivities. Because these metabolites are biosynthesized only under specific conditions, the vast majority of the fungal pharmacopeia awaits discovery. To discover the genetic networks that regulate the activity of secondary metabolites, we examined the genome-wide profiles of gene activity of the cell factory Aspergillus niger across hundreds of conditions. By constructing global networks that link genes with similar activities across conditions, we identified six putative global and pathway-specific regulators of secondary metabolite biosynthesis. Our study shows that elucidating the behavior of the genetic networks of fungi under diverse conditions harbors enormous promise for understanding fungal secondary metabolism, which ultimately may lead to novel drug candidates.
Collapse
|
29
|
Boruta T, Ścigaczewska A, Bizukojć M. "Microbial Wars" in a Stirred Tank Bioreactor: Investigating the Co-Cultures of Streptomyces rimosus and Aspergillus terreus, Filamentous Microorganisms Equipped With a Rich Arsenal of Secondary Metabolites. Front Bioeng Biotechnol 2021; 9:713639. [PMID: 34660550 PMCID: PMC8511322 DOI: 10.3389/fbioe.2021.713639] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial co-cultivation is an approach frequently used for the induction of secondary metabolic pathways and the discovery of novel molecules. The studies of this kind are typically focused on the chemical and ecological aspects of inter-species interactions rather than on the bioprocess characterization. In the present work, the co-cultivation of two textbook producers of secondary metabolites, namely Aspergillus terreus (a filamentous fungus used for the manufacturing of lovastatin, a cholesterol-lowering drug) and Streptomyces rimosus (an actinobacterial producer of an antibiotic oxytetracycline) in a 5.5-L stirred tank bioreactor was investigated in the context of metabolic production, utilization of carbon substrates and dissolved oxygen levels. The cultivation runs differed in terms of the applied co-culture initiation strategy and the composition of growth medium. All the experiments were performed in three bioreactors running in parallel (corresponding to a co-culture and two respective monoculture controls). The analysis based upon mass spectrometry and liquid chromatography revealed a broad spectrum of more than 40 secondary metabolites, including the molecules identified as the oxidized derivatives of rimocidin and milbemycin that were observed solely under the conditions of co-cultivation. S. rimosus showed a tendency to dominate over A. terreus, except for the runs where S. rimosus was inoculated into the already developed bioreactor cultures of A. terreus. Despite being dominated, the less aggressive strain still had an observable influence on the production of secondary metabolites and the utilization of substrates in co-culture. The monitoring of dissolved oxygen levels was evaluated as a fast approach of identifying the dominant microorganism during the co-cultivation process.
Collapse
Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Anna Ścigaczewska
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Marcin Bizukojć
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| |
Collapse
|
30
|
Gupta G, Ndiaye A, Filteau M. Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions. Front Microbiol 2021; 12:700752. [PMID: 34646243 PMCID: PMC8503676 DOI: 10.3389/fmicb.2021.700752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022] Open
Abstract
Microorganisms are a fundamental part of virtually every ecosystem on earth. Understanding how collectively they interact, assemble, and function as communities has become a prevalent topic both in fundamental and applied research. Owing to multiple advances in technology, answering questions at the microbial system or network level is now within our grasp. To map and characterize microbial interaction networks, numerous computational approaches have been developed; however, experimentally validating microbial interactions is no trivial task. Microbial interactions are context-dependent, and their complex nature can result in an array of outcomes, not only in terms of fitness or growth, but also in other relevant functions and phenotypes. Thus, approaches to experimentally capture microbial interactions involve a combination of culture methods and phenotypic or functional characterization methods. Here, through our perspective of food microbiologists, we highlight the breadth of innovative and promising experimental strategies for their potential to capture the different dimensions of microbial interactions and their high-throughput application to answer the question; are microbial interaction patterns or network architecture similar along different contextual scales? We further discuss the experimental approaches used to build various types of networks and study their architecture in the context of cell biology and how they translate at the level of microbial ecosystem.
Collapse
Affiliation(s)
- Gunjan Gupta
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Amadou Ndiaye
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Marie Filteau
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| |
Collapse
|
31
|
Rämä T, Quandt CA. Improving Fungal Cultivability for Natural Products Discovery. Front Microbiol 2021; 12:706044. [PMID: 34603232 PMCID: PMC8481835 DOI: 10.3389/fmicb.2021.706044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.
Collapse
Affiliation(s)
- Teppo Rämä
- Marbio, Norwegian College of Fishery Science, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| |
Collapse
|
32
|
Hu R, Zhao H, Xu X, Wang Z, Yu K, Shu L, Yan Q, Wu B, Mo C, He Z, Wang C. Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities. ENVIRONMENT INTERNATIONAL 2021; 154:106560. [PMID: 33866059 DOI: 10.1016/j.envint.2021.106560] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/15/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.
Collapse
Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Haiming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cehui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
| |
Collapse
|
33
|
Mencher A, Morales P, Tronchoni J, Gonzalez R. Mechanisms Involved in Interspecific Communication between Wine Yeasts. Foods 2021; 10:foods10081734. [PMID: 34441512 PMCID: PMC8394882 DOI: 10.3390/foods10081734] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022] Open
Abstract
In parallel with the development of non-Saccharomyces starter cultures in oenology, a growing interest has developed around the interactions between the microorganisms involved in the transformation of grape must into wine. Nowadays, it is widely accepted that the outcome of a fermentation process involving two or more inoculated yeast species will be different from the weighted average of the corresponding individual cultures. Interspecific interactions between wine yeasts take place on several levels, including interference competition, exploitation competition, exchange of metabolic intermediates, and others. Some interactions could be a simple consequence of each yeast running its own metabolic programme in a context where metabolic intermediates and end products from other yeasts are present. However, there are clear indications, in some cases, of specific recognition between interacting yeasts. In this article we discuss the mechanisms that may be involved in the communication between wine yeasts during alcoholic fermentation.
Collapse
Affiliation(s)
- Ana Mencher
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera LO-20, Salida 13, 26007 Logroño, Spain; (A.M.); (P.M.)
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera LO-20, Salida 13, 26007 Logroño, Spain; (A.M.); (P.M.)
| | - Jordi Tronchoni
- Faculty of Health Sciences, Valencian International University (VIU), C/Pintor Sorolla 21, 46002 Valencia, Spain;
| | - Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera LO-20, Salida 13, 26007 Logroño, Spain; (A.M.); (P.M.)
- Correspondence: ; Tel.: +34-941-894-980
| |
Collapse
|
34
|
Something old, something new: challenges and developments in Aspergillus niger biotechnology. Essays Biochem 2021; 65:213-224. [PMID: 33955461 PMCID: PMC8314004 DOI: 10.1042/ebc20200139] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
The filamentous ascomycete fungus Aspergillus niger is a prolific secretor of organic acids, proteins, enzymes and secondary metabolites. Throughout the last century, biotechnologists have developed A. niger into a multipurpose cell factory with a product portfolio worth billions of dollars each year. Recent technological advances, from genome editing to other molecular and omics tools, promise to revolutionize our understanding of A. niger biology, ultimately to increase efficiency of existing industrial applications or even to make entirely new products. However, various challenges to this biotechnological vision, many several decades old, still limit applications of this fungus. These include an inability to tightly control A. niger growth for optimal productivity, and a lack of high-throughput cultivation conditions for mutant screening. In this mini-review, we summarize the current state-of-the-art for A. niger biotechnology with special focus on organic acids (citric acid, malic acid, gluconic acid and itaconic acid), secreted proteins and secondary metabolites, and discuss how new technological developments can be applied to comprehensively address a variety of old and persistent challenges.
Collapse
|
35
|
Turning Inside Out: Filamentous Fungal Secretion and Its Applications in Biotechnology, Agriculture, and the Clinic. J Fungi (Basel) 2021; 7:jof7070535. [PMID: 34356914 PMCID: PMC8307877 DOI: 10.3390/jof7070535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/25/2021] [Indexed: 12/15/2022] Open
Abstract
Filamentous fungi are found in virtually every marine and terrestrial habitat. Vital to this success is their ability to secrete a diverse range of molecules, including hydrolytic enzymes, organic acids, and small molecular weight natural products. Industrial biotechnologists have successfully harnessed and re-engineered the secretory capacity of dozens of filamentous fungal species to make a diverse portfolio of useful molecules. The study of fungal secretion outside fermenters, e.g., during host infection or in mixed microbial communities, has also led to the development of novel and emerging technological breakthroughs, ranging from ultra-sensitive biosensors of fungal disease to the efficient bioremediation of polluted environments. In this review, we consider filamentous fungal secretion across multiple disciplinary boundaries (e.g., white, green, and red biotechnology) and product classes (protein, organic acid, and secondary metabolite). We summarize the mechanistic understanding for how various molecules are secreted and present numerous applications for extracellular products. Additionally, we discuss how the control of secretory pathways and the polar growth of filamentous hyphae can be utilized in diverse settings, including industrial biotechnology, agriculture, and the clinic.
Collapse
|
36
|
|
37
|
Hu B, Xu P, Ma L, Chen D, Wang J, Dai X, Huang L, Du W. One cell at a time: droplet-based microbial cultivation, screening and sequencing. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:169-188. [PMID: 37073344 PMCID: PMC10077293 DOI: 10.1007/s42995-020-00082-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.
Collapse
Affiliation(s)
- Beiyu Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xu
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 USA
| | - Liang Ma
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
| | - Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049 China
| |
Collapse
|
38
|
Buijs Y, Zhang SD, Jørgensen KM, Isbrandt T, Larsen TO, Gram L. Enhancement of antibiotic production by co-cultivation of two antibiotic producing marine Vibrionaceae strains. FEMS Microbiol Ecol 2021; 97:6164864. [PMID: 33693627 DOI: 10.1093/femsec/fiab041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/05/2021] [Indexed: 01/07/2023] Open
Abstract
Deciphering the cues that stimulate microorganisms to produce their full secondary metabolic potential promises to speed up the discovery of novel drugs. Ecology-relevant conditions, including carbon-source(s) and microbial interactions, are important effectors of secondary metabolite production. Vice versa secondary metabolites are important mediators in microbial interactions, although their exact natural functions are not always completely understood. In this study, we investigated the effects of microbial interactions and in-culture produced antibiotics on the production of secondary metabolites by Vibrio coralliilyticus and Photobacterium galatheae, two co-occurring marine Vibrionaceae. In co-culture, production of andrimid by V. coralliilyticus and holomycin by P. galatheae, were, compared to monocultures, increased 4.3 and 2.7 fold, respectively. Co-cultures with the antibiotic deficient mutant strains (andrimid- and holomycin-) did not reveal a significant role for the competitor's antibiotic as stimulator of own secondary metabolite production. Furthermore, we observed that V. coralliilyticus detoxifies holomycin by sulphur-methylation. Results presented here indicate that ecological competition in Vibrionaceae is mediated by, and a cue for, antibiotic secondary metabolite production.
Collapse
Affiliation(s)
- Yannick Buijs
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Karen Marie Jørgensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Thomas Isbrandt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| |
Collapse
|
39
|
Junier P, Cailleau G, Palmieri I, Vallotton C, Trautschold OC, Junier T, Paul C, Bregnard D, Palmieri F, Estoppey A, Buffi M, Lohberger A, Robinson A, Kelliher JM, Davenport K, House GL, Morales D, Gallegos-Graves LV, Dichosa AEK, Lupini S, Nguyen HN, Young JD, Rodrigues DF, Parra-Vasquez ANG, Bindschedler S, Chain PSG. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS Microbiol Ecol 2021; 97:6095729. [PMID: 33440006 PMCID: PMC7878174 DOI: 10.1093/femsec/fiab003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria–fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments.
Collapse
Affiliation(s)
- Pilar Junier
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Ilona Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Celine Vallotton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Olivia C Trautschold
- Materials Science and Technology, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, CH, 1015, Lausanne, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Danae Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aaron Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Julia M Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Karen Davenport
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Demosthenes Morales
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | | | - Armand E K Dichosa
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Simone Lupini
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Hang N Nguyen
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212, USA
| | - Debora F Rodrigues
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | | | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
| |
Collapse
|
40
|
Liu F, Giometto A, Wu M. Microfluidic and mathematical modeling of aquatic microbial communities. Anal Bioanal Chem 2021; 413:2331-2344. [PMID: 33244684 PMCID: PMC7990691 DOI: 10.1007/s00216-020-03085-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 01/27/2023]
Abstract
Aquatic microbial communities contribute fundamentally to biogeochemical transformations in natural ecosystems, and disruption of these communities can lead to ecological disasters such as harmful algal blooms. Microbial communities are highly dynamic, and their composition and function are tightly controlled by the biophysical (e.g., light, fluid flow, and temperature) and biochemical (e.g., chemical gradients and cell concentration) parameters of the surrounding environment. Due to the large number of environmental factors involved, a systematic understanding of the microbial community-environment interactions is lacking. In this article, we show that microfluidic platforms present a unique opportunity to recreate well-defined environmental factors in a laboratory setting in a high throughput way, enabling quantitative studies of microbial communities that are amenable to theoretical modeling. The focus of this article is on aquatic microbial communities, but the microfluidic and mathematical models discussed here can be readily applied to investigate other microbiomes.
Collapse
Affiliation(s)
- Fangchen Liu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Andrea Giometto
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Mingming Wu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|
41
|
Duncan TR, Werner-Washburne M, Northup DE. DIVERSITY OF SIDEROPHORE-PRODUCING BACTERIAL CULTURES FROM CARLSBAD CAVERNS NATIONAL PARK (CCNP) CAVES, CARLSBAD, NEW MEXICO. JOURNAL OF CAVE AND KARST STUDIES : THE NATIONAL SPELEOLOGICAL SOCIETY BULLETIN 2021; 83:29-43. [PMID: 34556971 PMCID: PMC8455092 DOI: 10.4311/2019es0118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Siderophores are microbially-produced ferric iron chelators. They are essential for microbial survival, but their presence and function for cave microorganisms have not been extensively studied. Cave environments are nutrient-limited and previous evidence suggests siderophore usage in carbonate caves. We hypothesize that siderophores are likely used as a mechanism in caves to obtain critical nutrients such as iron. Cave bacteria were collected from Long-term parent cultures (LT PC) or Short-term parent cultures (ST PC) inoculated with ferromanganese deposits (FMD) and carbonate secondary minerals from Lechuguilla and Spider caves in Carlsbad Caverns National Park (CCNP), NM. LT PC were incubated for 10-11 years to identify potential chemolithoheterotrophic cultures able to survive in nutrient-limited conditions. ST PC were incubated for 1-3 days to identify a broader diversity of cave isolates. A total of 170 LT and ST cultures,18 pure and 152 mixed, were collected and used to classify siderophore production and type and to identify siderophore producers. Siderophore production was slow to develop (>10 days) in LT cultures with a greater number of weak siderophore producers in comparison to the ST cultures that produced siderophores in <10 days, with a majority of strong siderophore producers. Overall, 64% of the total cultures were siderophore producers, which the majority preferred hydroxamate siderophores. Siderophore producers were classified into Proteobacteria (Alpha-, Beta-, or Gamma-), Actinobacteria, Bacteroidetes, and Firmicutes phyla using 16S rRNA gene sequencing. Our study supports our hypothesis that cave bacteria have the capability to produce siderophores in the subsurface to obtain critical ferric iron.
Collapse
|
42
|
Utilizing cross-species co-cultures for discovery of novel natural products. Curr Opin Biotechnol 2021; 69:252-262. [PMID: 33647849 DOI: 10.1016/j.copbio.2021.01.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/12/2021] [Accepted: 01/24/2021] [Indexed: 12/11/2022]
Abstract
Discovery of new natural products, especially those with high biological activities and application values, is of great research significance. However, conventional methods based on the cultivation of microbial mono-cultures can hardly satisfy the increasing need of novel natural product generation. Recently, the development of co-cultures composed of different species has emerged as an effective approach for mining novel natural products. Inspired by microbial communities in nature, these co-culture systems create favorable environmental conditions to promote interactions between co-culture members for activating the natural product biosynthesis that is hard to induce otherwise. A large variety of novel natural products have been identified using this robust approach. This review summarizes the recent achievements of using cross-species co-cultures for natural products discovery and discusses the existing challenges and future directions.
Collapse
|
43
|
Bio-Guided Isolation of Antimalarial Metabolites from the Coculture of Two Red Sea Sponge-Derived Actinokineospora and Rhodococcus spp. Mar Drugs 2021; 19:md19020109. [PMID: 33673168 PMCID: PMC7918646 DOI: 10.3390/md19020109] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Coculture is a productive technique to trigger microbes’ biosynthetic capacity by mimicking the natural habitats’ features principally by competition for food and space and interspecies cross-talks. Mixed cultivation of two Red Sea-derived actinobacteria, Actinokineospora spheciospongiae strain EG49 and Rhodococcus sp. UR59, resulted in the induction of several non-traced metabolites in their axenic cultures, which were detected using LC–HRMS metabolomics analysis. Antimalarial guided isolation of the cocultured fermentation led to the isolation of the angucyclines actinosporins E (1), H (2), G (3), tetragulol (5) and the anthraquinone capillasterquinone B (6), which were not reported under axenic conditions. Interestingly, actinosporins were previously induced when the axenic culture of the Actinokineospora spheciospongiae strain EG49 was treated with signalling molecule N-acetyl-d-glucosamine (GluNAc); this finding confirmed the effectiveness of coculture in the discovery of microbial metabolites yet to be discovered in the axenic fermentation with the potential that could be comparable to adding chemical signalling molecules in the fermentation flask. The isolated angucycline and anthraquinone compounds exhibited in vitro antimalarial activity and good biding affinity against lysyl-tRNA synthetase (PfKRS1), highlighting their potential developability as new antimalarial structural motif.
Collapse
|
44
|
Alkayyali T, Pope E, Wheatley SK, Cartmell C, Haltli B, Kerr RG, Ahmadi A. Development of a microbe domestication pod (MD Pod) for in situ cultivation of micro-encapsulated marine bacteria. Biotechnol Bioeng 2020; 118:1166-1176. [PMID: 33241862 DOI: 10.1002/bit.27633] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/01/2020] [Accepted: 11/20/2020] [Indexed: 11/10/2022]
Abstract
Microbial marine natural products hold significant potential for the discovery of new bioactive therapeutics such as antibiotics. Unfortunately, this discovery is hindered by the inability to culture the majority of microbes using traditional laboratory approaches. While many new methods have been developed to increase cultivability, a high-throughput in situ incubation chamber capable of simultaneously isolating individual microbes while allowing cellular communication has not previously been reported. Development of such a device would expedite the discovery of new microbial taxa and, thus, facilitate access to their associated natural products. In this study, this concept is achieved by the development of a new device termed by the authors as the microbe domestication (MD) Pod. The MD Pod enables single-cell cultivation by isolating marine bacterial cells in agarose microbeads produced using microfluidics, while allowing potential transmission of chemical signals between cells during in situ incubation in a chamber, or "Pod," that is deployed in the environment. The design of the MD Pod was optimized to ensure the use of biocompatible materials, allow for simple assembly in a field setting, and maintain sterility throughout incubation. The encapsulation process was designed to ensure that the viability of marine sediment bacteria was not adversely impacted by the encapsulation process. The process was validated using representative bacteria isolated from temperate marine sediment samples: Marinomonas polaris, Psychrobacter aquimaris, and Bacillus licheniformis. The overall process appeared to promote metabolic activity of most representative species. Thus, microfluidic encapsulation of marine bacteria and subsequent in situ incubation in the MD Pod is expected to accelerate marine natural products discovery by increasing the cultivability of marine bacteria.
Collapse
Affiliation(s)
- Tartela Alkayyali
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| | - Emily Pope
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada
| | - Sydney K Wheatley
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| | - Christopher Cartmell
- Departments of Chemistry, University of Prince Edward Island, Prince Edward Island, Canada
| | - Bradley Haltli
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Prince Edward Island, Canada
| | - Russell G Kerr
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada.,Departments of Chemistry, University of Prince Edward Island, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Prince Edward Island, Canada
| | - Ali Ahmadi
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| |
Collapse
|
45
|
Zhang B, Yu P, Wang Z, Alvarez PJJ. Hormetic Promotion of Biofilm Growth by Polyvalent Bacteriophages at Low Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:12358-12365. [PMID: 32886494 DOI: 10.1021/acs.est.0c03558] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Interactions between bacteriophages (phages) and biofilms are poorly understood despite their broad ecological and water quality implications. Here, we report that biofilm exposure to lytic polyvalent phages at low concentrations (i.e., 102-104 phages/mL) can counterintuitively promote biofilm growth and densification (corroborated by confocal laser scanning microscopy (CLSM)). Such exposure hormetically upregulated quorum sensing genes (by 4.1- to 24.9-fold), polysaccharide production genes (by 3.7- to 9.3-fold), and curli synthesis genes (by 4.5- to 6.5-fold) in the biofilm-dwelling bacterial hosts (i.e., Escherichia coli and Pseudomonas aeruginosa) relative to unexposed controls. Accordingly, the biofilm matrix increased its polysaccharide and extracellular DNA content relative to unexposed controls (by 41.8 ± 2.3 and 81.4 ± 2.2%, respectively), which decreased biofilm permeability and increased structural integrity. This contributed to enhanced resistance to disinfection with chlorine (bacteria half-lives were 6.08 ± 0.05 vs 3.91 ± 0.03 min for unexposed controls) and to subsequent phage infection (biomass removal was 18.2 ± 1.2 vs 32.3 ± 1.2% for unexposed controls), apparently by mitigating diffusion of these antibacterial agents through the biofilm. Overall, low concentrations of phages reaching a biofilm may result in unintended biofilm stimulation, which might accelerate biofouling, biocorrosion, or other biofilm-related water quality problems.
Collapse
Affiliation(s)
- Bo Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston 77005, United States
| | - Zijian Wang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston 77005, United States
| |
Collapse
|
46
|
Abstract
Interactions among microbes are key drivers of evolutionary progress and constantly shape ecological niches. Microorganisms rely on chemical communication to interact with each other and surrounding organisms. They synthesize natural products as signaling molecules, antibiotics, or modulators of cellular processes that may be applied in agriculture and medicine. Whereas major insight has been gained into the principles of intraspecies interaction, much less is known about the molecular basis of interspecies interplay. In this review, we summarize recent progress in the understanding of chemically mediated bacterial-fungal interrelations. We discuss pairwise interactions among defined species and systems involving additional organisms as well as complex interactions among microbial communities encountered in the soil or defined as microbiota of higher organisms. Finally, we give examples of how the growing understanding of microbial interactions has contributed to drug discovery and hypothesize what may be future directions in studying and engineering microbiota for agricultural or medicinal purposes.
Collapse
Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07745 Jena, Germany
| |
Collapse
|
47
|
Gao CH, Cao H, Cai P, Sørensen SJ. The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity. ISME JOURNAL 2020; 15:29-40. [PMID: 32887945 PMCID: PMC7852870 DOI: 10.1038/s41396-020-00751-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Coculture is an important model system in microbial ecology studies. As a key experimental parameter, the initial inoculation ratio has a crucial impact on the results of the coculture system. However, such an effect has never been investigated under multiple niche conditions. In this study, we established a simple coculture system with two model bacteria in various carbon sources and investigated the influence of initial inoculum ratios of 1:1000 to 1000:1 on community structure, function, and bacterial interaction. We found that the final ratio of the cocultures with different initial inoculum ratios differed in approximately five-sixths of the carbon sources, suggesting that the final ratio is highly dependent on the initial inoculum ratio, while the carbon source preferences of bacteria could not predict the final ratio of cocultures. Furthermore, we found that the initial ratio could regulate the metabolic capacity of the coculture, as only cocultures with initial ratios of 1:1 and 1000:1 gained high capacity on 14 specific carbon sources. The underlying reason may be that the pattern of species interaction is changed by the initial ratio. In conclusion, we showed that the initial ratio can induce emergent properties in coculture. These findings suggest that the initial ratio not only impacts the reproducibility of coculture experiments but also can influence our understanding of generic microbial ecology.
Collapse
Affiliation(s)
- Chun-Hui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hui Cao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| |
Collapse
|
48
|
Cuvas-Limon RB, Nobre C, Cruz M, Rodriguez-Jasso RM, Ruíz HA, Loredo-Treviño A, Texeira JA, Belmares R. Spontaneously fermented traditional beverages as a source of bioactive compounds: an overview. Crit Rev Food Sci Nutr 2020; 61:2984-3006. [PMID: 32662286 DOI: 10.1080/10408398.2020.1791050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fermented food has been present throughout history, since fermentation not only helps preserving food, but also provides specific organoleptic characteristics typically associated to these foods. Most of the traditional fermented foods and artisanal beverages are produced by spontaneous generation, meaning no control of the microbiota, or the substrate used. Nevertheless, even not being standardized, they are an important source of bioactive compounds, such as antioxidant compounds, bioactive beeps, short chain fatty acids, amino acids, vitamins, and minerals. This review compiles a list of relevant traditional fermented beverages around the world, aiming to detail the fermentation process itself-including source of microorganisms, substrates, produced metabolites and the operational conditions involved. As well as to list the bioactive compounds present in each fermented food, together with their impact in the human health. Traditional fermented beverages from Mexico will be highlighted. These compounds are of high interest for the food, pharmaceutical and cosmetics industry. To scale-up the home fermentation processes, it is necessary to fully understand the microbiology and biochemistry behind these traditional products. The use of good quality raw materials with standardized methodologies and defined microorganisms, may improve and increase the production of the desirable bioactive compounds and open a market for novel functional products.
Collapse
Affiliation(s)
- R B Cuvas-Limon
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Clarisse Nobre
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Mario Cruz
- Department of Food Science and Technology, Antonio Narro Autonomous Agricultural University, Saltillo, Coahuila, Mexico
| | - Rosa M Rodriguez-Jasso
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico
| | - Héctor A Ruíz
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico
| | - Araceli Loredo-Treviño
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico
| | - J A Texeira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ruth Belmares
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico
| |
Collapse
|
49
|
The contest of microbial pigeon neighbors: Interspecies competition between Serratia marcescens and the human pathogen Cryptococcus neoformans. Fungal Biol 2020; 124:629-638. [PMID: 32540186 DOI: 10.1016/j.funbio.2020.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 11/21/2022]
Abstract
In nature, microorganisms often exhibit competitive behavior for nutrients and limited space, allowing them to alter the virulence determinants of pathogens. The human pathogenic yeast Cryptococcus neoformans can be found organized in biofilms, a complex community composed of an extracellular matrix which confers protection against predation. The aim of this study was to evaluate and characterize antagonistic interactions between two cohabiting microorganisms: C. neoformans and the bacteria Serratia marcescens. The interaction of S. marcescens with C. neoformans expressed a negative effect on biofilm formation, polysaccharide capsule, production of urease, and melanization of the yeast. These findings evidence that competition in mixed communities can result in dominance by one species, with direct impact on the physiological modulation of virulence determinants. Such an approach is key for understating the response of communities to the presence of competitors and, ultimately, rationally designing communities to prevent and treat certain diseases.
Collapse
|
50
|
Shahab RL, Brethauer S, Luterbacher JS, Studer MH. Engineering of ecological niches to create stable artificial consortia for complex biotransformations. Curr Opin Biotechnol 2020; 62:129-136. [DOI: 10.1016/j.copbio.2019.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022]
|