Rapid Classification and Identification of Microcystis aeruginosa Strains Using MALDI-TOF MS and Polygenetic Analysis

Rapid Cyanobacteria Species Identification with High Sensitivity Using Native Mass Spectrometry

Cyanobacteria have evolved over billions of years to adapt and survive in diverse climates. Environmentally, this presents a huge challenge because cyanobacteria can now rapidly form algae blooms that are detrimental to aquatic life. In addition, many cyanobacteria produce toxins, making them hazardous to animals and humans that they encounter. Rapid identification of cyanobacteria is essential to monitor and prevent toxic algae blooms. Here, we show for the first time how native mass spectrometry can quickly and precisely identify cyanobacteria from diverse aquatic environments. By monitoring phycobiliproteins, abundant protein complexes within cyanobacteria, simple, easy-to-understand mass spectral "fingerprints" were created that were unique to each species. Moreover, our method is 10-fold more sensitive than the current MALDI-TOF mass spectrometric methods, meaning that cyanobacteria can be monitored using this technology prior to bloom formation. Together, the data show great promise for the simultaneous detection and identification of co-existing cyanobacteria in situ.

The Influence of Metabolic Inhibitors, Antibiotics, and Microgravity on Intact Cell MALDI-TOF Mass Spectra of the Cyanobacterium Synechococcus Sp. UPOC S4

The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp. UPOC S4 and to check the impact on reliability of identification. Defining the limits of this method is important for its use in biology and applied science. The compounds included inhibitors of respiration, glycolysis, citrate cycle, and proteosynthesis. They were used at 1–10 μM concentrations and different periods of up to 3 weeks. Cells were also grown without inhibitors in a microgravity because of expected strong effects. Mass spectra were evaluated using controls and interpreted in terms of differential peaks and their assignment to protein sequences by mass. Antibiotics, azide, and bromopyruvate had the greatest impact. The spectral patterns were markedly altered after a prolonged incubation at higher concentrations, which precluded identification in the database of reference spectra. The incubation in microgravity showed a similar effect. These differences were evident in dendrograms constructed from the spectral data. Enzyme inhibitors affected the spectra to a smaller extent. This study shows that only a long-term presence of antibiotics and strong metabolic inhibitors in the medium at 10⁻⁵ M concentrations hinders the correct identification of cyanobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF).

Cyanobacterial Classification with the Toxicity Using MALDI Biotyper

An abnormal growth of cyanobacteria in eutrophicated freshwaters can cause various environmental problems. In particular, Microcystis producing hepatotoxic cyclic heptapeptides microcystins (MCs) has been globally observed. Recent studies have demonstrated that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) offers a rapid classification of cyanobacteria; however, they have not fully considered the toxicity yet. In this study, we have performed MALDI-TOF MS for intact cyanobacterial cells using Biotyper software and optimized their conditions to achieve cyanobacterial classification with the toxicity. The detection mass range used for Biotyper was extended to cover small molecules, but their intense ions were suppressed as a function of the used instrument Autoflex Speed, which enabled simultaneous observations of large molecular fingerprints and small MCs with comparable ion intensity. Hierarchical clustering of mass spectra obtained under the optimized conditions differentiated toxic and non-toxic clusters of Microcystis strains and furthermore formed a tight cluster of non-toxic strains possessing the MC biosynthesis gene mcyG. Spectral libraries were expanded to >30 genera (>80 strains) under the default and optimized conditions to improve the confidence of cyanobacterial classification. Consequently, spectral library searching allowed for characterization of cyanobacteria from a field sample as mixed toxic and non-toxic Microcystis cells, without isolating those cells.

Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae

"Omics" represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and 'blind'-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism's inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.

A two-enzyme constituted mixture to improve the degradation of Arthrospira platensis microalga cell wall for monogastric diets

The main goal of this study was to test a rational combination of pre‐selected carbohydrate‐active enzymes (CAZymes) and sulphatases, individually or in combination, in order to evaluate its capacity to disrupt Arthrospira platensis cell wall, allowing the release of its valuable nutritional bioactive compounds. By the end, a two‐enzyme constituted mixture (Mix), composed by a lysozyme and a α‐amylase, was incubated with A. platensis suspension. The microalga cell wall disruption was evaluated through the amount of reducing sugars released from the cell wall complemented with the oligosaccharide profile by HPLC. An increase of the amount of reducing sugars up to 2.42 g/L in microalgae treated with the Mix relative to no treatment (p < .05), as well as a 7‐fold increase of oligosaccharides amount (p < .001), were obtained. With resort of fluorescence microscopy, a 36% reduction of fluorescence intensity (p < .001) was observed using Calcofluor White staining. In the supernatant, the Mix caused a 1.34‐fold increase in protein content (p = .018) relative to the control. Similarly, n‐6 polyunsaturated fatty acids (PUFA) (p = .007), in particular 18:2n‐6 (p = .016), monounsaturated fatty acids (MUFA) (p = .049) and chlorophyll a (p = .025) contents were higher in the supernatant of microalgae treated with the enzyme mixture in relation to the control. Taken together, these results point towards the disclosure of a novel two‐enzyme mixture able to partial degrade A. platensis cell wall, improving its nutrients bioavailability for monogastric diets with the cost‐effective advantage use of microalgae in animal feed industry.

Control of a toxic cyanobacterial bloom species, Microcystis aeruginosa, using the peptide HPA3NT3-A2

Microcystis aeruginosa, a species of freshwater cyanobacteria, is known to be one of the dominant species causing cyanobacterial harmful algal blooms (CyanoHABs). M. aeruginosa blooms have the potential to produce neurotoxins and peptide hepatotoxins, such as microcystins and lipopolysaccharides (LPSs). Currently, technologies for CyanoHAB control do not provide any ultimate solution because of the secondary pollution associated with the control measures. In this study, we attempted to use the peptide HPA3NT3-A2, which has been reported to be nontoxic and has antimicrobial properties, for the development of an eco-friendly control against CyanoHABs. HPA3NT3-A2 displayed significant algicidal effects against M. aeruginosa cells. HPA3NT3-A2 induced cell aggregation and flotation (thereby facilitating harvest), inhibited cell growth through sedimentation, and eventually destroyed the cells. HPA3NT3-A2 had no algicidal effect on other microalgal species such as Haematococcus pluvialis and Chlorella vulgaris. Additionally, HPA3NT3-A2 was not toxic to Daphnia magna. The algicidal mechanism of HPA3NT3-A2 was intracellular penetration. The results of this study suggest the novel possibility of controlling CyanoHABs using HPA3NT3-A2.

Global Metabolomic Characterizations of Microcystis spp. Highlights Clonal Diversity in Natural Bloom-Forming Populations and Expands Metabolite Structural Diversity

Cyanobacteria are photosynthetic prokaryotes capable of synthesizing a large variety of secondary metabolites that exhibit significant bioactivity or toxicity. Microcystis constitutes one of the most common cyanobacterial genera, forming the intensive blooms that nowadays arise in freshwater ecosystems worldwide. Species in this genus can produce numerous cyanotoxins (i.e., toxic cyanobacterial metabolites), which can be harmful to human health and aquatic organisms. To better understand variations in cyanotoxin production between clones of Microcystis species, we investigated the diversity of 24 strains isolated from the same blooms or from different populations in various geographical areas. Strains were compared by genotyping with 16S-ITS fragment sequencing and metabolite chemotyping using LC ESI-qTOF mass spectrometry. While genotyping can help to discriminate among different species, the global metabolome analysis revealed clearly discriminating molecular profiles among strains. These profiles could be clustered primarily according to their global metabolite content, then according to their genotype, and finally according to their sampling location. A global molecular network of all metabolites produced by Microcystis species highlights the production of a wide set of chemically diverse metabolites, including a few microcystins, many aeruginosins, microginins, cyanopeptolins, and anabaenopeptins, together with a large set of unknown molecules. These components, which constitute the molecular biodiversity of Microcystis species, still need to be investigated in terms of their structure and potential bioactivites (e.g., toxicity).

Intact cell MALDI-TOF mass spectrometric analysis of Chroococcidiopsis cyanobacteria for classification purposes and identification of possible marker proteins

Cyanobacteria represent a bacterial phyllum characteristic by the ability to photosynthesize. They are potentially applicable for the production of useful compounds but may also cause poisoning or at least health problems as they can produce cyanotoxins. The introduction of a fast methodology is important not only for fundamental taxonomic purposes, but also for reliable identifications in biological studies. In this work, we have used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells to study Chroococcidiopsis strains. A library of the obtained reference mass spectra containing characteristic peptide/protein profiles was examined by software tools to characterize similarities and differences applicable for diagnostics and taxonomy. Both a similarity tree and heat map constructed from the mass spectrometric data proved consistent with 16S rRNA sequencing results. We show as novelty that a binary matrix combining ferulic and sinapinic acids performs well in acquiring reproducible mass spectra of cyanobacteria. Using the matrix solvent, a protein extraction from cells was done. After polyacrylamide gel electrophoresis, the separated protein fractions were in-gel digested and the resulting peptides analyzed by liquid chromatography coupled with tandem mass spectrometry. For the first time, photosystem protein components, phycobilisome proteins, electron transport proteins, nitrogen-metabolism and nucleic acids binding-proteins, cytochromes plus other enzymes and various uncharacterized proteins could be assigned to characteristic peaks in the mass spectrometric profiles and some of them suggested as markers in addition to 30S and 50S ribosomal proteins known from previous studies employing intact cell mass spectrometry of microorganisms.

Identification and detection sensitivity of Microcystis aeruginosa from mixed and field samples using MALDI-TOF MS

To verify the applicability of identifying Microcystis aeruginosa by matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (MALDI-TOF MS), mixed and field samples were employed to study the sensitivity and the analysis power, respectively. Series diluted samples and artificially mixed samples by the M. aeruginosa NIES-843 strain were designed to verify the sensitivity. The lowest detection limit was 1.955 × 10⁶ cells in pure samples, while for mixed samples, the lowest detection limit and ratio of NIES-843 strain were 2.88 × 10⁶ cells and 33.7%, respectively. The results provided a reference for the reasonable volume of the water sample in which the M. aeruginosa could be detected. Ribosomal protein biomarkers for identifying M. aeruginosa which were successfully detected from the field samples in Taihu Lake, indicated that the identification of M. aeruginosa by MALDI-TOF MS could be applied in field samples. Furthermore, different genetic types of M. aeruginosa strains were also detected at different locations in Taihu Lake, which revealed the diversity of M. aeruginosa and the detection power of MALDI-TOF MS at the strain level for the field samples. The sensitivity and detection power in the analysis of M. aeruginosa by the MALDI-TOF MS demonstrated the applicability of this method in routine environmental monitoring.

Temperature modulates Fischerella thermalis ecotypes in Porcelana Hot Spring

In the Porcelana Hot Spring (Northern Patagonia), true-branching cyanobacteria are the dominant primary producers in microbial mats, and they are mainly responsible for carbon and nitrogen fixation. However, little is known about their metabolic and genomic adaptations at high temperatures. Therefore, in this study, a total of 81 Fischerella thermalis strains (also known as Mastigocladus laminosus) were isolated from mat samples in a thermal gradient between 61-46°C. The complementary use of proteomic comparisons from these strains, and comparative genomics of F. thermalis pangenomes, suggested that at least two different ecotypes were present within these populations. MALDI-TOF MS analysis separated the strains into three clusters; two with strains obtained from mats within the upper temperature range (61 and 54°C), and a third obtained from mats within the lower temperature range (51 and 46°C). Both groups possessed different but synonymous nifH alleles. The main proteomic differences were associated with the abundance of photosynthesis-related proteins. Three F. thermalis metagenome assembled genomes (MAGs) were described from 66, 58 and 48°C metagenomes. These pangenomes indicated a divergence of orthologous genes and a high abundance of exclusive genes at 66°C. These results improved the current understanding of thermal adaptation of F. thermalis and the evolution of these thermophilic cyanobacterial species.

Application of MALDI Biotyper to cyanobacterial profiling

RATIONALE

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been used for bacterial profiling. A few reports have shown MALDI-MS profiling of isolated/cultured cyanobacteria; however, these applications have been limited. In this study, we have investigated whether rapid profiling and differentiation of cyanobacteria including harmful genera Microcystis and Anabaena (Dolichospermum) can be performed by MALDI Biotyper analysis of intact cells.

METHODS

Twenty-two cyanobacterial strains including 12 Microcystis, 7 Anabaena, 1 Pseudanabaena, 1 Planktothrix, and 1 Synechocystis were cultured. Also, natural pond water containing cyanobacteria was collected. Intact cyanobacterial cells were deposited on a target plate, and analyzed using an Autoflex Speed MALDI-TOF mass spectrometer with Biotyper software. Mass spectra obtained from m/z 2000 to 20000 were used for clustering and spectral library searching of cyanobacterial strains.

RESULTS

MALDI-MS analysis of cultured cyanobacterial cells showed clear ion signals under optimized conditions. Hierarchical clustering of mass spectra using Biotyper resulted in a tight cluster of Microcystis strains which was clearly differentiated from a cluster of Anabaena strains. Spectral library searching was able to identify Microcystis aeruginosa NIES-298 and Synechocystis sp. PCC 6803 even when these two cells were mixed. Furthermore, cyanobacterial cells in the pond water were successfully classified as Anabaena.

CONCLUSIONS

We have demonstrated that MALDI-MS in combination with Biotyper analysis is applicable to cyanobacterial profiling. Increasing the size of the spectral library may facilitate monitoring of cyanobacteria in crude cyanobacterial blooms. Copyright © 2016 John Wiley & Sons, Ltd.