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Barcelo LAF, Lantican NB, Ventura RLG, Ventura JRS. Genetic characterization of biohydrogen-producing purple non-sulfur bacteria Rhodobacter johrii MAY2 isolate via whole genome analysis. Gene 2024; 924:148597. [PMID: 38782220 DOI: 10.1016/j.gene.2024.148597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Purple non-sulfur bacteria (PNSB) are a diverse group of bacteria studied for various possible applications. They are commonly surveyed in bioenergy research as they produce biohydrogen, a candidate for clean alternative energy. This study aimed to assess the biohydrogen production ability and genetically characterize a high biohydrogen-producing PNSB (MAY2) isolated from Los Baños, Laguna, Philippines via whole genome sequencing (WGS). MAY2, when grown in mixed volatile fatty acids, produced biogas with 38% hydrogen. WGS results revealed that the isolate is positively classified under the genus Rhodobacter johrii. Also, 82 genetic hallmarks for biohydrogen production were found in the isolated genome which are involved in the production of key enzymes and proteins relevant to the photofermentative and hydrogen regulation pathways. Its nitrogenase gene cluster is stringently regulated by two genes, nifA and rofN, whose function and expression are easily affected by several environmental factors.
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Affiliation(s)
- Leo Agustin F Barcelo
- Biomaterials and Environmental Engineering Laboratory, Department of Engineering Science, College of Engineering and Agro-Industrial Technology, University of the Philippines Los Baños, College, Laguna 4031 Philippines
| | - Nacita B Lantican
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, College, Laguna 4031 Philippines
| | - Ruby Lynn G Ventura
- University of the Philippines Rural High School, College of Arts and Sciences, University of the Philippines Los Baños, Paciano Rizal, Bay, Laguna, 4033, Philippines
| | - Jey-R S Ventura
- Biomaterials and Environmental Engineering Laboratory, Department of Engineering Science, College of Engineering and Agro-Industrial Technology, University of the Philippines Los Baños, College, Laguna 4031 Philippines.
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2
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Tang J, Jiang Y, Hu Z, Zhou H, You D, Daroch M. Genomic and phenotypic characterization of Thermosynechococcus-like strains reveals eight species within the genus Thermosynechococcus and a novel genus Parathermosynechococcus gen. nov. Mol Phylogenet Evol 2024; 197:108094. [PMID: 38723792 DOI: 10.1016/j.ympev.2024.108094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Thermophilic unicellular cyanobacteria of the family Thermosynechococcaceae are essential primary producers and integral components of many microbial mats found in hot springs of Asia and North America. Historically, based on their simple morphology, these organisms, along with members of taxonomically unrelated thermophilic Thermostichaceae have been described with a generic term, "Synechococcus", used for elongated unicellular cyanobacteria. This has created significant misperception in the scientific literature regarding the taxonomic status of these essential thermophilic primary producers and their relationship with Synechococcus sensu stricto. In this manuscript, we attempted a genome-driven taxonomic reevaluation of the family Thermosynechococcaceae. Application of genomic analyses such as GTDB classification, ANI/AAI and phylogenomics support the delineation of eight species within genus Thermosynechococcus. Two subspecies were further identified within T. taiwanensis by dDDH and phylogenomics. Moreover, the results also suggest the presence of two putative new genera phylogenetically alongside genus Thermosynechococcus, a thermophilic genus Parathermosynechococcus represented by PCC 6715 and a non-thermophilic genus represented by PCC 6312. The proposed genospecies and new genera were further integrated with morphological and/or ecological information. Interestingly, the phylogeny of 16S-23S ITS achieved a better taxonomic relationship than that of 16S rRNA and supported the genome-based classification of Thermosynechococcus spp. Finally, the pan-genome analysis indicated a conserved pattern of genomic core among known members of Thermosynechococcus.
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Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Ying Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Zhe Hu
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Dawei You
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China.
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3
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Lin L, Tao M, He WM, Wu QH, Huang HK, Murero AK, Shao XL, Wang LM, Qian GL. Identification of non-canonical antagonistic bacteria via interspecies contact-dependent killing. PEST MANAGEMENT SCIENCE 2024; 80:3997-4005. [PMID: 38527976 DOI: 10.1002/ps.8103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/18/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Canonical biocontrol bacteria were considered to inhibit pathogenic bacteria mainly by secreting antibiotic metabolites or enzymes. Recent studies revealed that some biocontrol bacteria can inhibit pathogenic bacteria through contact-dependent killing (CDK) mediated by contact-dependent secretion systems. The CDK was independent of antibiotic metabolites and often ignored in normal biocontrol activity assay. RESULTS In this study, we aimed to use a pathogen enrichment strategy to isolate non-canonical bacteria with CDK ability. Rhizosphere soil samples from Chinese cabbage showing soft rot symptom were collected and Pectobacterium carotovorum subsp. carotovorum (Pcc), the pathogen of cabbage soft rot, were added into these samples to enrich bacteria which attached on Pcc cells. By co-culture with Pcc, four bacteria strains (named as PcE1, PcE8, PcE12 and PcE13) showing antibacterial activity were isolated from Chinese cabbage rhizosphere. These four bacteria strains showed CDK abilities to different pathogenic bacteria of horticultural plants. Among them, PcE1 was identified as Chryseobacterium cucumeris. Genome sequencing showed that PcE1 genome encoded a type VI secretion system (T6SS) gene cluster. By heterologous expression, four predicted T6SS effectors of PcE1 showed antibacterial activity to Escherichia coli. CONCLUSION Overall, this study isolated four bacteria strains with CDK activity to various horticultural plant pathogens, and revealed possible involvement of T6SS of Chryseobacterium cucumeris in antibacterial activity. These results provide valuable insight for potential application of CDK activity in biocontrol bacteria. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Long Lin
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Min Tao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Wei-Mei He
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Qian-Hua Wu
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Hao-Kai Huang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Aprodisia Kavutu Murero
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Xiao-Long Shao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Li-Min Wang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Guo-Liang Qian
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
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Kumari S, Kumar A, Lepcha A, Kumar R. Cold-adapted Exiguobacterium sibiricum K1 as a potential bioinoculant in cold regions: Physiological and genomic elucidation of biocontrol and plant growth promotion. Gene 2024; 916:148439. [PMID: 38583819 DOI: 10.1016/j.gene.2024.148439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
The scarcity of soil nutrient availability under cold conditions of Himalayan regions needs a sustainable approach for better crop yields. The cold-adapted bacteria, Exiguobacterium sibiricum K1, with the potential to produce several plant growth-promoting (PGP) attributes, nitrogen fixation, indole acetic acid production, phosphate and potassium solubilization at 10 °C can provide an opportunity to promote crop yield improvement in an eco-friendly way under cold conditions. The bacterium also exhibited biocontrol activity against two phytopathogens and produced siderophore (53.0 ± 0.5 % psu). The strain's PGP properties were investigated using a spinach-based bioassay under controlled conditions. The bacterized seeds showed a notable increase in germination rate (23.2 %), shoot length (65.3 %), root length (56.6 %), leaf area (73.7 %), number of leaflets (65.2 %), and dry matter (65.2 %). Additionally, the leaf analysis indicated elevated chlorophyll pigments, i.e., chlorophyll a (55.5 %), chlorophyll b (42.8 %), carotenoids (35.2 %), percentage radical scavenging activity (47.4 %), and leaf nutrient uptake such as nitrogen (23.4 %), calcium (60.8 %), potassium (62.3 %), and magnesium (28.9 %). Moreover, the whole-genome sequencing and genome mining endorsed various biofertilisation-related genes, including genes for potassium and phosphate solubilization, iron and nitrogen acquisition, carbon dioxide fixation, and biocontrol ability of Exiguobacterium sibiricum K1. Overall, this study highlights the role of Exiguobacterium sibiricum K1 as a potential bioinoculant for improving crop yield under cold environments.
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Affiliation(s)
- Sareeka Kumari
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Anil Kumar
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Ayush Lepcha
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Rakshak Kumar
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India; Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India.
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Kumar P, Verma A, Yadav P, Das J, Kumar L, Krishnamurthi S. Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:172995. [PMID: 38719044 DOI: 10.1016/j.scitotenv.2024.172995] [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: 12/14/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.
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Affiliation(s)
- Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India; Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden; Umeå Marine Sciences Centre, Hörnefors, Sweden
| | - Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Lalit Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India.
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6
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Lu YT, Wu YY, Li YN, Zheng WY, Liu WZ. Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis. Arch Microbiol 2024; 206:342. [PMID: 38967823 DOI: 10.1007/s00203-024-04069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.
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Affiliation(s)
- Yi-Ting Lu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Yi-Yi Wu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Ya-Nan Li
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
- Department of Pharmaceutical Laboratory, Anhui Sunhere Pharmaceutical Excipients Co., Ltd, Huainan, Anhui Province, 232000, China
| | - Wei-Yi Zheng
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
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7
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Alghamdi AK, Parween S, Hirt H, Saad MM. Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina. BMC Genomics 2024; 25:672. [PMID: 38969999 DOI: 10.1186/s12864-024-10555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium's adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.
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Affiliation(s)
- Amal Khalaf Alghamdi
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sabiha Parween
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Max Perutz Laboratories, University of Vienna, Vienna, Austria.
| | - Maged M Saad
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Tan Gana NH, Ruz CP, Alcantara EP, Diaz MGQ, Marfori EC, Villegas LC, Creencia AR, Arguelles EDLR, Tan Gana NH, Monsalud RG, Opulencia RB. Genome drafts of Pseudogracilibacillus spp. from soil and sediment of Mount Makiling, a dormant volcano in the Philippines. Microbiol Resour Announc 2024:e0037424. [PMID: 38967465 DOI: 10.1128/mra.00374-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024] Open
Abstract
We present the draft whole-genome sequences of Pseudogracilibacillus spp. isolated from the soils and sediments of Sipit Creek located at Mount Makiling, a dormant volcano in the southern part of Luzon Island, Philippines. This Pseudogracilibacillus spp. genome report extends the body of knowledge on a lesser-known genus of Bacillaceae.
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Affiliation(s)
- Noel H Tan Gana
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Cernan P Ruz
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Edwin P Alcantara
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Maria Genaleen Q Diaz
- Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Eufrocinio C Marfori
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Lucille C Villegas
- Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Armi R Creencia
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Eldrin D L R Arguelles
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Neil H Tan Gana
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Arts and Sciences, City College of Calamba, Calamba, Laguna, Philippines
| | - Rosario G Monsalud
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Rina B Opulencia
- Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, College, Laguna, Philippines
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9
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Aldeia C, Campos-Madueno EI, Endimiani A. Genomic insights into Leminorella grimontii and its chromosomal class A GRI β-lactamase. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04888-7. [PMID: 38958811 DOI: 10.1007/s10096-024-04888-7] [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: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
Leminorella grimontii strain LG-KP-E1-2-T0 was isolated from Zophobas morio larvae. It showed a susceptibility phenotype compatible with the expression of an inducible extended-spectrum β-lactamase. The presence of a chromosomal bla gene encoding for the class A GRI-1 β-lactamase was revealed by whole-genome sequencing. GRI-1 shared the highest amino acid identity with RIC-1 and OXY-type β-lactamases (76-80%). Analysis of six further publicly-available L. grimontii draft genomes deposited in NCBI revealed that blaGRI-1 was always present. Core-genome analysis indicated that LG-KP-E1-2-T0 was unique from other strains. We provided the first complete genome of L. grimontii and new insights on its chromosomal β-lactamases.
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Affiliation(s)
- Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland.
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Samadpour M, Benoit L, Myoda S, Hans B, Nadala C, Kim SH, Themeli E, Cantera R, Nguyen T, Richter H. Microbiological survey and genomic analysis of Cronobacter sakazakii strains isolated from US households and retail foods. Appl Environ Microbiol 2024:e0070024. [PMID: 38953659 DOI: 10.1128/aem.00700-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Cronobacter species are opportunistic pathogens that are capable of causing morbidity and mortality, particularly in infants. Although the transmission dynamics involved in Cronobacter infections remain largely unknown, contaminated powdered infant formula (PIF) has been linked to 30% of Cronobacter sakazakii cases involving invasive illness in infants. As several lines of evidence have implicated the domestic environment in PIF contamination, we undertook a microbiological survey of homes (N = 263) across the US. Cronobacter spp. and C. sakazakii were isolated from 36.1% and 24.7% of US homes, respectively, with higher recovery rates observed for floor and kitchen surfaces. Multi-locus sequence typing indicated that the dominant strain was C. sakazakii ST4, the sequence type most commonly associated with neonatal meningitis. For comparison purposes, retail foods (N = 4,009) were also surveyed, with the highest contamination frequencies (10.1%-26.3%) seen for nut products, seeds, and grains/baked goods/flours. The sequence type profile of isolates recovered from homes mirrored that of isolates recovered from retail foods, with increased representation of ST1, ST4, ST13, ST17, and ST40. Analysis of 386 whole genomic sequences revealed significant diversity. Redundancies were only observed for isolates recovered from within the same domicile, and there were no identical matches with sequences archived at the NCBI pathogen database. Genes coding for putative virulence and antibiotic resistance factors did not segregate with clinically significant sequence types. Collectively, these findings support the possibility that contamination events occurring within the home should not be overlooked as a contributor to community-onset Cronobacter infections. IMPORTANCE Cronobacter sakazakii is an opportunistic pathogen that can cause significant morbidity and mortality in neonates. Its transmission dynamics are poorly understood, though powered infant formula (PIF) is thought to be the major transmission vehicle. How the PIF becomes contaminated remains unknown. Our survey shows that roughly 1/4 of US homes are contaminated with Cronobacter sakazakii, particularly in the kitchen setting. Our analyses suggest that the domestic environment may contribute to contamination of PIF and provides insights into mitigating the risk of transmission.
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Affiliation(s)
- Mansour Samadpour
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Lora Benoit
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Sam Myoda
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Bada Hans
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Cesar Nadala
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Seong Hong Kim
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Eni Themeli
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Ruth Cantera
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Truyen Nguyen
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Hans Richter
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
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11
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Schäfer L, Jehle JA, Kleespies RG, Wennmann JT. Pathogens of the oak processionary moth Thaumetopoea processionea: Developing a user-friendly bioassay system and metagenome analyses for microorganisms. J Invertebr Pathol 2024; 205:108121. [PMID: 38705355 DOI: 10.1016/j.jip.2024.108121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/05/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
The oak processionary moth (OPM) Thaumetopoea processionea is a pest of oak trees and poses health risks to humans due to the urticating setae of later instar larvae. For this reason, it is difficult to rear OPM under laboratory conditions, carry out bioassays or examine larvae for pathogens. Biological control targets the early larval instars and is based primarily on commercial preparations of Bacillus thuringiensis ssp. kurstaki (Btk). To test the entomopathogenic potential of other spore-forming bacteria, a user-friendly bioassay system was developed that (i) applies bacterial spore suspensions by oak bud dipping, (ii) targets first instar larvae through feeding exposure and (iii) takes into account their group-feeding behavior. A negligible mortality in the untreated control proved the functionality of the newly established bioassay system. Whereas the commercial Btk HD-1 strain was used as a bioassay standard and confirmed as being highly efficient, a Bacillus wiedmannii strain was ineffective in killing OPM larvae. Larvae, which died during the infection experiment, were further subjected to Nanopore sequencing for a metagenomic approach for entomopathogen detection. It further corroborated that B.wiedmannii was not able to infect and establish in OPM, but identified potential insect pathogenic species from the genera Serratia and Pseudomonas.
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Affiliation(s)
- Lea Schäfer
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
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12
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Behrendt U, Burghard V, Wende S, Ulrich K, Wolf J, Neumann-Schaal M, Ulrich A. Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus. Syst Appl Microbiol 2024; 47:126516. [PMID: 38772267 DOI: 10.1016/j.syapm.2024.126516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038T (=LMG 33092 T = DSM 115926 T). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.
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Affiliation(s)
- Undine Behrendt
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Valentin Burghard
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Sonja Wende
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Kristina Ulrich
- Johann Heinrich Von Thünen Institute, Institute of Forest Genetics, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany.
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Andreas Ulrich
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
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13
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Grabner F M, Grabner H M, Schein H, Schrank A, Töglhofer M, Weidenholzer E, Rückert-Reed C, Busche T, Buchebner-Jance M. Lacticaseibacillus parahuelsenbergensis sp. nov., Lacticaseibacillus styriensis sp. nov. and Lacticaseibacillus zeae subsp. silagei subsp. nov., isolated from different grass and corn silage. Int J Syst Evol Microbiol 2024; 74. [PMID: 38954457 DOI: 10.1099/ijsem.0.006441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024] Open
Abstract
Four rod-shaped, non-motile, non-spore-forming, facultative anaerobic, Gram-stain-positive lactic acid bacteria, designated as EB0058T, SCR0080, LD0937T and SCR0063T, were isolated from different corn and grass silage samples. The isolated strains were characterized using a polyphasic approach and EB0058T and SCR0080 were identified as Lacticaseibacillus zeae by 16S rRNA gene sequence analysis. Based on whole-genome sequence-based characterization, EB0058T and SCR0080 were separated into a distinct clade from Lacticaseibacillus zeae DSM 20178T, together with CECT9104 and UD2202, whose genomic sequences are available from NCBI GenBank. The average nucleotide identity (ANI) values within the new subgroup are 99.9 % and the digital DNA-DNA hybridization (dDDH) values are 99.3-99.9 %, respectively. In contrast, comparison of the new subgroup with publicly available genomic sequences of L. zeae strains, including the type strain DSM 20178T, revealed dDDH values of 70.2-72.5 % and ANI values of 96.2-96.6 %. Based on their chemotaxonomic, phenotypic and phylogenetic characteristics, EB0058T and SCR0080 represent a new subspecies of L. zeae. The name Lacticaseibacillus zeae subsp. silagei subsp. nov. is proposed with the type strain EB0058T (=DSM 116376T=NCIMB 15474T). According to the results of 16S rRNA gene sequencing, LD0937T and SCR0063T are members of the Lacticaseibacillus group. The dDDH value between the isolates LD0937T and SCR0063T was 67.6 %, which is below the species threshold of 70 %, clearly showing that these two isolates belong to different species. For both strains, whole genome-sequencing revealed that the closest relatives within the Lacticaseibacillus group were Lacticaseibacillus huelsenbergensis DSM 115425 (dDDH 66.5 and 65.9 %) and Lacticaseibacillus casei DSM 20011T (dDDH 64.1 and 64.9 %). Based on the genomic, chemotaxonomic and morphological data obtained in this study, two novel species, Lacticaseibacillus parahuelsenbergensis sp. nov. and Lacticaseibacillus styriensis sp. nov. are proposed and the type strains are LD0937T (=DSM 116105T=NCIMB 15471T) and SCR0063T (=DSM 116297T=NCIMB 15473T), respectively.
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Affiliation(s)
- Monika Grabner F
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | - Monika Grabner H
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | - Hermine Schein
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | - Andrea Schrank
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | - Manuela Töglhofer
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | | | | | - Tobias Busche
- Omics Core Facility NGS, Medical School OWL & CBTec, Bielefeld University, Bielefeld, Germany
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14
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Saticioglu IB, Ay H, Altun S, Ajmi N, Gunduz ES, Gocmen H, Duman M. Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov. Syst Appl Microbiol 2024; 47:126518. [PMID: 38761464 DOI: 10.1016/j.syapm.2024.126518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise analysis of the 16S rRNA gene sequences. The highest pairwise identity values were calculated as 98.8 % for strain F-30 T and Flavobacterium bizetiae, 99.0 % for strain F-65 T and Flavobacterium branchiarum, 98.7 % for strain F-126 T and Flavobacterium tructae, 98.2 % for strain F-323 T and Flavobacterium cupreum while 99.7 % identity level was detected for strain F-70 T and Flavobacterium geliluteum. In addition, strains F-33, Fl-77, and F-70 T shared 100 % identical 16S rRNA genes, while strains F-323 T and Fl-318 showed 99.9 % identity. A polyphasic approach including comparative analysis of whole-genome data was employed to ascertain the taxonomic provenance of the strains. In addition to the morphological, physiological, biochemical and chemotaxonomic characteristics of the strains, the overall genome-relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as five novel species within the genus Flavobacterium. The comprehensive genome analyses of the strains were also conducted to determine the biosynthetic gene clusters, virulence features and ecological distribution patterns. Based on the polyphasic characterisations, including comparative genome analyses, it is concluded that strains F-30 T, F-65 T, F-70 T, F126T and F-323 T represent five novel species within the genus Flavobacterium for which Flavobacterium piscisymbiosum sp. nov. F-30 T (=JCM 34194 T = KCTC 82254 T), Flavobacterium pisciphilum sp. nov. F-65 T (=JCM 34197 T = KCTC 82257 T), Flavobacterium flavipigmentatum sp. nov. F-70 T (Fl-33 = Fl-77 = JCM 34198 T = KCTC 82258 T), Flavobacterium lipolyticum sp. nov. F-126 T (JCM 34199 T = KCTC 82259 T) and Flavobacterium cupriresistens sp. nov. F-323 T (Fl-318 = JCM 34200 T = KCTC 82260 T), are proposed.
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, 16059, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yildiz Technical University, Istanbul, 34220, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, 16059, Turkey
| | - Nihed Ajmi
- Graduate School of Health Sciences, Bursa Uludag University, Bursa, 16059, Turkey
| | - Enes Said Gunduz
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Huban Gocmen
- Department of Microbiology, Faculty of Veterinary Medicine, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, 16059, Turkey
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15
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Velasquez MR, De Lay BD, Edmondson DG, Wormser GP, Norris SJ, Cafferky K, Munzer E, Rizk CC, Keller M. A Novel Treponema pallidum Subspecies pallidum Strain Associated With a Painful Oral Lesion Is a Member of a Potentially Emerging Nichols-Related Subgroup. Sex Transm Dis 2024; 51:486-492. [PMID: 38829929 DOI: 10.1097/olq.0000000000001971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
BACKGROUND Early syphilitic lesions are typically painless; however, several recent case studies have included patients with tender lesions and no evidence of concurrent infections. Here we present the manifestations and serological and molecular findings of a patient from New York State with a painful tongue lesion. METHODS The diagnosis of syphilis was based on a combination of physical examination, serologic, pathologic, and immunohistochemical findings. DNA obtained from a formalin-fixed, paraffin-embedded biopsy was used to characterize the infecting pathogen using polymerase chain reaction, multilocus sequence typing, and whole-genome sequencing methods. RESULTS Polymerase chain reaction and multilocus sequence typing of the biopsy specimen confirmed infection with T. pallidum subspecies pallidum ( T. pallidum ) of the Nichols cluster. Whole-genome sequencing analysis of this strain (herein called NYMC01) showed that it contained 17 unique single nucleotide variations and 4 more complex genetic differences; this novel genotype matched only 2 specimens, both from a patient in Seattle, Washington. The presence of this rare genotype in 2 geographically distinct locations suggests the potential emergence and spread of a new subgroup of the Nichols cluster. CONCLUSIONS To our knowledge, this is the first genomic sequence obtained from a T. pallidum strain linked to a painful lesion, and the third description of whole-genome sequencing of T. pallidum from formalin-fixed, paraffin-embedded tissue. Analysis of additional specimens may reveal that the NYMC01-related genotype represents an emerging T. pallidum subgroup and may also aid in determining whether the painful clinical presentation of primary syphilis is related to specific T. pallidum genotypes.
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Affiliation(s)
- Maria Rosa Velasquez
- From the Department of Internal Medicine, Division of Infectious Diseases, New York Medical College, Westchester Medical Center, Valhalla, NY
| | - Bridget D De Lay
- Department of Pathology and Laboratory Medicine, McGovern Medical School, UT Health Houston, Houston, TX
| | - Diane G Edmondson
- Department of Pathology and Laboratory Medicine, McGovern Medical School, UT Health Houston, Houston, TX
| | - Gary P Wormser
- From the Department of Internal Medicine, Division of Infectious Diseases, New York Medical College, Westchester Medical Center, Valhalla, NY
| | - Steven J Norris
- Department of Pathology and Laboratory Medicine, McGovern Medical School, UT Health Houston, Houston, TX
| | | | | | | | - Marina Keller
- From the Department of Internal Medicine, Division of Infectious Diseases, New York Medical College, Westchester Medical Center, Valhalla, NY
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16
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Bing H, Qi C, Gu J, Zhao T, Yu X, Cai Y, Zhang Y, Li A, Wang X, Zhao J, Xiang W. Isolation and identification of NEAU-CP5: A seed-endophytic strain of B. velezensis that controls tomato bacterial wilt. Microb Pathog 2024; 192:106707. [PMID: 38777241 DOI: 10.1016/j.micpath.2024.106707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/29/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
Bacterial wilt of tomato caused by Ralstonia solanacearum is a critical soilborne disease that drastically reduces yield. In the current study, an endophytic strain NEAU-CP5 with strong antagonistic activity against R. solanacearum was isolated from tomato seeds and characterized. The strain was identified as Bacillus velezensis based on 16S rRNA gene and whole genome sequence analysis. NEAU-CP5 can secrete amylase, protease, and cellulase, and also produce known antibacterial metabolites, including cyclo (leucylprolyl), cyclo (phenylalanyl-prolyl), cyclo (Pro-Gly), 3-benzyl-2,5-piperazinedione, pentadecanoic acid, eicosane, 2-methyoic acid, isovaleric acid, dibuty phthalate, and esters of fatty acids (HFDU), which may be responsible for its strong antibacterial activity. Fourteen gene clusters associated with antibacterial properties were also identified in the whole genome sequence of NEAU-CP5. Pot experiment demonstrated that the application of 108 CFU/mL NEAU-CP5 on tomato plants significantly reduced the incidence of tomato bacterial wilt by 68.36 ± 1.67 %. NEAU-CP5 also increased the activity of defense-related enzymes (CAT, POD, PPO, SOD, and PAL) in tomato plants. This is the first report of an effective control of bacterial wilt on tomato plants by B. velezensis and highlights the potential of NEAU-CP5 as a potential biocontrol agent for the management of tomato bacterial wilt.
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Affiliation(s)
- Hui Bing
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Cuiping Qi
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Jinzhao Gu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Tianxin Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Xiaoyan Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Yang Cai
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Yance Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Ailin Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.
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17
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Ercole TG, Kava VM, Petters-Vandresen DAL, Ribeiro RA, Hungria M, Galli LV. Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417. Curr Microbiol 2024; 81:247. [PMID: 38951210 DOI: 10.1007/s00284-024-03784-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024]
Abstract
Stenotrophomonas species are recognized as rhizobacteria that play a pivotal role in promoting plant growth by making substantial contributions to enhanced soil fertility, nutrient recycling, and phytopathogen control. Employing them as bioinputs constitutes an environmentally sound strategy, particularly within the rhizospheric community. This study revealed the draft genome sequence of Stenotrophomonas geniculata LGMB417, which was originally isolated from root samples of maize (Zea mays L.). This research assessed the potential of a bacterial strain at the molecular level through genome mining, aiming to identify genes with biotechnological significance for promoting plant growth and protection. The assembly findings indicate that strain LGMB417 possesses a genome size of 4,654,011 bp, with a G + C content of 66.50%. The draft genome sequence revealed the presence of gene clusters responsible for the synthesis of secondary metabolites and carbohydrate active enzymes (CAZymes), glycoside hydrolases (23), glycosyltransferases (18), carbohydrate esterases (5), polysaccharide lyases (2), carbohydrate-binding modules (2), and auxiliary activities (1). Several genes related to growth promotion were found in the genome, including those associated with phosphate transport and solubilization, nitrogen metabolism, siderophore production and iron transport, hormonal modulation, stress responses (such as to drought, temperature fluctuations, osmotic challenges, and oxidative conditions), and volatile organic compounds (VOCs). Subsequent phases will encompass investigations utilizing gene expression methodologies, with future explorations concentrating on facets pertinent to agricultural production, including comprehensive field studies.
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Affiliation(s)
- Tairine Graziella Ercole
- Postgraduate Program in Genetics, Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil.
| | - Vanessa Merlo Kava
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil
| | - Desirrê Alexia Lourenço Petters-Vandresen
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | | | - Lygia Vitoria Galli
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil.
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18
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Łopucki R, Stępień-Pyśniak D, Christensen H, Kubiński K, Lenarczyk E, Martinez-de-Tejada G, Kitowski I, Masłyk M. Interspecies transmission of antimicrobial-resistant bacteria between wild birds and mammals in urban environment. Vet Microbiol 2024; 294:110130. [PMID: 38820727 DOI: 10.1016/j.vetmic.2024.110130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
The transmission of antibiotic-resistant bacteria among wild animal species may hold significant epidemiological implications. However, this issue is seldom explored due to the perceived complexity of these systems, which discourages experimental investigation. To address this knowledge gap, we chose a configuration of birds and mammals coexisting in an urban green area as a research model: the rook Corvus frugilegus and the striped field mouse Apodemus agrarius. The indirect transmission of antimicrobial-resistant bacteria between these species is possible because rodents inhabiting rook colonies frequently come into contact with the birds' faeces and pellets. The study was conducted in two cities in eastern Poland (Central Europe) - Lublin and Chełm. Among 71 Escherichia (E.) coli isolates studied, 19.7% showed resistance to from one to six of the antibiotics tested, with much higher prevalence of antibiotic-resistant bacteria in the birds (32%) than in the rodents (7%). Whole genome sequencing was performed on 10 selected E. coli isolates representing similar resistance phenotypes. The following antimicrobial resistance genes were detected: blaTEM-1b, tet(A), tet(B), aph(6)-Id, aph(3'')-Ib, aadA1, aadA2, catA1, floR, cmlA, sul2, sul3, dfrA14, and dfrA2. Birds from the same city and also from both neighbouring cities shared E. coli bacteria with the same sequence types, whereas isolates detected in birds were not found to have been transferred to the mammalian population, despite close contact. This demonstrates that even intensive exposure to sources of these pathogens does not necessarily lead to effective transmission of antibiotic-resistant E. coli strains between birds and mammals. Further efforts should be dedicated to investigating actual transmission of antimicrobial-resistant bacteria in various ecological systems, including those that are crucial for public health, such as urban environments. This will facilitate the development of more accurate models for epidemiological threats and the formulation of well-balanced decisions regarding the coexistence of humans and urban wildlife.
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Affiliation(s)
- Rafał Łopucki
- John Paul II Catholic University of Lublin, Institute of Biological Sciences, Department of Biomedicine and Environmental Research, Konstantynów 1J, Lublin 20-708, Poland
| | - Dagmara Stępień-Pyśniak
- University of Life Sciences in Lublin, Faculty of Veterinary Medicine, Department of Veterinary Prevention and Avian Diseases, Głęboka 30, Lublin 20-612, Poland.
| | - Henrik Christensen
- University of Copenhagen, Department of Veterinary and Animal Sciences, Stigbøjlen 4, Frederiksberg C, Denmark
| | - Konrad Kubiński
- John Paul II Catholic University of Lublin, Institute of Biological Sciences, Department of Molecular Biology, Konstantynów 1J, Lublin 20-708, Poland
| | - Ewa Lenarczyk
- John Paul II Catholic University of Lublin, Institute of Biological Sciences, Department of Biomedicine and Environmental Research, Konstantynów 1J, Lublin 20-708, Poland
| | - Guillermo Martinez-de-Tejada
- University of Navarra, Department of Microbiology and Parasitology, IdiSNA (Navarra Institute for Health Research), Irunlarrea 1, Pamplona E-31008, Spain
| | - Ignacy Kitowski
- University College of Applied Sciences in Chełm, Pocztowa 54, Chełm 22-100, Poland
| | - Maciej Masłyk
- John Paul II Catholic University of Lublin, Institute of Biological Sciences, Department of Molecular Biology, Konstantynów 1J, Lublin 20-708, Poland
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19
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Kosmopoulos JC, Batstone-Doyle RT, Heath KD. Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis. Can J Microbiol 2024; 70:275-288. [PMID: 38507780 DOI: 10.1139/cjm-2023-0209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2) determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume-rhizobium dynamics in soil communities.
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Affiliation(s)
- James C Kosmopoulos
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, WI, USA
| | - Rebecca T Batstone-Doyle
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Katy D Heath
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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20
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Klages LJ, Kaup O, Busche T, Kalinowski J, Rückert-Reed C. Classification of a novel Serratia species, isolated from a wound swab in North Rhine-Westphalia: Proposal of Serratia sarumanii sp. nov. Syst Appl Microbiol 2024; 47:126527. [PMID: 38959748 DOI: 10.1016/j.syapm.2024.126527] [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: 01/11/2024] [Revised: 05/08/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Novel, white-pigmented, Gram-negative bacterial strains (K-M0706T, K-M0228, K-M0252, K-M0260) were isolated from clinical samples. With a similarity of up to 69.7 % to Serratia nevei S15T and up to 63.8 % to Serratia marcescens ATCC 13880T, as determined by digital DNA-DNA hybridization, the strains were assigned as novel species of the genus Serratia. The species can easily be differentiated from the red colored Serratia marcescens sensu stricto by its white phenotype. Discrimination between this strain and Serratia nevei is possible due to alpha-glucosidase activity and O/129-resistance, as shown for strain K-M0706T. The major fatty acids were determined as myristate, palmitate, cis-9,10-methylenehexadecanoate, linoleate, and (all cis-9,10)-methyleneoctadecanoate. These phenotypical and genomic data support the assignment of a novel species within the genus Serratia, named S. sarumanii due to its pathogenicity and white phenotype, with strain K-M0706T as the type strain.
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Affiliation(s)
- Levin Joe Klages
- Bielefeld University, Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Olaf Kaup
- Bielefeld University, Medical School and University Medical Center OWL, Bielefeld Hospital, Institute of Laboratory Medicine, Microbiology and Transfusion Medicine, Bielefeld, Germany
| | - Tobias Busche
- Bielefeld University, Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld, Germany; Bielefeld University, Medical School OWL, Bielefeld, Germany
| | - Jörn Kalinowski
- Bielefeld University, Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Christian Rückert-Reed
- Bielefeld University, Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld, Germany; Bielefeld University, Medical School OWL, Bielefeld, Germany.
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21
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Maw ZA, Grunwald AL, Haltli BA, Cartmell C, Kerr RG. Discovery of the Lipopeptides Albubactins A-H from Streptomyces albidoflavus RKJM0023 via Chemical Elicitation with Rhamnolipids and Synthesis of Albubactin A. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38940698 DOI: 10.1021/acs.jnatprod.3c01234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The marine tunicate-derived Streptomyces albidoflavus RKJM0023 was cultured in the presence of a rhamnolipid mixture in an effort to elicit the production of silent natural products. MS/MS-based molecular networking analysis enhanced with nonparametric statistics highlighted the upregulation of a molecular cluster (Kruskal-Wallis p = 1.6 e-6 for 1) in which no MS/MS features had library matches. Targeted isolation of these features resulted in the discovery of nine new N-acylated lipopeptides, albubactins A-H (1-8) each containing a unique glutamine tripeptide and a C-terminal ethyl ester moiety. Three related albubactin acids A-C (9-11) lacking the ethyl ester were also identified. NMR spectroscopy and UPLC-HR-ESI-MS/MS demonstrated that the albubactins were obtained as mixtures that shared a common m/z and differed only in their acylated terminal groups. Due to the complex spectroscopic elucidation with many overlapping shifts, a total synthesis of albubactin A (1) was completed and used to determine the absolute configuration of the new albubactins.
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Affiliation(s)
- Zacharie A Maw
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
| | - Alyssa L Grunwald
- Nautilus Biosciences, Croda Canada, Charlottetown, PEI C1A 4P3, Canada
| | - Bradley A Haltli
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
- Nautilus Biosciences, Croda Canada, Charlottetown, PEI C1A 4P3, Canada
| | - Christopher Cartmell
- Department of Pharmacology, College of Medicine; Comprehensive Center for Pain and Addiction, University of Arizona, Tucson, AZ 85724, United States
| | - Russell G Kerr
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
- Department of Chemistry, Faculty of Science, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
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22
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Burcham ZM. Comparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila. Microbiol Spectr 2024:e0415723. [PMID: 38934605 DOI: 10.1128/spectrum.04157-23] [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: 12/12/2023] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Thiopseudomonas alkaliphila, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how T. alkaliphila functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of T. alkaliphila includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in T. alkaliphila genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of T. alkaliphila, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.IMPORTANCEAs the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact. Thiopseudomonas alkaliphila is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification, T. alkaliphila has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that T. alkaliphila is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting T. alkaliphila may operate as an undescribed opportunistic pathogen.
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Affiliation(s)
- Zachary M Burcham
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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23
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Embarcadero-Jiménez S, Araujo-Palomares CL, Moreno-Perlín T, Ramírez-Álvarez N, Quezada-Hernández C, Batista-García RA, Sanchez-Flores A, Calcáneo-Hernández G, Silva-Jiménez H. Physiology and comparative genomics of the haloalkalitolerant and hydrocarbonoclastic marine strain Rhodococcus ruber MSA14. Arch Microbiol 2024; 206:328. [PMID: 38935150 DOI: 10.1007/s00203-024-04050-z] [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: 04/05/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Marine hydrocarbonoclastic bacteria can use polycyclic aromatic hydrocarbons as carbon and energy sources, that makes these bacteria highly attractive for bioremediation in oil-polluted waters. However, genomic and metabolic differences between species are still the subject of study to understand the evolution and strategies to degrade PAHs. This study presents Rhodococcus ruber MSA14, an isolated bacterium from marine sediments in Baja California, Mexico, which exhibits adaptability to saline environments, a high level of intrinsic pyrene tolerance (> 5 g L- 1), and efficient degradation of pyrene (0.2 g L- 1) by 30% in 27 days. Additionally, this strain demonstrates versatility by using naphthalene and phenanthrene as individual carbon sources. The genome sequencing of R. ruber MSA14 revealed a genome spanning 5.45 Mbp, a plasmid of 72 kbp, and three putative megaplasmids, lengths between 110 and 470 Kbp. The bioinformatics analysis of the R. ruber MSA14 genome revealed 56 genes that encode enzymes involved in the peripheral and central pathways of aromatic hydrocarbon catabolism, alkane, alkene, and polymer degradation. Within its genome, R. ruber MSA14 possesses genes responsible for salt tolerance and siderophore production. In addition, the genomic analysis of R. ruber MSA14 against 13 reference genomes revealed that all compared strains have at least one gene involved in the alkanes and catechol degradation pathway. Overall, physiological assays and genomic analysis suggest that R. ruber MSA14 is a new haloalkalitolerant and hydrocarbonoclastic strain toward a wide range of hydrocarbons, making it a promising candidate for in-depth characterization studies and bioremediation processes as part of a synthetic microbial consortium, as well as having a better understanding of the catabolic potential and functional diversity among the Rhodococci group.
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Affiliation(s)
- Salvador Embarcadero-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Cynthia Lizzeth Araujo-Palomares
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Tonatiuh Moreno-Perlín
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, C.P. 62209, México
| | - Nancy Ramírez-Álvarez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Cristina Quezada-Hernández
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, C.P. 62209, México
- Departamento de Biología Animal, Biología Vegetal y Ecología, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Jaén, 23071, España
| | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Unidad Universitaria de Secuenciación Masiva y Bioinformática, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, C.P. 62210, México
| | - Gabriela Calcáneo-Hernández
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, C.P. 04510, México
| | - Hortencia Silva-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México.
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24
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Borker SS, Sharma P, Thakur A, Kumar A, Kumar A, Kumar R. Physiological and genomic insights into a psychrotrophic drought-tolerant bacterial consortium for crop improvement in cold, semiarid regions. Microbiol Res 2024; 286:127818. [PMID: 38970906 DOI: 10.1016/j.micres.2024.127818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/12/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024]
Abstract
The agricultural land in the Indian Himalayan region (IHR) is susceptible to various spells of snowfall, which can cause nutrient leaching, low temperatures, and drought conditions. The current study, therefore, sought an indigenous psychrotrophic plant growth-promoting (PGP) bacterial inoculant with the potential to alleviate crop productivity under cold and drought stress. Psychrotrophic bacteria preisolated from the night-soil compost of the Lahaul Valley of northwestern Himalaya were screened for phosphate (P) and potash (K) solubilization, nitrogen fixation, indole acetic acid (IAA) production, siderophore and HCN production) in addition to their tolerance to drought conditions for consortia development. Furthermore, the effects of the selected consortium on the growth and development of wheat (Triticum aestivum L.) and maize (Zea mays L.) were assessed in pot experiments under cold semiarid conditions (50 % field capacity). Among 57 bacteria with P and K solubilization, nitrogen fixation, IAA production, siderophore and HCN production, Pseudomonas protegens LPH60, Pseudomonas atacamensis LSH24, Psychrobacter faecalis LUR13, Serratia proteamaculans LUR44, Pseudomonas mucidolens LUR70, and Glutamicibacter bergerei LUR77 exhibited tolerance to drought stress (-0.73 MPa). The colonization of wheat and maize seeds with these drought-tolerant PGP strains resulted in a germination index >150, indicating no phytotoxicity under drought stress. Remarkably, a particular strain, Pseudomonas sp. LPH60 demonstrated antagonistic activity against three phytopathogens Ustilago maydis, Fusarium oxysporum, and Fusarium graminearum. Treatment with the consortium significantly increased the foliage (100 % and 160 %) and root (200 % and 133 %) biomasses of the wheat and maize plants, respectively. Furthermore, whole-genome sequence comparisons of LPH60 and LUR13 with closely related strains revealed genes associated with plant nutrient uptake, phytohormone synthesis, siderophore production, hydrogen cyanide (HCN) synthesis, volatile organic compound production, trehalose and glycine betaine transport, cold shock response, superoxide dismutase activity, and gene clusters for nonribosomal peptide synthases and polyketide synthetases. With their PGP qualities, biocontrol activity, and ability to withstand environmental challenges, the developed consortium represents a promising cold- and drought-active PGP bioinoculant for cereal crops grown in cold semiarid regions.
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Affiliation(s)
- Shruti Sinai Borker
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pallavi Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Aman Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aman Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anil Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura 799022, India.
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25
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Zhang W, Zheng L, Xie J, Su X, Zhang M, Huang H, Schmitz-Esser S, Du S, Yang Y, Xie J, Zhang Q, Yu S, Guo Q, Wang H, Zhang L, Yang K, Hou R. The giant panda gut harbors a high diversity of lactic acid bacteria revealed by a novel culturomics pipeline. mSystems 2024:e0052024. [PMID: 38920380 DOI: 10.1128/msystems.00520-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Some lactic acid bacteria (LAB) can provide significant health benefits, which are critically important for the conservation of endangered animals, such as giant pandas. However, little is known about the diversity and culturability of LAB in the giant panda gut microbiota. To understand the roles of LAB in giant panda conservation, it is critical to culture bacterial strains of interest. In this study, we established a pipeline to culture bacterial strains using enrichment of target bacteria with different liquid media and growth conditions. Then, the strains were isolated in solid media to study their functions. Using 210 samples from the culture enrichment method and 138 culture-independent samples, we obtained 1120 amplicon sequencing variants (ASVs) belonging to Lactobacillales. Out of the 1120 ASVs, 812 ASVs from the culture enrichment approach were twofold more diverse than 336 ASVs from the culture-independent approach. Many ASVs of interest were not detected in the culture-independent approach. Using this pipeline, we isolated many relevant bacterial strains and established a giant panda gut bacteria strain collection that included strains with low-abundance in culture-independent samples and included most of the giant panda LAB described by other researchers. The strain collection consisted of 60 strains representing 35 species of 12 genera. Thus, our pipeline is powerful and provides guidance in culturing gut microbiota of interest in hosts such as the giant panda.IMPORTANCECultivation is necessary to screen strains to experimentally investigate microbial traits, and to confirm the activities of novel genes through functional characterization studies. In the long-term, such work can aid in the identification of potential health benefits conferred by bacteria and this could aid in the identification of bacterial candidate strains that can be applied as probiotics. In this study, we developed a pipeline with low-cost and user-friendly culture enrichment to reveal the diversity of LAB in giant pandas. We compared the difference between culture-independent and culture enrichment methods, screened strains of interest that produced high concentrations of short-chain fatty acids (SCFAs), and we investigated the catalog of virulence factors, antibiotic resistance, butyrate and lactate synthesis genes of the strains at a genomic level. This study will provide guidance for microbiota cultivation and a foundation for future research aiming to understand the functions of specific strains.
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Affiliation(s)
- Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
| | - Lijun Zheng
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Junjin Xie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Xiaoyan Su
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu, Sichuan, China
| | - He Huang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | | | - Shizhang Du
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
| | - Yu Yang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Jiqin Xie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Qinrong Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Shuran Yu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Qiang Guo
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Hairui Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Kong Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
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26
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Zeng J, Iizaka Y, Hamada M, Iwai A, Takeuchi R, Fukumoto A, Tamura T, Anzai Y. Actinoplanes kirromycinicus sp. nov., isolated from soil. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00756-w. [PMID: 38926493 DOI: 10.1038/s41429-024-00756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/22/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
A novel actinomycete, designated as TPMA0078T, was isolated from a soil sample collected in Shinjuku, Tokyo, Japan. 16S rRNA gene sequence analysis indicated that strain TPMA0078T belongs to the genus Actinoplanes and is closely related to Actinoplanes regularis IFO 12514T (99.86% 16S rRNA gene sequence similarity). The spores of strain TPMA0078T were motile, and the sporangia were cylindrical. The diamino acids in the cell wall peptidoglycan of strain TPMA0078T were meso-diaminopimelic acid and 3OH-meso-diaminopimelic acid. Whole-cell sugars were glucose and mannose, with galactose as a minor component. The major cellular fatty acids identified were iso-C15:0, iso-C16:0, and anteiso-C17:0. The predominant menaquinone was MK-9(H4), and the principal polar lipid was phosphatidylethanolamine. These chemotaxonomic properties of strain TPMA0078T were consistent with those of Actinoplanes. Meanwhile, digital DNA-DNA hybridization and average nucleotide identity values showed low relatedness between strain TPMA0078T and A. regularis NBRC 12514T. Furthermore, several phenotypic properties of strain TPMA0078T distinguished it from those of closely related species. Based on its genotypic and phenotypic characteristics, strain TPMA0078T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes kirromycinicus sp. nov. is proposed. The type strain is TPMA0078T (=NBRC 116422T = TBRC 18262T).
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Affiliation(s)
- Jiahao Zeng
- Faculty of Pharmaceutical Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Yohei Iizaka
- Faculty of Pharmaceutical Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan.
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Aya Iwai
- Faculty of Pharmaceutical Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Riku Takeuchi
- Faculty of Pharmaceutical Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Atsushi Fukumoto
- Faculty of Pharmaceutical Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yojiro Anzai
- Faculty of Pharmaceutical Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
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27
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Mahmoud FM, Pritsch K, Siani R, Benning S, Radl V, Kublik S, Bunk B, Spröer C, Schloter M. Comparative genomic analysis of strain Priestia megaterium B1 reveals conserved potential for adaptation to endophytism and plant growth promotion. Microbiol Spectr 2024:e0042224. [PMID: 38916310 DOI: 10.1128/spectrum.00422-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
In our study, we aimed to explore the genomic and phenotypic traits of Priestia megaterium strain B1, which was isolated from root material of healthy apple plants, to adapt to the endophytic lifestyle and promote plant growth. We identified putative genes encoding proteins involved in chemotaxis, flagella biosynthesis, biofilm formation, secretory systems, detoxification, transporters, and transcription regulation. Furthermore, B1 exhibited both swarming and swimming motilities, along with biofilm formation. Both genomic and physiological analyses revealed the potential of B1 to promote plant growth through the production of indole-3-acetic acid and siderophores, as well as the solubilization of phosphate and zinc. To deduce potential genomic features associated with endophytism across members of P. megaterium strains, we conducted a comparative genomic analysis involving 27 and 31 genomes of strains recovered from plant and soil habitats, respectively, in addition to our strain B1. Our results indicated a closed pan genome and comparable genome size of strains from both habitats, suggesting a facultative host association and adaptive lifestyle to both habitats. Additionally, we performed a sparse Partial Least Squares Discriminant Analysis to infer the most discriminative functional features of the two habitats based on Pfam annotation. Despite the distinctive clustering of both groups, functional enrichment analysis revealed no significant enrichment of any Pfam domain in both habitats. Furthermore, when assessing genetic elements related to adaptation to endophytism in each individual strain, we observed their widespread presence among strains from both habitats. Moreover, all members displayed potential genetic elements for promoting plant growth.IMPORTANCEBoth genomic and phenotypic analyses yielded valuable insights into the capacity of P. megaterium B1 to adapt to the plant niche and enhance its growth. The comparative genomic analysis revealed that P. megaterium members, whether derived from soil or plant sources, possess the essential genetic machinery for interacting with plants and enhancing their growth. The conservation of these traits across various strains of this species extends its potential application as a bio-stimulant in diverse environments. This significance also applies to strain B1, particularly regarding its application to enhance the growth of plants facing apple replant disease conditions.
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Affiliation(s)
- Fatma M Mahmoud
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Karin Pritsch
- Research Unit for Environmental Simulations, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Environmental Microbiology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
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Millán-López S, Zurita-Artaloitia JM, Silva-Jiménez H, Pardo-López L, Sanchez-Flores A. Genomic sequence of three hydrocarbonoclastic pseudomonadaceae strains isolated from marine sediments of the port of Rosarito, Baja California, Mexico. Microbiol Resour Announc 2024:e0033524. [PMID: 38916305 DOI: 10.1128/mra.00335-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/24/2024] [Indexed: 06/26/2024] Open
Abstract
We report the draft genome sequence of three marine bacteria belonging to Pseudomonas and Stutzerimonas genera, with hydrocarbonoclastic metabolism for oil and monoaromatic hydrocarbon degradation. The genomic information of these organisms contributes to the knowledge of natural and polluted marine environments with ubiquitous presence of hydrocarbons as a selective pressure.
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Affiliation(s)
- Sofía Millán-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Juan M Zurita-Artaloitia
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Hortencia Silva-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Dao VHT, Nguyen LT, Tran PMT, Nguyen TX, Le HHT, Dinh ST. Whole-genome sequence of Micrococcus sp. strain HOU01 isolated from potato root. Microbiol Resour Announc 2024:e0026824. [PMID: 38916298 DOI: 10.1128/mra.00268-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Endophytes play important roles in potato production. The whole genome of endophytic Micrococcus sp. Strain HOU01, isolated from potato root grown at Vietnam National University of Agriculture, Hanoi, Vietnam, was sequenced using Oxford Nanopore's PromethION platform. The complete circular genome is 2,552,707 bp with a GC content of 72.5%.
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Affiliation(s)
| | - Loan To Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
| | - Phuong Minh Thi Tran
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Truong Xuan Nguyen
- Institute of Agrobiology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | | | - Son Truong Dinh
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
- Institute of Agrobiology, Vietnam National University of Agriculture, Hanoi, Vietnam
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Wang S, Yuan C, Xu C, Li D, Zhang H, Wang J, Wang X, Li Y, Jiao D, Yuan S, Chen H, Qiu D. Denitrificimonas halotolerans sp. nov., a novel species isolated from UASB sludge treating landfill leachate. Antonie Van Leeuwenhoek 2024; 117:91. [PMID: 38907751 DOI: 10.1007/s10482-024-01987-5] [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: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
A Gram-stain-negative, facultative anaerobe, rod-shaped strain JX-1T was isolated from UASB sludge treating landfill leachate in Wuhan, China. The isolate is capable of growing under conditions of pH 6.0-11.0 (optimum, pH 7.0-8.0), temperature 4-42 ℃ (optimum, 20-30 ℃), 0-8.0% (w/v) NaCl (optimum, 5.0%), and ammonia nitrogen concentration of 200-5000 mg/L (optimum, 500 mg/L) on LB plates. The microorganism can utilize malic acid, D-galactose, L-rhamnose, inosine, and L-glutamic acid as carbon sources, but does not reduce nitrates and nitrites. The major fatty acids are C18:1ω7c/C18:1ω6c, iso-C15:0, and anteiso-C15:0. The respiratory quinones are Q9 (91.92%) and Q8 (8.08%). Polar lipids include aminolipid, aminophospholipid, diphosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylglycerol, and phospholipid. Compared with other strains, strain JX-1T and Denitrificimonas caeni HY-14T have the highest values in terms of 16S rRNA gene sequence similarity (96.79%), average nucleotide identity (ANI; 76.06%), and average amino acid identity (AAI; 78.89%). Its digital DNA-DNA hybridization (dDDH) result is 20.3%. The genome of strain JX-1T, with a size of 2.78 Mb and 46.12 mol% G + C content, lacks genes for denitrification and dissimilatory nitrate reduction to ammonium (DNRA), but contains genes for ectoine synthesis as a secondary metabolite. The results of this polyphasic study allow genotypic and phenotypic differentiation of the analysed strain from the closest related species and confirm that the strain represents a novel species within the genus Denitrificimonas, for which the name Denitrificimonas halotolerans sp. nov. is proposed with JX-1T (= MCCC 1K08958T = KCTC 8395T) as the type strain.
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Affiliation(s)
- Shanhui Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chu Yuan
- Unikleen Filtration Technology (Wuhan) Co., Ltd, Wuhan, 430205, China
| | - Chengbin Xu
- Unikleen Filtration Technology (Wuhan) Co., Ltd, Wuhan, 430205, China
| | - Ditian Li
- Unikleen Filtration Technology (Wuhan) Co., Ltd, Wuhan, 430205, China
| | - Han Zhang
- Unikleen Filtration Technology (Wuhan) Co., Ltd, Wuhan, 430205, China
| | - Jing Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Li
- China University of Geosciences (CUG), Wuhan, 430074, China
| | - Dian Jiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siliang Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Han Chen
- Jingchu University of Technology, Jingmen, 448000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongru Qiu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Tomita S, Nakai R, Kuroda K, Kurashita H, Hatamoto M, Yamaguchi T, Narihiro T. Corallococcus caeni sp. nov., a novel myxobacterium isolated from activated sludge. Arch Microbiol 2024; 206:317. [PMID: 38904779 DOI: 10.1007/s00203-024-04037-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 06/22/2024]
Abstract
Two myxobacterial strains (KH5-1T and NO1) were isolated from the activated sludge tanks treating municipal sewage wastewater in Japan. These strains were recognised as myxobacteria based on their phenotypic characteristics of swarming colonies and fruiting bodies. Phylogenetic analyses using the 16S rRNA gene revealed that strains KH5-1T and NO1 were affiliated with the genus Corallococcus, with the closest neighbours being Corallococcus exercitus AB043AT (99.77% and 99.84%, respectively). Genome comparisons using orthologous average nucleotide identity (orthoANI) and digital DNA-DNA hybridisation similarity (dDDH) with strains KH5-1T and NO1 and their phylogenetically close relatives in Corallococcus spp. were below the thresholds. The major cellular fatty acids of strains KH5-1T and NO1 were iso-C15:0 (31.9%, 30.0%), summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) (20.2%, 17.7%), and iso-C17:0 (12.1%, 14.8%), and the major respiratory quinone was found to be menaquinone (MK)-8. Based on the phenotypic, chemotaxonomic, and phylogenetic evidence, strains KH5-1T and NO1 represent a new species in the genus Corallococcus, for which the proposed name is Corallococcus caeni sp. nov. The type strain is KH5-1T (= NCIMB 15510T = JCM 36609T).
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Affiliation(s)
- Shun Tomita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan.
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Hazuki Kurashita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan.
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Zang M, Ma ZH, Xu YL, Long XF. Taxonomic identification, phenol biodegradation and soil remediation of the strain Rhodococcus sacchari sp. nov. Z13 T. Arch Microbiol 2024; 206:313. [PMID: 38900186 DOI: 10.1007/s00203-024-04048-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
Phenols are highly toxic chemicals that are extensively used in industry and produce large amounts of emissions. Notably, phenols released into the soil are highly persistent, causing long-term harm to human health and the environment. In this study, a gram-positive, aerobic, and rod-shaped bacterial strain, Z13T, with efficient phenol degradation ability, was isolated from the soil of sugarcane fields. Based on the physiological properties and genomic features, strain Z13T is considered as a novel species of the genus Rhodococcus, for which the name Rhodococcus sacchari sp. nov. is proposed. The type strain is Z13T (= CCTCC AB 2022327T = JCM 35797T). This strain can use phenol as its sole carbon source. Z13T was able to completely degrade 1200 mg/L phenol within 20 h; the maximum specific growth rate was μmax = 0.93174 h-1, and the maximum specific degradation rate was qmax = 0.47405 h-1. Based on whole-genome sequencing and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, strain Z13T contains a series of phenol degradation genes, including dmpP, CatA, dmpB, pcaG, and pcaH, and can metabolize aromatic compounds. Moreover, the potential of strain Z13T for soil remediation was investigated by introducing Z13T into simulated phenol-contaminated soil, and the soil microbial diversity was analyzed. The results showed that 100% of the phenol in the soil was removed within 7.5 d. Furthermore, microbial diversity analysis revealed an increase in the relative species richness of Oceanobacillus, Chungangia, and Bacillus.
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Affiliation(s)
- Meng Zang
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, People's Republic of China
- Guangxi Key Laboratory of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, People's Republic of China
| | - Zhen-Hua Ma
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, People's Republic of China
- Guangxi Key Laboratory of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, People's Republic of China
| | - Yu-Lei Xu
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, People's Republic of China
- Guangxi Key Laboratory of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, People's Republic of China
| | - Xiu-Feng Long
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, People's Republic of China.
- Guangxi Key Laboratory of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, People's Republic of China.
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Du Y, Han W, Hao P, Hu Y, Hu T, Zeng Y. A Genomics-Based Discovery of Secondary Metabolite Biosynthetic Gene Clusters in the Potential Novel Strain Streptomyces sp. 21So2-11 Isolated from Antarctic Soil. Microorganisms 2024; 12:1228. [PMID: 38930610 PMCID: PMC11205464 DOI: 10.3390/microorganisms12061228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Streptomyces species are attractive sources of secondary metabolites that serve as major sources of antibiotics and other drugs. In this study, genome mining was used to determine the biosynthetic potential of Streptomyces sp. 21So2-11 isolated from Antarctic soil. 16S rRNA gene sequencing revealed that this strain is most closely related to Streptomyces drozdowiczii NBRC 101007T, with a similarity of 98.02%. Genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) showed that strain 21So2-11 represents a novel species of the genus Streptomyces. In addition to a large number of genes related to environmental adaptation and ecological function, a total of 28 putative biosynthetic gene clusters (BGCs) responsible for the biosynthesis of known and/or novel secondary metabolites, including terpenes, lantipeptides, polyketides, nonribosomal peptides, RiPPs and siderophores, were detected in the genome of strain 21So2-11. In addition, a total of 1456 BGCs were predicted to contribute to the biosynthesis of more than 300 secondary metabolites based on the genomes of 47 Streptomyces strains originating from polar regions. The results indicate the potential of Streptomyces sp. 21So2-11 for bioactive secondary metabolite production and are helpful for understanding bacterial adaptability and ecological function in cold terrestrial environments.
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Affiliation(s)
- Yu Du
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
| | - Wei Han
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
| | - Puyu Hao
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Yongqiang Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
| | - Ting Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
| | - Yinxin Zeng
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
- Shanghai Key Laboratory of Polar Life and Environment Sciences, Shanghai Jiao Tong University, Shanghai 200030, China
- Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Ministry of Education, Shanghai 200030, China
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Sukpanoa S, Kaewkla O, Suriyachadkun C, Papayrata C, Klankeo P, Franco CMM. Streptomyces mahasarakhamensis sp. nov., an Endophytic Actinobacterium Isolated from Jasmine Rice and its Potential as plant Growth Promoter. Curr Microbiol 2024; 81:223. [PMID: 38874598 DOI: 10.1007/s00284-024-03747-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/19/2024] [Indexed: 06/15/2024]
Abstract
Two endophytic actinobacteria, strains MK5T and MK7, were isolated from the surface-sterilized root of Jasmine rice (Oryza sativa KDML 105). These strains were aerobic actinobacteria with a well-developed substrate and aerial mycelia that formed spiral spore chains. The type strains that shared the high 16S rRNA gene sequence similarity with both strains were Streptomyces naganishii NBRC 12892T (99.4%), "Streptomyces griseicoloratus" TRM S81-3T (99.2%), and Streptomyces spiralis NBRC 14215T (98.9%). Strains MK5T and MK7 are the same species sharing a digital DNA-DNA hybridization (dDDH) value of 95.3% and a 16S rRNA gene sequence similarity of 100%. Chemotaxonomic data confirmed the affiliation of strains MK5T and MK7 to the genus Streptomyces. Strains MK5T and MK7 contained MK-9(H4) as a major menaquinone; the whole-cell sugar of both strains was galactose and glucose. The strain MK5T shared 93.4% average nucleotide identity (ANI)-Blast, 95.5% ANI-MUMmer, 93% average amino acid identity, and 61.3% dDDH with S. spiralis NBRC 14215T. The polyphasic approach confirmed that strain MK5T represents a novel species, and the name Streptomyces mahasarakhamensis sp. nov. is proposed. The type strain is MK5T (= TBRC 17754 = NRRL B-65683). Genome mining, using an in silico approach and searching biosynthesis gene clusters of strains MK5T and MK7, revealed that the genomes contained genes encoding proteins relating to plant growth promotion, bioactive compounds, and beneficial enzymes. Strains MK5T and MK7 could produce indole acetic acid and solubilize phosphate in vitro.
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Affiliation(s)
- Sudarat Sukpanoa
- Faculty of Science, Department of Biology, Mahasarakham University, Kham Riang, 44150, Maha Sarakham Province, Thailand
| | - Onuma Kaewkla
- Faculty of Science, Department of Biology, Mahasarakham University, Kham Riang, 44150, Maha Sarakham Province, Thailand.
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, 12120, Pathumthani, Thailand
| | - Chanakran Papayrata
- Central Laboratory of Mahasarakham University, Mahasarakham University, Kham Riang, 44150, Maha Sarakham Province, Thailand
| | - Piriya Klankeo
- Faculty of Science, Omics Science and Bioinformatics Center, Chulalongkorn University, Pathumwan, 10330, Bangkok, Thailand
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Malfent F, Zehl M, Kirkegaard RH, Oberhofer M, Zotchev SB. Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum. Front Microbiol 2024; 15:1408479. [PMID: 38946903 PMCID: PMC11212599 DOI: 10.3389/fmicb.2024.1408479] [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: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 07/02/2024] Open
Abstract
Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.
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Affiliation(s)
- Fabian Malfent
- Division of Pharmacognosy, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rasmus H. Kirkegaard
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Martina Oberhofer
- Division of Pharmacognosy, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Sergey B. Zotchev
- Division of Pharmacognosy, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
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Wang X, Pan H, Zhou H, Feng Z, Li A, Guan X. Draft genome of Pseudomonas sp. XK-1, a marine bacterium capable of degrading lignin and Mn(II) oxidation. Microbiol Resour Announc 2024:e0041124. [PMID: 38864618 DOI: 10.1128/mra.00411-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
We report the draft genome sequence of marine bacteria, Pseudomonas sp. XK-1. Strain XK-1 could facilitate Mn(II) oxidation with lignin as the sole carbon source. The genome length of XK-1 is 4,751,776 bp, with a G + C content of 62.61%. Genome analyses reveal the carbon and manganese cycling driven by bacteria.
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Affiliation(s)
- Xukang Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, Panjin, China
| | - Haixia Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, Panjin, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, Panjin, China
| | - Zhongqing Feng
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, Panjin, China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Xiaoyan Guan
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
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Cea-Torrescassana E, Howard TP, Stach J, Montero-Calasanz MDC. Whole-genome sequence of the plant-associated bacterium Pseudomonas granadensis CT364 isolated in Seville, Spain. Microbiol Resour Announc 2024; 13:e0073523. [PMID: 38682778 DOI: 10.1128/mra.00735-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
Pseudomonas sp. CT364 was isolated from olive tree rhizosphere in Seville (Spain). We report its complete genome sequence, acquired by co-assembling Illumina and Nanopore reads. The genome comprises a circular chromosome of 6.2 Mbp and a G + C content of 60.0%. Taxonomic analyses confirmed it to be Pseudomonas granadensis.
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Affiliation(s)
- Eva Cea-Torrescassana
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas P Howard
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jem Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maria Del Carmen Montero-Calasanz
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- IFAPA Las Torres- Andalusian Institute of Agricultural and Fisheries Research and Training, Junta de Andalucía, Cra. Sevilla-Cazalla, Alcalá del Río, Seville, Spain
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Kundlacz C, Aldeia C, Eddoubaji Y, Campos-Madueno EI, Endimiani A. Complete genome sequence of Pseudomonas canadensis strain Pcan-CK-23 isolated from Zophobas morio larvae. Microbiol Resour Announc 2024; 13:e0002324. [PMID: 38682776 DOI: 10.1128/mra.00023-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
We present the complete genome sequence of Pseudomonas canadensis. The strain (Pcan-CK-23) was isolated from Zophobas morio (superworm) larvae. The genome consisted of a 6,424,469 bp chromosome with a GC content of 60.3% and 5,973 genes. Pcan-CK-23 can be used as a reference genome for further studies with P. canadensis.
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Affiliation(s)
- Cindy Kundlacz
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Yasmine Eddoubaji
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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Ramzan R, Ali A, Farooq M, Ali H, Khaliq S, Rashid MH. Draft genome sequence of extracellular enzyme-producing Bacillus paralicheniformis strain NBG-07. Microbiol Resour Announc 2024:e0009624. [PMID: 38860803 DOI: 10.1128/mra.00096-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024] Open
Abstract
The genome of Bacillus paralicheniformis strain NBG-07 was sequenced using Illumina sequencing due to its ability to produce thermostable enzymes of industrial importance. The strain was isolated from the soil. Annotation of the draft genome revealed genes involved in the production of different enzymes, including alpha-amylase, protease, cellulase, and laccase.
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Affiliation(s)
- Rubab Ramzan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Asad Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Hamid Rashid
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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40
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Attéré SA, Piché LC, Intertaglia L, Lami R, Charette SJ, Vincent AT. Complete sequences of two Paenibacillus sp. strains and one Lysinibacillus strain isolated from the environment on STAA medium highlight biotechnological potential. Microbiol Resour Announc 2024; 13:e0019924. [PMID: 38682917 DOI: 10.1128/mra.00199-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024] Open
Abstract
Streptomycin thallous acetate actidione medium is typically used to isolate Brochothrix thermosphacta bacteria from food. Using this medium, three bacterial strains were isolated from the environment. Genomic sequences demonstrated that these bacteria are of the genera Lysinibacillus and Paenibacillus and are of biotechnological interest.
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Affiliation(s)
- Sabrina A Attéré
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Hôpital Laval, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
| | - Laurie C Piché
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, rue de l'Agriculture, Université Laval, Quebec City, Quebec, Canada
| | - Laurent Intertaglia
- Sorbonne Université, CNRS, Bio2mar, Observatoire Océanologique de Banyuls-sur-Mer, Avenue Pierre Fabre, Banyuls-sur-Mer, France
| | - Raphaël Lami
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, Observatoire Océanologique de Banyuls-sur-Mer, Avenue Pierre Fabre, Banyuls-sur-Mer, France
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Hôpital Laval, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
| | - Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, rue de l'Agriculture, Université Laval, Quebec City, Quebec, Canada
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Tanaka T, Okano K, Iwaki H. Complete genome sequence of Paraburkholderia terrae strain KU-46, a 2,4-dinitrophenol-degrading bacterium. Microbiol Resour Announc 2024; 13:e0028224. [PMID: 38700342 DOI: 10.1128/mra.00282-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
Paraburkholderia terrae strain KU-46 has been studied for its capability to degrade 2,4-dinitrophenol. Here, we present the complete 10,833,180bp genome of this microorganism, comprising five circular chromosomes housing 9,797 protein-coding sequences. The genes responsible for 2,4-dinitrophenol and 4-nitrophenol degradation are located on chromosome 2.
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Affiliation(s)
- Tomoki Tanaka
- Department of Life Science and Biotechnology, Kansai University, Suita, Osaka, Japan
| | - Kenji Okano
- Department of Life Science and Biotechnology, Kansai University, Suita, Osaka, Japan
| | - Hiroaki Iwaki
- Department of Life Science and Biotechnology, Kansai University, Suita, Osaka, Japan
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Dai M, Xu Y, Zhao L, Wu M, Ma H, Zhu L, Li W, Li X, Sun B. Caproicibacter sp. BJN0012, a potential new species isolated from cellar mud for caproic acid production from glucose. J Biotechnol 2024; 388:11-23. [PMID: 38614441 DOI: 10.1016/j.jbiotec.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Abstract
Acids play a crucial role in enhancing the flavor of strong-aroma Baijiu, and among them, caproic acid holds significant importance in determining the flavor of the final product. However, the metabolic synthesis of caproic acid during the production process of Baijiu has received limited attention, resulting in fluctuations in caproic acid content among fermentation batches and generating production instability. Acid-producing bacteria found in the cellar mud are the primary microorganisms responsible for caproic acid synthesis, but there is a lack of research on the related microbial resources and their metabolic properties. Therefore, it is essential to identify and investigate these acid-producing microorganisms from cellar mud to ensure stable caproic acid synthesis. In this study, a unique strain was isolated from the cellar mud, exhibiting a 98.12 % similarity in its 16 S rRNA sequence and an average nucleotide identity of 79.57 % with the reference specie, together with the DNA-DNA hybridization of 23.20 % similarity, confirming the distinct species boundaries. The strain was able to produce 1.22 ± 0.55 g/L caproic acid from glucose. Through genome sequencing, annotation, and bioinformatics analysis, the complete pathway of caproic acid synthesis from glucose was elucidated, and the catalytic mechanism of the key thiolase for caproic acid synthesis was investigated. These findings provide useful fundamental data for revealing the metabolic properties of caproic acid-producing bacteria found in cellar mud.
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Affiliation(s)
- Mengqi Dai
- School of Food and Health, Beijing Technology and Businmmess University, Beijing 100048, China
| | - Youqiang Xu
- School of Food and Health, Beijing Technology and Businmmess University, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China.
| | - Lei Zhao
- School of Food and Health, Beijing Technology and Businmmess University, Beijing 100048, China
| | - Mengqin Wu
- School of Food and Health, Beijing Technology and Businmmess University, Beijing 100048, China
| | - Huifeng Ma
- Hebei Fenglaiyi Wine Industry Co., Ltd, Xingtai, Hebei province 055550, China
| | - Lining Zhu
- Hebei Fenglaiyi Wine Industry Co., Ltd, Xingtai, Hebei province 055550, China
| | - Weiwei Li
- School of Food and Health, Beijing Technology and Businmmess University, Beijing 100048, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Xiuting Li
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 102401, China.
| | - Baoguo Sun
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing 100048, China
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Ercole TG, Kava VM, Petters-Vandresen DAL, Nassif Gomes ME, Aluizio R, Ribeiro RA, Hungria M, Galli LV. Unlocking the growth-promoting and antagonistic power: A comprehensive whole genome study on Bacillus velezensis strains. Gene 2024; 927:148669. [PMID: 38866259 DOI: 10.1016/j.gene.2024.148669] [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: 02/29/2024] [Revised: 05/14/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Bacillus species are extensively documented as plant growth-promoting rhizobacteria, contributing significantly to the enhancement of soil fertility, nutrient recycling, and the control of phytopathogens. Utilizing them as biocontrol agents represents an environmentally friendly strategy, particularly within the rhizospheric community. This study presents the comprehensive genome sequences of three B. velezensis strains (LGMB12, LGMB319, and LGMB426) which were previously isolated from root samples of maize (Zea mays L.), along with a type strain FZB42. The research assesses the capability of the three strains for antagonizing fungi, specifically Fusarium graminearum, Fusarium verticillioides, Colletotrichum graminicola, and Stenocarpella sp. In paired cultures involving maize fungi, treatments containing bacteria B. velezensis exhibited statistically significant differences compared to both negative and positive treatments in terms of antagonism. Furthermore, genome mining techniques were employed to explore their inherent antagonistic potential. The assembly revealed that strains LGMB12, LGMB319, LGMB426, and FZB42 exhibit genome sizes of 4,187,541 bp, 4,244,954 bp, 3,976,537 bp, and 3,990,518 respectively. Their respective G + C content stands at 46.42 %, 46.50 %, 46.51 %, and 46.38 %. Moreover, the genomes present multiple gene clusters responsible for the synthesis of secondary metabolites and carbohydrate-active enzymes (CAZymes). These clusters highlight a diverse array of antibacterial and antifungal properties, complemented by numerous plant growth-promoting genes. These results highlight the potential of B. velezensis LGMB12, LGMB319, and LGMB426 strains as biocontrol and plant growth promotion agents, being promising candidates for further studies in agricultural production, including field trials.
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Affiliation(s)
- Tairine Graziella Ercole
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Vanessa Merlo Kava
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Desirrê Alexia Lourenço Petters-Vandresen
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Maria Eduarda Nassif Gomes
- Pontifical Catholic University of Paraná, Imaculada Conceição St., 1155, 80215-901 Curitiba, PR, Brazil.
| | - Rodrigo Aluizio
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil.
| | | | - Lygia Vitoria Galli
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
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Pal S, Yuvaraj R, Krishnan H, Venkatraman B, Abraham J, Gopinathan A. Unraveling radiation resistance strategies in two bacterial strains from the high background radiation area of Chavara-Neendakara: A comprehensive whole genome analysis. PLoS One 2024; 19:e0304810. [PMID: 38857267 PMCID: PMC11164402 DOI: 10.1371/journal.pone.0304810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/18/2024] [Indexed: 06/12/2024] Open
Abstract
This paper reports the results of gamma irradiation experiments and whole genome sequencing (WGS) performed on vegetative cells of two radiation resistant bacterial strains, Metabacillus halosaccharovorans (VITHBRA001) and Bacillus paralicheniformis (VITHBRA024) (D10 values 2.32 kGy and 1.42 kGy, respectively), inhabiting the top-ranking high background radiation area (HBRA) of Chavara-Neendakara placer deposit (Kerala, India). The present investigation has been carried out in the context that information on strategies of bacteria having mid-range resistance for gamma radiation is inadequate. WGS, annotation, COG and KEGG analyses and manual curation of genes helped us address the possible pathways involved in the major domains of radiation resistance, involving recombination repair, base excision repair, nucleotide excision repair and mismatch repair, and the antioxidant genes, which the candidate could activate to survive under ionizing radiation. Additionally, with the help of these data, we could compare the candidate strains with that of the extremely radiation resistant model bacterium Deinococccus radiodurans, so as to find the commonalities existing in their strategies of resistance on the one hand, and also the rationale behind the difference in D10, on the other. Genomic analysis of VITHBRA001 and VITHBRA024 has further helped us ascertain the difference in capability of radiation resistance between the two strains. Significantly, the genes such as uvsE (NER), frnE (protein protection), ppk1 and ppx (non-enzymatic metabolite production) and those for carotenoid biosynthesis, are endogenous to VITHBRA001, but absent in VITHBRA024, which could explain the former's better radiation resistance. Further, this is the first-time study performed on any bacterial population inhabiting an HBRA. This study also brings forward the two species whose radiation resistance has not been reported thus far, and add to the knowledge on radiation resistant capabilities of the phylum Firmicutes which are abundantly observed in extreme environment.
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Affiliation(s)
- Sowptika Pal
- Molecular Endocrinology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramani Yuvaraj
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Hari Krishnan
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Balasubramanian Venkatraman
- Radiological and Environmental Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Jayanthi Abraham
- Microbial Biotechnology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anilkumar Gopinathan
- Molecular Endocrinology Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Stoll DA, Grimmler C, Hetzer B, Masoura A, Kulling SE, Huch M. Bosea rubneri sp. nov. Isolated from Organically Grown Allium cepa. Curr Microbiol 2024; 81:212. [PMID: 38839619 PMCID: PMC11153308 DOI: 10.1007/s00284-024-03717-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
Strain ZW T0_25T was isolated from an onion sample (Allium cepa var. Hytech F1) within a storage trial and proofed to be a novel, aerobic, Gram-stain negative, rod-shaped bacterial strain. Analyses of the 16S rRNA gene sequence and of the whole draft genome sequences, i.e., digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) showed that this strain represents a new species of the genus Bosea. The genome size of strain ZW T0_25T is 6.19 Mbp, and the GC content is 66.9%. As whole cell sugars, rhamnose, ribose and glucose were identified. Ubiquinone Q-10 is the major respiratory quinone with 97.8%. Polar lipids in strain ZW T0_25T are composed of one phosphatidylethanolamine, one phosphatidylglycerol, one aminophospholipid, two aminolipids, one glycolipid and two phospholipids whereas the fatty acid profile predominantly consists of C18:1 w7c (63.3%), C16:1 w7c (19.5%) and C16:0 (7.1%). Phenotypic traits were tested in the wet lab as well as predicted in silico from genome data. Therefore, according to this polyphasic approach, the new name Bosea rubneri sp. nov. with the type strain ZW T0_25T (= DSM 116094 T = LMG 33093 T) is proposed.
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Affiliation(s)
- Dominic A Stoll
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Christina Grimmler
- Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, E.-C.-Baumann-Straße 20, 95326, Kulmbach, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Alexandra Masoura
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Sabine E Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Melanie Huch
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany.
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Qiu X, Ye K, Ma Y, Zhao Q, Wang L, Yang J. Genome sequence-based species classification of Enterobacter cloacae complex: a study among clinical isolates. Microbiol Spectr 2024; 12:e0431223. [PMID: 38687068 DOI: 10.1128/spectrum.04312-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
Accurate species-level identification of Enterobacter cloacae complex (ECC) is crucial for related research. The classification of ECC is based on strain-to-strain phylogenetic congruence, as well as genomic features including average nucleotide identity (ANI) and digitalized DNA-DNA hybridization (dDDH). ANI and dDDH derived from whole-genome sequencing have emerged as a reliable metric for assessing genetic relatedness between genomes and are increasingly recognized as a standard for species delimitation. Up to now, there are two different classification methods for ECC. The first one categorizes E. hormaechei, a species within ECC, into five subspecies (E. hormaechei subsp. steigerwaltii, subsp. oharae, subsp. xiangfangensis, subsp. hoffmannii, and subsp. hormaechei). The second classifies E. hormaechei as three species: E. hormaechei, "E. xiangfangensis," "E. hoffmanii." While the former is well-accepted in the academic area, the latter may have a greater ability to distinguish different species of ECC. To assess the suitability of these identification criteria for clinical ECC isolates, we conducted a comprehensive analysis involving phylogenetic analysis, ANI and dDDH value alignment, virulence gene identification, and capsule typing on 256 clinical ECC strains isolated from the bloodstream. Our findings indicated that the method of categorizing E. hormaechei into five subspecies has better correlation and consistency with the molecular characteristics of clinical ECC isolates, as evidenced by phylogenetic analysis, virulence genes, and capsule typing. Therefore, the subspecies-based classification method appears more suitable for taxonomic assignments of clinical ECC isolates. IMPORTANCE Standardizing taxonomy of the Enterobacter cloacae complex (ECC) is necessary for data integration across diverse studies. The study utilized whole-genome data to accurately identify 256 clinical ECC isolated from bloodstream infections using average nucleotide identity (ANI), digitalized DNA-DNA hybridization (dDDH), and phylogenetic analysis. Through comprehensive assessments including phylogenetic analysis, ANI and dDDH comparisons, virulence gene, and capsule typing of the 256 clinical isolates, it was concluded that the classification method based on subspecies exhibited better correlation and consistency with the molecular characteristics of clinical ECC isolates. In summary, this research contributes to the precise identification of clinical ECC at the species level and expands our understanding of ECC.
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Affiliation(s)
- Xuemei Qiu
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
- Medical school of Chinese PLA, Beijing, China
| | - Kun Ye
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanning Ma
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qiang Zhao
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lifeng Wang
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jiyong Yang
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
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Steyaert S, Peeters C, Wieme AD, Muyldermans A, Vandoorslaer K, Spilker T, Wybo I, Piérard D, LiPuma JJ, Vandamme P. Novel Ralstonia species from human infections: improved matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification and analysis of antimicrobial resistance patterns. Microbiol Spectr 2024; 12:e0402123. [PMID: 38661349 DOI: 10.1128/spectrum.04021-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
A collection of 161 Ralstonia isolates, including 90 isolates from persons with cystic fibrosis, 27 isolates from other human clinical samples, 8 isolates from the hospital environment, 7 isolates from industrial samples, and 19 environmental isolates, was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification and yielded confident species level identification scores for only 62 (39%) of the isolates, including four that proved misidentified subsequently. Whole-genome sequence analysis of 32 representative isolates for which no confident MALDI-TOF MS species level identification was obtained revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively, and provided the basis for updating an in-house MALDI-TOF MS database. A reanalysis of all mass spectra with the updated MALDI-TOF MS database increased the percentage of isolates with confident species level identification up to 77%. The antimicrobial susceptibility of 30 isolates mainly representing novel human clinical and environmental Ralstonia species was tested toward 17 antimicrobial agents and demonstrated that the novel Ralstonia species were generally multi-resistant, yet susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline. An analysis of genomic antimicrobial resistance genes in 32 novel and publicly available genome sequences revealed broadly distributed beta-lactam resistance determinants.IMPORTANCEThe present study demonstrated that a commercial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification database can be tailored to improve the identification of Ralstonia species. It also revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively. An analysis of minimum inhibitory concentration values demonstrated that the novel Ralstonia species were generally multi-resistant but susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline.
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Affiliation(s)
- Stephanie Steyaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Astrid Muyldermans
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ingrid Wybo
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Denis Piérard
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
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48
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Stegman N, Steiling M, Jackson B, Sedano C, Putonti C. Draft genome assembly of Lactobacillus johnsonii UMB3423 from a voided urine sample. Microbiol Resour Announc 2024:e0033324. [PMID: 38832771 DOI: 10.1128/mra.00333-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/02/2024] [Indexed: 06/05/2024] Open
Abstract
While the urogenital microbiota of asymptomatic females is often dominated by species of Lactobacillus, Lactobacillus johnsonii is not a common member. It is more frequently found in the gastrointestinal tract. Here, we present the draft genome sequence of L. johnsonii UMB3423, which was isolated from a voided urine sample.
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Affiliation(s)
- Natalie Stegman
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Maria Steiling
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Briana Jackson
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Cerena Sedano
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
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49
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Petakh P, Oksenych V, Khovpey Y, Kamyshnyi O. Comprehensive Analysis of Antiphage Defense Mechanisms: Serovar-Specific Patterns. Antibiotics (Basel) 2024; 13:522. [PMID: 38927188 PMCID: PMC11201134 DOI: 10.3390/antibiotics13060522] [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: 05/05/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
Leptospirosis is a major zoonotic disease caused by pathogenic spirochetes in the genus Leptospira, affecting over a million people annually and causing approximately 60,000 deaths. Leptospira interrogans, a key causative agent, likely possesses defense systems against bacteriophages (leptophages), yet these systems are not well understood. We analyzed 402 genomes of L. interrogans using the DefenseFinder tool to identify and characterize the antiphage defense systems. We detected 24 unique systems, with CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins), PrrC, Borvo, and Restriction-Modification (R-M) being the most prevalent. Notably, Cas were identified in all strains, indicating their central role in phage defense. Furthermore, there were variations in the antiphage system distribution across different serovars, suggesting unique evolutionary adaptations. For instance, Retron was found exclusively in the Canicola serovar, while prokaryotic Argonaute proteins (pAgo) were only detected in the Grippotyphosa serovar. These findings significantly enhance our understanding of Leptospira's antiphage defense mechanisms. They reveal the potential for the development of serovar-specific phage-based therapies and underscore the importance of further exploring these defense systems.
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Affiliation(s)
- Pavlo Petakh
- Department of Biochemistry and Pharmacology, Uzhhorod National University, 88000 Uzhhorod, Ukraine; (P.P.); (Y.K.)
- Department of Microbiology, Virology and Immunology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Yevheniya Khovpey
- Department of Biochemistry and Pharmacology, Uzhhorod National University, 88000 Uzhhorod, Ukraine; (P.P.); (Y.K.)
| | - Oleksandr Kamyshnyi
- Department of Microbiology, Virology and Immunology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
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50
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Yasawong M, Songngamsuk T, Phatcharaharikarn M, Sriyapai P, Silprasit K, Ngamniyom A, Sriyapai T. Draft genome sequence data of multidrug-resistant Pseudomonas aeruginosa WO7 from a hospital wastewater treatment plant in Thailand. Data Brief 2024; 54:110344. [PMID: 38586145 PMCID: PMC10997946 DOI: 10.1016/j.dib.2024.110344] [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: 02/24/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
Multidrug-resistant Pseudomonas aeruginosa WO7 was isolated from an untreated water sample from a hospital wastewater treatment plant in Thailand. This report presents the draft genome sequence data of P. aeruginosa WO7. Genomic DNA was obtained from a pure culture of P. aeruginosa WO7, and paired-end reads were generated using an Illumina MiSeq sequencer. The draft genome consisted of 111 contigs with a total size of 6,784,206 base pairs, an N50 of 209,424 base pairs, and a GC content of 65.85%. The dDDH value between WO7 and Pseudomonas aeruginosa DSM 50071T was determined to be 90.7%, indicating that the strain is Pseudomonas aeruginosa. The data presented indicate the potential for bacterial classification, comparative genomics, comprehensive analysis of antimicrobial resistance, and assessment of bacterial virulence factors in P. aeruginosa. The draft genome sequence data have been deposited at the NCBI under Bioproject accession number PRJNA550309.
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Affiliation(s)
- Montri Yasawong
- Program on Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Thunwarat Songngamsuk
- Program on Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | | | - Pichapak Sriyapai
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Kun Silprasit
- Faculty of Environmental Culture and Ecotourism, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Arin Ngamniyom
- Faculty of Environmental Culture and Ecotourism, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Thayat Sriyapai
- Faculty of Environmental Culture and Ecotourism, Srinakharinwirot University, Bangkok 10110, Thailand
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