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Etheridge T, Swiston C, Harrie RP, Bernstein PS. ACUTE POST-TRAUMATIC ENDOPHTHALMITIS SECONDARY TO BACILLUS PUMILUS / SAFENSIS. Retin Cases Brief Rep 2024; 18:305-307. [PMID: 36729827 DOI: 10.1097/icb.0000000000001391] [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: 10/23/2022] [Accepted: 11/26/2022] [Indexed: 02/03/2023]
Abstract
PURPOSE To report a case of post-traumatic endophthalmitis secondary to Bacillus pumilus/safensis . METHODS Observational case report of a single patient. RESULTS A 62-year-old man presented with a traumatic corneal laceration because of baling wire while working on a sheep farm. Appropriate corneal laceration repair with injection of intravitreal antibiotics (ceftazidime, clindamycin, and vancomycin) was performed. A single organism, identified as B. pumilus or Bacillus safensis, was isolated from the vitreous aspirate. A subsequent pars plana vitrectomy, pars plana lensectomy, anterior capsulotomy, and fluid-air exchange was required because of severe inflammatory reaction from retained lens material, retinal edema, and vitreous opacities. Vision improved from hand motion to 20/60 at the three-month follow-up visit. CONCLUSION We describe a case of acute post-traumatic endophthalmitis secondary to B. pumilus/safensis.
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Affiliation(s)
- Tyler Etheridge
- John A. Moran Eye Center, University of Utah, Salt Lake City, Utah
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2
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Xia J, Si H, Huang X, Chen X, Fu X, Li G, Lai Q, Li F, Wang W, Shao Z. Metabolomics and Molecular Networking-Guided Screening of Bacillus-Derived Bioactive Compounds Against a Highly Lethal Vibrio Species. Anal Chem 2024; 96:4359-4368. [PMID: 38452345 DOI: 10.1021/acs.analchem.3c02958] [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: 03/09/2024]
Abstract
Microorganisms are important sources of bioactive natural products. However, the complexity of microbial metabolites and the low abundance of active compounds render the isolation and purification process laborious and inefficient. During our search for active substances capable of inhibiting the newly discovered highly lethal Vibrio strain vp-HL, we found that the fermentation broth of multiple Bacillus strains exhibited antibacterial activity. However, the substances responsible for the activity remained unclear. Metabolomics, molecular networking (MN), and the Structural similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS) were employed in conjunction with bioactivity screening to predict the antibacterial compounds from Bacillus strains. The analysis of fractions, and their isolation, NMR-based annotation, and bioactivity evaluation of an amicoumacin compound partially confirmed the prediction from these statistical analyses. This work presents the potential of marine Bacillus in producing active substances against Vibrio species. Additionally, it highlighted the significance and feasibility of metabolomics and MN in the dereplication of compounds and the determination of isolation targets.
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Affiliation(s)
- Jinmei Xia
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Hongkun Si
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Xiaomei Huang
- Department of Marine Biology, Xiamen Ocean Vocational College, Xiamen 361102, China
| | - Xiangwei Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Guangyu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Fang Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Weiyi Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
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3
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Golnari M, Bahrami N, Milanian Z, Rabbani Khorasgani M, Asadollahi MA, Shafiei R, Fatemi SSA. Isolation and characterization of novel Bacillus strains with superior probiotic potential: comparative analysis and safety evaluation. Sci Rep 2024; 14:1457. [PMID: 38228716 PMCID: PMC10791968 DOI: 10.1038/s41598-024-51823-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: 08/03/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024] Open
Abstract
Despite the current use of some Bacillus spp. as probiotics, looking for and introducing new efficient and safe potential probiotic strains is one of the most important topics in both microbiology and food industry. This study aimed to isolate, identify, and evaluate the probiotic characteristics and safety of some Bacillus spp. from natural sources. Thirty-six spore-forming, Gram-positive, and catalase-positive Bacillus isolates were identified in 54 samples of soil, feces and dairy products. Bacterial identification was performed using 16S rDNA sequencing. To evaluate the probiotic potential of isolates, the resistance of bacterial cells to simulated gastrointestinal tract (GIT) conditions, the presence of enterotoxin genes, their susceptibility to antibiotics, antimicrobial and hemolytic activities and biochemical profiles were investigated. The results revealed that eight sporulating Bacillus spp. isolates fulfilled all tested probiotic criteria. They showed a high growth rate, non-hemolytic and lecithinase activity, and resistance to simulated GIT conditions. These strains exhibited broad-spectrum antibacterial activity against pathogenic bacteria. In addition, they did not exhibit antibacterial resistance to the 12 tested antibiotics. The results of this study suggest that these isolates can be considered as candidates for functional foods and as safe additives to improve diet quality.
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Affiliation(s)
- Mohsen Golnari
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Nastaran Bahrami
- Department of Microbiology, NourDanesh Institute of Higher Education, Meymeh, Iran
| | - Zahra Milanian
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohammad Rabbani Khorasgani
- Department of Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Rasoul Shafiei
- Department of Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Seyed Safa-Ali Fatemi
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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4
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Chebotar VK, Zaplatkin AN, Chizhevskaya EP, Gancheva MS, Voshol GP, Malfanova NV, Baganova ME, Khomyakov YV, Pishchik VN. Phytohormone Production by the Endophyte Bacillus safensis TS3 Increases Plant Yield and Alleviates Salt Stress. PLANTS (BASEL, SWITZERLAND) 2023; 13:75. [PMID: 38202382 PMCID: PMC10780329 DOI: 10.3390/plants13010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Endophytic bacteria can be used to overcome the effect of salinity stress and promote plant growth and nutrient uptake. Bacillus safensis colonizes a wide range of habitats due to survival in extreme environments and unique physiological characteristics, such as a high tolerance for salt, heavy metals, and ultraviolet and gamma radiations. The aim of our study was to examine the salt resistance of the endophytic strain TS3 B. safensis and its ability to produce phytohormones and verify its effect on plant yield in field trials and the alleviation of salt stress in pot experiments. We demonstrate that the strain TS3 is capable of producing enzymes and phytohormones such as IAA, ABA and tZ. In pot experiments with radish and oat plants in salinization, the strain TS3 contributed to the partial removal of the negative effect of salinization. The compensatory effect of the strain TS3 on radish plants during salinization was 46.7%, and for oats, it was 108%. We suppose that such a pronounced effect on the plants grown and the salt stress is connected with its ability to produce phytohormones. Genome analysis of the strain TS3 showed the presence of the necessary genes for the synthesis of compounds responsible for the alleviation of the salt stress. Strain B. safensis TS3 can be considered a promising candidate for developing biofertilizer to alleviate salt stress and increase plant yield.
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Affiliation(s)
- Vladimir K. Chebotar
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
| | - Alexander N. Zaplatkin
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
| | - Elena P. Chizhevskaya
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
| | - Maria S. Gancheva
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| | - Gerben P. Voshol
- Institute of Biology Leiden, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (G.P.V.); (N.V.M.)
| | - Natalia V. Malfanova
- Institute of Biology Leiden, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (G.P.V.); (N.V.M.)
| | - Maria E. Baganova
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
| | - Yuriy V. Khomyakov
- Agrophysical Scientific Research Institute, Grazhdansky pr. 14, 195220 St. Petersburg, Russia;
| | - Veronika N. Pishchik
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
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Padayao MHR, Padayao FRP, Patalinghug JM, Raña GS, Yee J, Geraldino PJ, Quilantang N. Antimicrobial and quorum sensing inhibitory activity of epiphytic bacteria isolated from the red alga Halymenia durvillei. Access Microbiol 2023; 5:000563.v4. [PMID: 38188234 PMCID: PMC10765052 DOI: 10.1099/acmi.0.000563.v4] [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: 01/12/2023] [Accepted: 11/10/2023] [Indexed: 01/09/2024] Open
Abstract
Halymenia durvillei is a red alga that is commonly utilized in the Philippines as food and as a source of high-value natural products for industrial applications. However, there are no studies regarding the microbial community associated with H. durvillei and its potential applications. This study aimed to isolate and identify the epiphytic bacteria of H. durvillei and determine their antimicrobial and quorum sensing inhibitory (QSI) effects. The thalli of H. durvillei were collected at the shores of Santa Fe, Bantayan, Cebu, Philippines. Bacterial isolates were identified using 16S rRNA, and their ethyl acetate (EtOAc) extracts were subjected to antimicrobial susceptibility tests against representative species of yeast and Gram-negative and Gram-positive bacteria. Their QSI activity against Chromobacterium violaceum was also determined. Fourteen distinct bacterial colonies belonging to four genera, namely Alteromonas (3), Bacillus (5), Oceanobacillus (1) and Vibrio (5), were successfully isolated and identified. All 14 bacterial isolates exhibited antibacterial effects. EPB9, identified as Bacillus safensis , consistently showed the strongest inhibition against Escherichia coli , Staphylococcus aureus and Staphylococcus epidermidis , with minimum inhibitory concentrations (MICs) ranging from 0.0625 to 1.0 mg ml-1. In contrast, all 14 isolates showed weak antifungal effects. Both B. safensis (EPB9) and Bacillus australimaris (EPB15) exhibited QSI effects at 100 mg ml-1, showing opaque zones of 3.1±0.9 and 3.8±0.4 mm, respectively. This study is the first to isolate and identify the distinct microbial epiphytic bacterial community of H. durvillei and its potential as an abundant resource for new antibacterial and QSI bioactives.
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Affiliation(s)
- Mary Hannah Rose Padayao
- Applied Microbiology and Molecular Biology Laboratory, Department of Biology, University of San Carlos, Cebu City 6000, Philippines
- Tuklas Lunas Development Center, University of San Carlos, Cebu City 6000, Philippines
| | - Francis Reuben Paul Padayao
- Applied Microbiology and Molecular Biology Laboratory, Department of Biology, University of San Carlos, Cebu City 6000, Philippines
| | - Jenny Marie Patalinghug
- Applied Microbiology and Molecular Biology Laboratory, Department of Biology, University of San Carlos, Cebu City 6000, Philippines
| | - Gem Stephen Raña
- Applied Microbiology and Molecular Biology Laboratory, Department of Biology, University of San Carlos, Cebu City 6000, Philippines
| | - Jonie Yee
- Applied Microbiology and Molecular Biology Laboratory, Department of Biology, University of San Carlos, Cebu City 6000, Philippines
- Tuklas Lunas Development Center, University of San Carlos, Cebu City 6000, Philippines
| | - Paul John Geraldino
- Applied Microbiology and Molecular Biology Laboratory, Department of Biology, University of San Carlos, Cebu City 6000, Philippines
- Tuklas Lunas Development Center, University of San Carlos, Cebu City 6000, Philippines
| | - Norman Quilantang
- Applied Microbiology and Molecular Biology Laboratory, Department of Biology, University of San Carlos, Cebu City 6000, Philippines
- Tuklas Lunas Development Center, University of San Carlos, Cebu City 6000, Philippines
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Uvarova YE, Demenkov PS, Kuzmicheva IN, Venzel AS, Mischenko EL, Ivanisenko TV, Efimov VM, Bannikova SV, Vasilieva AR, Ivanisenko VA, Peltek SE. Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder. J Integr Bioinform 2023; 20:jib-2023-0017. [PMID: 37978847 PMCID: PMC10757077 DOI: 10.1515/jib-2023-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 11/19/2023] Open
Abstract
Bacillus strains are ubiquitous in the environment and are widely used in the microbiological industry as valuable enzyme sources, as well as in agriculture to stimulate plant growth. The Bacillus genus comprises several closely related groups of species. The rapid classification of these remains challenging using existing methods. Techniques based on MALDI-TOF MS data analysis hold significant promise for fast and precise microbial strains classification at both the genus and species levels. In previous work, we proposed a geometric approach to Bacillus strain classification based on mass spectra analysis via the centroid method (CM). One limitation of such methods is the noise in MS spectra. In this study, we used a denoising autoencoder (DAE) to improve bacteria classification accuracy under noisy MS spectra conditions. We employed a denoising autoencoder approach to convert noisy MS spectra into latent variables representing molecular patterns in the original MS data, and the Random Forest method to classify bacterial strains by latent variables. Comparison of the DAE-RF with the CM method using the artificially noisy test samples showed that DAE-RF offers higher noise robustness. Hence, the DAE-RF method could be utilized for noise-robust, fast, and neat classification of Bacillus species according to MALDI-TOF MS data.
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Affiliation(s)
- Yulia E. Uvarova
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Pavel S. Demenkov
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | | | - Artur S. Venzel
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | - Elena L. Mischenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Timofey V. Ivanisenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Vadim M. Efimov
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Svetlana V. Bannikova
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Asya R. Vasilieva
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Vladimir A. Ivanisenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | - Sergey E. Peltek
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
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Schubert WW, Seto EP, Hinzer AA, Guan L. Identification and Archive of Mars 2020 Spacecraft Microbial Isolates. ASTROBIOLOGY 2023; 23:835-845. [PMID: 37584746 DOI: 10.1089/ast.2022.0052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
To support NASA's Mars 2020 mission, bioassays were performed to ensure the biological cleanliness of the spacecraft, instruments, and hardware assembly areas. Bioassays began in May 2014, as the first components were assembled, and continued until their launch in July 2020. Over this 6-year period, 1811 bioassay sampling sessions were conducted. To understand the nature of microbiological presence on and around the spacecraft, an archive of organisms resulting from the bioassays was assembled. This archive included 4232 microbial specimens preserved as frozen stocks. To date, more than 3489 microbial isolates have been tested by MALDI-TOF mass spectrometry analysis. Identifications were based on high confidence level matches to known microorganisms in the reference spectra database where 39 distinct genera were identified. Gram-positive bacteria were isolated almost exclusively. Most, but not all, were spore-forming genera. The most prevalent genera isolated in order of frequency were Bacillus, Priestia, Paenibacillus, Staphylococcus, Micrococcus, and Streptomyces. Within the largely represented Bacillus-like genera, the five most prevalent species were cereus, licheniformis, horneckiae, subtilis, and safensis.
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Affiliation(s)
- Wayne W Schubert
- Biotechnology and Planetary Protection Group, California Institute of Technology, Jet Propulsion Laboratory, Pasadena, California, USA
| | - Emily P Seto
- Biotechnology and Planetary Protection Group, California Institute of Technology, Jet Propulsion Laboratory, Pasadena, California, USA
| | - Akemi A Hinzer
- Department of Chemistry and Biochemistry, California State University, Northridge, California, USA
| | - Lisa Guan
- Biotechnology and Planetary Protection Group, California Institute of Technology, Jet Propulsion Laboratory, Pasadena, California, USA
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Reale A, Messia MC, Pulvento C, Lavini A, Nazzaro S, Di Renzo T. Microbial and Qualitative Traits of Quinoa and Amaranth Seeds from Experimental Fields in Southern Italy. Foods 2023; 12:foods12091866. [PMID: 37174403 PMCID: PMC10177794 DOI: 10.3390/foods12091866] [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: 04/06/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Quinoa and amaranth are of special interest since they are increasingly used for the development of new bakery products with enhanced nutritional value. The aim of the study was to evaluate the agronomic, microbiological, and nutritional characteristics of quinoa and amaranth seeds grown in Southern Italy. For this reason, quinoa Titicaca and three amaranth accessions (5, 12, and 14) were cultivated in different experimental fields in the Campania Region and analyzed for the cultivation aspects, chemical composition, and microbiological quality of the seeds. All seeds showed a good adaptability to cultivation in the experimental areas of the Mediterranean basin. Quinoa seeds were characterized by their higher protein, fat, and ash content than the amaranth seeds, which were characterized by their higher value in dietary fiber. All seeds, regardless of the geographical area of production, were contaminated with yeasts, moulds, and spore-forming bacteria, mainly Bacillus cereus, B. licheniformis, B. safensis and B. subtilis, as identified by 16S rRNA sequencing analysis. So, the detection of Bacillus spp. must be strongly monitored, as quinoa and amaranth seeds could be used in bread production, where they can cause ropiness, resulting in great economic losses for the industries.
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Affiliation(s)
- Anna Reale
- Institute of Food Sciences, National Research Council (CNR-ISA), Via Roma 64, 83100 Avellino, Italy
| | - Maria Cristina Messia
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise, Via De Sanctis, 86100 Campobasso, Italy
| | - Cataldo Pulvento
- Department of Soil, Plant and Food Science (DISSPA), University of Bari "A. Moro", Via Amendola, 165/A, 70126 Bari, Italy
| | - Antonella Lavini
- Institute for Agricultural and Forestry Systems in the Mediterranean (ISAFOM), National Research Council of Italy (CNR), 80055 Portici, Italy
| | - Stefania Nazzaro
- Institute of Food Sciences, National Research Council (CNR-ISA), Via Roma 64, 83100 Avellino, Italy
| | - Tiziana Di Renzo
- Institute of Food Sciences, National Research Council (CNR-ISA), Via Roma 64, 83100 Avellino, Italy
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Sánchez-Díaz R, Molina-Garza ZJ, Cruz-Suárez LE, Selvin J, Kiran GS, Gómez-Gil B, Galaviz-Silva L, Ibarra-Gámez JC. Draft genome sequences of Bacillus pumilus 36R ATNSAL and B. safensis 13L LOBSAL, two potential candidate probiotic strains for shrimp aquaculture. J Glob Antimicrob Resist 2022; 31:304-308. [PMID: 36272706 DOI: 10.1016/j.jgar.2022.10.002] [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: 04/08/2020] [Revised: 09/21/2022] [Accepted: 10/06/2022] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES This work aimed to isolate bacterial strains with antagonist activity against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (VPAHPND) that was isolated from outbreaks in Mexico. Here, we report the draft genome sequences of two antagonistic strains, isolated from saline sediment in Sonora, Mexico. METHODS Cross-streak and well diffusion tests were employed to find the bacterial strains with higher inhibitory activity against VPAHPND. The whole genomes of B. pumilus 36R ATNSAL and B. safensis 13L LOBSAL were sequenced using Ion TorrentTM (PGM) and Illumina MiseqTM platforms, respectively. Annotation was performed using the RAST server, and the genes involved in the biosynthesis of bacterial secondary metabolites were predicted using antiSMASH. RESULTS Two bacterial isolates, B. safensis 13L LOBSAL and B. pumilus 36R ATNSAL, were chosen based on their strong antagonistic profiles. The genome of 36R ATNSAL was 3.94 Mbp in length and contained 3824 genes and a total of 4116 coding sequences (CDSs); the genome of 13L LOBSAL was 3.68 Mbp and contained 3619 genes and 3688 CDSs. Twenty-eight and 32 biosynthetic gene clusters responsible for putative antimicrobial metabolite production were identified in 36R ATNSAL and 13L LOBSAL, respectively. CONCLUSIONS The two strains 13L LOBSAL and 36R ATNSAL showed excellent probiotic profiles in vitro. The genome sequences will help with the mining and reconstruction of metabolic pathways in Bacillus strains. Genome sequence-guided strain improvement could augment the probiotic potential of Bacillus strains for applications in shrimp aquaculture.
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Affiliation(s)
- Ricardo Sánchez-Díaz
- Technological Institute of Sonora (ITSON), 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora,CP 85000, México
| | - Zinnia Judith Molina-Garza
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico
| | - Lucía Elizabeth Cruz-Suárez
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, India
| | - Bruno Gómez-Gil
- Research Center for Food and Development (CIAD), Mazatlan Unit, Av. Sábalo Cerritos S/N, Mazatlán, Sinaloa, C.P. 82112. Mexico
| | - Lucio Galaviz-Silva
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico.
| | - José Cuauhtémoc Ibarra-Gámez
- Technological Institute of Sonora (ITSON), 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora,CP 85000, México.
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10
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Laamarti M, Chemao-Elfihri MW, Essabbar A, Manni A, Kartti S, Alouane T, Temsamani L, Eljamali JE, Sbabou L, Ouadghiri M, Filali-Maltouf A, Belyamani L, Ibrahimi A. Genomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits. Funct Integr Genomics 2022; 22:1173-1187. [PMID: 36175602 DOI: 10.1007/s10142-022-00905-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/04/2022]
Abstract
Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, sequenced, and assembled the genomes of Bacillus safensis strains BcP62 and Bcs93, to which we performed comparative genome analyses. Using the DDH and ANI of both strains with the available B. safensis genomes, we identified three potential subspecies within this group. Intra-species core genome phylogenetic analysis did not result in clustering genomes by niche type, with some exceptions. This study also revealed that the genomes of the analyzed strains possessed plant growth-promoting characteristics, most of which were conserved in all B. safensis strains. Furthermore, we highlight the genetic features of B. safensis BcP62 and Bcs93 related to survival in the Merzouga desert in Morocco. These strains could be potentially used in agriculture as PGPB in extreme environments, given their high tolerability to unfavorable conditions.
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Affiliation(s)
- Meriem Laamarti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Mohammed Walid Chemao-Elfihri
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelmounim Essabbar
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Amina Manni
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Souad Kartti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarek Alouane
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Loubna Temsamani
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jamal-Eddine Eljamali
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco.,Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco
| | - Mouna Ouadghiri
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco.,Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco. .,Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco.
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11
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Huynh-Phuoc V, Ly TQ, Purbiantoro W, Ngo HVT, Afonso F, Vu NU, Cheng TC. Bacillus safensis isolated from white-leg shrimp, Penaeus vannamei in Taiwan with antagonistic activity against common Vibrio pathogens. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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12
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Kamala Jayanthi PD, Vyas M. Exploring the Transient Microbe Population on Citrus Butterfly Wings. Microbiol Spectr 2022; 10:e0205521. [PMID: 35856677 PMCID: PMC9431565 DOI: 10.1128/spectrum.02055-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
Microbes carve out dwelling niches in unusual environments. Insects, in general, have been hosts to microbes in different ways. Some insects incorporate microbes as endosymbionts that help with metabolic functions, while some vector pathogenic microbes that cause serious plant and animal diseases, including humans. Microbes isolated from insect sources have been beneficial and a huge information repository. The fascinating and evolutionarily successful insect community has survived mass extinctions as a result of their unique biological traits. Wings have been one of the most important factors contributing to the evolutionary success of insects. In the current study, wings of Papilio polytes, a citrus butterfly, were investigated for the presence of ecologically significant microbes within hours of eclosing under aseptic conditions. Scanning electron microscopy (SEM) revealed the presence of bacteria dwelling in crevices created by a specific arrangement of scales on the butterfly wing. A total of 38 bacterial isolates were obtained from the patched wings of the citrus butterfly, and Bacillus spp. were predominant among them. We probed the occurrence of these microbes to assess their significance to the insect. Many of the isolates displayed antibacterial, antifungal, and biosurfactant properties. Interestingly, one of the isolates displayed entomopathogenic potential toward the notorious agricultural pest mealybug. All the wing isolates were seen to cluster together consistently in a phylogenetic analysis, except for one isolate of Bacillus zhangzhouensis (Papilio polytes isolate [Pp] no. 28), suggesting they are distinct strains. IMPORTANCE This is a first study reporting the presence of culturable microbes on an unusual ecological niche such as butterfly wings. Our findings also establish that microbes inhabit these niches before the butterfly has contact with the environment. The findings in this report have opened up a new area of research which will not only help understand the microbiome of insect wings but might prove beneficial in other specialized studies.
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Affiliation(s)
- P. D. Kamala Jayanthi
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, India
| | - Meenal Vyas
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, India
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13
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A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations. Microorganisms 2022; 10:microorganisms10091720. [PMID: 36144322 PMCID: PMC9505155 DOI: 10.3390/microorganisms10091720] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As fingerprints, we denote those core proteins of a certain lineage that are present only in that particular lineage and absent in any other Bacillus lineage. Thus, these lineage-specific fingerprints are expected to be involved in particular adaptations of that lineage. Intriguingly, with a few notable exceptions, the majority of the Bacillus species demonstrate a rather low number of species-specific fingerprints, with the majority of them being of unknown function. Therefore, species-specific adaptations are mostly attributed to highly unstable (in evolutionary terms) accessory proteomes and possibly to changes at the gene regulation level. A series of comparative analyses consistently demonstrated that the progenitor of the Cereus Clade underwent an extensive genomic expansion of chromosomal protein-coding genes. In addition, the majority (76–82%) of the B. subtilis proteins that are essential or play a significant role in sporulation have close homologs in most species of both the Subtilis and the Cereus Clades. Finally, the identification of lineage-specific fingerprints by this study may allow for the future development of highly specific vaccines, therapeutic molecules, or rapid and low-cost molecular tests for species identification.
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14
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Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD. Appl Environ Microbiol 2022; 88:e0091622. [PMID: 35762789 PMCID: PMC9317851 DOI: 10.1128/aem.00916-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the biochemistry and metabolic pathways of cyanide degradation is necessary to improve the efficacy of cyanide bioremediation processes and industrial requirements. We have isolated and sequenced the genome of a cyanide-degrading Bacillus strain from water in contact with mine tailings from Lima, Peru. This strain was classified as Bacillus safensis based on 16S rRNA gene sequencing and core genome analyses and named B. safensis PER-URP-08. We searched for possible cyanide-degradation enzymes in the genome of this strain and identified a putative cyanide dihydratase (CynD) gene similar to a previously characterized CynD from Bacillus pumilus C1. Sequence analysis of CynD from B. safensis and B. pumilus allow us to identify C-terminal residues that differentiate both CynDs. We then cloned, expressed in Escherichia coli, and purified recombinant CynD from B. safensis PER-URP-08 (CynDPER-URP-08) and showed that in contrast to CynD from B. pumilus C1, this recombinant CynD remains active at up to pH 9. We also showed that oligomerization of CynDPER-URP-08 decreases as a function of increased pH. Finally, we demonstrated that transcripts of CynDPER-URP-08 in B. safensis PER-URP-08 are strongly induced in the presence of cyanide. Our results suggest that the use of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tool for cyanide bioremediation warrants further investigation. IMPORTANCE Despite being of environmental concern around the world due to its toxicity, cyanide continues to be used in many important industrial processes. Thus, searching for cyanide bioremediation methods is a matter of societal concern and must be present on the political agenda of all governments. Here, we report the isolation, genome sequencing and characterization of cyanide degradation capacity of a bacterial strain isolated from an industrial mining site in Peru. We characterize a cyanide dehydratase (CynD) homolog from one of these bacteria, Bacillus safensis PER-URP-08.
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15
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Stott KV, Morgan L, Shearer C, Steadham MB, Ballarotto M, Hendrickson R. Qualification of Membrane Filtration for Planetary Protection Flight Implementation. Front Microbiol 2022; 13:871110. [PMID: 35572631 PMCID: PMC9100389 DOI: 10.3389/fmicb.2022.871110] [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: 02/07/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
Planetary protection is the practice of preventing forward and backward contamination of solar system bodies. Spacecraft and associated surfaces are sampled to ensure compliance with bioburden requirements. Current planetary protection sampling and processing methodologies consist of extracting microbial cells from wipe or swab samples through a procedure (NASA Standard Assay) that includes sonication, heat shock, and pour-plate steps. The pour-plate steps are laborious and prolonged. Moreover, results can be imprecise because only a fraction of the sample fluid is plated for CFU enumeration (80% for swabs and 25% for wipes). Thus, analysis requires that a pour fraction extrapolation factor be applied to CFU counts to account for bioburden in the remaining sample volume that is not plated. This extrapolation results in large variances for data, decreasing the accuracy of spore bioburden estimation of spacecraft hardware. In this study, we investigated the use of membrane filtration as an alternative method to pour-plate processing. Membrane filtration is an appealing methodology for planetary protection because it can process greater sample volumes and reduces the data variance for bioburden enumeration. A pour fraction extrapolation factor is still applied for both swabs and wipes (92%), however, it is a greater pour fraction than the pour-plate method. Here we present data collected by the Jet Propulsion Laboratory and the Applied Physics Laboratory to experimentally determine the equivalency of membrane filtration to pour-plate methodology for implementation during the NASA Standard Assay. Additionally, we outline the planned procedures for two membrane filtration systems: Pall® Laboratory Manifold system and Milliflex® Plus Vacuum Pump System. Both systems demonstrated equivalence of the membrane filtration method to the pour-plate method.
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Affiliation(s)
| | - Lyssa Morgan
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Caitlin Shearer
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
| | | | - Mihaela Ballarotto
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
| | - Ryan Hendrickson
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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16
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Cai G, Li J, Zhou M, Zhu G, Li Y, Lv N, Wang R, Li C, Pan X. Compost-derived indole-3-acetic-acid-producing bacteria and their effects on enhancing the secondary fermentation of a swine manure-corn stalk composting. CHEMOSPHERE 2022; 291:132750. [PMID: 34740695 DOI: 10.1016/j.chemosphere.2021.132750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 06/13/2023]
Abstract
Composting, as an effectively bio-oxidative process, has been widely used for converting organic waste to organic fertilizer. However, the low fertilizer efficiency of composting product limited its application in agriculture. To improve the growth-promoting effect of composting product, the present study investigated the bioaugmentation strategy of inoculating indole-3-acetic-acid (IAA)-producing bacteria. Firstly, two IAA-producing bacteria (Bacillus safensis 33C and Rhodococcus rhodochrous YZ) were isolated from composting products with high IAA yields of 39.18 and 16.32 μg mL-1, respectively. Secondly, the microbial inoculants were prepared with 33C, YZ and a previously isolated IAA-producing strain Corynebacterium stationis 29B. To increase the accumulation of microbial secondary metabolites, microbial inoculants were amended at the secondary fermentation stage of composting. Physicochemical characterization showed that the maturity of composting product was significantly promoted by inoculating microbial inoculants prepared with 33C and 29B (single and combined inoculants). Finally, bioaugmentation with 33C and 29B increased the IAA contents of composting products by 2.9-5.2 times, which benefited the germination and early vegetative growth of plants. In summary, inoculating proper IAA-producing bacteria during secondary fermentation of composting could improve the quality of composting product and expand its application.
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Affiliation(s)
- Guanjing Cai
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; School of Environment and Natural Resources, Renmin University of China, Beijing, 100872, China; Key Laboratory of Energy Resource Utilization from Agriculture Residue, Ministry of Agriculture and Rural Affairs, China
| | - Junjie Li
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingdian Zhou
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Gefu Zhu
- School of Environment and Natural Resources, Renmin University of China, Beijing, 100872, China; Key Laboratory of Energy Resource Utilization from Agriculture Residue, Ministry of Agriculture and Rural Affairs, China.
| | - Yanlin Li
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Lv
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruming Wang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxing Li
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK, 2800, Denmark
| | - Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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17
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Coelho LF, Madden J, Kaltenegger L, Zinder S, Philpot W, Esquível MG, Canário J, Costa R, Vincent WF, Martins Z. Color Catalogue of Life in Ice: Surface Biosignatures on Icy Worlds. ASTROBIOLOGY 2022; 22:313-321. [PMID: 34964651 DOI: 10.1089/ast.2021.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With thousands of discovered planets orbiting other stars and new missions that will explore our solar system, the search for life in the universe has entered a new era. However, a reference database to enable our search for life on the surface of icy exoplanets and exomoons by using records from Earth's icy biota is missing. Therefore, we developed a spectra catalogue of life in ice to facilitate the search for extraterrestrial signs of life. We measured the reflection spectra of 80 microorganisms-with a wide range of pigments-isolated from ice and water. We show that carotenoid signatures are wide-ranged and intriguing signs of life. Our measurements allow for the identification of such surface life on icy extraterrestrial environments in preparation for observations with the upcoming ground- and space-based telescopes. Dried samples reveal even higher reflectance, which suggests that signatures of surface biota could be more intense on exoplanets and moons that are drier than Earth or on environments like Titan where potential life-forms may use a different solvent. Our spectra library covers the visible to near-infrared and is available online. It provides a guide for the search for surface life on icy worlds based on biota from Earth's icy environments.
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Affiliation(s)
- Lígia F Coelho
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Jack Madden
- Department of Astronomy, Cornell University, Ithaca, New York, USA
- Carl Sagan Institute, Ithaca, New York, USA
| | - Lisa Kaltenegger
- Department of Astronomy, Cornell University, Ithaca, New York, USA
- Carl Sagan Institute, Ithaca, New York, USA
| | - Stephen Zinder
- Carl Sagan Institute, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - William Philpot
- Carl Sagan Institute, Ithaca, New York, USA
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - M Glória Esquível
- Landscape, Environment, Agriculture and Food-LEAF Centre, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - João Canário
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Warwick F Vincent
- Centre for Northern Studies (CEN), Takuvik & Biology Department, Université Laval, Québec, Canada
| | - Zita Martins
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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18
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Vejar N, Gutiérrez S, Tareelap N, Alvarado C, Solís R, Guerra C, Pineda F, Sancy M, Páez M. Influence of Bacillus safensis and Bacillus pumilus on the electrochemical behavior of 2024-T3 aluminum alloy. Bioelectrochemistry 2022; 143:107950. [PMID: 34592630 DOI: 10.1016/j.bioelechem.2021.107950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/18/2021] [Accepted: 09/15/2021] [Indexed: 11/20/2022]
Abstract
In this work, electrochemical techniques were employed to evaluate the contribution to the corrosion and corrosion inhibition of 2024-T3 aluminum alloy by two Gram-positive bacteria. In addition, polarized impedance was used to determine the microbial effect on the cathodic and anodic reactions. These microorganisms were collected from a tropical environment due to the favorable bacterial growth of this kind of climate. The alloy was exposed to the sterile medium and inoculated for up to 12 days evaluating the microbiological and electrochemical behavior. The results by linear scanning voltammetry showed that the B. safensis and B. pumilus caused a dual effect of increase and decrease currents, and through electrochemical impedance spectroscopy, showed in some cases, inductive loop, which could be associated with local corrosion and another case, an increasing impedance could be related to protection. In addition, a morphological characterization was performed by scanning electron microscopy before and after exposure, showing an increase in copper precipitation in the vicinity of the intermetallic phases by bacteria, attributed to local corrosion, but, in general, a significant effect of damages was not observed.
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Affiliation(s)
- Nelson Vejar
- Centro de Investigación y Desarrollo en Ciencias Aeroespaciales, Fuerza Aérea de Chile, Av. José Miguel Carrera 11087, Santiago, Chile.
| | - Sebastián Gutiérrez
- Centro de Investigación y Desarrollo en Ciencias Aeroespaciales, Fuerza Aérea de Chile, Av. José Miguel Carrera 11087, Santiago, Chile
| | - Napachat Tareelap
- School of Energy, Environment and Materials, King Mongkut's University of Technology Thonburi, 126 Pracha Uthit Road, Bangmod, Thungkru, Bangkok 10140, Thailand
| | - Claudia Alvarado
- Centro de Investigación y Desarrollo en Ciencias Aeroespaciales, Fuerza Aérea de Chile, Av. José Miguel Carrera 11087, Santiago, Chile
| | - Roberto Solís
- Centro de Investigación y Desarrollo en Ciencias Aeroespaciales, Fuerza Aérea de Chile, Av. José Miguel Carrera 11087, Santiago, Chile
| | - Carolina Guerra
- Escuela de Construcción Civil, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Fabiola Pineda
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile
| | - Mamié Sancy
- Escuela de Construcción Civil, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Maritza Páez
- Universidad de Santiago de Chile, Av. Libertador Bernardo ÓHiggins 3363, Santiago, Chile
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Fernandes T, da Silva KT, Carvalho BF, Schwan RF, Pereira RAN, Pereira MN, da Silva Ávila CL. Effect of amylases and storage length on losses, nutritional value, fermentation, and microbiology of silages of corn and sorghum kernels. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Wu PS, Liu CH, Hu SY. Probiotic Bacillus safensis NPUST1 Administration Improves Growth Performance, Gut Microbiota, and Innate Immunity against Streptococcus iniae in Nile tilapia ( Oreochromis niloticus). Microorganisms 2021; 9:2494. [PMID: 34946096 PMCID: PMC8703608 DOI: 10.3390/microorganisms9122494] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Probiotics are considered ecofriendly alternatives to antibiotics as immunostimulants against pathogen infections in aquaculture. In the present study, protease-, amylase-, cellulase-, and xylanase-producing Bacillus safensis NPUST1 were isolated from the gut of Nile tilapia, and the beneficial effects of B. safensis NPUST1 on growth, innate immunity, disease resistance and gut microbiota in Nile tilapia were evaluated by feeding tilapia a basal diet or basal diet containing 105 and 106-107 CFU/g for 8 weeks. The results showed that the weight gain, feed efficiency and specific growth rate were significantly increased in tilapia fed a diet containing 106 CFU/g and 107 CFU/g B. safensis NPUST1. Intestinal digestive enzymes, including protease, amylase and lipase, and hepatic mRNA expression of glucose metabolism and growth-related genes, such as GK, G6Pase, GHR and IGF-1, were also significantly increased in the 106 CFU/g and 107 CFU/g B. safensis NPUST1 treated groups. Immune parameters such as phagocytic activity, respiratory burst and superoxide dismutase activity in head kidney leukocytes, serum lysozyme, and the mRNA expression of IL-1β, IL-8, TNF-α and lysozyme genes were significantly induced in the head kidney and spleen of 106 CFU/g and 107 CFU/g B. safensis NPUST1 treated fish. The cumulative survival rate was significantly increased in fish fed a diet containing 106 CFU/g and 107 CFU/g B. safensis NPUST1 after challenge with Streptococcus iniae. Dietary supplementation with B. safensis NPUST1 improves the gut microbiota of Nile tilapia, which increases the abundance of potential probiotics and reduces the abundance of pathogenic pathogens. The present study is the first to report the use of B. safensis as a potential probiotic in aquaculture, and a diet containing 106 CFU/g B. safensis NPUST1 is adequate for providing beneficial effects on growth performance and health status in tilapia.
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Affiliation(s)
- Pei-Shan Wu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912, Taiwan;
| | - Chun-Hong Liu
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan;
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Shao-Yang Hu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912, Taiwan;
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
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21
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Romero-Severson J, Moran TE, Shrader DG, Fields FR, Pandey-Joshi S, Thomas CL, Palmer EC, Shrout JD, Pfrender ME, Lee SW. A Seed-Endophytic Bacillus safensis Strain With Antimicrobial Activity Has Genes for Novel Bacteriocin-Like Antimicrobial Peptides. Front Microbiol 2021; 12:734216. [PMID: 34646254 PMCID: PMC8503640 DOI: 10.3389/fmicb.2021.734216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/20/2021] [Indexed: 12/04/2022] Open
Abstract
Bacteriocins are a highly diverse group of antimicrobial peptides that have been identified in a wide range of commensal and probiotic organisms, especially those resident in host microbiomes. Rising antibiotic resistance have fueled renewed research into new drug scaffolds such as antimicrobial peptides for use in therapeutics. In this investigation, we examined mung bean seeds for endophytes possessing activity against human and plant pathogens. We isolated a novel strain of Bacillus safensis, from the contents of surface-sterilized mung bean seed, which we termed B. safensis C3. Genome sequencing of C3 identified three distinct biosynthetic systems that produce bacteriocin-based peptides. C3 exhibited antibacterial activity against Escherichia coli, Xanthomonas axonopodis, and Pseudomonas syringae. Robust antimicrobial activity of B. safensis C3 was observed when C3 was co-cultured with Bacillus subtilis. Using the cell-free supernatant of C3 and cation exchange chromatography, we enriched a product that retained antimicrobial activity against B. subtilis. The peptide was found to be approximately 3.3 kDa in size by mass spectrometry, and resistant to proteolysis by Carboxypeptidase Y and Endoproteinase GluC, suggesting that it is a modified variant of an AS-48 like bacteriocin. Our findings open new avenues into further development of novel bacteriocin-based scaffolds for therapeutic development, as well as further investigations into how our discoveries of bacteriocin-producing plant commensal microorganisms may have the potential for an immediate impact on the safety of food supplies.
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Affiliation(s)
- Jeanne Romero-Severson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Thomas E Moran
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Donna G Shrader
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Francisco R Fields
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Susan Pandey-Joshi
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Clayton L Thomas
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Emily C Palmer
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States.,Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Joshua D Shrout
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States.,Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
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Cruz CS, Ricci MF, Vieira AT. Gut Microbiota Modulation as a Potential Target for the Treatment of Lung Infections. Front Pharmacol 2021; 12:724033. [PMID: 34557097 PMCID: PMC8453009 DOI: 10.3389/fphar.2021.724033] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal and respiratory systems are colonized by a complex ecosystem of microorganisms called the microbiota. These microorganisms co-evolved over millions of years with the host, creating a symbiotic relationship that is fundamental for promoting host homeostasis by producing bioactive metabolites and antimicrobial molecules, and regulating the immune and inflammatory responses. Imbalance in the abundance, diversity, and function of the gut microbiota (known as dysbiosis) have been shown to increase host susceptibility to infections in the lungs, suggesting crosstalk between these organs. This crosstalk is now referred to as the gut-lung axis. Hence, the use of probiotics, prebiotics, and synbiotics for modulation of gut microbiota has been studied based on their effectiveness in reducing the duration and severity of respiratory tract infections, mainly owing to their effects on preventing pathogen colonization and modulating the immune system. This review discusses the role and responses of probiotics, prebiotics, and synbiotics in the gut-lung axis in the face of lung infections.
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Affiliation(s)
- Clênio Silva Cruz
- Laboratory of Microbiota and Immunomodulation (LMI), Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Mayra Fernanda Ricci
- Laboratory of Microbiota and Immunomodulation (LMI), Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Angélica Thomaz Vieira
- Laboratory of Microbiota and Immunomodulation (LMI), Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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Draft Genome Sequences of Heat Shock-Tolerant Microbes Isolated from a Spacecraft Assembly Facility. Microbiol Resour Announc 2021; 10:e0065321. [PMID: 34498924 PMCID: PMC8428253 DOI: 10.1128/mra.00653-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heat shock-tolerant microorganisms belonging to the orders Bacillales and Micrococcales were isolated from the Spacecraft Assembly Facility at the Jet Propulsion Laboratory, and 63 draft genome sequences were assembled and identified. Further analyses of these genomes can provide insight into methods for preventing forward contamination.
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Husni AAA, Ismail SI, Jaafar NM, Zulperi D. Current Classification of the Bacillus pumilus Group Species, the Rubber-Pathogenic Bacteria Causing Trunk Bulges Disease in Malaysia as Assessed by MLSA and Multi rep-PCR Approaches. THE PLANT PATHOLOGY JOURNAL 2021; 37:243-257. [PMID: 34111914 PMCID: PMC8200583 DOI: 10.5423/ppj.oa.02.2021.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Bacillus pumilus is the causal agent of trunk bulges disease affecting rubber and rubberwood quality and yield production. In this study, B. pumilus and other closely related species were included in B. pumilus group, as they shared over 99.5% similarity from 16S rRNA analysis. Multilocus sequence analysis (MLSA) of five housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using REP, ERIC, and BOX primers conducted to analyze the diversity and systematic relationships of 20 isolates of B. pumilus group from four rubber tree plantations in Peninsular Malaysia (Serdang, Tanah Merah, Baling, and Rawang). Multi rep-PCR results revealed the genetic profiling among the B. pumilus group isolates, while MLSA results showed 98-100% similarity across the 20 isolates of B. pumilus group species. These 20 isolates, formerly established as B. pumilus, were found not to be grouped with B. pumilus. However, being distributed within distinctive groups of the B. pumilus group comprising of two clusters, A and B. Cluster A contained of 17 isolates close to B. altitudinis, whereas Cluster B consisted of three isolates attributed to B. safensis. This is the first MLSA and rep-PCR study on B. pumilus group, which provides an in-depth understanding of the diversity of these rubber-pathogenic isolates in Malaysia.
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Affiliation(s)
- Ainur Ainiah Azman Husni
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Noraini Md. Jaafar
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Dzarifah Zulperi
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Laboratory of Sustainable Resources Management, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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Fu X, Gong L, Liu Y, Lai Q, Li G, Shao Z. Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation. Front Microbiol 2021; 12:571212. [PMID: 34025591 PMCID: PMC8139322 DOI: 10.3389/fmicb.2021.571212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation. Results Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair. Conclusion Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
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Affiliation(s)
- Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Full-Genome Sequence of Bacillus safensis Strain IDN1, Isolated from Commercially Available Natto in Indonesia. Microbiol Resour Announc 2021; 10:10/15/e00180-21. [PMID: 33858928 PMCID: PMC8050970 DOI: 10.1128/mra.00180-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated a strain of Bacillus safensis, which we called IDN1, from natto sold in Indonesia. In order to gain insights into its genomic structure and understand its biology, we used the Oxford Nanopore MinION platform followed by PCR to verify the ends and determine its full circular genome sequence. We isolated a strain of Bacillus safensis, which we called IDN1, from natto sold in Indonesia. In order to gain insights into its genomic structure and understand its biology, we used the Oxford Nanopore MinION platform followed by PCR to verify the ends and determine its full circular genome sequence.
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Olajide AM, Chen S, LaPointe G. Markers to Rapidly Distinguish Bacillus paralicheniformis From the Very Close Relative, Bacillus licheniformis. Front Microbiol 2021; 11:596828. [PMID: 33505369 PMCID: PMC7829221 DOI: 10.3389/fmicb.2020.596828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
As close relatives, Bacillus paralicheniformis is often wrongly identified as Bacillus licheniformis. In this study, two genetic markers are presented based on fenC and fenD from the fengycin operon of B. paralicheniformis to rapidly distinguish it from B. licheniformis. The fengycin operon is one of the few present in B. paralicheniformis but absent in B. lichenformis up to date. Using these markers, two presumptive B. paralicheniformis isolates each were recovered from a set of isolates previously identified as B. licheniformis by Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) or identified only to genus level as Bacillus by 16S ribosomal RNA (rRNA) gene sequencing, respectively. Whole genome sequencing of the four isolates confirmed their identity as B. paralicheniformis having the closest similarity with B. paralicheniformis ATCC 9945a (GenBank: CP005965.1) with a 7,682 k-mer score and 97.22% Average Nucleotide Identity (ANI). ANI of 100% suggests that the four isolates are highly similar. Further analysis will be necessary to determine if finer differences exist among these isolates at the level of single nucleotide polymorphisms.
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Affiliation(s)
- Atinuke M Olajide
- CRIFS, Department of Food Science, University of Guelph, Ontario, ON, Canada
| | - Shu Chen
- Agriculture and Food Laboratory, Laboratory Services Division, University of Guelph, Ontario, ON, Canada
| | - Gisèle LaPointe
- CRIFS, Department of Food Science, University of Guelph, Ontario, ON, Canada
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Mhatre S, Singh NK, Wood JM, Parker CW, Pukall R, Verbarg S, Tindall BJ, Neumann-Schaal M, Venkateswaran K. Description of Chloramphenicol Resistant Kineococcus rubinsiae sp. nov. Isolated From a Spacecraft Assembly Facility. Front Microbiol 2020; 11:1957. [PMID: 32973710 PMCID: PMC7472656 DOI: 10.3389/fmicb.2020.01957] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 07/24/2020] [Indexed: 11/13/2022] Open
Abstract
A Gram-positive, coccoid, motile, aerobic bacterium, designated strain B12T was isolated from a Jet Propulsion Laboratory spacecraft assembly cleanroom, Pasadena, CA, United States. Strain B12T was resistant to chloramphenicol (100 μg/mL), and is a relatively slow grower (3-5 days optimal). Strain B12T was found to grow optimally at 28 to 32°C, pH 7 to 8, and 0.5% NaCl. Fatty acid methyl ester analysis showed that the major fatty acid of the strain B12T was anteiso C15 : 0 (66.3%), which is also produced by other Kineococcus species. However, arachidonic acid (C20 : 4 ω6,9,12,16c) was present in strain B12T and Kineococcus glutinatus YIM 75677T but absent in all other Kineococcus species. 16S rRNA analysis revealed that strain B12T was 97.9% similar to Kineococcus radiotolerans and falls within the Kineococcus clade. Low 16S rRNA gene sequence similarities (<94%) with other genera in the family Kineosporiaceae, including Angustibacter (93%), Kineosporia (94% to 95%), Pseudokineococcus (93%), Quadrisphaera (93%), and Thalassiella (94%) demonstrated that the strain B12T does not belong to these genera. Phylogenetic analysis of the gyrB gene show that all known Kineococcus species exhibited <86% sequence similarity with B12T. Multi-locus sequence and whole genome sequence analyses confirmed that B12T clades with other Kineococcus species. Average nucleotide identity of strain B12T were 75-78% with other Kineococcus species, while values ranged from 72-75% with species from other genera within family Kineosporiaceae. Average amino-acid identities were 66-72% with other Kineococcus species, while they ranged from 50-58% with species from other genera. The dDDH comparison of strain B12T genome with members of genera Kineococcus showed 20-22% similarity, again demonstrating that B12T is distantly related to other members of the genus. Furthermore, analysis of whole proteome deduced from WGS places strain B12T in order Kineosporiales, confirming that strain B12T is a novel member of family Kineosporiaceae. Based on these analyses and other genome characteristics, strain B12T is assigned to a novel species within the genus Kineococcus, and the name Kineococcus rubinsiae sp. nov., is proposed. The type strain is B12T (=FJII-L1-CM-PAB2T; NRRL B-65556T, DSM 110506T).
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Affiliation(s)
- Snehit Mhatre
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Jason M. Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Susanne Verbarg
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Rcheulishvili N, Zhang Y, Papukashvili D, Deng YL. Survey and Evaluation of Spacecraft-Associated Aluminum-Degrading Microbes and Their Rapid Identification Methods. ASTROBIOLOGY 2020; 20:925-934. [PMID: 32783563 DOI: 10.1089/ast.2019.2078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aluminum corrosion has become a major obstacle in spacecraft construction given that aluminum is used extensively throughout the construction process. Despite its many attributes in strength and durability, aluminum is susceptible to corrosion, in particular, corrosion due to microbial contamination. Scientists have encountered a number of problems with microbial aluminum corrosion within spacecraft components. Here, we summarize recent findings with regard to the phenomenon of microbiologically influenced corrosion (MIC) on space stations in the context of microbial strains isolated from the Mir space station (Mir) and the International Space Station (ISS). Given that strains found on spacecraft are of terrestrial origin, an understanding of the contribution of Al-corrosive microbes to corrosion and related risks to space travel and astronaut health is essential for implementation of prevention strategies. Accordingly, an efficient rapid identification method of microbes with the capability to degrade aluminum is proposed. In particular, onboard implementation of a matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) is addressed. The use of a MALDI-TOF MS on board spacecraft will be crucial to future successes in space travel given that traditional methods of identifying corrosive species are far more time-consuming. Identification of microbes by way of a MALDI-TOF MS may also aid in the study of microbial corrosion and be a valuable asset for MIC prevention.
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Affiliation(s)
- Nino Rcheulishvili
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
| | - Ying Zhang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
| | - Dimitri Papukashvili
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
| | - Yu-Lin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
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30
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Differential antioxidant activity of glucuronoxylooligosaccharides (UXOS) and arabinoxylooligosaccharides (AXOS) produced by two novel xylanases. Int J Biol Macromol 2020; 155:1075-1083. [DOI: 10.1016/j.ijbiomac.2019.11.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/24/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023]
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Huang Y, Łężyk M, Herbst FA, Busk PK, Lange L. Novel keratinolytic enzymes, discovered from a talented and efficient bacterial keratin degrader. Sci Rep 2020; 10:10033. [PMID: 32572051 PMCID: PMC7308268 DOI: 10.1038/s41598-020-66792-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/21/2020] [Indexed: 11/30/2022] Open
Abstract
Huge quantities of keratinaceous waste are a substantial and almost totally unexploited protein resource which could be upgraded for use as high value-added products by efficient keratinolytic enzymes. In this study, we found that Bacillus sp. 8A6 can efficiently degrade chicken feather after 24 h growth. According to phylogenetic analysis, the strain (formerly identified as Bacillus pumilus 8A6) belongs to the B. pumilus species clade but it is more closely related to B. safensis. Hotpep predicted 233 putative proteases from Bacillus sp. 8A6 genome. Proteomic analysis of culture broths from Bacillus sp. 8A6 cultured on chicken feathers or on a mixture of bristles and hooves showed high abundance of proteins with functions related to peptidase activity. Five proteases (one from family M12, one from family S01A, two from family S08A and one from family T3) and four oligopeptide and dipeptide binding proteins were highly expressed when Bacillus sp. 8A6 was grown in keratin media compared to LB medium. This study is the first to report that bacterial proteases in families M12, S01A and T3 are involved in keratin degradation together with proteases from family S08.
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Affiliation(s)
- Yuhong Huang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- Beijing Key Laboratory of Ionic Liquids Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Mateusz Łężyk
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg East, Denmark
| | - Peter Kamp Busk
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
| | - Lene Lange
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800, Kongens Lyngby, Denmark.
- Bioeconomy, Research & Advisory, Karensgade 5, DK-2500, Valby, Denmark.
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Liu G, Lin X, Xu S, Liu G, Liu F, Mu W. Screening, identification and application of soil bacteria with nematicidal activity against root-knot nematode (Meloidogyne incognita) on tomato. PEST MANAGEMENT SCIENCE 2020; 76:2217-2224. [PMID: 31970922 DOI: 10.1002/ps.5759] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 01/16/2020] [Accepted: 01/22/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Root-knot nematodes (Meloidogyne spp.) are soilborne pathogens that can cause great damage to and economic loss of crops globally. Owing to the high toxicity of chemicals toward humans and the environment, the use of biocontrol bacteria, a promising method for controlling root-knot nematodes, has gained attention. RESULTS To screen novel bacterial strains for their ability to control root-knot nematodes, 106 bacterial strains were isolated from soil. Eight of the obtained isolates exhibited satisfactory nematicidal activity against Meloidogyne incognita at 2-fold dilutions (approximately 3 × 1012 CFU mL-1 ) after 12 h of exposure. Based on their physiological, biochemical and molecular (16S rRNA and gyrB gene sequences) characteristics, the eight strains were identified as Bacillus halotolerans, B. kochii, B. oceanisediminis, B. pumilus, B. toyonensis, B. cereus, Pseudomonas aeruginosa and B. pseudomycoides. In greenhouse and field experiments, the eight isolates suppressed M. incognita up to 69.96% compared to the control. Additionally, the yield of tomato increased 1.4-26.1% over that of the control. CONCLUSION The strains of B. halotolerans DDWA, B. kochii DDWB, B. oceanisediminis DDWC and B. pseudomycoides JNC have potential to control M. incognita, which has not been previously reported. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Guangying Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection Shandong Agricultural University, Tai'an, PR China
- College of Plant Protection, Shandong Agricultural University, Tai'an, PR China
| | - Xu Lin
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection Shandong Agricultural University, Tai'an, PR China
- College of Plant Protection, Shandong Agricultural University, Tai'an, PR China
| | - Shuangyu Xu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection Shandong Agricultural University, Tai'an, PR China
- College of Plant Protection, Shandong Agricultural University, Tai'an, PR China
| | - Guang Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection Shandong Agricultural University, Tai'an, PR China
- College of Plant Protection, Shandong Agricultural University, Tai'an, PR China
| | - Feng Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection Shandong Agricultural University, Tai'an, PR China
- College of Plant Protection, Shandong Agricultural University, Tai'an, PR China
| | - Wei Mu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection Shandong Agricultural University, Tai'an, PR China
- College of Plant Protection, Shandong Agricultural University, Tai'an, PR China
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Little SV, Hillhouse AE, Lawhon SD. Whole-Genome Sequences of an Abortive Bacillus safensis Strain Isolated from a Mare's Uterus. Microbiol Resour Announc 2020; 9:e00342-20. [PMID: 32409543 PMCID: PMC7225542 DOI: 10.1128/mra.00342-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/21/2020] [Indexed: 11/21/2022] Open
Abstract
This is a report of two Bacillus safensis genomes sequenced from separate cultures isolated from the uterus of a 16-year-old Westphalian mare that aborted a dead fetus. This strain represents the first case of a B. safensis-associated equine abortion and the first case of infection caused by this bacterium.
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Affiliation(s)
- Sara V Little
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Andrew E Hillhouse
- Texas A&M Institute for Genome Sciences and Society, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Sara D Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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Tait AW, Gagen EJ, Wilson SA, Tomkins AG, Southam G. Eukaryotic Colonization of Micrometer-Scale Cracks in Rocks: A "Microfluidics" Experiment Using Naturally Weathered Meteorites from the Nullarbor Plain, Australia. ASTROBIOLOGY 2020; 20:364-374. [PMID: 31873039 DOI: 10.1089/ast.2019.2077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The advent of microfluidics has revolutionized the way we understand how microorganisms propagate through microporous spaces. Here, we apply this understanding to the study of how endolithic environmental microorganisms colonize the interiors of sterile rock. The substrates used for our study are stony meteorites from the Nullarbor Plain, Australia; a semiarid limestone karst that provides an ideal setting for preserving meteorites. Periodic flooding of the Nullarbor provides a mechanism by which microorganisms and exogenous nutrients may infiltrate meteorites. Our laboratory experiments show that environmental microorganisms reach depths greater than 400 μm by propagating through existing brecciation, passing through cracks no wider than the diameter of a resident cell (i.e., ∼5 μm). Our observations are consistent with the propagation of these eukaryotic cells via growth and cell division rather than motility. The morphology of the microorganisms changed as a result of propagation through micrometer-scale cracks, as has been observed previously for bacteria on microfluidic chips. It has been suggested that meteorites could have served as preferred habitats for microorganisms on ancient Mars. Based on our results, the depths reached by terrestrial microorganisms within meteorites would be sufficient to mitigate against the harmful effects of ionizing radiation, such as UV light, in Earth's deserts and potentially on Mars, if similar processes of microbial colonization had once been active there. Thus, meteorites landing in ancient lakes on Mars, that later dried out, could have been some of the last inhabited locations on the surface, serving as refugia before the planet's surface became inhospitable. Finally, our observations suggest that terrestrial microorganisms can colonize very fine cracks within meteorites (and potentially spaceships and rovers) on unexpectedly short timescales, with important implications for both recognition of extraterrestrial life in returned geological samples and planetary protection.
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Affiliation(s)
- Alastair W Tait
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Australia
- Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
| | - Emma J Gagen
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Australia
| | - Siobhan A Wilson
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Australia
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Andrew G Tomkins
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Australia
| | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Australia
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Seuylemezian A, Ott L, Wolf S, Fragante J, Yip O, Pukall R, Schumann P, Vaishampayan P. Bacillus glennii sp. nov. and Bacillus saganii sp. nov., isolated from the vehicle assembly building at Kennedy Space Center where the Viking spacecraft were assembled. Int J Syst Evol Microbiol 2020; 70:71-76. [PMID: 31622233 DOI: 10.1099/ijsem.0.003714] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, motile, endospore-forming, aerobic strains, designated V44-8T and V47-23aT, were isolated from environmental air sampling at the vehicle assembly building at Cape Canaveral, Florida, where the Viking spacecraft were assembled. Growth was observed at pH 7-9 (optimum, pH 9) for strain V44-8T, and pH 5-10 (pH 9) for strain V47-23aT. Both strains displayed growth in 0-5 % NaCl with an optimum at 1 % for strain V44-8T; 0 % for strain V47-23aT. Strains V44-8T and V47-23aT grew optimally at 32 °C, (15-32 °C) and 25 °C (20-45 °C), respectively. The cell wall of both strains contained meso-diaminopimelic acid as the diagnostic diamino acid. Both strains contained phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C14 : 0 and iso-C15 : 0. Strain V47.23aT shared its highest 16S rRNA sequence similarity with Bacillus cavernae DSM-105484T at 96.9%, and V44.8T with Bacillus zeae DSM-103964T at 96.6 %. Based on their phenotypic characteristics and phylogenetic position inferred from 16S rRNA gene sequence analyses, the isolates were identified as being a members of the genus Bacillus that forms a separate clade when compared to close relatives. Average nucleotide identity and average amino acid identity values between strains V44-8T and DSM-103964T were 72.1% and 67.5 %; V47-23aT and DSM-105484T were 62.4% and 69.1%, respectively. Based on the phenotypic, genomic and biochemical data, strains V44-8T and V47-23aT represent two novel species in the genus Bacillus for which the names Bacillus glennii sp. nov. [type strain, V44-8T (=ATCC BAA-2860T =DSM 105192T)], and Bacillus saganii sp. nov. [V47-23aT (=ATCC BAA-2861T=DSM 105190T)] are proposed.
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Affiliation(s)
- Arman Seuylemezian
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Logan Ott
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Sarah Wolf
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Jomel Fragante
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Oscar Yip
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B D-38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B D-38124 Braunschweig, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
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36
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Fischer S, Krause T, Lederer F, Merroun ML, Shevchenko A, Hübner R, Firkala T, Stumpf T, Jordan N, Jain R. Bacillus safensis JG-B5T affects the fate of selenium by extracellular production of colloidally less stable selenium nanoparticles. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121146. [PMID: 31771888 DOI: 10.1016/j.jhazmat.2019.121146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 06/10/2023]
Abstract
Understanding the impact of microorganisms on the mobility of selenium (Se) is important for predicting the fate of toxic Se in the environment and improving wastewater treatment technologies. The bacteria strain Bacillus safensis JG-B5T, isolated from soil in a uranium mining waste pile, can influence the Se speciation in the environment and engineered systems. However, the mechanism and conditions of this process remain unknown. This study found that the B. safensis JG-B5T is an obligate aerobic microorganism with an ability to reduce 70% of 2.5 mM selenite to produce red spherical biogenic elemental selenium nanoparticles (BioSeNPs). Only extracellular production of BioSeNPs was observed using transmission electron microscopy. The two-chamber reactor experiments, genome analysis and corona proteins identified on BioSeNPs suggested that the selenite reduction process was primarily mediated through membrane-associated proteins, like succinate dehydrogenase. Extracellular presence and low colloidal stability of BioSeNPs as indicated by ζ-potential measurements, render B. safensis JG-B5T an attractive candidate in wastewater treatment as it provides easy way of recovering Se while maintaining low Se discharge. As this microorganism decreases Se mobility, it will affect Se bioavailability in the environment and decreases its toxicity.
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Affiliation(s)
- Sarah Fischer
- Helmholtz-Zentrum Dresden - Rossendorf e. V., Institute of Resource Ecology, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Thomas Krause
- Technische Universität Dresden, Institute of Microbiology, Chair of Molecular Biotechnology, 01062 Dresden, Germany
| | - Franziska Lederer
- Helmholtz-Zentrum Dresden - Rossendorf e. V., Helmholtz Institute Freiberg for Resource Technology, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Mohamed L Merroun
- University of Granada, Department of Microbiology, Campus Fuentenueva, E-18071 Granada, Spain
| | - Anna Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - René Hübner
- Helmholtz-Zentrum Dresden - Rossendorf e. V., Institute of Ion Beam Physics and Materials Research, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Tamas Firkala
- Helmholtz-Zentrum Dresden - Rossendorf e. V., Helmholtz Institute Freiberg for Resource Technology, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Thorsten Stumpf
- Helmholtz-Zentrum Dresden - Rossendorf e. V., Institute of Resource Ecology, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Norbert Jordan
- Helmholtz-Zentrum Dresden - Rossendorf e. V., Institute of Resource Ecology, Bautzner Landstrasse 400, 01328 Dresden, Germany.
| | - Rohan Jain
- Helmholtz-Zentrum Dresden - Rossendorf e. V., Helmholtz Institute Freiberg for Resource Technology, Bautzner Landstrasse 400, 01328 Dresden, Germany.
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37
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Elyasi Far B, Yari Khosroushahi A, Dilmaghani A. In Silico Study of Alkaline Serine Protease and Production Optimization in Bacillus sp. Khoz1 Closed Bacillus safensis Isolated from Honey. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10016-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Rong S, Xu H, Li L, Chen R, Gao X, Xu Z. Antifungal activity of endophytic Bacillus safensis B21 and its potential application as a biopesticide to control rice blast. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 162:69-77. [PMID: 31836057 DOI: 10.1016/j.pestbp.2019.09.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 08/29/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Endophytic bacteria are potential biocontrol agents for the control of fungal diseases. Here, an endophyte strain, B21, was isolated from Osmanthus fragrans Lour. fruits and identified as Bacillus safensis by analysis of its 16S rDNA gene sequence and its biochemical and physiological characteristics. The culture filtrate showed antifungal activity against Magnaporthe oryzae, which causes rice blast disease, and the IC50 of the methanol extract was 15.56 μg/mL, which was significantly lower than that of carbendazim (25.16 μg/mL). The antifungal activity of the methanol extract was stable at a wide range of pH values (1-9) and temperatures (40-100 °C). Two antifungal compounds were isolated by organic extraction, silica gel column chromatography and high-performance liquid chromatography (HPLC). Based on electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance spectrometry (NMR) analyses, the structures of the antifungal compounds were identified as iturin A2 and iturin A6. Additionally, the hyphae treated with iturin (iturin A2 or iturin A6) could be stained with the fluorescent dye propidium iodide (PI), indicating that these two compounds inhibited the growth of hyphae by changing the hyphal membrane permeability. In field experiments, spray treatment with fermentation broth resulted in a lower disease index than treatment with carbendazim, as did the culture filtrate. The results suggest that strain B21 and its bioactive compounds have the potential to be developed into a biopesticide for the biocontrol of rice blast.
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Affiliation(s)
- Songhao Rong
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Hong Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Lihua Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Rongjun Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Xiaoling Gao
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Zhengjun Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China.
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39
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Hou F, Chang Y, Huang Z, Han N, Bin L, Deng H, Li Z, Pan Z, Ding L, Gao H, Yang R, Zhi F, Bi Y. Application of LpxC enzyme inhibitor to inhibit some fast-growing bacteria in human gut bacterial culturomics. BMC Microbiol 2019; 19:308. [PMID: 31888576 PMCID: PMC6937742 DOI: 10.1186/s12866-019-1681-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/11/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Culturomics can ascertain traces of microorganisms to be cultivated using different strategies and identified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry or 16S rDNA sequencing. However, to cater to all requirements of microorganisms and isolate as many species as possible, multiple culture conditions must be used, imposing a heavy workload. In addition, the fast-growing bacteria (e.g., Escherichia) surpass the slow-growing bacteria in culture by occupying space and using up nutrients. Besides, some bacteria (e.g., Pseudomonas) suppress others by secreting antibacterial metabolites, making it difficult to isolate bacteria with lower competence. Applying inhibitors to restrain fast-growing bacteria is one method to cultivate more bacterial species from human feces. RESULTS We applied CHIR-090, an LpxC enzyme inhibitor that has antibacterial activity against most Gram-negative bacteria, to culturomics of human fresh feces. The antibacterial activity of CHIR-090 was first assessed on five Gram-negative species of bacteria (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus vulgaris, and Bacteroides vulgatus), all of which are commonly isolated from the human gut. Then, we assessed suitable concentrations of the inhibitor. Finally, CHIR-090 was applied in blood culture bottles for bacterial cultivation. In total, 102 species from five samples were identified. Of these, we found one new species, two species not reported previously in the human gut, and 11 species not previously isolated from humans. CONCLUSIONS CHIR-090 can suppress E. coli, P. aeruginosa, K. pneumoniae, Pro. vulgaris, but not B. vulgatus. Compared with the non-inhibitor group, CHIR-090 increased bacteria isolation by 23.50%, including four species not reported in humans and one new species. Application of LpxC enzyme inhibitor in culturomics increased the number of species isolated from the human gut.
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Affiliation(s)
- Fengyi Hou
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuxiao Chang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zongyu Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ni Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Bin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Huimin Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhengchao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhiyuan Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Ding
- Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong Gao
- Shijitan Hospital, Capital Medical University, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fachao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
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40
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Molecular characterization of Bacillus, lactic acid bacteria and yeast as potential probiotic isolated from fermented food. SCIENTIFIC AFRICAN 2019. [DOI: 10.1016/j.sciaf.2019.e00175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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41
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Draft Genome Sequence of Bacillus safensis RP10, Isolated from Soil in the Atacama Desert, Chile. Microbiol Resour Announc 2019; 8:8/44/e01150-19. [PMID: 31672748 PMCID: PMC6953511 DOI: 10.1128/mra.01150-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Genome analysis of Bacillus safensis RP10, a strain from the soil of Atacama Desert in northern Chile, reflects a bacterium adapted to live in soil containing high levels of heavy metals, high salt conditions, and low carbon and energy sources.
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42
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Microscopic Characterization of Biological and Inert Particles Associated with Spacecraft Assembly Cleanroom. Sci Rep 2019; 9:14251. [PMID: 31582832 PMCID: PMC6776515 DOI: 10.1038/s41598-019-50782-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/05/2019] [Indexed: 11/18/2022] Open
Abstract
NASA cleanrooms are certified by particle counts and are humidity-controlled, temperature-regulated, and oligotrophic in nature for assembling spacecraft subsystems. Microorganisms, which are not part of the cleanroom certification metrics, should not be overlooked when assessing the cleanliness of the facility since they can enter through soil or air, shed from humans, adapt to the oligotrophic conditions, and subsequently could contaminate spacecraft. These biogenic particles need to be identified to extend our knowledge of biological contamination for future NASA mission use. This study collected particles from the cleanroom and estimated the distribution of fallout microbial cell and inert dust particles using microscopy and molecular techniques. Aluminum coupon-based polycarbonate filter assemblies were deployed in the spacecraft assembly cleanroom facility to collect fallout particles. Epifluorescence and electron microscopy showed that particles varied in size and structure, and displayed live/dead biological and inert particle signatures from sources that include spores and fungal hyphae. Additionally, correlative epifluorescence and field emission scanning electron microscopy, combined with energy-dispersive X-ray analysis (for elemental compositions) methods, differentiated whether microbes adhering to particles were live/dead cells or inert particles. This visualization approach allowed for the classification of microorganisms as being standalone (free-living) or associated with a particle, as well as its characteristic size. Furthermore, time-course microscopy was used to determine the microbial cell growth and confirm the biological/molecular identification. Routine investigation of cleanroom biological and inert fallout particles will help to determine the biological load of spacecraft components and will also have direct relevance to the pharmaceutical and medical industries. One of the main objectives for NASA’s current and future missions is to prevent forward and back contamination of exploring planets. The goal of this study is to determine the association of microorganisms with the inert, natural cleanroom fallout particles and to ascertain whether microorganisms prefer to adhere to a particle size. A novel microscopy technique was developed, and by utilizing various molecular techniques, particles and associated microbial phylogeny were characterized. An accurate assessment of the microbes associated with cleanroom particles is necessary to protect the health of the people who occupy the room for long duration for aeronautical, medical, and pharmaceutical industries.
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Li J, Wu ZB, Zhang Z, Zha JW, Qu SY, Qi XZ, Wang GX, Ling F. Effects of potential probiotic Bacillus velezensis K2 on growth, immunity and resistance to Vibrio harveyi infection of hybrid grouper (Epinephelus lanceolatus♂ × E. fuscoguttatus♀). FISH & SHELLFISH IMMUNOLOGY 2019; 93:1047-1055. [PMID: 31425831 DOI: 10.1016/j.fsi.2019.08.047] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Nowadays, there is no suitable treatment for vibriosis in groupers. So an eco-efficient and environmentally friendly treatment is necessary for the grouper industry. Probiotic-feeding has been a promising strategy to control the bacterial pathogens in aquaculture. A new Bacillus velezensis strain named K2 was isolated from the intestinal tract of healthy grouper, and exhibited wide antimicrobial spectrum of against fish pathogens, including Vibrio harveyi, Vibrio alginolyticus, Aeromonas hydrophila, Aeromonas veronii, Aeromonas caviae, Enterococcus casseliflavus and Lactococcus garvieae. Moreover, results of the safety of B. velezensis K2 showed that intraperitoneal injection of K2 in healthy grouper did not cause any pathological abnormality or death, indicating this bacteria could be considered as a candidate probiotic in aquaculture. Groupers were fed with the diets containing 1 × 107 cfu/g of B. velezensis K2 for 4 weeks. Various immune parameters were examined at 1, 2, 3, and 4 weeks of post-feeding. Results showed that diets supplemented with K2 significantly increased serum acid phosphatase (ACP) activity (P < 0.05). Results of the mRNA expression of immune-related genes in the head kidney of hybrid grouper showed that the expression of lysozyme gene was significantly upregulated after 1 and 2 weeks of feeding (P < 0.05). A significant up-regulation of the expression of piscidin, IgM and MyD88 were detected at day 21, whereas the TLR3 and TLR5 showed lower expression compared to the controls during 21 days, and a significant decrease of TLR3 gene was found at day 28 (P < 0.05). After challenge with V. harveyi, the survival rate of fish administrated with the strain K2 for 28 days was signifiacantly higher than the controls without this strain (P < 0.05). These results collectively suggest that B. velezensis K2 is a potential probiotic species to improve health status and disease resistance and can be developed as a probiotic agent in grouper industry.
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Affiliation(s)
- Jing Li
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Zhi-Bin Wu
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Zhao Zhang
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Ji-Wei Zha
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Shen-Ye Qu
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Xiao-Zhou Qi
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China
| | - Gao-Xue Wang
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China.
| | - Fei Ling
- Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China.
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Kelley DE, Hodo CL, Aceino A, Lawhon SD, Hinrichs K, Brinsko SP. Abortion due to
Bacillus safensis
in a mare. EQUINE VET EDUC 2019. [DOI: 10.1111/eve.13181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- D. E. Kelley
- Department of Large Animal Clinical Sciences College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas USA
| | - C. L. Hodo
- Department of Veterinary Pathobiology College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas USA
| | - A. Aceino
- Department of Veterinary Pathobiology College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas USA
| | - S. D. Lawhon
- Department of Veterinary Pathobiology College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas USA
| | - K. Hinrichs
- Department of Veterinary Pathobiology College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas USA
- Department of Veterinary Physiology and Pharmacology College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas USA
| | - S. P. Brinsko
- Department of Large Animal Clinical Sciences College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas USA
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45
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Juárez-Jiménez B, Pesciaroli C, Maza-Márquez P, López-Martínez S, Vílchez-Quero JL, Zafra-Gómez A. Biodegradation of methyl and butylparaben by bacterial strains isolated from amended and non-amended agricultural soil. Identification, behavior and enzyme activities of microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 245:245-254. [PMID: 31154171 DOI: 10.1016/j.jenvman.2019.05.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/17/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
The aim of the present study was to investigate the kinetics of methylparaben (MPB) and butylparaben (BPB) removal, two emerging pollutants with possible endocrine disrupting effects, from agricultural soil with and without amendment with compost from sewage sludge used as biostimulant. Compound removal is explained by a first-order kinetic model with half-life times of 6.5/6.7 days and 11.4/8.2 days, in presence/absence of compost, for MPB and BPB respectively. % R2 for the fitted model were higher than 96% in all cases. Additionally, isolation of bacteria capable to grow using MPB or BPB as carbon source was also carry out. Laboratory tests demonstrated the ability of these bacteria to biodegrade MPB and BPB from culture media in more than 95% in some cases. These strains showed high ability to biodegrade the compounds. Ten isolates, most of them related to Gram positive bacteria of the genus Bacillus, were identified by 16S rRNA gene sequencing. The study of the enzymatic activities of the isolates revealed both esterase (C4) and esterase-lipase activities.
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Affiliation(s)
- Belén Juárez-Jiménez
- Research Group of Environmental Microbiology, Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, And Water Institute, C/ Ramon y Cajal s/n, University of Granada, E-18071, Granada, Spain.
| | - Chiara Pesciaroli
- Department of Biotechnology and Bioscience, University of Milan Bicocca, Italy
| | - Paula Maza-Márquez
- Research Group of Environmental Microbiology, Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, And Water Institute, C/ Ramon y Cajal s/n, University of Granada, E-18071, Granada, Spain
| | - Sergio López-Martínez
- Research Group of Analytical Chemistry and Life Sciences, Department of Analytical Chemistry, University of Granada, Campus of Fuentenueva, E-18071, Granada, Spain
| | - José Luís Vílchez-Quero
- Research Group of Analytical Chemistry and Life Sciences, Department of Analytical Chemistry, University of Granada, Campus of Fuentenueva, E-18071, Granada, Spain
| | - Alberto Zafra-Gómez
- Research Group of Analytical Chemistry and Life Sciences, Department of Analytical Chemistry, University of Granada, Campus of Fuentenueva, E-18071, Granada, Spain.
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Rettberg P, Antunes A, Brucato J, Cabezas P, Collins G, Haddaji A, Kminek G, Leuko S, McKenna-Lawlor S, Moissl-Eichinger C, Fellous JL, Olsson-Francis K, Pearce D, Rabbow E, Royle S, Saunders M, Sephton M, Spry A, Walter N, Wimmer Schweingruber R, Treuet JC. Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know? ASTROBIOLOGY 2019; 19:951-974. [PMID: 30762429 PMCID: PMC6767865 DOI: 10.1089/ast.2018.1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
To ensure that scientific investments in space exploration are not compromised by terrestrial contamination of celestial bodies, special care needs to be taken to preserve planetary conditions for future astrobiological exploration. Significant effort has been made and is being taken to address planetary protection in the context of inner Solar System exploration. In particular for missions to Mars, detailed internationally accepted guidelines have been established. For missions to the icy moons in the outer Solar System, Europa and Enceladus, the planetary protection requirements are so far based on a probabilistic approach and a conservative estimate of poorly known parameters. One objective of the European Commission-funded project, Planetary Protection of Outer Solar System, was to assess the existing planetary protection approach, to identify inherent knowledge gaps, and to recommend scientific investigations necessary to update the requirements for missions to the icy moons.
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Affiliation(s)
- Petra Rettberg
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
- Address correspondence to: Petra Rettberg, German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Research Group Astrobiology, Linder Höhe, 51147 Köln, Germany
| | - André Antunes
- GEMM—Group for Extreme and Marine Microbiology, Department of Biology, Edge Hill University, Ormskirk, United Kingdom
| | - John Brucato
- Department of Physics and Astronomy, Astrophysical Observatory of Arcetri, National Institute for Astrophysics (INAF), Florence, Italy
| | - Patricia Cabezas
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Geoffrey Collins
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Alissa Haddaji
- Committee on Space Research (COSPAR), Montpellier, France
| | - Gerhard Kminek
- Committee on Space Research (COSPAR), Montpellier, France
| | - Stefan Leuko
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | | | | | - Jean-Louis Fellous
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Karen Olsson-Francis
- Faculty of Science, Technology, Engineering & Mathematics, School of Environment, Earth & Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | - David Pearce
- Department of Applied Sciences, Northumbria University, Newcastle, United Kingdom
| | - Elke Rabbow
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Samuel Royle
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Mark Saunders
- Independent Consultant for the US National Academies of Sciences (NAS), Washington, District of Columbia
| | - Mark Sephton
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Andy Spry
- Carl Sagan Center, SETI, Mountain View, California
| | - Nicolas Walter
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Robert Wimmer Schweingruber
- Institut für Experimentelle und Angewandte Physik, Abteilung Extraterrestrische Physik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Guarcello R, Gaglio R, Todaro A, Alfonzo A, Schicchi R, Cirlincione F, Moschetti G, Francesca N. Insights Into the Cultivable Microbial Ecology of "Manna" Ash Products Extracted From Fraxinus angustifolia ( Oleaceae) Trees in Sicily, Italy. Front Microbiol 2019; 10:984. [PMID: 31164870 PMCID: PMC6536662 DOI: 10.3389/fmicb.2019.00984] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/18/2019] [Indexed: 02/04/2023] Open
Abstract
Microbial communities characterizing a specific food matrix, generally, strongly contribute to both its composition, and properties for food applications. To our knowledge, this is the first study to investigate the cultivable microbial ecology of Sicilian “Manna” ash products in order to acquire new information on the hygienic quality, shelf-life and potential application of this traditional food. To this purpose, several manna samples belonging to different commercial categories were collected and subjected to the analysis of bacteria, yeasts, and filamentous fungi. Furthermore, an investigation of the sugar content and physicochemical parameters was performed. The results of our study followed the trend generally reported for other sugary foods. Conversely, as regards microbiological analyses, in the present study, the presence of microorganisms at high levels confirmed their survival in stressing conditions characterizing this food matrix in a viable and cultivable form. Most species were osmophilic, endophytic bacteria, antagonistic of fungi pathogen of plants. Yeasts were the most abundant microbial populations and a total of six species were identified: Candida aaseri, Candida lactis-condensi, Citeromyces matritensis, Lachancea thermotolerans, Saccharomyces cerevisiae, and Zygosaccharomyces bailii. Filamentous fungi included five genera, which were considered common contaminants of honey and of other foods due to their xerophilic characteristics. Interestingly, our results suggest that the strains of L. thermotolerans isolated in this study might be evaluated for their potential to act as starters either singly or in multi-combination for food applications.
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Affiliation(s)
- Rosa Guarcello
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Raimondo Gaglio
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Aldo Todaro
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Antonio Alfonzo
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Rosario Schicchi
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Fortunato Cirlincione
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Giancarlo Moschetti
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Nicola Francesca
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, Italy
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48
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Wu T, Xu J, Liu J, Guo WH, Li XB, Xia JB, Xie WJ, Yao ZG, Zhang YM, Wang RQ. Characterization and Initial Application of Endophytic Bacillus safensis Strain ZY16 for Improving Phytoremediation of Oil-Contaminated Saline Soils. Front Microbiol 2019; 10:991. [PMID: 31134029 PMCID: PMC6515983 DOI: 10.3389/fmicb.2019.00991] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/18/2019] [Indexed: 11/16/2022] Open
Abstract
Hydrocarbon-degrading and plant-growth-promoting bacterial endophytes have proven useful for facilitating the phytoremediation of petroleum-contaminated soils with high salinity. In this study, we identified Bacillus safensis strain ZY16 as an endophytic bacterium that can degrade hydrocarbons, produce biosurfactants, tolerate salt, and promote plant growth. The strain was isolated from the root of Chloris virgata Sw., a halotolerant plant collected from the Yellow River Delta. ZY16 survived in Luria-Bertani (LB) broth with 0–16% (w/v) sodium chloride (NaCl) and grew well in LB broth supplemented with 0–8% NaCl, indicating its high salt tolerance. The endophytic strain ZY16 effectively degraded C12–C32n-alkanes of diesel oil effectively, as well as common polycyclic aromatic hydrocarbons under hypersaline conditions. For example, in mineral salts (MS) liquid medium supplemented with 6% NaCl, ZY16 degraded n-undecane, n-hexadecane, n-octacosane, naphthalene, phenanthrene, and pyrene, with degradation percentages of 94.5, 98.2, 64.8, 72.1, 59.4, and 27.6%, respectively. In addition, ZY16 produced biosurfactant, as confirmed by the oil spreading technique, surface tension detection, and emulsification of para-xylene and paraffin. The biosurfactant production ability of ZY16 under hypersaline conditions was also determined. Moreover, ZY16 showed plant-growth-promoting attributes, such as siderophore and indole-3-acetic acid production, as well as phosphate solubilization. To assess the enhanced phytoremediation of saline soils polluted by hydrocarbons and the plant-growth-promotion ability of ZY16, a pot trial with and without inoculation of the endophyte was designed and performed. Inoculated and non-inoculated plantlets of C. virgata Sw. were grown in oil-polluted saline soil, with oil and salt contents of 10462 mg/kg and 0.51%, respectively. After 120 days of growth, significant enhancement of both the aerial and underground biomass of ZY16-inoculated plants was observed. The soil total petroleum hydrocarbon degradation percentage (a metric of phytoremediation) after incubation with ZY16 was 63.2%, representing an elevation of 25.7% over phytoremediation without ZY16 inoculation. Our study should promote the application of endophytic B. safensis ZY16 in phytoremediation by extending our understanding of the mutualistic interactions between endophytes and their host plants.
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Affiliation(s)
- Tao Wu
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China.,Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China.,Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
| | - Jie Xu
- Department of Bioengineering, Binzhou Vocational College, Binzhou, China
| | - Jian Liu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
| | - Wei-Hua Guo
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiao-Bin Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiang-Bao Xia
- Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China
| | - Wen-Jun Xie
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China.,Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China
| | - Zhi-Gang Yao
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Yu-Miao Zhang
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China.,Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, China
| | - Ren-Qing Wang
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao, China
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The Spectrum of Interactions between Cryptococcus neoformans and Bacteria. J Fungi (Basel) 2019; 5:jof5020031. [PMID: 31013706 PMCID: PMC6617360 DOI: 10.3390/jof5020031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/08/2019] [Accepted: 04/11/2019] [Indexed: 01/08/2023] Open
Abstract
Cryptococcus neoformans is a major fungal pathogen that infects immunocompromised people and causes life-threatening meningoencephalitis. C. neoformans does not occur in isolation either in the environment or in the human host, but is surrounded by other microorganisms. Bacteria are ubiquitously distributed in nature, including soil, and make up the dominant part of the human microbiota. Pioneering studies in the 1950s demonstrated antifungal activity of environmental bacteria against C. neoformans. However, the mechanisms and implications of these interactions remain largely unknown. Recently, interest in polymicrobial interaction studies has been reignited by the development of improved sequencing methodologies, and by the realization that such interactions may have a huge impact on ecology and human health. In this review, we summarize our current understanding of the interaction of bacteria with C. neoformans.
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Anyasi RO, Atagana HI, Sutherland R. Comparative Study of the Colonization of Chromolaena and Tobacco Plants by Bacteria safensis CS4 using Different Methods of Inoculation. Pak J Biol Sci 2019; 22:309-317. [PMID: 31930841 DOI: 10.3923/pjbs.2019.309.317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVES This study entails the effectiveness of colonization of bacterial endophytes following inoculation of the cells in plants. METHODOLOGY Different methods of inoculation including seed immersion, root immersion and foliar spray were studied on Chromolaena odorata and Nicotiana tabacum for 10, 20 and 30 days. This was to ascertain the colonization ability of the endophytic strain amongst the two set of plants. The foliar parts of the plants were assessed post inoculation for the presence of the bacteria strain, followed by the growth parameters in the plant. Significant differences at p<0.05 of colonization were established by the different inoculation methods. RESULTS Foliar spray demonstrated the highest colonization in both Chromolaena and tobacco plants followed by root immersion. Leaf inoculation in tobacco plant demonstrated a positive colonization which is not significant. However, seed inoculation provided colonization in Chromolaena plant at 10, 20 and 30 days post inoculation at a frequency lower than that of tobacco. With root immersion in Chromolaena, there was colonization at 10 days post inoculation, no colonization at 20 days post inoculation, but colonization re-appeared at 30 days (PI). Growth index measured demonstrated a positive relationship between the inoculation of the endophyte and the growth parameters which included stem length and germination rate. CONCLUSION This study, therefore, showed that the bacteria strain B. safensis CS4 can effectively be horizontally transferred into tobacco and Chromolaena plants using different methods. Foliar spraying demonstrated the optimal colonization of the strain in the plant leaves.
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