Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)

Discrimination of Euglena gracilis strains Z and bacillaris by MALDI-TOF MS

AIMS

Euglena gracilis is used as model organism for various microbiological, molecular biological and biotechnological studies. Its most studied wild type strains are Z and bacillaris, but their discrimination by standard molecular methods is difficult. Therefore, we decided to test the suitability of MALDI-TOF MS (matrix assisted laser desorption/ionization - time of flight mass spectrometry) for identification of E. gracilis and for discrimination of these two strains possessing functional chloroplasts. MALDI-TOF MS profiling was also tested for two white (non-photosynthetic) stable E. gracilis mutant strains W_gm ZOflL and W₁₀ BSmL.

METHODS AND RESULTS

We have successfully obtained main spectrum profiles (MSPs) of E. gracilis strains Z, SAG 1224-5/25 and bacillaris, SAG 1224-5/15 using protein extraction procedure. Subsequent MALDI-TOF MS profiling of a number of tested samples and the comparison of the obtained protein profiles with our in-house database including MSPs of both strains has revealed that these two strains can be easily distinguished by MALDI-TOF MS based on score values over two in most cases. This method has also confirmed the ancestry of white mutant strains W_gm ZOflL and W₁₀ BSmL, originally derived from strains Z and bacillaris, respectively.

CONCLUSIONS

MALDI-TOF MS is suitable, accurate and rapid method for discrimination of E. gracilis strains.

SIGNIFICANCE AND IMPACT OF STUDY

These results can have broad practical implications for laboratories cultivating various strains of euglenids, and they can be applied for their discrimination by MALDI-TOF MS.

Microalgae Bioactive Carbohydrates as a Novel Sustainable and Eco-Friendly Source of Prebiotics: Emerging Health Functionality and Recent Technologies for Extraction and Detection

There is a global interest in the novel consumption, nutritional trends, and the market of new prebiotic sources and their potential functional impacts. Commercially available nutritional supplements based on microalgae that are approved to be edible by FDA, like Arthrospira platensis (Cyanobacteria) and Chlorella vulgaris (Chlorophyta) become widely attractive. Microalgae are rich in carbohydrates, proteins, and polyunsaturated fatty acids that have high bioactivity. Recently, scientists are studying the microalgae polysaccharides (PS) or their derivatives (as dietary fibers) for their potential action as a novel prebiotic source for functional foods. Besides, the microalgae prebiotic polysaccharides are used for medication due to their antioxidant, anticancer, and antihypertensive bioactivities. This review provides an overview of microalgae prebiotics and other macromolecules’ health benefits. The phytochemistry of various species as alternative future sources of novel polysaccharides were mentioned. The application as well as the production constraints and multidisciplinary approaches for evaluating microalgae phytochemistry were discussed. Additionally, the association between this potential of combining techniques like spectroscopic, chromatographic, and electrochemical analyses for microalgae sensation and analysis novelty compared to the chemical methods was emphasized.

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.

A new glance at the chemosphere of macroalgal-bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

Symbiosis is a dominant form of life that has been observed numerous times in marine ecosystems. For example, macroalgae coexist with bacteria that produce factors that promote algal growth and morphogenesis. The green macroalga Ulva mutabilis (Chlorophyta) develops into a callus-like phenotype in the absence of its essential bacterial symbionts Roseovarius sp. MS2 and Maribacter sp. MS6. Spatially resolved studies are required to understand symbiont interactions at the microscale level. Therefore, we used mass spectrometry profiling and imaging techniques with high spatial resolution and sensitivity to gain a new perspective on the mutualistic interactions between bacteria and macroalgae. Using atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionisation high-resolution mass spectrometry (AP-SMALDI-HRMS), low-molecular-weight polar compounds were identified by comparative metabolomics in the chemosphere of Ulva. Choline (2-hydroxy-N,N,N-trimethylethan-1-aminium) was only determined in the alga grown under axenic conditions, whereas ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was found in bacterial presence. Ectoine was used as a metabolic marker for localisation studies of Roseovarius sp. within the tripartite community because it was produced exclusively by these bacteria. By combining confocal laser scanning microscopy (cLSM) and AP-SMALDI-HRMS, we proved that Roseovarius sp. MS2 settled mainly in the rhizoidal zone (holdfast) of U. mutabilis. Our findings provide the fundament to decipher bacterial symbioses with multicellular hosts in aquatic ecosystems in an ecologically relevant context. As a versatile tool for microbiome research, the combined AP-SMALDI and cLSM imaging analysis with a resolution to level of a single bacterial cell can be easily applied to other microbial consortia and their hosts. The novelty of this contribution is the use of an in situ setup designed to avoid all types of external contamination and interferences while resolving spatial distributions of metabolites and identifying specific symbiotic bacteria.

Microalgae with artificial intelligence: A digitalized perspective on genetics, systems and products

With recent advances in novel gene-editing tools such as RNAi, ZFNs, TALENs, and CRISPR-Cas9, the possibility of altering microalgae toward designed properties for various application is becoming a reality. Alteration of microalgae genomes can modify metabolic pathways to give elevated yields in lipids, biomass, and other components. The potential of such genetically optimized microalgae can give a "domino effect" in further providing optimization leverages down the supply chain, in aspects such as cultivation, processing, system design, process integration, and revolutionary products. However, the current level of understanding the functional information of various microalgae gene sequences is still primitive and insufficient as microalgae genome sequences are long and complex. From this perspective, this work proposes to link up this knowledge gap between microalgae genetic information and optimized bioproducts using Artificial Intelligence (AI). With the recent acceleration of AI research, large and complex data from microalgae research can be properly analyzed by combining the cutting-edge of both fields. In this work, the most suitable class of AI algorithms (such as active learning, semi-supervised learning, and meta-learning) are discussed for different cases of microalgae applications. This work concisely reviews the current state of the research milestones and highlight some of the state-of-art that has been carried out, providing insightful future pathways. The utilization of AI algorithms in microalgae cultivation, system optimization, and other aspects of the supply chain is also discussed. This work opens the pathway to a digitalized future for microalgae research and applications.

Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry

INTRODUCTION

Marine planktonic communities are complex microbial consortia often dominated by microscopic algae. The taxonomic identification of individual phytoplankton cells usually relies on their morphology and demands expert knowledge. Recently, a live single-cell mass spectrometry (LSC-MS) pipeline was developed to generate metabolic profiles of microalgae.

OBJECTIVE

Taxonomic identification of diverse microalgal single cells from collection strains and plankton samples based on the metabolic fingerprints analyzed with matrix-free laser desorption/ionization high-resolution mass spectrometry.

METHODS

Matrix-free atmospheric pressure laser-desorption ionization mass spectrometry was performed to acquire single-cell mass spectra from collection strains and prior identified environmental isolates. The computational identification of microalgal species was performed by spectral pattern matching (SPM). Three similarity scores and a bootstrap-derived confidence score were evaluated in terms of their classification performance. The effects of high and low-mass resolutions on the classification success were evaluated.

RESULTS

Several hundred single-cell mass spectra from nine genera and nine species of marine microalgae were obtained. SPM enabled the identification of single cells at the genus and species level with high accuracies. The receiver operating characteristic (ROC) curves indicated a good performance of the similarity measures but were outperformed by the bootstrap-derived confidence scores.

CONCLUSION

This is the first study to solve taxonomic identification of microalgae based on the metabolic fingerprints of the individual cell using an SPM approach.

MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats

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.

Direct MALDI-TOF MS Identification of Bacterial Mixtures

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now widely used to characterize bacterial samples for clinical diagnosis, food safety control, environmental monitoring, and so on. However, existing standard approaches are only applied to analyze single colonies purified by plate culture, which limits the approaches to cultivable bacteria and makes the whole approaches time-consuming. In this work, we propose a new framework to analyze MALDI-TOF spectra of bacterial mixtures and to directly characterize each component without purification procedures. The framework is a combination of a synthetic mixture model based on a non-negative linear combination of candidate reference spectra and a statistical assessment by in silico generated spectra via a jackknife resampling. Ninety-seven model bacterial mixture samples and 8 cocultured blind-coded bacterial mixture samples, containing up to 6 strains in varied ratios in each sample, together with a reference database containing the mass spectra of 1081 strains, were used to validate the framework. High sensitivity (>80%, with error rate <5%) was achieved for balanced binary and ternary mixtures. The sensitivity was >60% for balanced quaternary and pentabasic mixtures, and 48%-71% for asymmetric situation, with error rate <5%. The work can facilitate rapid and reliable characterization of bacterial mixtures without purification procedures, which is of practical value in clinical diagnosis, food safety control, environmental monitoring, and so on. The framework can be further applied to many other spectroscopy-based analytics to interpret spectra from mixed samples.

Characterization of microbial mixtures by mass spectrometry

MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.

Development of a MALDI-TOF MS-Based Protein Fingerprint Database of Common Food Fish Allowing Fast and Reliable Identification of Fraud and Substitution

Fish substitution and fish fraud are widely observed in the global food market. To detect and prevent substitution, DNA-based methods do not always meet the demand of being time- and cost-efficient; therefore, methodology improvements are needed. The use of species-specific protein patterns, as determined by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, has recently improved species identification of prokaryotes both time- and cost-wise. We used the method to establish a database containing protein patterns of common food fish prone to substitution. The database currently comprises 54 fish species. Aspects such as the sensitivity of identification on the species level and the impact of bacterial contamination of fish filets are assessed. Most database entries are characterized by low intraspecies but high interspecies variability. Hitherto, 118 validation samples were successfully determined. The results presented herein underline the potential and reliability of eukaryotic species identification via MALDI-TOF mass spectrometry.

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.

Identification of Microalgae by Laser Desorption/Ionization Mass Spectrometry Coupled with Multiple Nanomatrices

In this study, we demonstrate a simple method to identify microalgae by surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) using three different substrates: HgSe, HgTe, and HgTeSe nanostructures. The fragmentation/ionization processes of complex molecules in algae varied according to the heat absorption and transfer efficiency of the nanostructured matrices (NMs). Therefore, the mass spectra obtained for microalgae showed different patterns of m/z values for different NMs. The spectra contained both significant and nonsignificant peaks. Constructing a Venn diagram with the significant peaks obtained for algae when using HgSe, HgTe, and HgTeSe NMs in m/z ratio range 100-1000, a unique relationship among the three sets of values was obtained. This unique relationship of sets is different for each species of microalgae. Therefore, by observing the particular relationship of sets, we successfully identified different algae such as Isochrysis galbana, Emiliania huxleyi, Thalassiosira weissflogii, Nannochloris sp., Skeletonema cf. costatum, and Tetraselmis chui. This simple and cost-effective SALDI-MS analysis method coupled with multi-nanomaterials as substrates may be extended to identify other microalgae and microorganisms in real samples. Graphical Abstract Identification of microalgae by surface-assisted laser desorption/ionization mass spectrometry coupled with three different mercury-based nanosubstrates.

Letter: The potential of amine-containing dendrimer mass standards for internal calibration of peptides

In order to ensure accurate mass determinations, MALDI-TOF mass spectrometers must be calibrated regularly. While peptides and proteins represent the most widely used calibration standards due to their monodispersity, known masses and availability, their limited shelf-life complicates their use. Recently, polyester dendrimer calibrants have been introduced as an alternative because, in addition to monodispersity and relative molecular masses as high as 30,000, they exhibit vastly improved stability and broad compatibility with both matrices and solvents. However, the use of these initially reported polyester dendrimers as internal calibrants for the analysis of peptides or proteins presents a unique problem because these dendrimers typically require ionization with metal cations, while amino acid-based compounds preferentially ionize via protonation of an amine. To address this complication, dendrimers bearing a single amine were prepared which demonstrate the ability to easily ionize via protonation with either acidic matrices or dilute solutions of trifluoroacetic acid. This class of amine-containing dendrimers shows promise as a calibrant system specifically designed for the internal calibration of peptides.