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Santos Ferreira DA, de Castro Levatti EV, Santa Cruz LM, Costa AR, Migotto ÁE, Yamada AY, Camargo CH, Christodoulides M, Lago JHG, Tempone AG. Saturated Iso-Type Fatty Acids from the Marine Bacterium Mesoflavibacter zeaxanthinifaciens with Anti-Trypanosomal Potential. Pharmaceuticals (Basel) 2024; 17:499. [PMID: 38675459 PMCID: PMC11053438 DOI: 10.3390/ph17040499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Chagas disease is a Neglected Tropical Disease with limited and ineffective therapy. In a search for new anti-trypanosomal compounds, we investigated the potential of the metabolites from the bacteria living in the corals and sediments of the southeastern Brazilian coast. Three corals, Tubastraea coccinea, Mussismilia hispida, Madracis decactis, and sediments yielded 11 bacterial strains that were fully identified by MALDI-ToF/MS or gene sequencing, resulting in six genera-Vibrio, Shewanella, Mesoflavibacter, Halomonas, Bacillus, and Alteromonas. To conduct this study, EtOAc extracts were prepared and tested against Trypanosoma cruzi. The crude extracts showed IC50 values ranging from 15 to 51 μg/mL against the trypomastigotes. The bacterium Mesoflavibacter zeaxanthinifaciens was selected for fractionation, resulting in an active fraction (FII) with IC50 values of 17.7 μg/mL and 23.8 μg/mL against the trypomastigotes and amastigotes, respectively, with neither mammalian cytotoxicity nor hemolytic activity. Using an NMR and ESI-HRMS analysis, the FII revealed the presence of unsaturated iso-type fatty acids. Its lethal action was investigated, leading to a protein spectral profile of the parasite altered after treatment. The FII also induced a rapid permeabilization of the plasma membrane of the parasite, leading to cell death. These findings demonstrate that these unsaturated iso-type fatty acids are possible new hits against T. cruzi.
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Affiliation(s)
- Dayana Agnes Santos Ferreira
- Pathophysiology Laboratory, Instituto Butantan, Av. Vital Brazil, 1500, Sao Paulo 05503-900, SP, Brazil; (D.A.S.F.); (E.V.d.C.L.)
| | | | - Lucas Monteiro Santa Cruz
- Centre of Organic Contaminants, Instituto Adolfo Lutz, Av. Dr. Arnaldo, 355, Sao Paulo 01246-000, SP, Brazil; (L.M.S.C.); (A.R.C.)
| | - Alan Roberto Costa
- Centre of Organic Contaminants, Instituto Adolfo Lutz, Av. Dr. Arnaldo, 355, Sao Paulo 01246-000, SP, Brazil; (L.M.S.C.); (A.R.C.)
| | - Álvaro E. Migotto
- Centre for Marine Biology, Universidade de São Paulo, Rodovia Doutor Manoel Hipólito do Rego, km. 131,5, Pitangueiras, Sao Sebastiao 11612-109, SP, Brazil;
| | - Amanda Yaeko Yamada
- Centre of Bacteriology, Instituto Adolfo Lutz, Av. Dr. Arnaldo, 351, Sao Paulo 01246-000, SP, Brazil; (A.Y.Y.); (C.H.C.)
| | - Carlos Henrique Camargo
- Centre of Bacteriology, Instituto Adolfo Lutz, Av. Dr. Arnaldo, 351, Sao Paulo 01246-000, SP, Brazil; (A.Y.Y.); (C.H.C.)
| | - Myron Christodoulides
- Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | - João Henrique G. Lago
- Centre of Natural Sciences and Humanities, Universidade Federal do ABC, Sao Paulo 09210-580, SP, Brazil
| | - Andre Gustavo Tempone
- Pathophysiology Laboratory, Instituto Butantan, Av. Vital Brazil, 1500, Sao Paulo 05503-900, SP, Brazil; (D.A.S.F.); (E.V.d.C.L.)
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Bielen A, Babić I, Vuk Surjan M, Kazazić S, Šimatović A, Lajtner J, Udiković-Kolić N, Mesić Z, Hudina S. Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21752-21764. [PMID: 38393570 DOI: 10.1007/s11356-024-32537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.
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Affiliation(s)
- Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia.
| | - Ivana Babić
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Marija Vuk Surjan
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Ana Šimatović
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Jasna Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Zrinka Mesić
- Oikon Ltd., Trg Senjskih Uskoka 1-2, 10020, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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Changes in the bacterial community in port waters during ship’s ballast water discharge. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02963-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Liu T, Kang L, Xu J, Wang J, Gao S, Li Y, Li J, Yuan Y, Yuan B, Wang J, Zhao B, Xin W. PVBase: A MALDI-TOF MS Database for Fast Identification and Characterization of Potentially Pathogenic Vibrio Species From Multiple Regions of China. Front Microbiol 2022; 13:872825. [PMID: 35656002 PMCID: PMC9152771 DOI: 10.3389/fmicb.2022.872825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
The potentially pathogenic species of the genus Vibrio pose a threat to both humans and animals, creating medical burdens and economic losses to the mariculture industry. Improvements in surveillance and diagnosis are needed to successfully manage vibriosis outbreaks. Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) can provide rapid diagnosis and has been widely used in the identification of Vibrio spp. The main weakness of this technology is the limited number of strains and species of Vibrio in the existing commercial database. Here, we develop a new in-house database named PVBase containing 790 main spectra projections (MSP) of ten Vibrio species that come from various regions of China and include abundant clinical and environmental strains. PVBase was validated through a blind test of 65 Vibrio strains. The identification accuracy and scoring of Vibrio strains was greatly improved through the addition of PVBase. Identification accuracy increased from 73.4 to 100%. The number of strains with identification scores above 2.2 increased from 53.1% to 96.9% and 53.1% of strains had an identification score above 2.59. Moreover, perfect discrimination was obtained when using all of the MSPs created for the Vibrio species, even for very closely related species such as V. cholerae, V. albensis, and V. mimicus or V. alginolyticus, V. parahaemolyticus, and V. harveyi. In addition, we used phyloproteomic analysis to study whether there are differences in protein fingerprints of different regions or pathogenic strains. We found that MSP characteristics of Vibrio species were not related to their region or source. With the construction of PVBase, the identification efficiency of potentially pathogenic Vibrio species has been greatly improved, which is an important advance for epidemic prevention and control, and aquaculture disease detection.
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Affiliation(s)
- Tingting Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jinglin Xu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yanwei Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jiaxin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Baohua Zhao
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
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5
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Ashfaq MY, Da'na DA, Al-Ghouti MA. Application of MALDI-TOF MS for identification of environmental bacteria: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114359. [PMID: 34959061 DOI: 10.1016/j.jenvman.2021.114359] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 05/22/2023]
Abstract
Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.
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Affiliation(s)
- Mohammad Y Ashfaq
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Dana A Da'na
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar.
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6
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Modern Analytical Techniques for Detection of Bacteria in Surface and Wastewaters. SUSTAINABILITY 2021. [DOI: 10.3390/su13137229] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Contamination of surface waters with pathogens as well as all diseases associated with such events are a significant concern worldwide. In recent decades, there has been a growing interest in developing analytical methods with good performance for the detection of this category of contaminants. The most important analytical methods applied for the determination of bacteria in waters are traditional ones (such as bacterial culturing methods, enzyme-linked immunoassay, polymerase chain reaction, and loop-mediated isothermal amplification) and advanced alternative methods (such as spectrometry, chromatography, capillary electrophoresis, surface-enhanced Raman scattering, and magnetic field-assisted and hyphenated techniques). In addition, optical and electrochemical sensors have gained much attention as essential alternatives for the conventional detection of bacteria. The large number of available methods have been materialized by many publications in this field aimed to ensure the control of water quality in water resources. This study represents a critical synthesis of the literature regarding the latest analytical methods covering comparative aspects of pathogen contamination of water resources. All these aspects are presented as representative examples, focusing on two important bacteria with essential implications on the health of the population, namely Pseudomonas aeruginosa and Escherichia coli.
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7
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Wang C, Bi H. Super-fast seafood authenticity analysis by One-step pretreatment and comparison of mass spectral patterns. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107751] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Shao M, Bi H. Direct identification of fish species by surface molecular transferring. Analyst 2021; 145:4148-4155. [PMID: 32386286 DOI: 10.1039/d0an00510j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
With the expansion of the aquatic market and the large quantity of seafood consumption, the issues on safety, traceability and authenticity of seafood are becoming more and more important. Herein, a mass spectrometric method by direct analysis of fish samples was developed for fish authentication. A high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) technique was applied to analyze the substances on the fish skin, or the surface molecularly imprinted substances on the surface of muscle tissues using a MALDI-target plate. A multivariate analysis was executed on the obtained mass spectra, and plots of principal component analysis (PCA) for different fish samples were differently clustered in a 95% confidence level. The developed strategy was capable of classifying and identifying fish species. The molecular imprinting method was found with good analytical reproducibility. The strategy enables the distinguishment of fish samples in a quick, efficient and easy mode. It is promising to apply the presently developed strategy for the authentication of seafood and extend the protocol for the detection of other protein food products.
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Affiliation(s)
- Mingke Shao
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China.
| | - Hongyan Bi
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China.
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Schaerer LG, Webb PN, Corazzola A, Christian WC, Techtmann SM. Impact of air, water and dock microbial communities on boat microbial community composition. J Appl Microbiol 2020; 131:768-779. [PMID: 33128819 DOI: 10.1111/jam.14916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/15/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
Abstract
AIMS This study explores the microbial diversity of sources which may influence boat microbial communities. We investigated the impact of dock, air and water microbial communities on the hull, transom and bilge microbial communities over the span of 11 days. METHODS AND RESULTS Using source tracking software, we investigated the extent to which each of our potential sources (air, water and dock) influenced the overall microbial community. This study concluded that the dock impacted 14-64% of the hull and transom microbial community. Micro-organisms from the water were shown to impact 5·6% the bilge microbial community but had minimal impact on hull and transom microbial communities. Micro-organisms from the air had minimal impact in all areas of the boat. CONCLUSIONS Our results demonstrate that micro-organisms from sources other than water can influence the microbial community of a boat, suggesting that terrestrial micro-organisms can impact the boat microbial community. SIGNIFICANCE AND IMPACT OF THE STUDY Outside of ballast tanks, microbial diversity on boats is largely unexplored. While ballast water is widely recognized as a route for dispersal of allochthonous micro-organisms, comparatively little is known about the microbial diversity on other areas of the boat. If the organisms on a boat originate from sources other than water, there is potential that terrestrial micro-organisms could be dispersed by shipping activity.
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Affiliation(s)
- L G Schaerer
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - P N Webb
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - A Corazzola
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - W C Christian
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - S M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
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Khandeparker L, Kuchi N, Desai DV, Anil AC. Changes in the ballast water tank bacterial community during a trans-sea voyage: Elucidation through next generation DNA sequencing. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 273:111018. [PMID: 32741756 DOI: 10.1016/j.jenvman.2020.111018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Ballast water (BW) mediated bioinvasion is one of the greatest threats to the health of aquatic ecosystems. Bacteria, unlike higher organisms, are transferred in large numbers through BW. Owing to their abundance and potential pathogenicity, they pose a direct threat to the prevailing microbiome in the recipient waters and also to human health. This study investigated the changes in the BW tank bacterial community during a trans-sea voyage from Visakhapatnam port, located along the east coast of India (Bay of Bengal) to Mumbai port, located along the west coast of India (Arabian Sea). Next generation sequencing was used to explore the unculturable segment of bacteria. The BW tank conditions led to a decrease in photoautotrophs and non-spore forming bacteria. On the other hand, biofilm forming and antibiotic producing bacteria, nutrient limiting condition sustaining bacteria, and those capable of synthesizing enzymes prerequisite for active metabolism under stress, increased over time. The shifts in the bacterial community were dependent on mechanisms adopted by the clades to cope with the BW tank conditions. Functional prediction of the bacterial community revealed a significant increase in the core metabolic functions, which enabled the survival of such bacteria. As the voyage progressed, an increase in the total viable bacteria in BW tanks could be attributed to the decrease in the abundance of phytoplankton and zooplankton. At the end of the voyage, the bacterial community in the BW tanks was significantly different, and the species diversity and richness were higher than that of the natural seawater (source water). Pathogenic species were more abundant during mid-voyage than at the end of the voyage, suggesting that voyage duration influences the pathogenic bacterial community. Investigating the fate of the discharged bacterial population at the deballasting point is a way forward in the assessment of marine bioinvasion.
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Affiliation(s)
| | - Nishanth Kuchi
- CSIR - National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Dattesh V Desai
- CSIR - National Institute of Oceanography, Dona Paula, Goa, 403004, India.
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11
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Brockmann M, Aupperle-Lellbach H, Gentil M, Heusinger A, Müller E, Marschang RE, Pees M. Challenges in microbiological identification of aerobic bacteria isolated from the skin of reptiles. PLoS One 2020; 15:e0240085. [PMID: 33075077 PMCID: PMC7571677 DOI: 10.1371/journal.pone.0240085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/19/2020] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Bacterial pathogens are often involved in dermatitis in reptiles. Exact identification of reptile-specific but otherwise uncommon bacterial species may be challenging. However, identification is crucial to evaluate the importance of the detected bacterial species. OBJECTIVE The aim of this study was to assess the number of aerobic bacterial isolates cultured from skin-derived samples of reptiles which were not reliably identified by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS), and to determine their identity. MATERIAL AND METHODS Routine bacterial diagnostics were performed on 235 skin samples, and 417 bacterial isolates were analysed by MALDI-TOF MS. The isolates were grouped into categories based on their first score: category I (≥ 2.00), category II (≥ 1.70 and < 2.00), and category III (< 1.70). Isolates from category III were further investigated by 16S rRNA gene sequencing and the following criteria were applied: query cover 100%, e-value rounded to 0.0 and sequence identity (%) > 98.00% for genus identification, and > 99.00% for species identification. RESULTS The majority of bacterial isolates were in category I (85.1%) or category II (8.4%). In category III (6.5%) results achieved at first by MALDI-TOF MS corresponded to the results of the molecular analysis in 8.0% of isolates at the species level and in 24.0% at the genus level. Bacterial isolates classified as category III were heterogenic in genus (e.g. Chryseobacterium, Devriesea, Pseudomonas, Staphylococcus, Uruburuella), and some have only been described in reptiles so far. CONCLUSIONS Most of the aerobic bacterial isolates cultured from reptile skin achieved high scores by MALDI-TOF MS. However, in the majority of category III isolates MALDI-TOF MS results were different from those of the molecular analysis. This strengthens the need to carefully examine low-scored results for plausibility and to be familiar with the occurrence and morphology of relevant reptile-specific bacterial species (e.g. Devriesea agamarum) as well as with the limits of the database used.
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MESH Headings
- Animals
- Bacteria, Aerobic/chemistry
- Bacteria, Aerobic/genetics
- Bacteria, Aerobic/isolation & purification
- Gram-Negative Bacteria/genetics
- Gram-Negative Bacteria/isolation & purification
- Gram-Negative Bacteria/metabolism
- Gram-Positive Bacteria/genetics
- Gram-Positive Bacteria/isolation & purification
- Gram-Positive Bacteria/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Reptiles/microbiology
- Skin/microbiology
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
| | | | | | | | | | | | - Michael Pees
- Clinic for Birds and Reptiles, University of Leipzig, Leipzig, Germany
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Mougin J, Flahaut C, Roquigny R, Bonnin-Jusserand M, Grard T, Le Bris C. Rapid Identification of Vibrio Species of the Harveyi Clade Using MALDI-TOF MS Profiling With Main Spectral Profile Database Implemented With an In-House Database: Luvibase. Front Microbiol 2020; 11:586536. [PMID: 33162963 PMCID: PMC7581793 DOI: 10.3389/fmicb.2020.586536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/17/2020] [Indexed: 12/02/2022] Open
Abstract
Vibrio bacteria, and particularly members of the Harveyi clade, are the causative agents of vibriosis. This disease is responsible for mass mortality events and important economic losses on aquaculture farms. Improvements in surveillance and diagnosis are needed to successfully manage vibriosis outbreaks. 16S rRNA gene sequencing is generally considered to be the gold standard for bacterial identification but the cost and long processing time make it difficult to apply for routine identification. In contrast, MALDI-TOF MS offers rapid diagnosis and is commonly used in veterinary laboratories today. The major limiting factor for using this technique is the low environmental bacterial diversity in the commonly available databases. Here, we demonstrate that the sole use of the commercially available Bruker BioTyper database is not fully adequate for identifying Vibrio bacteria isolated from aquaculture farms. We therefore developed a new in-house database named Luvibase, composed of 23 reference MALDI-TOF mass spectra profiles obtained from Vibrio collection strains, mostly belonging to the Harveyi clade. The comparison of the accuracy of MALDI-TOF MS profiling and 16S rRNA gene sequencing revealed a lack of resolution for 16S rRNA gene sequencing. In contrast, MALDI-TOF MS profiling proved to be a more reliable tool for resolving species-level variations within the Harveyi clade. Finally, combining the Luvibase with the Bruker ver.9.0.0.0 database, led to successful identification of 47 Vibrio isolates obtained from moribund abalone, seabass and oysters. Thus, the use of Luvibase allow for increased confidence in identifying Vibrio species belonging to the Harveyi clade.
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Affiliation(s)
- Julia Mougin
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Christophe Flahaut
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Roxane Roquigny
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Maryse Bonnin-Jusserand
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Thierry Grard
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Cédric Le Bris
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
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13
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Wang C, Bi H, Xie J. Visualization of the Distance among Fishes by MALDI MS for Rapid Determination of the Taxonomic Status of Fish Fillets. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8438-8446. [PMID: 32648743 DOI: 10.1021/acs.jafc.0c01291] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Taxonomic research plays an important role in the classification of organisms. Molecular techniques provide useful tools for the determination of the taxonomic status of species, although often time-consuming and not cost-efficient. Herein, we developed a strategy to analyze fish samples in a rapid mode. Experimentally, fish fillet samples were pretreated with trifluoroacetic acid aqueous solution, and the obtained protein fraction was analyzed by matrix-assisted laser desorption/ionization mass spectrometry. Principal component analysis of mass spectrometric datasets was used to visualize the taxonomical distance among the analyzed 13 seafood species. The results were illustrated using treemaps where the fish relationship distance can be visualized. The obtained mass spectral results can be taken as reference and successfully used for the identification of unknown fish fillet samples. It is promising to utilize the present strategy to provide clues for the taxonomy study among ambiguous species and identify fish species.
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Affiliation(s)
- Chengyu Wang
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China
| | - Hongyan Bi
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China
| | - Jing Xie
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, 201306 Shanghai, China
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14
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Vidal LMR, Venas TM, Gonçalves ARP, Mattsson HK, Silva RVP, Nóbrega MS, Azevedo GPR, Garcia GD, Tschoeke DA, Vieira VV, Thompson FL, Thompson CC. Rapid screening of marine bacterial symbionts using MALDI-TOF MS. Arch Microbiol 2020; 202:2329-2336. [PMID: 32529508 DOI: 10.1007/s00203-020-01917-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 11/30/2022]
Abstract
Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.
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Affiliation(s)
- Livia M R Vidal
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tainá M Venas
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Aline R P Gonçalves
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Hannah K Mattsson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Raphael V P Silva
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Maria S Nóbrega
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gustavo P R Azevedo
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Departamento de Ensino de Graduação, Campus UFRJ - Macaé Professor Aloisio Teixeira, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, RJ, Brazil
| | - Diogo A Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Biomedical Engineer Program - COPPE (UFRJ), Rio de Janeiro, Brazil
| | - Verônica V Vieira
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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15
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Global Comparison of the Bacterial Communities of Bilge Water, Boat Surfaces, and External Port Water. Appl Environ Microbiol 2019; 85:AEM.01804-19. [PMID: 31585994 DOI: 10.1128/aem.01804-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/16/2019] [Indexed: 01/07/2023] Open
Abstract
In the past, ballast water has been a key vector in the ship-mediated dispersal of invasive species. Here, we evaluate the potential for port microorganisms to enter and colonize the hull and bilge water of ships. Due to the small size and ubiquitous nature of bacteria, they also have the potential to be spread through hull fouling and bilge water discharge. The goal of this study was to identify the extent to which the boat microbial community is shaped by the microbial community in the port water where the boat spends most of its time. Here, we compared the microbial communities of the hull and bilge compartments of 20 boats to those of the port water in 20 different ports in five regions around the world. We found that there was a significant difference in microbial diversity between boat and port microbial communities. Despite these differences, we found that Cyanobacteria were present at high abundances in the bilge water of most vessels. Due to the limited light in the bilge, the presence of Cyanobacteria suggests that port microorganisms can enter the bilge. Using source-tracking software, we found that, on average, 40% of the bilge and 52% of the hull microbial communities were derived from water. These findings suggest that the bilge of a vessel contains a diverse microbial community that is influenced by the port microbial community and has the potential to serve as an underappreciated vector for dispersal of life.IMPORTANCE Invasive species have been a worldwide problem for many years. However, the potential for microorganisms to become invasive is relatively underexplored. As the tools to study bacterial communities become more affordable, we are able to perform large-scale studies and examine bacterial communities in higher resolution than was previously practical. This study looked at the potential for bacteria to colonize both boat surfaces and bilge water. We describe the bacterial communities on boats in 20 shipping ports in five regions around the world, describing how these microorganisms were similar to microorganisms found in port water. This suggests that the water influences the bacterial community of a boat and that microorganisms living on a boat could be moved from place to place when the boat travels.
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16
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Kazazić SP, Topić Popović N, Strunjak-Perović I, Babić S, Florio D, Fioravanti M, Bojanić K, Čož-Rakovac R. Matrix-assisted laser desorption/ionization time of flight mass spectrometry identification of Vibrio (Listonella) anguillarum isolated from sea bass and sea bream. PLoS One 2019; 14:e0225343. [PMID: 31738803 PMCID: PMC6860450 DOI: 10.1371/journal.pone.0225343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/01/2019] [Indexed: 11/18/2022] Open
Abstract
Vibrio (Listonella) anguillarum is a pathogenic bacterium causing septicaemia in a wide range of marine organisms and inducing severe mortalities, thus it is crucial to conduct its accurate and rapid identification. The aim of this study was to assess MALDI-TOF MS as a method of choice for identification of clinical V. anguillarum isolates from affected marine fish. Since the method accuracy might be influenced by the type of the medium used, as well as by the incubation conditions, we tested V. anguillarum isolates grown on standard media with and without the addition of NaCl, cultured at three incubation temperatures, and at three incubation periods. The best scores were retrieved for V. anguillarum strains grown on NaCl-supplemented tryptone soy agar (TSA) at 22°C and incubated for 48h (100% identification to species level; overall score 2.232), followed by incubation at 37°C and 48h (100% to species level; score 2.192). The strains grown on non-supplemented TSA gave the best readings when incubated at 22°C for 72h (100% identification to species level; overall score 2.182), followed by incubation at 15°C for 72h (100% to species level; score 2.160). Unreliable identifications and no-identifications were growing with the incubation duration at 37°C, on both media, amounting to 88.89% for 7d incubation on supplemented TSA, and 92.60% for 7d incubation on non-supplemented TSA. The age of the cultured strains and use of media significantly impacted the mass spectra, demonstrating that for reliable identification, MALDI-TOF MS protein fingerprinting with the on-target extraction should be performed on strains grown on a NaCl-supplemented medium at temperatures between 15 and 22°C, incubated for 48–72 hours.
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Affiliation(s)
- Snježana P Kazazić
- Laboratory for Mass Spectrometry and Functional Proteomics, Rudjer Bošković Institute, Zagreb, Croatia
| | - Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Sanja Babić
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Daniela Florio
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Ozzano Emilia, Italy
| | - Marialetizia Fioravanti
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Ozzano Emilia, Italy
| | - Krunoslav Bojanić
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
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17
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Daae HL, Heldal KK, Madsen AM, Olsen R, Skaugset NP, Graff P. Occupational exposure during treatment of offshore drilling waste and characterization of microbiological diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:533-540. [PMID: 31121403 DOI: 10.1016/j.scitotenv.2019.05.131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
The exposure for workers handling and recycling offshore drilling waste are previously not described, and given the potential for exposure to hazardous components, there is a need for characterizing this occupational exposure. In this study five plants recycling offshore drilling waste with different techniques were included. Measurements were conducted in both winter and summer to include seasonal exposure variations. Altogether >200 personal air-exposure measurements for oil mist, oil vapor, volatile organic compounds (VOC), hydrogen sulfide (H2S) and solvents were carried out respectively. Microorganisms related to drilling waste were identified in bulk samples and in stationary air measurements from two of the plants. The exposure to oil mist and oil vapor were below 10% of the current Norwegian occupational exposure limits (OEL) for all measured components. The plants using the Resoil or TCC method had a statistically significant higher exposure to oil vapor than the plant using complete combustion (p-value <0.05). No statistically significant difference was found between the different treatment methods for oil mist. The exposure to solvents was generally low (additive factor < 0.03). Endotoxin measurements done during winter showed a median concentration of 5.4 endotoxin units (EU)/m3. Levels of H2S above the odor threshold of 0.1 ppm were measured at four plants. Both drill mud and slop water contained a high number and diversity of bacteria (2-4 × 104 colony forming unit (CFU)/mL), where a large fraction was Gram-negative species. Some of the identified microorganisms are classified as potentially infectious pathogens for humans and thus might be a hazard to workers.
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Affiliation(s)
- Hanne Line Daae
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Kari Kulvik Heldal
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Anne Mette Madsen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
| | - Raymond Olsen
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Nils Petter Skaugset
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway
| | - Pål Graff
- National Institute of Occupational Health, Pb 5330 Majorstuen, N-0304 Oslo, Norway.
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18
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Ratiu IA, Railean Plugaru V, Pomastowski P, Milanowski M, Mametov R, Bocos-Bintintan V, Buszewski B. Temporal influence of different antibiotics onto the inhibition of Escherichia coli bacterium grown in different media. Anal Biochem 2019; 585:113407. [PMID: 31449777 DOI: 10.1016/j.ab.2019.113407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 01/08/2023]
Abstract
Escherichia coli (E. coli) is a Gram-negative bacterium commonly found in the lower intestine of warm-blooded organisms, including humans. Although the majority of the strains are considerably harmless, some serotypes are pathogenic, frequently causing diarrhea and other illnesses outside the intestinal tract. The standard antidote against bacteria is the use of antibiotics. Depending on their type, the antibiotics have various mechanisms of action on bacteria. Moreover, in case of in-vitro cultivation of bacteria, the used growth media plays a crucial role, since it influences bacterial inhibition as well. In the present study, we emphasize the importance of cultivability in bacterial inhibition under the treatment with five different antibiotics belonging to different classes. Consequently, E. coli was cultivated in three different growth media: trypcase soy broth (TSB), Mueller Hinton (MH), and minimal salts (M9) enriched with glucose, respectively. MALDI-TOF MS (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) analyses, that were used for fast characterization of changes that occur in ribosomal protein profiles, revealed differentiation and similarities between investigated cases, while flow cytometry (FCM) tests better explained the given changes that occurred in the analyzed samples after 3, 24 and 48 h of experimental campaign.
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Affiliation(s)
- Ileana Andreea Ratiu
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland; Babeş-Bolyai University, Faculty of Chemistry and Chemical Engineering, 11 Arany Janos Str., RO, 400028, Cluj-Napoca, Romania.
| | - Viorica Railean Plugaru
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland
| | - Pawel Pomastowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland
| | - Maciej Milanowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland
| | - Radik Mametov
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland
| | - Victor Bocos-Bintintan
- Faculty of Environmental Science and Engineering, Babeş-Bolyai University, 30 Fântânele Str., RO, 400294, Cluj-Napoca, Romania
| | - Boguslaw Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland.
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19
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Anderson HE, Santos IC, Hildenbrand ZL, Schug KA. A review of the analytical methods used for beer ingredient and finished product analysis and quality control. Anal Chim Acta 2019; 1085:1-20. [PMID: 31522723 DOI: 10.1016/j.aca.2019.07.061] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 07/28/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022]
Abstract
Beer is an incredibly complex beverage containing more than 3000 different compounds, including carbohydrates, proteins, ions, microbes, organic acids, and polyphenols, among others. Beer becomes even more complex during storage, for over time it may undergo chemical changes that negatively affect the flavor, aroma, and appearance. Thus, it can be expected that maintaining the quality of beer throughout its lifetime is a difficult task. Since it is such a popular drink throughout the world, being familiar with proper analytical techniques for beer evaluation is useful for researchers and brewers. These techniques include, but are not limited to, gas chromatography, liquid chromatography, matrix assisted laser desorption/ionization, capillary electrophoresis, mass spectrometry, ultraviolet-visible spectroscopy, and flame ionization detection. This review aims to summarize the various ingredients and components of beer, discuss how they affect the finished product, and present some of the analytical methods used for quality control and understanding the formation of chemicals in beer during the brewing process.
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Affiliation(s)
- Hailee E Anderson
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, TX, 76019, USA
| | - Ines C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, TX, 76019, USA; Affiliate of Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Zacariah L Hildenbrand
- Affiliate of Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, 76019, USA; Inform Environmental, LLC, 6060 N. Central Expressway, Suite 500, Dallas, TX, 75206, USA
| | - Kevin A Schug
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, TX, 76019, USA; Affiliate of Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, 76019, USA.
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20
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Blondeau LD, Rubin JE, Deneer H, Kanthan R, Sanche S, Hamula C, Blondeau JM. Forensic, investigative and diagnostic microbiology: similar technologies but different priorities. Future Microbiol 2019; 14:553-558. [PMID: 31148476 DOI: 10.2217/fmb-2019-0088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Joseph E Rubin
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Harry Deneer
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Rani Kanthan
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Stephen Sanche
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Camille Hamula
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Joseph M Blondeau
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Ophthalmology, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
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21
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Ashfaq MY, Al-Ghouti MA, Qiblawey H, Rodrigues DF, Hu Y, Zouari N. Isolation, identification and biodiversity of antiscalant degrading seawater bacteria using MALDI-TOF-MS and multivariate analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:910-920. [PMID: 30625677 DOI: 10.1016/j.scitotenv.2018.11.477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Seawater reverse osmosis (SWRO) is a commonly used desalination technique owing to its lesser environmental and economic impacts as compared to thermal desalination techniques. Antiscalants are used in SWRO to reduce membrane scaling caused by the supersaturation of salts present in feed water. However, to remain effective in reducing membrane scaling, antiscalants should be highly stable and resistant to biological degradation by seawater microorganisms. In this research, several bacteria from Qatar's seawater were isolated and screened for their ability to use antiscalants as a carbon and energy source. The biodiversity of antiscalant degrading seawater bacteria was demonstrated through combining the techniques of MALDI-TOF MS and principle component analysis. It was found that the bacteria isolated from Qatar's seawater such as H. aquamarina, H. elongata, P. fragi, P. stutzeri and others can degrade antiscalants and use them as a carbon and energy source. It was observed that the growth rates varied based on the type of antiscalant and the bacteria used. Among the tested strains, H. aquamarina, which is also known for its potential to cause biofouling, demonstrated the highest growth rates in antiscalants media. Thus, it was concluded that there is wide variety of bacteria in Qatar's seawater that can biodegrade the antiscalants; reducing their efficiency to combat membrane scaling. Since, these antiscalants will be used as a source of carbon and energy, microbial growth will increase resulting in enhanced membrane biofouling in SWRO.
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Affiliation(s)
- Mohammad Y Ashfaq
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar.
| | - Hazim Qiblawey
- Department of Chemical Engineering, College of Engineering, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Debora F Rodrigues
- Department of Civil and Environmental Engineering, Cullen College of Engineering, University of Houston, Houston, TX, USA
| | - Yandi Hu
- Department of Civil and Environmental Engineering, Cullen College of Engineering, University of Houston, Houston, TX, USA
| | - Nabil Zouari
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar
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22
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Gerhard WA, Gunsch CK. Metabarcoding and machine learning analysis of environmental DNA in ballast water arriving to hub ports. ENVIRONMENT INTERNATIONAL 2019; 124:312-319. [PMID: 30660844 DOI: 10.1016/j.envint.2018.12.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
While ballast water has long been linked to the global transport of invasive species, little is known about its microbiome. Herein, we used 16S rRNA gene sequencing and metabarcoding to perform the most comprehensive microbiological survey of ballast water arriving to hub ports to date. In total, we characterized 41 ballast, 20 harbor, and 6 open ocean water samples from four world ports (Shanghai, China; Singapore; Durban, South Africa; Los Angeles, California). In addition, we cultured Enterococcus and E. coli to evaluate adherence to International Maritime Organization standards for ballast discharge. Five of the 41 vessels - all of which were loaded in China - did not comply with standards for at least one indicator organism. Dominant bacterial taxa of ballast water at the class level were Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia. Ballast water samples were composed of significantly lower proportions of Oxyphotobacteria than either ocean or harbor samples. Linear discriminant analysis (LDA) effect size (LEfSe) and machine learning were used to identify and test potential biomarkers for classifying sample types (ocean, harbor, ballast). Eight candidate biomarkers were used to achieve 81% (k nearest neighbors) to 88% (random forest) classification accuracy. Further research of these biomarkers could aid the development of techniques to rapidly assess ballast water origin.
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Affiliation(s)
- William A Gerhard
- Duke University, Department of Civil and Environmental Engineering, 121 Hudson Hall, Durham, NC 27708-0287, United States
| | - Claudia K Gunsch
- Duke University, Department of Civil and Environmental Engineering, 121 Hudson Hall, Durham, NC 27708-0287, United States.
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23
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Tuohy JM, Mueller-Spitz SR, Albert CM, Scholz-Ng SE, Wall ME, Noutsios GT, Gutierrez AJ, Sandrin TR. MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats. Front Microbiol 2018; 9:2442. [PMID: 30374340 PMCID: PMC6196315 DOI: 10.3389/fmicb.2018.02442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/24/2018] [Indexed: 12/13/2022] Open
Abstract
Matrix-assisted Laser Desorption Ionization-Time of Flight Mass Spectroscopy (MALDI-TOF MS) has been used routinely over the past decade in clinical microbiology laboratories to rapidly characterize diverse microorganisms of medical importance both at the genus and species levels. Currently, there is keen interest in applying MALDI-TOF MS at taxonomic levels beyond species and to characterize environmental isolates. We constructed a model system consisting of 19 isolates of Deinococcus aquaticus obtained from biofilm communities indigenous to diverse substrates (concrete, leaf tissue, metal, and wood) in the Fox River - Lake Winnebago system of Wisconsin to: (1) develop rapid sample preparation methods that produce high quality, reproducible MALDI-TOF spectra and (2) compare the performance of MALDI-TOF MS-based profiling to common DNA-based approaches including 16S rRNA sequencing and genomic diversity by BOX-A1R fingerprinting. Our results suggest that MALDI-TOF MS can be used to rapidly and reproducibly characterize environmental isolates of D. aquaticus at the subpopulation level. MALDI-TOF MS provided higher taxonomic resolution than either 16S rRNA gene sequence analysis or BOX-A1R fingerprinting. Spectra contained features that appeared to permit characterization of isolates into two co-occurring subpopulations. However, reliable strain-level performance required rigorous and systematic standardization of culture conditions and sample preparation. Our work suggests that MALDI-TOF MS offers promise as a rapid, reproducible, and high-resolution approach to characterize environmental isolates of members of the genus Deinococcus. Future work will focus upon application of methods described here to additional members of this ecologically diverse and ubiquitous genus.
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Affiliation(s)
- James M Tuohy
- Biology Department, Glendale Community College, Glendale, AZ, United States
| | - Sabrina R Mueller-Spitz
- Biology Department, University of Wisconsin Oshkosh, Oshkosh, WI, United States.,Sustainability Institute for Regional Transformations, University of Wisconsin Oshkosh, Oshkosh, WI, United States
| | - Chad M Albert
- Biology Department, Glendale Community College, Glendale, AZ, United States.,Department of Natural Sciences, Western New Mexico University, Silver City, NM, United States
| | - Stacy E Scholz-Ng
- Biology Department, Glendale Community College, Glendale, AZ, United States.,Department of Natural Sciences, Western New Mexico University, Silver City, NM, United States
| | - Melinda E Wall
- Biology Department, Glendale Community College, Glendale, AZ, United States.,Department of Natural Sciences, Western New Mexico University, Silver City, NM, United States
| | - George T Noutsios
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, United States
| | - Anthony J Gutierrez
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, United States
| | - Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, United States.,Julie Ann Wrigley Global Institute of Sustainability, Arizona State University, Tempe, AZ, United States
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da Silva Câmara A, de Almeida Fernandes LD. Evaluation of the interactions between the marine bacterium Pseudomonas fluorescens and the microalga Isochrysis galbana in simulated ballast tank environment. Arch Microbiol 2018; 201:35-44. [PMID: 30187094 DOI: 10.1007/s00203-018-1569-0] [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: 05/22/2018] [Revised: 08/11/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
Abstract
To evaluate the impacts of the interaction between bacteria and microalgae has been the object of study by many research groups around the world. However, little is known about the interference that pigments produced by bacteria, such as the pyoverdine siderophore, can cause to microalgae like Isochrysis galbana. Pyoverdine is a fluorochrome produced by certain Pseudomonas strains, such as P. fluorescens, which plays a role in capturing and transporting iron ions from the environment to the cell. Unlike the oceans where Fe concentrations are extremely low (< 10-15 µM), in a ballast tank it is expected that there is a great supply of iron to the cells and that the absence of light is the main limiting factor until the water is discarded. Interestingly, under certain conditions, bacteria such as P. fluorescens absorb most of the water soluble iron ions and prevent the growth of phytoplankton even if there is sufficient light. Changes in the patterns of light distribution in aquatic environments may affect the physiological characteristics of certain microalgae. This study aimed to evaluate the impacts of the presence of P. fluorescens on the survival and growth of I. galbana inside the tank. For the study, an experiment was carried out to study the interaction between P. fluorescens and I. galbana under simulated conditions of a vessel in the presence/absence of Pseudomonas and light. The results showed that the presence of the bacteria is not the main limiting factor for microalga growth. The effect of the light factor was determinant on the reproduction rate. It is believed that pyoverdine produced by P. fluorescens affected I. galbana stock either by increasing mortality or decreasing growth rate as revealed by laboratory experiments. However, it was not possible to check if the pigment concentration was affected by the growth of microalgae.
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Affiliation(s)
- Aline da Silva Câmara
- Laboratory of Microbiology and Cytometry, Biofouling and Bioinvasion Division, Marine Biotechnology Department, Instituto de Estudos do Mar Almirante Paulo Moreira - IEAPM - Brazilian Navy, Rua Kioto 253, Praia dos Anjos, Arraial do Cabo, Rio De Janeiro, 28930-000, Brazil. .,Programa de Pós-graduação em Biotecnologia Marinha - IEAPM, Rua Daniel Barreto s/n - Prédio Amazônia Azul - Praia dos Anjos, Arraial do Cabo, 28930-000, Brazil.
| | - Lohengrin Dias de Almeida Fernandes
- Laboratory of Microbiology and Cytometry, Biofouling and Bioinvasion Division, Marine Biotechnology Department, Instituto de Estudos do Mar Almirante Paulo Moreira - IEAPM - Brazilian Navy, Rua Kioto 253, Praia dos Anjos, Arraial do Cabo, Rio De Janeiro, 28930-000, Brazil.,Programa de Pós-graduação em Biotecnologia Marinha - IEAPM, Rua Daniel Barreto s/n - Prédio Amazônia Azul - Praia dos Anjos, Arraial do Cabo, 28930-000, Brazil
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Lv B, Cui Y, Tian W, Li J, Xie B, Yin F. Abundances and profiles of antibiotic resistance genes as well as co-occurrences with human bacterial pathogens in ship ballast tank sediments from a shipyard in Jiangsu Province, China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 157:169-175. [PMID: 29621708 DOI: 10.1016/j.ecoenv.2018.03.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/18/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Ship ballasting operations may transfer harmful aquatic organisms across global ocean. This study aims to reveal the occurrences and abundances of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs) in ballast tank sediments. Nine samples were collected and respectively analyzed by real-time quantitative PCR and high-throughput sequencing technologies. Ten ARGs (aadA1, blaCTX-M, blaTEM, ermB, mefA, strB, sul1, sul2, tetM, and tetQ) and the Class-I integron gene (intI1) were highly prevalent (105-109 gene copies/g) in ballast tank sediments. The sul1 was the most abundant ARG with the concentration of 108-109 copies/g and intI1 was much more abundant than the ARGs in ballast tank sediments. The strong positive correlations between intI1 and ARGs (blaCTX-M, sul1, sul2 and tetM) indicated the potential spread of ARGs via horizontal gene transfer. In ballast tank sediments, 44 bacterial species were identified as HBPs and accounted for 0.13-21.46% of the total bacterial population although the three indicator pathogenic microbes (Vibrio cholerae, Escherichia coli, and Enterococci) proposed by the International Maritime Organization were not detected. Pseudomonas pseudoalcaligenes, Enterococcus hirae, Shigella sonnei and Bacillus anthracis were the dominant pathogens in ballast tank sediments. Zn and P in sediments had positive effects on the ARGs. Network analysis results indicated that sul1 and sul2 genes existed in several bacterial pathogens. Ballast tank sediments could be regarded as a carrier for the migration of ARGs. It is important to manage ballast tank sediments reasonably in order to prevent the dissemination of ARGs and bacterial pathogens.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), Shanghai Maritime University, Shanghai 201306, China.
| | - Yuxue Cui
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
| | - Wen Tian
- Jiangyin Entry-Exit Inspection and Quarantine Bureau, Jiangyin 214442, China
| | - Jing Li
- Jiangyin Entry-Exit Inspection and Quarantine Bureau, Jiangyin 214442, China
| | - Bing Xie
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
| | - Fang Yin
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), Shanghai Maritime University, Shanghai 201306, China
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26
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Hede N, Khandeparker L. Influence of Darkness and Aging on Marine and Freshwater Biofilm Microbial Communities Using Microcosm Experiments. MICROBIAL ECOLOGY 2018; 76:314-327. [PMID: 29380028 DOI: 10.1007/s00248-018-1149-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Ballast tank biofilms pose an additional risk of microbial invasion if sloughed off during ballasting operations, yet their significance and invasion biology is poorly understood. In this study, biofilms developed in marine and freshwater locations were exposed to prolonged darkness and aging by mimicking ballast water conditions in the laboratory. Upon prolonged darkness, the decay of phytoplankton, as indicated by the decrease in chlorophyll a in marine biofilms, led to remineralization and enhanced bacterial and protist populations. However, the same trend was not observed in the case of freshwater biofilms wherein the microbial parameters (i.e., bacteria, protists) and chlorophyll a decreased drastically. The bacterial community structure in such conditions was evaluated by real-time quantitative PCR (qPCR), and results showed that the biofilm bacterial communities changed significantly over a period of time. α-Proteobacteria was the most stable taxonomic group in the marine biofilms under dark conditions. However, β-proteobacteria dominated the freshwater biofilms and seemed to play an important role in organic matter remineralization. γ-Proteobacteria, which includes most of the pathogenic genera, were affected significantly and decreased in both the types of biofilms. This study revealed that marine biofilm communities were able to adapt better to the dark conditions while freshwater biofilm communities collapsed. Adaptation of tolerant bacterial communities, regeneration of nutrients via cell lysis, and presence of grazers appeared to be key factors for survival upon prolonged darkness. However, the fate of biofilm communities upon discharge in the new environment and their invasion potential is an important topic for future investigation.
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Affiliation(s)
- Niyati Hede
- CSIR - National Institute of Oceanography, Dona Paula, Goa, 403 004, India
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Bronzato GF, Oliva MS, Alvin MG, Pribul BR, Rodrigues DP, Coelho SM, Coelho IS, Souza MM. MALDI-TOF MS as a tool for the identification of Vibrio alginolyticus from Perna perna mussels (Linnaeus, 1758). PESQUISA VETERINARIA BRASILEIRA 2018. [DOI: 10.1590/1678-5150-pvb-5233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
ABSTRACT: Vibrio species are ubiquitous in aquatic environments, including coastal and marine habitats. Vibrio alginolyticus is an opportunistic pathogen for fish, crustaceans and mussels and their identification by biochemical tests may be impaired due their nutritional requirements. The study used Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to identify 49 Vibrio spp. isolates associated with mussels (Perna perna) from different locations along the Rio de Janeiro coast. The rpoA gene was used as a genus-specific marker of Vibrio spp. and was positive in all 209 isolates. MALDI-TOF MS confirmed 87.8% of V. alginolyticus when compared to the results of the biochemical tests. Four isolates were identified as Shewanella putrefaciens (8.16%) and one was identified as V. parahaemolyticus (2.0%). Just one isolate was not identified by this technique (2.0%). The pyrH sequencing confirmed 75% of the proteomic technique results. MALDI-TOF MS is an excellent option for characterization of bacterial species, as it is efficient, fast and easy to apply. In addition, our study confirms its high specificity and sensitivity in these marine bacteria identification.
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El-Jeni R, Böhme K, El Bour M, Calo-Mata P, Kefi R, Barros-Velázquez J, Bouhaouala-Zahar B. Rapid genus identification of selected lactic acid bacteria isolated from Mugil cephalis and Oreochromis niloticus organs using MALDI-TOF. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1357-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Martin MS, Santos IC, Carlton DD, Stigler-Granados P, Hildenbrand ZL, Schug KA. Characterization of bacterial diversity in contaminated groundwater using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 622-623:1562-1571. [PMID: 29054663 DOI: 10.1016/j.scitotenv.2017.10.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 06/07/2023]
Abstract
Groundwater is a major source for drinking water in the United States, and therefore, its quality and quantity is of extreme importance. One major concern that has emerged is the possible contamination of groundwater due to the unconventional oil and gas extraction activities. As such, the impacts of exogenous contaminants on microbial ecology is an area to be explored to understand what are the chemical and physical conditions that allow the proliferation of pathogenic bacteria and to find alternatives for water treatment by identifying organic-degrading bacteria. In this work, we assess the interplay between groundwater quality and the microbiome in contaminated groundwaters rich in hydrocarbon gases, volatile organic and inorganic compounds, and various metals. Opportunistic pathogenic bacteria, such as Aeromonas hydrophila, Bacillus cereus, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia, were identified, increasing the risk for consumption of and exposure to these contaminated groundwaters. Additionally, antimicrobial tests revealed that many of the identified bacteria were resistant to different antibiotics. The MALDI-TOF MS results were successfully confirmed with 16S rRNA gene sequencing, proving the accuracy of this high-throughput method. Collectively, these data provide a seminal understanding of the microbial populations in contaminated groundwater overlying anthropogenic activities like unconventional oil and gas development.
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Affiliation(s)
- Misty S Martin
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, USA
| | - Inês C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, USA; Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, USA
| | - Doug D Carlton
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, USA; Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, USA
| | | | - Zacariah L Hildenbrand
- Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, USA; Inform Environmental, LLC, Dallas, TX, USA.
| | - Kevin A Schug
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, USA; Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, USA.
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Darling JA, Frederick RM. Nucleic acids-based tools for ballast water surveillance, monitoring, and research. JOURNAL OF SEA RESEARCH 2018; 133:43-52. [PMID: 30147432 PMCID: PMC6104837 DOI: 10.1016/j.seares.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Understanding the risks of biological invasion posed by ballast water-whether in the context of compliance testing, routine monitoring, or basic research-is fundamentally an exercise in biodiversity assessment, and as such should take advantage of the best tools available for tackling that problem. The past several decades have seen growing application of genetic methods for the study of biodiversity, driven in large part by dramatic technological advances in nucleic acids analysis. Monitoring approaches based on such methods have the potential to increase dramatically sampling throughput for biodiversity assessments, and to improve on the sensitivity, specificity, and taxonomic accuracy of traditional approaches. The application of targeted detection tools (largely focused on PCR but increasingly incorporating novel probe-based methodologies) has led to a paradigm shift in rare species monitoring, and such tools have already been applied for early detection in the context of ballast water surveillance. Rapid improvements in community profiling approaches based on high throughput sequencing (HTS) could similarly impact broader efforts to catalogue biodiversity present in ballast tanks, and could provide novel opportunities to better understand the risks of biotic exchange posed by ballast water transport-and the effectiveness of attempts to mitigate those risks. These various approaches still face considerable challenges to effective implementation, depending on particular management or research needs. Compliance testing, for instance, remains dependent on accurate quantification of viable target organisms; while tools based on RNA detection show promise in this context, the demands of such testing require considerable additional investment in methods development. In general surveillance and research contexts, both targeted and community-based approaches are still limited by various factors: quantification remains a challenge (especially for taxa in larger size classes), gaps in nucleic acids reference databases are still considerable, uncertainties in taxonomic assignment methods persist, and many applications have not yet matured sufficiently to offer standardized methods capable of meeting rigorous quality assurance standards. Nevertheless, the potential value of these tools, their growing utilization in biodiversity monitoring, and the rapid methodological advances over the past decade all suggest that they should be seriously considered for inclusion in the ballast water surveillance toolkit.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Raymond M. Frederick
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, Edison, NJ, USA
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31
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Abundance and community composition of bacterioplankton in the Northern South China Sea during winter: geographic position and water layer influences. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0023-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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The current status on the taxonomy of Pseudomonas revisited: An update. INFECTION GENETICS AND EVOLUTION 2017; 57:106-116. [PMID: 29104095 DOI: 10.1016/j.meegid.2017.10.026] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
The genus Pseudomonas described in 1894 is one of the most diverse and ubiquitous bacterial genera which encompass species isolated worldwide. In the last years more than 70 new species have been described, which were isolated from different environments, including soil, water, sediments, air, animals, plants, fungi, algae, compost, human and animal related sources. Some of these species have been isolated in extreme environments, such as Antarctica or Atacama desert, and from contaminated water or soil. Also, some species recently described are plant or animal pathogens. In this review, we revised the current status of the taxonomy of genus Pseudomonas and the methodologies currently used for the description of novel species which includes, in addition to the classic ones, new methodologies such as MALDI-TOF MS, MLSA and genome analyses. The novel Pseudomonas species described in the last years are listed, together with the available genome sequences of the type strains of Pseudomonas species present in different databases.
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Mass spectrometric techniques for the analysis of volatile organic compounds emitted from bacteria. Bioanalysis 2017; 9:1069-1092. [PMID: 28737423 DOI: 10.4155/bio-2017-0051] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Bacteria are the main cause of many human diseases. Typical bacterial identification methods, for example culture-based, serological and genetic methods, are time-consuming, delaying the potential for an early and accurate diagnosis and the appropriate subsequent treatment. Nevertheless, there is a stringent need for in situ tests that are rapid, noninvasive and sensitive, which will greatly facilitate timely treatment of the patients. This review article presents volatile organic metabolites emitted from various micro-organism strains responsible for common bacterial infections in humans. Additionally, the manuscript shows the application of different analytical techniques for fast bacterial identification. Details of these techniques are given, which focuses on their advantages and drawbacks in using for volatile organic components analysis.
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Christ APG, Ramos SR, Cayô R, Gales AC, Hachich EM, Sato MIZ. Characterization of Enterococcus species isolated from marine recreational waters by MALDI-TOF MS and Rapid ID API® 20 Strep system. MARINE POLLUTION BULLETIN 2017; 118:376-381. [PMID: 28318563 DOI: 10.1016/j.marpolbul.2017.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 06/06/2023]
Abstract
MALDI-TOF Mass Spectrometry Biotyping has proven to be a reliable method for identifying bacteria at the species level based on the analysis of the ribosomal proteins mass fingerprint. We evaluate the usefulness of this method to identify Enterococcus species isolated from marine recreational water at Brazilian beaches. A total of 127 Enterococcus spp. isolates were identified to species level by bioMérieux's API® 20 Strep and MALDI-TOF systems. The biochemical test identified 117/127 isolates (92%), whereas MALDI identified 100% of the isolates, with an agreement of 63% between the methods. The 16S rRNA gene sequencing of isolates with discrepant results showed that MALDI-TOF and API® correctly identified 74% and 11% of these isolates, respectively. This discrepancy probably relies on the bias of the API® has to identify clinical isolates. MALDI-TOF proved to be a feasible approach for identifying Enterococcus from environmental matrices increasing the rapidness and accuracy of results.
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Affiliation(s)
- Ana Paula Guarnieri Christ
- CETESB - Companhia Ambiental do Estado de São Paulo, Department of Environmental Analysis, São Paulo - SP, Brazil
| | - Solange Rodrigues Ramos
- CETESB - Companhia Ambiental do Estado de São Paulo, Department of Environmental Analysis, São Paulo - SP, Brazil
| | - Rodrigo Cayô
- UNIFESP - Universidade Federal de São Paulo, Department of Medicine, ALERTA Laboratory, São Paulo - SP, Brazil
| | - Ana Cristina Gales
- UNIFESP - Universidade Federal de São Paulo, Department of Medicine, ALERTA Laboratory, São Paulo - SP, Brazil
| | - Elayse Maria Hachich
- CETESB - Companhia Ambiental do Estado de São Paulo, Department of Environmental Analysis, São Paulo - SP, Brazil
| | - Maria Inês Zanoli Sato
- CETESB - Companhia Ambiental do Estado de São Paulo, Department of Environmental Analysis, São Paulo - SP, Brazil.
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Lymperopoulou DS, Dobbs FC. Bacterial Diversity in Ships' Ballast Water, Ballast-Water Exchange, and Implications for Ship-Mediated Dispersal of Microorganisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:1962-1972. [PMID: 28135081 DOI: 10.1021/acs.est.6b03108] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Using next-generation DNA sequencing of the 16S rRNA gene, we analyzed the composition and diversity of bacterial assemblages in ballast water from tanks of 17 commercial ships arriving to Hampton Roads, Virginia (USA) following voyages in the North Atlantic Ocean. Amplicon sequencing analysis showed the heterogeneous assemblages were (1) dominated by Alpha- and Gammaproteobacteria, Bacteroidetes, and unclassified Bacteria; (2) temporally distinct (June vs August/September); and (3) highly fidelitous among replicate samples. Whether tanks were exchanged at sea or not, their bacterial assemblages differed from those of local, coastal water. Compositional data suggested at-sea exchange did not fully flush coastal Bacteria from all tanks; there were several instances of a genetic geographic signal. Quantitative PCR yielded no Escherichia coli and few instances of Vibrio species. Salinity, but not ballast-water age or temperature, contributed significantly to bacterial diversity. Whether anthropogenic mixing of marine Bacteria restructures their biogeography remains to be tested.
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Affiliation(s)
- Despoina S Lymperopoulou
- Department of Plant and Microbial Biology, University of California-Berkeley , 331 Koshland Hall, Berkeley, California 94720, United States
| | - Fred C Dobbs
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University , 4600 Elkhorn Avenue, Norfolk, Virginia 23529, United States
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36
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Santos IC, Hildenbrand ZL, Schug KA. Mass Spectrometry for the Study of Microbial Communities in Environmental Waters. ADVANCES IN CHEMICAL POLLUTION, ENVIRONMENTAL MANAGEMENT AND PROTECTION 2017. [DOI: 10.1016/bs.apmp.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Popović NT, Kazazić SP, Strunjak-Perović I, Čož-Rakovac R. Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS. ENVIRONMENTAL RESEARCH 2017; 152:7-16. [PMID: 27741451 DOI: 10.1016/j.envres.2016.09.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 09/20/2016] [Accepted: 09/24/2016] [Indexed: 05/20/2023]
Abstract
Identification of bacteria in aquatic and environmental applications, for monitoring purposes and research, for health assessments and therapy considerations of farmed and free-living aquatic organisms, still relies on conventional phenotypic and biochemical protocols. Although molecular techniques based on DNA amplification and sequencing are finding ways into diagnostic laboratories, they are time-consuming, costly and difficult in the case of multiplex assays. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate proteomic method reliable for identification of unknown bacteria to the genus and species level. Upon extension of databases, it will certainly find its position in environmental sciences. The paper presents an overview of the principle of the method, its effectiveness in comparison with conventional and molecular identification procedures, and applicability on environmental and aquatic isolates, discussing its advantages and shortcomings, as well as possible future implementations.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Snježana P Kazazić
- Laboratory for Mass Spectrometry, Division of Physical Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
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Rahi P, Prakash O, Shouche YS. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists. Front Microbiol 2016; 7:1359. [PMID: 27625644 PMCID: PMC5003876 DOI: 10.3389/fmicb.2016.01359] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
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Affiliation(s)
- Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science Pune, India
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Sala-Comorera L, Vilaró C, Galofré B, Blanch AR, García-Aljaro C. Use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant. Int J Hyg Environ Health 2016; 219:577-584. [PMID: 26809219 DOI: 10.1016/j.ijheh.2016.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 11/28/2022]
Abstract
The study of bacterial communities throughout a drinking water treatment plant could provide a basic understanding of the effects of water processing that could then be used to improve the management of such plants. However, it is necessary to develop new analytical techniques that are sufficiently efficient, robust and fast for their effective and useful application in routine analysis. The aim of this study is therefore to assess the performance of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), as compared to the PhenePlate™ system, for routine analysis in a drinking water treatment plant. To this end we studied a total of 277 colonies isolated in different seasons and from different points throughout the water treatment process, including: raw water, sand filtration, ultrafiltration, reverse osmosis and chlorination. The colonies were analysed using MALDI-TOF MS by direct deposition of the cells on the plate. The colonies were also biochemically fingerprinted using the PhenePlate™ system, clustered according to their similarity and a representative strain was selected for 16S rRNA gene sequencing and API® gallery-based identification. The use of MALDI-TOF MS was reliable compared to the PhenePlate™ system and has the advantage of being faster and relatively cheap. Bacteria typing by MALDI-TOF MS is therefore a promising method to replace conventional routine phenotypic methods for the identification of bacteria in drinking water laboratories, thanks to its robustness. The major limiting factor for MALDI-TOF MS is the lack of a suitable mass spectra database; although each laboratory can develop its own library. This methodology will provide a tracking tool for companies to use in risk management and the detection of possible failures in both the water treatment processes and the distribution network, as well as offering characterization of the intrinsic microbial populations.
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Affiliation(s)
- Laura Sala-Comorera
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Carles Vilaró
- Aigües de Barcelona, EMGCIA, C/General Batet 1-7, 08028 Barcelona, Spain
| | - Belén Galofré
- Aigües de Barcelona, EMGCIA, C/General Batet 1-7, 08028 Barcelona, Spain
| | - Anicet R Blanch
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Cristina García-Aljaro
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
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Emami K, Nelson A, Hack E, Zhang J, Green DH, Caldwell GS, Mesbahi E. MALDI-TOF Mass Spectrometry Discriminates Known Species and Marine Environmental Isolates of Pseudoalteromonas. Front Microbiol 2016; 7:104. [PMID: 26903983 PMCID: PMC4751257 DOI: 10.3389/fmicb.2016.00104] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/19/2016] [Indexed: 02/05/2023] Open
Abstract
The genus Pseudoalteromonas constitutes an ecologically significant group of marine Gammaproteobacteria with potential biotechnological value as producers of bioactive compounds and of enzymes. Understanding their roles in the environment and bioprospecting for novel products depend on efficient ways of identifying environmental isolates. Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) biotyping has promise as a rapid and reliable method of identifying and distinguishing between different types of bacteria, but has had relatively limited application to marine bacteria and has not been applied systematically to Pseudoalteromonas. Therefore, we constructed a MALDI-TOF MS database of 31 known Pseudoalteromonas species, to which new isolates can be compared by MALDI-TOF biotyping. The ability of MALDI-TOF MS to distinguish between species was scrutinized by comparison with 16S rRNA gene sequencing. The patterns of similarity given by the two approaches were broadly but not completely consistent. In general, the resolution of MALDI-TOF MS was greater than that of 16S rRNA gene sequencing. The database was tested with 13 environmental Pseudoalteromonas isolates from UK waters. All of the test strains could be identified to genus level by MALDI-TOF MS biotyping, but most could not be definitely identified to species level. We conclude that several of these isolates, and possibly most, represent new species. Thus, further taxonomic investigation of Pseudoalteromonas is needed before MALDI-TOF MS biotyping can be used reliably for species identification. It is, however, a powerful tool for characterizing and distinguishing among environmental isolates and can make an important contribution to taxonomic studies.
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Affiliation(s)
- Kaveh Emami
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University Newcastle upon Tyne, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University Newcastle upon Tyne, UK
| | - Ethan Hack
- School of Biology, Newcastle University Newcastle upon Tyne, UK
| | - Jinwei Zhang
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee Dundee, UK
| | - David H Green
- Microbial and Molecular Biology, Scottish Association for Marine Science, Scottish Marine Institute Oban, UK
| | - Gary S Caldwell
- School of Marine Science and Technology, Newcastle University Newcastle upon Tyne, UK
| | - Ehsan Mesbahi
- Faculty of Science, Agriculture and Engineering, Newcastle University Newcastle upon Tyne, UK
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Santos IC, Hildenbrand ZL, Schug KA. Applications of MALDI-TOF MS in environmental microbiology. Analyst 2016; 141:2827-37. [DOI: 10.1039/c6an00131a] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is an emerging technique for microbial identification, characterization, and typing.
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Affiliation(s)
- Inês C. Santos
- Department of Chemistry and Biochemistry
- The University of Texas at Arlington
- Arlington
- USA
| | - Zacariah L. Hildenbrand
- Inform Environmental
- LLC
- Dallas
- USA
- Affiliate of the Collaborative Laboratories for Environmental Analysis and Remediation
| | - Kevin A. Schug
- Department of Chemistry and Biochemistry
- The University of Texas at Arlington
- Arlington
- USA
- Affiliate of the Collaborative Laboratories for Environmental Analysis and Remediation
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Novel Electrokinetic Microfluidic Detector for Evaluating Effectiveness of Microalgae Disinfection in Ship Ballast Water. Int J Mol Sci 2015; 16:25560-75. [PMID: 26516836 PMCID: PMC4632816 DOI: 10.3390/ijms161025560] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/13/2015] [Accepted: 10/13/2015] [Indexed: 11/17/2022] Open
Abstract
Ship ballast water treatment methods face many technical challenges. The effectiveness of every treatment method usually is evaluated by using large scale equipment and a large volume of samples, which involves time-consuming, laborious, and complex operations. This paper reports the development of a novel, simple and fast platform of methodology in evaluating the efficiency and the best parameters for ballast water treatment systems, particularly in chemical disinfection. In this study, a microfluidic chip with six sample wells and a waste well was designed, where sample transportation was controlled by electrokinetic flow. The performance of this microfluidic platform was evaluated by detecting the disinfection of Dunaliella salina (D. salina) algae in ballast water treated by sodium hypochlorite (NaClO) solution. Light-induced chlorophyll fluorescence (LICF) intensity was used to determine the viability of microalgae cells in the system, which can be operated automatically with the dimension of the detector as small as 50 mm × 24 mm × 5 mm. The 40 µL volume of sample solution was used for each treatment condition test and the validity of detection can be accomplished within about five min. The results show that the viability of microalgae cells under different treatment conditions can be determined accurately and further optimal treatment conditions including concentrations of NaClO and treatment time can also be obtained. These results can provide accurate evaluation and optimal parameters for ballast water treatment methods.
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Khandeparker L, Anil AC, Naik SD, Gaonkar CC. Daily variations in pathogenic bacterial populations in a monsoon influenced tropical environment. MARINE POLLUTION BULLETIN 2015; 96:337-343. [PMID: 25956443 DOI: 10.1016/j.marpolbul.2015.04.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/22/2015] [Accepted: 04/25/2015] [Indexed: 06/04/2023]
Abstract
Changing climatic conditions have influenced the monsoon pattern in recent years. Variations in bacterial population in one such tropical environment were observed everyday over two years and point out intra and inter annual changes driven by the intensity of rainfall. Vibrio spp. were abundant during the monsoon and so were faecal coliforms. Vibrio alginolyticus were negatively influenced by nitrate, whereas, silicate and rainfall positively influenced Vibrio parahaemolyticus numbers. It is also known that pathogenic bacteria are associated with the plankton. Changes in the abundance of plankton, which are governed mainly by environmental changes, could be responsible for variation in pathogenic bacterial abundance during monsoon, other than the land runoff due to precipitation and influx of fresh water.
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Affiliation(s)
| | | | - Sneha D Naik
- CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
| | - Chetan C Gaonkar
- CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India
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Suh SS, Park M, Hwang J, Kil EJ, Jung SW, Lee S, Lee TK. Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea. PLoS One 2015; 10:e0131633. [PMID: 26121668 PMCID: PMC4487691 DOI: 10.1371/journal.pone.0131633] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/05/2015] [Indexed: 11/19/2022] Open
Abstract
High-resolution 16S rRNA tag pyrosequencing was used to obtain seasonal snapshots of the bacterial diversity and community structure at two locations in Gosung Bay (South Sea, Korea) over a one year period. Seasonal sampling from the water column at each site revealed highly diverse bacterial communities containing up to 900 estimated Operational Taxonomic Units (OTUs). The Alphaproteobacteria and Gammaproteobacteria were the most abundant groups, and the most frequently recorded OTUs were members of Pelagibacter and Glaciecola. In particular, it was observed that Arcobacter, a genus of the Epsilonproteobacteria, dominated during summer. In addition, Psedoalteromonadaceae, Vibrionaceae and SAR11-1 were predominant members of the OTUs found in all sampling seasons. Environmental factors significantly influenced the bacterial community structure among season, with the phosphate and nitrate concentrations contributing strongly to the spatial distribution of the Alphaproteobacteria; the Gammaproteobacteria, Flavobacteria, and Actinobacteria all showed marked negative correlations with all measured nutrients, particularly silicon dioxide and chlorophyll-a. The results suggest that seasonal changes in environmental variables contribute to the dynamic structure of the bacterial community in the study area.
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Affiliation(s)
- Sung-Suk Suh
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje, 656–830, Republic of Korea
| | - Mirye Park
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje, 656–830, Republic of Korea
- Korea University of Science and Technology, Daejeon, 305–350, Republic of Korea
| | - Jinik Hwang
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje, 656–830, Republic of Korea
- Korea University of Science and Technology, Daejeon, 305–350, Republic of Korea
| | - Eui-Joon Kil
- Department of Genetic Engineering Sungkyunkwan University, Suwon, 440–746, Republic of Korea
| | - Seung Won Jung
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje, 656–830, Republic of Korea
| | - Sukchan Lee
- Department of Genetic Engineering Sungkyunkwan University, Suwon, 440–746, Republic of Korea
| | - Taek-Kyun Lee
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje, 656–830, Republic of Korea
- Korea University of Science and Technology, Daejeon, 305–350, Republic of Korea
- * E-mail:
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Kryazhevskikh NA, Loiko NG, Demkina EV, Mulyukin AL, Lebedev AT, Gaponov AM, Tutel’yan AV, Nikolaev YA, El’-Registan GI. Applicability of MALDI mass spectrometry for diagnostics of phase variants in bacterial populations. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715030121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Mohanty BP, Mitra T, Banerjee S, Bhattacharjee S, Mahanty A, Ganguly S, Purohit GK, Karunakaran D, Mohanty S. Proteomic profiling of white muscle from freshwater catfish Rita rita. FISH PHYSIOLOGY AND BIOCHEMISTRY 2015; 41:789-802. [PMID: 25810140 DOI: 10.1007/s10695-015-0046-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/19/2015] [Indexed: 06/04/2023]
Abstract
Muscle tissues contribute 34-48 % of the total body mass in fish. Proteomic analysis enables better understanding of the skeletal muscle physiology and metabolism. A proteome map reflects the general fingerprinting of the fish species and has the potential to identify novel proteins which could serve as biomarkers for many aspects of aquaculture including fish physiology and growth, flesh quality, food safety and aquatic environmental monitoring. The freshwater catfish Rita rita of the family Bagridae inhabiting the tropical rivers and estuaries is an important food fish with high nutritive value and is also considered a species of choice in riverine pollution monitoring. Omics information that could enhance utility of this species in molecular research is meager. Therefore, in the present study, proteomic analysis of Rita rita muscle has been carried out and functional genomics data have been generated. A reference muscle proteome has been developed, and 23 protein spots, representing 18 proteins, have been identified by MALDI-TOF/TOF-MS and LC-MS/MS. Besides, transcript information on a battery of heat shock proteins (Hsps) has been generated. The functional genomics information generated could act as the baseline data for further molecular research on this species.
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Affiliation(s)
- Bimal Prasanna Mohanty
- Proteomics Unit, Biochemistry Laboratory, Fishery Resource and Environmental Management Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, India,
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Erler R, Wichels A, Heinemeyer EA, Hauk G, Hippelein M, Reyes NT, Gerdts G. VibrioBase: A MALDI-TOF MS database for fast identification of Vibrio spp. that are potentially pathogenic in humans. Syst Appl Microbiol 2014; 38:16-25. [PMID: 25466918 DOI: 10.1016/j.syapm.2014.10.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 10/20/2014] [Accepted: 10/27/2014] [Indexed: 11/17/2022]
Abstract
Mesophilic marine bacteria of the family Vibrionaceae, specifically V. cholerae, V. parahaemolyticus and V. vulnificus, are considered to cause severe illness in humans. Due to climate-change-driven temperature increases, higher Vibrio abundances and infections are predicted for Northern Europe, which in turn necessitates environmental surveillance programs to evaluate this risk. We propose that whole-cell matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling is a promising tool for the fast and reliable species classification of environmental isolates. Because the reference database does not contain sufficient Vibrio spectra we generated the VibrioBase database in this study. Mass spectrometric data were generated from 997 largely environmental strains and filed in this new database. MALDI-TOF MS clusters were assigned based on the species classification obtained by analysis of partial rpoB (RNA polymerase beta-subunit) sequences. The affiliation of strains to species-specific clusters was consistent in 97% of all cases using both approaches, and the extended VibrioBase generated more specific species identifications with higher matching scores compared to the commercially available database. Therefore, we have made the VibrioBase database freely accessible, which paves the way for detailed risk assessment studies of potentially pathogenic Vibrio spp. from marine environments.
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Affiliation(s)
- René Erler
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany.
| | - Antje Wichels
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Ernst-August Heinemeyer
- Governmental Institute of Public Health of Lower Saxony, Lüchtenburger Weg 24, 26603 Aurich, Germany
| | - Gerhard Hauk
- Regional Office for Health and Social Affairs of Mecklenburg-Western Pomerania, Gertrudenstraße 11, 18057 Rostock, Germany
| | - Martin Hippelein
- University Medical Center Schleswig-Holstein, Central Facility: Medical Investigation Office and Hygiene, Brunswiker Straße 4, 24105 Kiel, Germany
| | - Nadja Torres Reyes
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Telegrafenberg, 14473 Potsdam, Germany
| | - Gunnar Gerdts
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
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Suh SS, Park M, Hwang J, Lee S, Chung Y, Lee TK. Distinct patterns of marine bacterial communities in the South and North Pacific Oceans. J Microbiol 2014; 52:834-41. [PMID: 25269604 DOI: 10.1007/s12275-014-4287-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/22/2014] [Accepted: 08/06/2014] [Indexed: 12/27/2022]
Abstract
The study of oceanic microbial communities is crucial for our understanding of the role of microbes in terms of biomass, diversity and ecosystem function. In this study, 16S rRNA gene tag pyrosequencing was used to investigate change in bacterial community structure between summer and winter water masses from Gosung Bay in the South Sea of Korea and Chuuk in Micronesia, located in the North and South Pacific Oceans, respectively. Summer and winter sampling from each water mass revealed highly diverse bacterial communities, containing ~900 Operational Taxonomic Units (OTUs). The microbial distribution and highly heterogeneous composition observed at both sampling sites were different from those of most macroorganisms. The bacterial communities in the seawater at both sites were most abundant in Proteobacteria during the summer in Gosung and in Bacterioidetes during the winter. The proportion of Cyanobacteria was higher in summer than in winter in Chuuk and similar in Gosung. Additionally, the microbial community during summer in Gosung was significantly different from other communities observed based on the unweighted UniFrac distance. These data suggest that in both oceanic areas sampled, the bacterial communities had distinct distribution patterns with spatially- and temporally-heterogeneous distributions.
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Affiliation(s)
- Sung-Suk Suh
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje, 656-830, Republic of Korea
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Altug G, Gurun S, Cardak M, Ciftci PS, Kalkan S. The occurrence of pathogenic bacteria in some ships' ballast water incoming from various marine regions to the Sea of Marmara, Turkey. MARINE ENVIRONMENTAL RESEARCH 2012; 81:35-42. [PMID: 22998778 DOI: 10.1016/j.marenvres.2012.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/15/2012] [Accepted: 08/18/2012] [Indexed: 06/01/2023]
Abstract
The composition and frequency of antibiotic resistance of pathogenic bacteria, the abundance of heterotrophic aerobic bacteria (HPC) and possible in-situ use of chromogenic agar were investigated in the ships' ballast water coming from different regions of the world to the Sea of Marmara, Turkey for the first time. The samples that were taken from 21 unit ships coming from various marine environments of the Southern China Sea, the Atlantic Ocean, the Mediterranean and the Black Sea to the Sea of Marmara, Turkey in 2009 and 2010 were tested. 38 bacteria species, 27 of them pathogenic bacteria belonging to 17 familia, were detected. Vibrio cholera was not detected in the samples. However, the presence of a high number of HPC, including a cocktail of pathogenic bacteria showed that the ships carry a potential risk for the Sea of Marmara.
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Affiliation(s)
- Gulsen Altug
- Istanbul University, Department of Marine Biology, Istanbul, Turkey.
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