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Kumar G, Kallscheuer N, Kashif M, Ahamad S, Jagadeeshwari U, Pannikurungottu S, Haufschild T, Kabuu M, Sasikala C, Jogler C, Ramana CV. Gemmata algarum, a Novel Planctomycete Isolated from an Algal Mat, Displays Antimicrobial Activity. Mar Drugs 2023; 22:10. [PMID: 38276648 PMCID: PMC10817699 DOI: 10.3390/md22010010] [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: 09/05/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Axenic cultures of two strains, JC673T and JC717, both belonging to the phylum Planctomycetota, were isolated from distinct geographical locations in India. Strain JC673T was obtained from algal mats of a wetland situated in the state of Kerala, India, while strain JC717 originated from the Central Marine Fisheries Research Institute (CMFRI), state of Tamil Nadu, India. The two strains share 99.9% 16S rRNA gene sequence similarity and are most closely related to Gemmata obscuriglobus UQM 2246T (99.3% 16S rRNA gene sequence identity). The newly isolated strains are Gram-negative, grow aerobically and tolerate up to 4% (w/v) NaCl and a pH of up to 9.0. Cells are spherical and form pink-pigmented colonies. The respiratory quinone is MK-6. Major fatty acids are C18:0, C16:1ω5c and C16:0. Polar lipids include phosphatidylcholine, phosphatidylethanolamine, several unidentified amino lipids, unidentified phospholipids, additional unidentified lipids, and an unidentified choline lipid. The polyamine spermidine is produced by the two strains. The strains have a genome size of about 8.2 Mb with a DNA G+C content of 67.6%. Solvent-based culture extracts of the isolates showed antimicrobial activity against three bacterial test strains. Their phylogenetic position along with differences in morphological, physiological, and genomic features support the classification as a new species of the genus Gemmata, for which we propose the name Gemmata algarum sp. nov. Strain JC673T (=KCTC 72851T = NBRC 114340T) and JC717 are the type and non-type strain of the new species, respectively.
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Affiliation(s)
- Gaurav Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, 07743 Jena, Germany
| | - Nicolai Kallscheuer
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Mohammad Kashif
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
| | - Shabbir Ahamad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
| | - Uppada Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Sreya Pannikurungottu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
| | - Tom Haufschild
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Moses Kabuu
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, 07743 Jena, Germany
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
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Ge ZB, Zhai ZQ, Xie WY, Dai J, Huang K, Johnson DR, Zhao FJ, Wang P. Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria. THE ISME JOURNAL 2023; 17:2090-2102. [PMID: 37737252 PMCID: PMC10579247 DOI: 10.1038/s41396-023-01519-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms that underlie these interactions and their association with metal/metalloid biogeochemistry, however, remain poorly understood. Here, we identified two soil bacteria, Bacillus sp. BP-3 and Delftia sp. DT-2, that engage in a two-tiered mutualism. Strain BP-3 has low utilization ability of pyruvic acid while strain DT-2 lacks hexokinase, lacks a phosphotransferase system, and is defective in glucose utilization. When strain BP-3 is grown in isolation with glucose, it releases pyruvic acid to the environment resulting in acidification and eventual self-killing. However, when strain BP-3 is grown together with strain DT-2, strain DT-2 utilizes the released pyruvic acid to meet its energy requirements, consequently rescuing strain BP-3 from pyruvic acid-induced growth inhibition. The two bacteria further enhance their collective competitiveness against other microbes by using arsenic as a weapon. Strain DT-2 reduces relatively non-toxic methylarsenate [MAs(V)] to highly toxic methylarsenite [MAs(III)], which kills or suppresses competitors, while strain BP-3 detoxifies MAs(III) by methylation to non-toxic dimethylarsenate [DMAs(V)]. These two arsenic transformations are enhanced when strains DT-2 and BP-3 are grown together. The two strains, along with their close relatives, widely co-occur in soils and their abundances increase with the soil arsenic concentration. Our results reveal that these bacterial types employ a two-tiered mutualism to ensure their collective metabolic activity and maintain their ecological competitive against other soil microbes. These findings shed light on the intricateness of bacterial interactions and their roles in ecosystem functioning.
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Affiliation(s)
- Zhan-Biao Ge
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Qiang Zhai
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wan-Ying Xie
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Dai
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ke Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
- Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Fang-Jie Zhao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China.
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Jiang B, Shen Y, Lu X, Du Y, Jin N, Li G, Zhang D, Xing Y. Toxicity assessment and microbial response to soil antibiotic exposure: differences between individual and mixed antibiotics. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:460-473. [PMID: 35166274 DOI: 10.1039/d1em00405k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Increasing amounts of antibiotics are introduced into soils, raising great concerns on their ecotoxicological impacts on the soil environment. This work investigated the individual and joint toxicity of three antibiotics, tetracycline (TC), sulfonamide (SD) and erythromycin (EM) via a whole-cell bioreporter assay. TC, SD and EM in aqueous solution demonstrated cytotoxicity, whilst soil exposure showed genotoxicity, indicating that soil particles possibly affected the bioavailability of antibiotics. Toxicity of soils exposed to TC, SD and EM changed over time, demonstrating cytotoxic effects within 14-d exposure and genotoxic effects after 30 days. Joint toxicity of TC, SD and EM in soils instead showed cytotoxicity, suggesting a synergetic effect. High-throughput sequencing suggested that the soil microbial response to individual antibiotics and their mixtures showed a different pattern. Soil microbial community composition was more sensitive to TC, in which the abundance of Pseudomonas, Pirellula, Subdivision3_genera_incertae_sedis and Gemmata varied significantly. Microbial community functions were significantly shifted by EM amendments, including signal transduction mechanisms, cytoskeleton, cell wall/membrane/envelope biogenesis, transcription, chromatin structure and dynamics, and carbohydrate transport and metabolism. This work contributes to a better understanding of the ecological effects and potential risks of individual and joint antibiotics on the soil environment.
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Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Yaoxin Shen
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Xin Lu
- Petrochina North China Gas Marketing Company, Beijing, 100029, PR China
| | - Yufan Du
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Naifu Jin
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
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Vitorino IR, Lage OM. The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes. Antonie van Leeuwenhoek 2022; 115:169-201. [PMID: 35037113 DOI: 10.1007/s10482-021-01699-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 01/21/2023]
Abstract
The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
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Ivanova AA, Kulichevskaya IS, Dedysh SN. Gemmata palustris sp. nov., a Novel Planctomycete from a Fen in Northwestern Russia. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kallscheuer N, Jogler C. The bacterial phylum Planctomycetes as novel source for bioactive small molecules. Biotechnol Adv 2021; 53:107818. [PMID: 34537319 DOI: 10.1016/j.biotechadv.2021.107818] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Extensive knowledge and methodological expertise on the bacterial cell biology have been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technological processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The characterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state of planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study of additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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Kulichevskaya IS, Ivanova AA, Naumoff DG, Beletsky AV, Rijpstra WIC, Sinninghe Damsté JS, Mardanov AV, Ravin NV, Dedysh SN. Frigoriglobus tundricola gen. nov., sp. nov., a psychrotolerant cellulolytic planctomycete of the family Gemmataceae from a littoral tundra wetland. Syst Appl Microbiol 2020; 43:126129. [PMID: 32847778 PMCID: PMC7534041 DOI: 10.1016/j.syapm.2020.126129] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 11/25/2022]
Abstract
Planctomycetes of the family Gemmataceae are characterized by large genome sizes and cosmopolitan distribution in freshwater and terrestrial environments but their ecological functions remain poorly understood. In this study, we characterized a novel representative of this family, strain PL17T, which was isolated from a littoral tundra wetland and was capable of growth on xylan and cellulose. Cells of this isolate were represented by pink-pigmented spheres that multiplied by budding and occurred singly or in short chains and aggregates. Strain PL17T was obligately aerobic, mildly acidophilic chemoorganotrophic bacterium, which displayed good tolerance of low temperatures. The major fatty acids were C18:0, C16:1ω5, and βOH-C16:1; the major polar lipid was trimethylornithine. The genome of strain PL17T consisted of a 9.83 Mb chromosome and a 24.69kb plasmid. The G+C contents of the chromosomal and plasmid DNA were 67.4 and 62.3mol%, respectively. Over 8900 potential protein-coding genes were identified in the genome including a putative cellulase that contains a domain from the GH5 family of glycoside hydrolases. The genome of strain PL17T contained one linked and one unlinked rRNA operons with 16S rRNA gene sequences displaying 94.5% similarity to that in Gemmata obscuriglobus UQM2246T. Based on the results of comparative phenotypic, chemotaxonomic and phylogenomic analyses, we propose to classify strain PL17T (= CECT 9407T=VKM B-3467T) as representing a novel genus and species of the family Gemmataceae, Frigoriglobus tundricola gen. nov., sp. nov.
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Affiliation(s)
- Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Daniil G Naumoff
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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Noyer M, Reoyo-Prats B, Aubert D, Bernard M, Verneau O, Palacios C. Particle-attached riverine bacteriome shifts in a pollutant-resistant and pathogenic community during a Mediterranean extreme storm event. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 732:139047. [PMID: 32473395 DOI: 10.1016/j.scitotenv.2020.139047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/22/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Rivers are representative of the overall contamination found in their catchment area. Contaminant concentrations in watercourses depend on numerous factors including land use and rainfall events. Globally, in Mediterranean regions, rainstorms are at the origin of fluvial multipollution phenomena as a result of Combined Sewer Overflows (CSOs) and floods. Large loads of urban-associated microorganisms, including faecal bacteria, are released from CSOs which place public health - as well as ecosystems - at risk. The impacts of freshwater contamination on river ecosystems have not yet been adequately addressed, as is the case for the release of pollutant mixtures linked to extreme weather events. In this context, microbial communities provide critical ecosystem services as they are the only biological compartment capable of degrading or transforming pollutants. Through the use of 16S rRNA gene metabarcoding of environmental DNA at different seasons and during a flood event in a typical Mediterranean coastal river, we show that the impacts of multipollution phenomena on structural shifts in the particle-attached riverine bacteriome were greater than those of seasonality. Key players were identified via multivariate statistical modelling combined with network module eigengene analysis. These included species highly resistant to pollutants as well as pathogens. Their rapid response to contaminant mixtures makes them ideal candidates as potential early biosignatures of multipollution stress. Multiple resistance gene transfer is likely enhanced with drastic consequences for the environment and human-health, particularly in a scenario of intensification of extreme hydrological events.
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Affiliation(s)
- Mégane Noyer
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | - Brice Reoyo-Prats
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | - Dominique Aubert
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | - Maria Bernard
- Univ. Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; INRAE, SIGENAE, 78350 Jouy-en-Josas, France
| | - Olivier Verneau
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France; Unit. for Environmental Sciences and Management, North-West University, ZA-2520 Potchefstroom, South Africa
| | - Carmen Palacios
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France.
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10
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Kulichevskaya IS, Naumoff DG, Miroshnikov KK, Ivanova AA, Philippov DA, Hakobyan A, Rijpstra WIC, Damsté JSS, Liesack W, Dedysh SN. Limnoglobus roseus gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family Gemmataceae. Int J Syst Evol Microbiol 2020; 70:1240-1249. [PMID: 31800383 PMCID: PMC7397252 DOI: 10.1099/ijsem.0.003904] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/16/2019] [Indexed: 11/18/2022] Open
Abstract
The family Gemmataceae accommodates aerobic, chemoorganotrophic planctomycetes, which inhabit various freshwater ecosystems, wetlands and soils. Here, we describe a novel member of this family, strain PX52T, which was isolated from a boreal eutrophic lake in Northern Russia. This isolate formed pink-pigmented colonies and was represented by spherical cells that occurred singly, in pairs or aggregates and multiplied by budding. Daughter cells were highly motile. PX52T was an obligate aerobic chemoorganotroph, which utilized various sugars and some heteropolysaccharides. Growth occurred at pH 5.0-7.5 (optimum pH 6.5) and at temperatures between 10 and 30 °C (optimum 20-25 °C). The major fatty acids were C18 : 1ɷ7c, C18 : 0 and βOH-C16:0; the major intact polar lipid was trimethylornithine, and the quinone was MK-6. The complete genome of PX52T was 9.38 Mb in size and contained nearly 8000 potential protein-coding genes. Among those were genes encoding a wide repertoire of carbohydrate-active enzymes (CAZymes) including 33 glycoside hydrolases (GH) and 87 glycosyltransferases (GT) affiliated with 17 and 12 CAZy families, respectively. DNA G+C content was 65.6 mol%. PX52T displayed only 86.0-89.8 % 16S rRNA gene sequence similarity to taxonomically described Gemmataceae planctomycetes and differed from them by a number of phenotypic characteristics and by fatty acid composition. We, therefore, propose to classify it as representing a novel genus and species, Limnoglobus roseus gen. nov., sp. nov. The type strain is strain PX52T (=KCTC 72397T=VKM B-3275T).
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Affiliation(s)
- Irina S. Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Daniil G. Naumoff
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Anna Hakobyan
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - W. Irene C. Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Werner Liesack
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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Kaboré OD, Aghnatios R, Godreuil S, Drancourt M. Escherichia coli Culture Filtrate Enhances the Growth of Gemmata spp. Front Microbiol 2019; 10:2552. [PMID: 31781064 PMCID: PMC6851166 DOI: 10.3389/fmicb.2019.02552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/22/2019] [Indexed: 12/05/2022] Open
Abstract
Background Planctomycetes bacteria are known to be difficult to isolate, we hypothesized this may be due to missing iron compounds known to be important for other bacteria. We tested the growth-enhancement effect of complementing two standard media with Escherichia coli culture filtrate on two cultured strains of Gemmata spp. Also, the acquisition of iron by Gemmata spp. was evaluated by measuring various molecules involved in iron metabolism. Materials and Methods Gemmata obscuriglobus and Gemmata massiliana were cultured in Caulobacter and Staley’s medium supplemented or not with E. coli culture filtrate, likely containing siderophores and extracellular ferrireductases. We performed iron metabolism studies with FeSO4, FeCl3 and deferoxamine in the cultures with the E. coli filtrate and the controls. Results and Discussion The numbers of G. obscuriglobus and G. massiliana colonies on Caulobacter medium or Staley’s medium supplemented with E. coli culture filtrate were significantly higher than those on the standard medium (p < 0.0001). Agar plate assays revealed that the Gemmata colonies near E. coli colonies were larger than the more distant colonies, suggesting the diffusion of unknown growth promoting molecules. The inclusion of 10–4 to 10–3 M FeSO4 resulted in rapid Gemmata spp. growth (4–5 days compared with 8–9 days for the controls), suggesting that both species can utilize FeSO4 to boost their growth. In contrast, deferoxamine slowed down and prevented Gemmata spp. growth. Further studies revealed that the complementation of Caulobacter medium with E. coli culture filtrate and 10–4 M FeSO4 exerted a significant growth-enhancement effect compared with that obtained with Caulobacter medium supplemented with E. coli culture filtrate alone (p < 0.0122). Moreover, the intracellular iron concentrations in G. obscuriglobus and G. massiliana cultures in iron-depleted broth supplemented with the E. coli filtrate were 0.63 ± 0.16 and 0.78 ± 0.12 μmol/L, respectively, whereas concentrations of 1.72 ± 0.13 and 1.56± 0.11 μmol/L were found in the G. obscuriglobus and G. massiliana cultures grown in broth supplemented with the E. coli filtrate and FeSO4. The data reported here indicated that both E. coli culture filtrate and FeSO4 act as growth factors for Gemmata spp. via a potentiation mechanism.
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Affiliation(s)
- Odilon D Kaboré
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rita Aghnatios
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Département de Bactériologie-Virologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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12
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Kaboré OD, Godreuil S, Drancourt M. Improved culture of fastidious Gemmata spp. bacteria using marine sponge skeletons. Sci Rep 2019; 9:11707. [PMID: 31406238 PMCID: PMC6690866 DOI: 10.1038/s41598-019-48293-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023] Open
Abstract
Gemmata are Planctomycetes bacteria recalcitrant to traditional cultivation in the clinical microbiology laboratory and they have been seldom documented in patients. Based on previously known relationships of Planctomycetes with marine sponges, we designed a new culture medium A incorporating marine sponge skeleton of Spongia sp. to the standard culture medium; and culture medium B incorporating Spongia sp. skeleton heat aqueous filtrate into medium A; and inoculating the three culture media (standard, A and B) with Gemmata obscuriglobus DSM 5831T and Gemmata massiliana DSM 26013T in the presence of negative controls. Cultures were observed by naked eyes for 7 days and bacterial growth was quantified by microscopic observations and culture-based enumerations. Macroscopic observations at day-3 revealed a pink bacterial pellet in medium B tubes while standard medium tubes remained limpid until day-8. Growing Gemmata spp. bacteria in medium A yielded air bubbles released by bacterial respiration, whereas control tubes remained bubble-free. The number of colonies in standard medium (1.363 ± 115 for G. obscuriglobus, 1.288 ± 83 for G. massiliana) was significantly lower than those counted from medium B (2.552 ± 128 for G. obscuriglobus, 1.870 ± 112 for G. massiliana) and from medium A (2.851 ± 137 for G. obscuriglobus, 2.035 ± 163 for G. massiliana) (p < 0.10-4) at day-2 incubation. At day-3 incubation, the number of colonies counted from supplemented media A and B increased up to one log than those counted from the control medium (p < 0.10-4). Along the following day-4-7 incubation, the number of colonies counted from media A and B remained significantly higher compared to standard medium (p < 0.10-4). These data indicate that incorporation of spongin-based marine sponge skeleton and heat aqueous filtrate of sponge skeleton significantly improved growth of Gemmata spp. bacteria. These observations pave the way towards improved isolation and culture of Gemmata spp. from environmental and clinical specimens.
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Affiliation(s)
- Odilon D Kaboré
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm 1058, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.
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13
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Antibiotic susceptibility of marine Planctomycetes. Antonie van Leeuwenhoek 2019; 112:1273-1280. [DOI: 10.1007/s10482-019-01259-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
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14
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Kaboré OD, Loukil A, Godreuil S, Drancourt M. Co-culture models illustrate the digestion of Gemmata spp. by phagocytes. Sci Rep 2018; 8:13311. [PMID: 30190504 PMCID: PMC6127157 DOI: 10.1038/s41598-018-31667-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 08/10/2018] [Indexed: 11/25/2022] Open
Abstract
Gemmata spp. bacteria thrive in the same aquatic environments as free-living amoebae. DNA-based detection of Gemmata spp. sequences in the microbiota of the human digestive tract and blood further questioned the susceptibility of Gemmata spp. to phagocytes. Here, Gemmata obscuriglobus and Gemmata massiliana were co-cultured with the amoebae Acanthamoeba polyphaga, Acanthamoeba castellanii, Acanthamoeba griffini and THP-1 macrophage-like phagocytes. All experiments were performed in five independant replicates. The ratio amoeba/bacteria was 1:20 and the ratio THP-1/bacteria was 1:10. After a 2-hour co-culture, extracellular bacteria were killed by kanamycin or amikacin and eliminated. The intracellular location of Gemmata bacteria was specified by confocal microscopy. Microscopic enumerations and culture-based enumerations of colony-forming units were performed at T = 0, 1, 2, 3, 4, 8, 16, 24, 48 and 72 hours post-infection. Then, Gemmata bacteria were engulfed into the phagocytes’ cytoplasmic vacuoles, more than (98 ± 2)% of Gemmata bacteria, compared to controls, were destroyed by phagocytic cells after a 48-h co-culture according to microscopy and culture results, and no positive culture was observed at T = 72-hours. Under our co-culture conditions, Gemmata bacteria were therefore susceptible to the environmental and host phagocytes here investigated. These data suggest that these Acanthamoeba species and THP-1 cells cannot be used to isolate G. massiliana and G. obscuriglobus under the co-culture conditions applied in this study. Although the THP-1 response can point towards potential responses that might occur in vivo, these responses should first bevalidated by in vivo studies to draw definite conclusions.
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Affiliation(s)
- Odilon D Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ahmed Loukil
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, 1058, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.
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15
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Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
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16
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Franke JD, Blomberg WR, Todd RT, Thomas RW, Selmecki AM. Assembly of a complete genome sequence for Gemmata obscuriglobus reveals a novel prokaryotic rRNA operon gene architecture. Antonie van Leeuwenhoek 2018; 111:2095-2105. [DOI: 10.1007/s10482-018-1102-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/16/2018] [Indexed: 11/28/2022]
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17
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Christen JR, Edmond E, Drancourt M. Methods for detecting Gemmata spp. bacteremia in the microbiology laboratory. BMC Res Notes 2018; 11:11. [PMID: 29310696 PMCID: PMC5759251 DOI: 10.1186/s13104-017-3119-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 12/29/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Gemmata bacteria are fastidious, Gram-negative and aerobic. The only representatives are Gemmata obscuriglobus and Gemmata massiliana. These Planctomycetes appear to be a part of human digestive tract microbiome, and G. massiliana has been isolated from water. Further specific detection in the blood of two patients with febrile neutropenia suggests that Gemmata bacteremia may remain under-documented. The objective of this study was to develop an effective protocol to document Gemmata spp. bacteremia in the laboratory. Using mock-infected and control blood specimens, three methods for detecting Gemmata bacteremia, namely, automated microbial detection, culture on solid medium, and quantitative polymerase chain reaction (PCR), have been developed and studied. RESULTS Gemmata spp. were undetected by automated blood culture system but culturing mock-infected blood on Caulobacter agar detected ≥ 102 G. obscuriglobus bacteria/mL and ≥ 104 G. massiliana bacteria/mL. Specific real-time PCR detected 102 Gemmata bacteria/mL. These protocols may be used to investigate the epidemiology of Gemmata spp. bacteremia.
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Affiliation(s)
- Jacques-Robert Christen
- URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Aix Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Department of Infectious Diseases and Tropical Medicine, Laveran Military Teaching Hospital, Marseille, France
| | - Edwin Edmond
- URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Aix Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Michel Drancourt
- URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Aix Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France.
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18
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Zablocki O, van Zyl LJ, Kirby B, Trindade M. Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy. Viruses 2017; 9:E348. [PMID: 29156552 PMCID: PMC5707555 DOI: 10.3390/v9110348] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 01/15/2023] Open
Abstract
The current view of virus diversity in terrestrial hot springs is limited to a few sampling sites. To expand our current understanding of hot spring viral community diversity, this study aimed to investigate the first African hot spring (Brandvlei hot spring; 60 °C, pH 5.7) by means of electron microscopy and sequencing of the virus fraction. Microscopy analysis revealed a mixture of regular- and 'jumbo'-sized tailed morphotypes (Caudovirales), lemon-shaped virions (Fuselloviridae-like; salterprovirus-like) and pleiomorphic virus-like particles. Metavirome analysis corroborated the presence of His1-like viruses and has expanded the current clade of salterproviruses using a polymerase B gene phylogeny. The most represented viral contig was to a cyanophage genome fragment, which may underline basic ecosystem functioning provided by these viruses. Furthermore, a putative Gemmata-related phage was assembled with high coverage, a previously undocumented phage-host association. This study demonstrated that a moderately thermophilic spring environment contained a highly novel pool of viruses and should encourage future characterization of a wider temperature range of hot springs throughout the world.
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Affiliation(s)
- Olivier Zablocki
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Bronwyn Kirby
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
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19
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Kulichevskaya IS, Ivanova AA, Baulina OI, Rijpstra WIC, Sinninghe Damsté JS, Dedysh SN. Fimbriiglobus ruber gen. nov., sp. nov., a Gemmata-like planctomycete from Sphagnum peat bog and the proposal of Gemmataceae fam. nov. Int J Syst Evol Microbiol 2017; 67:218-224. [PMID: 27902209 DOI: 10.1099/ijsem.0.001598] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, budding, dark pink to red-pigmented bacterium was isolated from an acidic boreal Sphagnum peat bog and designated strain SP5T. Cells of this strain were non-motile spheres that were uniformly covered with crateriform pits and fimbria, and tended to form aggregates during growth in liquid media. Strain SP5T was capable of growth between pH 4.0 and pH 6.8 (optimum at pH 5.5-6.0) and at temperatures between 10 and 30 °C (optimum at 20-25 °C). The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C20 : 1ω9c, C16 : 1ω9c and C16 : 0, and the major polar lipid was trimethylornithine. Cells contained also significant amounts of bound (ω-1)OH-C30 : 1 fatty acid. The quinone was menaquinone-6, and the G+C content of the DNA was 60.7 mol%. Strain SP5T was a member of the order Planctomycetales and belonged to the phylogenetic lineage defined by the genus Gemmata. It displayed 88 and 89 % 16S rRNA gene sequence similarity to Gemmata obscuriglobusUQM 2246T and 'Gemmata massiliana' IIL30, 89 % to Zavarzinella formosa A10T and 86 % to Telmatocola sphagniphila SP2T. However, strain SP5T differed from members of these genera by cell morphology, substrate utilization pattern and fatty acid composition. Based on these data, the novel isolate should be considered as representing a novel species of a new genus of planctomycetes, for which the name Fimbriiglobus ruber gen. nov., sp. nov, is proposed. The type strain is SP5T (=LMG 29572T=VKM B-3045T). We also suggest the establishment of a novel family, Gemmataceaefam. nov., which includes the phylogenetically related genera Gemmata, Zavarzinella, Telmatocola and Fimbriiglobus.
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Affiliation(s)
- Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Olga I Baulina
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, GSP-1, Moscow 119234, Russia
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, Utrecht, The Netherlands.,Department of Marine Microbiology and Biogeochemistry and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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20
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Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia. Anaerobe 2017; 43:47-55. [DOI: 10.1016/j.anaerobe.2016.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
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21
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Kohn T, Heuer A, Jogler M, Vollmers J, Boedeker C, Bunk B, Rast P, Borchert D, Glöckner I, Freese HM, Klenk HP, Overmann J, Kaster AK, Rohde M, Wiegand S, Jogler C. Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea. Front Microbiol 2016; 7:2079. [PMID: 28066393 PMCID: PMC5177795 DOI: 10.3389/fmicb.2016.02079] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/08/2016] [Indexed: 11/23/2022] Open
Abstract
Members of the phylum Planctomycetes are ubiquitous bacteria that dwell in aquatic and terrestrial habitats. While planctomycetal species are important players in the global carbon and nitrogen cycle, this phylum is still undersampled and only few genome sequences are available. Here we describe strain NH11T, a novel planctomycete obtained from a crustacean shell (Wadden Sea, Germany). The phylogenetically closest related cultivated species is Gimesia maris, sharing only 87% 16S rRNA sequence identity. Previous isolation attempts have mostly yielded members of the genus Rhodopirellula from water of the German North Sea. On the other hand, only one axenic culture of the genus Pirellula was obtained from a crustacean thus far. However, the 16S rRNA gene sequence of strain NH11T shares only 80% sequence identity with the closest relative of both genera, Rhodopirellula and Pirellula. Thus, strain NH11T is unique in terms of origin and phylogeny. While the pear to ovoid shaped cells of strain NH11T are typical planctomycetal, light-, and electron microscopic observations point toward an unusual variation of cell division through budding: during the division process daughter- and mother cells are connected by an unseen thin tubular-like structure. Furthermore, the periplasmic space of strain NH11T was unusually enlarged and differed from previously known planctomycetes. The complete genome of strain NH11T, with almost 9 Mb in size, is among the largest planctomycetal genomes sequenced thus far, but harbors only 6645 protein-coding genes. The acquisition of genomic components by horizontal gene transfer is indicated by the presence of numerous putative genomic islands. Strikingly, 45 “giant genes” were found within the genome of NH11T. Subsequent analysis of all available planctomycetal genomes revealed that Planctomycetes as such are especially rich in “giant genes”. Furthermore, Multilocus Sequence Analysis (MLSA) tree reconstruction support the phylogenetic distance of strain NH11T from other cultivated Planctomycetes of the same phylogenetic cluster. Thus, based on our findings, we propose to classify strain NH11T as Fuerstia marisgermanicae gen. nov., sp. nov., with the type strain NH11T, within the phylum Planctomycetes.
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Affiliation(s)
- Timo Kohn
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Anja Heuer
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Mareike Jogler
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - John Vollmers
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Christian Boedeker
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Patrick Rast
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Daniela Borchert
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Ines Glöckner
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Heike M Freese
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | | | - Jörg Overmann
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Anne-Kristin Kaster
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Manfred Rohde
- Helmholtz Centre for Infectious Disease Braunschweig, Germany
| | - Sandra Wiegand
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Christian Jogler
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
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Graça AP, Calisto R, Lage OM. Planctomycetes as Novel Source of Bioactive Molecules. Front Microbiol 2016; 7:1241. [PMID: 27570520 PMCID: PMC4982196 DOI: 10.3389/fmicb.2016.01241] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022] Open
Abstract
Marine environments are a fruitful source of bioactive compounds some of which are the newest leading drugs in medicinal therapeutics. Of particular importance are organisms like sponges and macroalgae and their associated microbiome. Planctomycetes, abundant in macroalgae biofilms, are promising producers of bioactive compounds since they share characteristics, like large genomes and complex life cycles, with the most bioactive bacteria, the Actinobacteria. Furthermore, genome mining revealed the presence of secondary metabolite pathway genes or clusters in 13 analyzed Planctomycetes genomes. In order to assess the antimicrobial production of a large and diverse collection of Planctomycetes isolated from macroalgae from the Portuguese coast, molecular, and bioactivity assays were performed in 40 bacteria from several taxa. Two genes commonly associated with the production of bioactive compounds, nonribosomal peptide synthetases (NRPS), and polyketide synthases (PKS) genes were screened. Molecular analysis revealed that 95% of the planctomycetes potentially have one or both secondary bioactive genes; 85% amplified with PKS-I primers and 55% with NRPS primers. Some of the amplified genes were confirmed to be involved in secondary metabolite pathways. Using bioinformatic tools their biosynthetic pathways were predicted. The secondary metabolite genomic potential of strains LF1, UC8, and FC18 was assessed using in silico analysis of their genomes. Aqueous and organic extracts of the Planctomycetes were evaluated for their antimicrobial activity against an environmental Escherichia coli, E. coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 25923, Bacillus subtilis ATCC 6633, and a clinical isolate of Candida albicans. The screening assays showed a high number of planctomycetes with bioactive extracts revealing antifungal (43%) and antibacterial (54%) activity against C. albicans and B. subtilis, respectively. Bioactivity was observed in strains from Rhodopirellula lusitana, R. rubra, R. baltica, Roseimaritima ulvae, and Planctomyces brasiliensis. This study confirms the bioactive capacity of Planctomycetes to produce antimicrobial compounds and encourages further studies envisaging molecule isolation and characterization for the possible discovery of new drugs.
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Affiliation(s)
- Ana P Graça
- Departamento de Biologia, Faculdade de Ciências, Universidade do PortoPorto, Portugal; CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental-Universidade do PortoPorto, Portugal
| | - Rita Calisto
- Departamento de Biologia, Faculdade de Ciências, Universidade do PortoPorto, Portugal; CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental-Universidade do PortoPorto, Portugal
| | - Olga M Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do PortoPorto, Portugal; CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental-Universidade do PortoPorto, Portugal
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Abstract
The Planctomycetes genus Gemmata is represented by both uncultured organisms and cultured Gemmata obscuriglobus and 'Gemmata massiliana' organisms. Their plasmidless 9.2 Mb genomes encode a complex cell plan, cell signaling capacities, antibiotic and trace metal resistance and multidrug resistance efflux pumps. As they lack iron metabolism pathways, they are fastidious. Gemmata spp. are mainly found in aquatic and soil environments but have also been found in hospital water networks in close proximity to patients, in animals, on human skin, the gut microbiota and in the blood of aplastic leukemic patients. Due to their panoply of attack and defense mechanisms and their recently demonstrated association with humans, the potential of Gemmata organisms to behave as opportunistic pathogens should be more widely recognized.
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Affiliation(s)
- Rita Aghnatios
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille 13005, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille 13005, France
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24
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Durand G, Lagier JC, Khelaifia S, Armstrong N, Robert C, Rathored J, Fournier PE, Raoult D. Drancourtella massiliensis gen. nov., sp. nov. isolated from fresh healthy human faecal sample from South France. New Microbes New Infect 2016; 11:34-42. [PMID: 27257490 PMCID: PMC4877409 DOI: 10.1016/j.nmni.2016.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 01/30/2016] [Accepted: 02/03/2016] [Indexed: 11/01/2022] Open
Abstract
Strain GD1(T) gen. nov., sp. nov., is the type strain of the newly proposed genus and species Drancourtella massiliensis, belonging to the Clostridiales order. This strain, isolated from the stool of a healthy person, is a Gram-positive rod, oxygen intolerant and nonmotile, with spore-forming activity. The features of this organism and its genome sequence are described. The draft genome is 3 057 334 bp long with 45.24% G + C content; it contains 2861 protein-coding genes and 64 RNA genes.
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Affiliation(s)
- G.A. Durand
- URMITE UM63, CNRS7278, IRD198, INSERM1085, Faculté de Médecine, Aix Marseille Université, Marseille, France
- Pôle des Maladies Infectieuses, Hôpital La Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - J.-C. Lagier
- URMITE UM63, CNRS7278, IRD198, INSERM1085, Faculté de Médecine, Aix Marseille Université, Marseille, France
- Pôle des Maladies Infectieuses, Hôpital La Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - S. Khelaifia
- URMITE UM63, CNRS7278, IRD198, INSERM1085, Faculté de Médecine, Aix Marseille Université, Marseille, France
| | - N. Armstrong
- URMITE UM63, CNRS7278, IRD198, INSERM1085, Faculté de Médecine, Aix Marseille Université, Marseille, France
| | - C. Robert
- URMITE UM63, CNRS7278, IRD198, INSERM1085, Faculté de Médecine, Aix Marseille Université, Marseille, France
| | - J. Rathored
- URMITE UM63, CNRS7278, IRD198, INSERM1085, Faculté de Médecine, Aix Marseille Université, Marseille, France
| | - P.-E. Fournier
- URMITE UM63, CNRS7278, IRD198, INSERM1085, Faculté de Médecine, Aix Marseille Université, Marseille, France
- Pôle des Maladies Infectieuses, Hôpital La Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - D. Raoult
- URMITE UM63, CNRS7278, IRD198, INSERM1085, Faculté de Médecine, Aix Marseille Université, Marseille, France
- Pôle des Maladies Infectieuses, Hôpital La Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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