Potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of freshwater zooplankton: A pilot study with three Eudiaptomus (Copepoda: Diaptomidae) species
Riccardi N.,CNR Institute of Ecosystem Study |
Lucini L.,Cantonal Institute of Microbiology |
Benagli C.,Cantonal Institute of Microbiology |
Welker M.,AnagnosTec GmbH |
And 3 more authors.
Journal of Plankton Research | Year: 2012
The accurate identification of individuals in zooplankton samples is a crucial step in many plankton studies. Up to now, this has been done primarily by microscopic analysis of morphological characters, and new molecular methodologies are still relatively rarely applied. Another promising technology is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), which has had a major impact in applied and systematic microbiology, where it is used for routine high throughput identification of bacteria and fungi. For the present study, we developed a protocol for the rapid acquisition of mass spectra from whole individual copepods. The final protocol enabled us to obtain mass spectra with more than 100 distinct peaks in the mass range of 2000-20 000 Da. A comparison of the mass spectra of three species of Eudiaptomus showed that they could all be clearly discriminated, whereas the mass spectra of different developmental stages and sexes of each particular species were highly similar. Further, a discrimination of con-specific individuals from different habitats was achieved, at least partly, even without extensive optimization of the analytical and statistical procedures. These results indicate the feasibility of identifying copepods by a rapid and simple MALDI-TOF MS analysis, e.g. for population ecology studies. © 2012 The Author. Source
Welker M.,AnagnosTec GmbH
Proteomics | Year: 2011
The invention of MALDI-TOF-MS enormously contributed to the understanding of protein chemistry and cell biology. Without this technique proteomics would most likely not be the important discipline it is today. Besides 'true' proteomics, MALDI-TOF-MS was applied for the analysis of microorganisms for their taxonomic characterization from its beginning. This approach has since been developed as a diagnostic tool readily available for routine, high-throughput analysis of microbial isolates from clinical specimens by intact-cell mass spectrometry (ICMS), the direct analysis of whole bacterial cell without a preceding fractionation or separation by chromatography or electrophoresis. ICMS exploits the reproducibility of mass fingerprints for individual bacterial and fungal strains as well as the high similarity of mass fingerprints within a species. Comparison of mass spectral data to genomic sequences emphasized the validity of peak patterns as taxonomic markers. Supported by comprehensive databases, MALDI-TOF-MS-based identification has been widely accepted in clinical laboratories within only a few years. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source
Okello W.,Austrian Academy of Sciences |
Okello W.,National Fisheries Resources Research Institute NaFIRRI |
Portmann C.,Ecole Polytechnique Federale de Lausanne |
Erhard M.,AnagnosTec GmbH |
And 2 more authors.
Environmental Toxicology | Year: 2010
Microcystins (MCs) are cyclic heptapeptides, which are the most abundant toxins produced by cyanobacteria in freshwater. The phytoplankton of many freshwater lakes in Eastern Africa is dominated by cyanobacteria. Less is known, however, on the occurrence of MC producers and the production of MCs. Twelve Ugandan freshwater habitats ranging from mesotrophic to hypertrophic conditions were sampled in May and June of 2004 and April of 2008 and were analyzed for their physicochemical parameters, phytoplankton composition, and MC concentrations. Among the group of the potential MC-producing cyanobacteria, Anabaena (0-107 cells ml-1) and Microcystis (10 3-107 cells ml-1) occurred most frequently and dominated in eutrophic systems. A significant linear relationship (n = 31, r2 = 0.38, P < 0.001) between the Microcystis cell numbers and MC concentration (1.3-93 fg of MC cell-1) was observed. Besides [MeAsp3, Mdha7]-MC-RR, two new MCs, [Asp 3]-MC-RY and [MeAsp3]-MC-RY, were isolated and their constitution was assigned by LC-MS2. To identify the MC-producing organism in the water samples, (i) the conserved aminotransferase domain part of the mcyE gene that is indicative of MC production was amplified by general primers and cloned and sequenced, and (ii) genus-specific primers were used to amplify the mcyE gene of the genera Microcystis, Anabaena, and Planktothrix. Only mcyE genotypes that are indicative of Microcystis sp. were obtained via the environmental cloning approach (337 bp, 96.1-96.7% similarity to the Microcystis aeruginosa strain PCC7806). Accordingly, only the mcyE primers, which are specific for Microcystis, revealed PCR products. We concluded that Microcystis is the major MC-producer in Ugandan freshwater. © 2009 Wiley Periodicals, Inc. Source
Fathalli A.,Institute National Agronomique Of Tunisie |
Jenhani A.B.R.,Institute National Agronomique Of Tunisie |
Moreira C.,CIIMAR - Interdisciplinary Center of Marine and Environmental |
Azevedo J.,CIIMAR - Interdisciplinary Center of Marine and Environmental |
And 6 more authors.
Archives of Microbiology | Year: 2011
Cylindrospermopsis raciborskii is an invasive freshwater cyanobacteria of tropical origin, also found in temperate regions. Due to its known ability to produce potent toxins, such as cylindrospermopsin and the paralytic shellfish poisoning, this species is of major concern from a water quality perspective. This study presents a genetic characterization of four C. raciborskii strains isolated from the Bir M'cherga Tunisian reservoir. The toxicity assessment was investigated via molecular biology tools, which suggested that all the isolated strains were not producing cylindrospermopsin, saxitoxin, or microcystin. This result was further confirmed by HPLC and MALDI-TOF analyses. However, we report for the first time in C. raciborskii the presence of mcyA and mcyE, two segments of the microcystin synthetase mcy cluster. All the strains were identified taxonomically based on the 16S rRNA sequences, and their phylogenetic relationships were assessed using the rpoC1 region. Tunisian strains formed a distinct clade separated from the other African strains. © 2011 Springer-Verlag. Source
A polyphasic approach leading to the revision of the genus Planktothrix (Cyanobacteria) and its type species, P. agardhii, and proposal for integrating the emended valid botanical taxa, as well as three new species, Planktothrix paucivesiculata sp. nov.ICNP, Planktothrix tepida sp. nov.ICNP, and Planktothrix serta sp. nov.ICNP
Gaget V.,Institute Pasteur Paris |
Gaget V.,Center dAnalyse Environnementales |
Welker M.,AnagnosTec GmbH |
Welker M.,bioMerieux |
And 3 more authors.
Systematic and Applied Microbiology | Year: 2015
Twenty strains of Planktothrix and five of 'Oscillatoria' were characterized by a polyphasic approach, for clarification of their taxonomic relationships. Emphasis was given to the strains (17) of the Pasteur Culture Collection of Cyanobacteria (PCC). Phenotypic characters analyzed comprised morphology, phycobiliprotein composition, temperature and salinity tolerance. The gvpA gas vesicle gene was detected by PCR in all strains, and transmission electron microscopy confirmed gas vesicle formation in the strains of 'Oscillatoria'. MALDI-TOF mass spectrometry revealed 13 chemotypes, nine of which produce microcystins. A multi-locus sequence typing (MLST) analysis was conducted using individual and concatenated nucleotide sequences of the 16S rDNA, internal transcribed spacer (ITS), gyrB, rpoC1 and rpoB. The results highlighted an unexpected diversity within the genus Planktothrix, showing that the five strains of 'Oscillatoria' need to be included in this taxon. Consequently, the genus consists of seven phylogenetic clusters, three of which represent new species, named Planktothrix paucivesiculata sp. nov.ICNP (type strain: PCC 8926T), Planktothrix tepida sp. nov.ICNP (type strain: PCC 9214T) and Planktothrix serta sp. nov.ICNP (type strain: PCC 8927T). These, together with the emended genus Planktothrix and its type species P. agardhii, valid taxa under the ICN, are described/re-described for gaining nomenclatural standing under the ICNP. © 2015 Elsevier GmbH. Source