Genetic diversity and phylogeny of toxic cyanobacteria determined by DNA polymorphisms within the phycocyanin locus

A new quantitative PCR assay for detection of potentially anatoxin-producing cyanobacteria

Anatoxins (ATX) are globally occurring toxins produced by some species of cyanobacteria in aquatic habitats. They can cause acute poisoning in animals, leading to muscle paralysis and respiratory failure, and might also pose a long-term health risk to humans. Thanks to advances in molecular methods and genomic knowledge, it is now possible to rapidly detect and quantify the genes associated with cyanotoxin production for most major groups of cyanotoxins except ATX. The aim of this study was to develop and validate a new quantitative PCR (qPCR) assay for general detection of all potential ATX producers in the environment. After specificity testing in silico and in vitro with 16 cyanobacterial strains (endpoint PCR, amplicon sequencing and qPCR), two assays targeting the anaC gene were thoroughly validated for linearity, amplification efficiency, sensitivity, dynamic range, inter-assay and intra-assay variability, and the influence of background DNA. The assays were then applied to 144 environmental samples of plankton and biofilm from lakes and rivers whose ATX content had previously been measured by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Amplification efficiency of the two designed assays was between 94 % and 103 %, and the limits of quantification and detection were up to, but mostly below, 322 and 32 cells/mL, respectively. Both assays showed better or equal specificity in cyanobacterial cultures than currently available PCR assays and were able to predict the presence of ATX detected by LC-MS/MS in most environmental samples (83 % in plankton and 52-62 % in biofilm). A higher number of discrepancies between qPCR and LC-MS/MS results in biofilm than in plankton samples indicates limited knowledge and sparse genomic data on benthic cyanobacteria. These assays are the first published general qPCR assays targeting all ATX producers and could provide water managers with a rapid and cost-effective risk assessment to better protect human and animal health.

Widespread distribution of chlorophyll f-producing Leptodesmis cyanobacteria

Chlorophyll (Chl) f was reported as the fifth Chl in oxygenic photoautotrophs. Chlorophyll f production expanded the utilization of photosynthetically active radiation into the far-red light (FR) region in some cyanobacterial genera. In this study, 11 filamentous cyanobacterial strains were isolated from FR-enriched habitats, including hydrophyte, moss, shady stone, shallow ditch, and microbial mat across Central and Southern China. Polyphasic analysis classified them into the same genus of Leptodesmis and further recognized them as four new species, including Leptodesmis atroviridis sp. nov., Leptodesmis fuscus sp. nov., Leptodesmis olivacea sp. nov., and Leptodesmis undulata sp. nov. These cyanobacteria had absorption peaks beyond 700 nm due to Chl f production and red-shifted phycobiliprotein complexes under FR conditions. All but L. undulata produced phycoerythrin and showed varying degrees of a reddish-brown to dark green color under white light conditions. However, the phycoerythrin contents were sharply decreased under FR conditions, and these three Leptodesmis species appeared green. In summary, the Leptodesmis genus contains diverse species with the capacity to synthesize Chl f and is likely a ubiquitous group of Chl f-producing cyanobacteria.

Enhancement mechanism of xanthan gum production in Xanthomonas campestris induced by atmospheric and room-temperature plasma (ARTP) mutagenesis

Xanthan gum, produced by the aerobic fermentation of carbohydrates by Xanthomonas campestris, is a significant natural and industrial biopolymer known for its exceptional properties. Enhancing the yield of xanthan gum production remains a critical challenge. This study employed atmospheric and room temperature plasma (ARTP) technology to induce mutagenesis in X. campestris, resulting in a high-yielding strain, X20. The X20 mutant exhibited a substantial increase in xanthan gum yield, ranging from 13.3 % to 30.0 % over the starting strain across NaCl concentrations of 0, 6.0, and 8.0 g/L, along with improved viscosity and molecular weight. In the whole genome of X20 mutant, a total of 80 variant sites differing from the reference genome were identified, involving 76 mutated genes. Among these, 19 were missense mutations primarily associated with the two-component system. Transcriptome analysis highlighted their role in enhancing flagellar movement, biofilm formation, and metabolic synthesis, thereby elevating the capability of the mutant strain in xanthan gum production. This study demonstrates the potential of ARTP as an effective tool for microbial mutagenesis breeding, providing theoretical guidance for future studies on the synthesis regulation of xanthan gum and the engineering modification of X. campestris.

Diversity and networking of uni-cyanobacterial cultures and associated heterotrophic bacteria from the benthic microbial mat of a desert hydrothermal spring

Thermal springs harbour microorganisms, often dominated by cyanobacteria, which form biofilms and microbial mats. These phototrophic organisms release organic exudates into their immediate surroundings, attracting heterotrophic bacteria that contribute to the diversity and functioning of these ecosystems. In this study, the microbial mats from a hydrothermal pool in the Ksar Ghilane oasis in the Grand Erg Oriental of the Desert Tunisia were collected to obtain cyanobacterial cultures formed by single cyanobacterial species. High-throughput analysis showed that while the microbial mat hosted diverse cyanobacteria, laboratory cultures selectively enriched cyanobacteria from the Leptolyngbya, Nodosilinea, and Arthronema. Per each of these genera, multiple non-axenic uni-cyanobacterial cultures were established, totalling 41 cultures. Cyanobacteria taxa mediated the assembly of distinct heterotrophic bacterial communities, with members of the Proteobacteria and Actinobacteria phyla dominating. The bacterial communities of uni-cyanobacterial cultures were densely interconnected, with heterotrophic bacteria preferentially co-occurring with each other. Our study highlighted the complex structures of non-axenic uni-cyanobacterial cultures, where taxonomically distinct cyanobacteria consistently associate with specific groups of heterotrophic bacteria. The observed associations were likely driven by common selection pressures in the laboratory, such as cultivation conditions and specific hosts, and may not necessarily reflect the microbial dynamic occurring in the spring microbial mats.

Effects of salinity and nutrient stress on a toxic freshwater cyanobacterial community and its associated microbiome: An experimental study

We aimed to evaluate the ability of naturally occurring colonies of Microcystis, embedded in a thick mucilage, to persist in estuarine waters. In two batch experiments, we examined the dynamics of microbial communities, including cyanobacteria and associated heterotrophic bacteria, sampled from the field during both a cyanobacterial bloom (non-limiting nutrient condition) and the post-bloom period (limiting nutrient condition), and subjected them to a salinity gradient representative of the freshwater-marine continuum. We demonstrated that both Microcystis aeruginosa and M. wesenbergii survived high salinities due to osmolyte accumulation. Specifically, prolonged exposure to high salinity led to betaine accumulation in the cyanobacterial biomass. The relative abundance of the mcyB gene remained around 30%, suggesting no selection for toxic genotypes with salinity or nutrient changes. Microcystins were predominantly intracellular, except at high salinity levels (>15), where more than 50% of the total microcystin concentration was extracellular. In both nutrient conditions, over 70% of the heterotrophic bacterial community belonged to the Gammaproteobacteria family, followed by the Bacteroidota. Bacterial community composition differed in both size fractions, as well as along the salinity gradient over time. Finally, genus-specific core microbiomes were identified and conserved even under highly stressful conditions, suggesting interactions that support community stability and resilience.

Molecular Screening for Cyanobacteria and Their Cyanotoxin Potential in Diverse Habitats

Cyanobacteria are adaptable and dominant organisms that exist in many harsh and extreme environments due to their great ecological tolerance. They produce various secondary metabolites, including cyanotoxins. While cyanobacteria are well studied in surface waters and some aerial habitats, numerous other habitats and niches remain underexplored. We collected 61 samples of: (i) biofilms from springs, (ii) aerial microbial mats from buildings and subaerial mats from caves, and (iii) water from borehole wells, caves, alkaline, saline, sulphidic, thermal, and iron springs, rivers, seas, and melted cave ice from five countries (Croatia, Georgia, Italy, Serbia, and Slovenia). We used (q)PCR to detect cyanobacteria (phycocyanin intergenic spacer-PC-IGS and cyanobacteria-specific 16S rRNA gene) and cyanotoxin genes (microcystins-mcyE, saxitoxins-sxtA, cylindrospermopsins-cyrJ), as well as amplicon sequencing and morphological observations for taxonomic identification. Cyanobacteria were detected in samples from caves, a saline spring, and an alkaline spring. While mcyE or sxtA genes were not observed in any sample, cyrJ results showed the presence of a potential cylindrospermopsin producer in a biofilm from a sulphidic spring in Slovenia. This study contributes to our understanding of cyanobacteria occurrence in diverse habitats, including rare and extreme ones, and provides relevant methodological considerations for future research in such environments.

Distribution of toxigenic cyanobacteria in Alpine lakes and rivers as revealed by molecular screening

The increasing frequency of cyanobacteria blooms in waterbodies caused by ecosystem eutrophication could endanger human health. This risk can be mitigated by effective monitoring incorporating molecular methods. To date, most molecular studies on toxigenic cyanobacteria have been limited to microcystins (MCs), disregarding other cyanotoxins, to freshwater planktic habitats while ignoring benthic habitats, and to limited geographic areas (usually one or a few specific waterbodies). In this study, we used PCR-based methods including PCR product sequencing and chemical-analytical methods (LC-MS/MS) to screen many plankton (n = 123) and biofilm samples (n = 113) originating from 29 Alpine lakes and 18 rivers for their cyanotoxin production potential. Both mcyE (indicating MC synthesis) and anaC (indicating anatoxin (ATX) synthesis) gene fragments were able to qualitatively predict MC or ATX occurrence. The abundance of mcyE gene fragments was significantly related to MC concentrations in plankton samples (R2 = 0.61). mcyE gene fragments indicative of MC synthesis were most abundant in planktic samples (65 %) and were assigned to the genera Planktothrix and Microcystis. However, mcyE rarely occurred in biofilms of lakes and rivers, i.e., 4 % and 5 %, respectively, and were assigned to Microcystis, Planktothrix, and Nostoc. In contrast, anaC gene fragments occurred frequently in planktic samples (14 % assigned to Tychonema, Phormidium (Microcoleus), and Oscillatoria), but also in biofilms of lakes (49 %) and rivers (18 %) and were assigned to the genera Phormidium, Oscillatoria, and Nostocales. The cyrJ gene fragment indicating cylindrospermopsin synthesis occurred only once in plankton (assigned to Dolichospermum), while saxitoxin synthesis potential was not detected. For plankton samples, monomictic and less eutrophic conditions were positively related to mcyE/MC occurrence frequency, while oligomictic conditions were related to anaC/ATX frequency. The anaC/ATX frequency in biofilm was related to the lake habitats generally showing higher biodiversity as revealed from metabarcoding in a parallel study.

Characterization of Neowestiellopsis persica A1387 (Hapalosiphonaceae) based on the cpcA, psbA, rpoC1, nifH and nifD gene sequences

BACKGROUND

Complex descriptions of new strains of cyanobacteria appear very frequently. The main importance of these descriptions concerns potential new substances that they could synthesise, as well as their different properties as a result of their different ecological niches. The main gene used for these descriptions is 16 S with ITS or whole genome sequencing. Neowestiellopsis persica represents a unique example of the influence of ecology on morphological changes, with almost identical 16 S identity. Although our previously described Neowestiellopsis persica strain A1387 was characterized by 16 S analysis, we used different molecular markers to provide a way to separate strains of this genus that are closely related at the genetic level.

MATERIALS AND METHODS

In order to conduct an in-depth study, several molecular markers, namely psbA, rpoC1, nifD, nifH and cpcA were sequenced and studied in Neowestiellopsis persica strain A1387.

RESULTS

The results of the phylogenetic analysis, based on cpcA, showed that the studied strain A 1387 falls into a separate clade than N. persica, indicating that this signature sequence could be a useful molecular marker for phylogenetic separation of similar strains isolated in the future.

CONCLUSIONS

Analysis of strain A1387 based on gene differences confirmed that it is a Neowestiellopsis strain. The morphological changes observed in the previous study could be due to different ecological and cultivation conditions compared to the type species. At the same time, the sequences obtained have increased our understanding of this species and will help in the future to better identify strains belonging to the genus Neowestiellopsis.

Comparative genomic analysis of Microcystis strain diversity using conserved marker genes

Microcystis-dominated cyanobacterial harmful algal blooms (cyanoHABs) have a global impact on freshwater environments, affecting both wildlife and human health. Microcystis diversity and function in field samples and laboratory cultures can be determined by sequencing whole genomes of cultured isolates or natural populations, but these methods remain computationally and financially expensive. Amplicon sequencing of marker genes is a lower cost and higher throughput alternative to characterize strain composition and diversity in mixed samples. However, the selection of appropriate marker gene region(s) and primers requires prior understanding of the relationship between single gene genotype, whole genome content, and phenotype. To identify phylogenetic markers of Microcystis strain diversity, we compared phylogenetic trees built from each of 2,351 individual core genes to an established phylogeny and assessed the ability of these core genes to predict whole genome content and bioactive compound genotypes. We identified single-copy core genes better able to resolve Microcystis phylogenies than previously identified marker genes. We developed primers suitable for current Illumina-based amplicon sequencing with near-complete coverage of available Microcystis genomes and demonstrate that they outperform existing options for assessing Microcystis strain composition. Results showed that genetic markers can be used to infer Microcystis gene content and phenotypes such as potential production of bioactive compounds , although marker performance varies by bioactive compound gene and sequence similarity. Finally, we demonstrate that these markers can be used to characterize the Microcystis strain composition of laboratory or field samples like those collected for surveillance and modeling of Microcystis-dominated cyanobacterial harmful algal blooms.

Occurrence of Harmful Algal Blooms in Freshwater Sources of Mindu and Nyumba ya Mungu Dams, Tanzania

Harmful algal blooms (HABs) pose a significant threat to aquatic ecosystems and human health due to the production of toxins. The identification and quantification of these toxins are crucial for water quality management decisions. This study used DNA analysis (PCR techniques) to identify toxin-producing strains and liquid-chromatography-tandem mass spectrometry (LC-MS/MS) to quantify microcystins in samples from Mindu and Nyumba ya Mungu Dams in Tanzania. The results showed that HABs were detected in both dams. The BLAST results revealed that the 16S gene sequences of uncultured samples were very similar to an Antarctic cyanobacterium, Leptolyngbya sp, Anabaena sp, and Microcystis aeruginosa. Sequences of the cultured samples were most similar to Nodularia spumigena, Amazoninema brasiliense, Anabaena sp, and Microcystis aeruginosa. Further analyses showed that the nucleotide sequence similarity of uncultured isolates from this study and those from the GenBank ranged from 85 to 100%. For cultured isolates from this study and others from the GenBank, nucleotide identity ranged from 81 to 100%. The molecular identification of Microcystis aeruginosa confirmed the presence of HABs in both Mindu and Nyumba ya Mungu Dams in Tanzania. At Mindu Dam, the mean concentrations (± standard deviation) of microcystin-LR, -RR, and -YR were 1.08 ± 0.749 ppm, 0.120 ± 0.0211 ppm, and 1.37 ± 0.862 ppm, respectively. Similarly, at Nyumba ya Mungu Dam, the concentrations of microcystin-LR, -RR, and -YR were 1.07 ± 0.499 ppm, 0.124 ± 0.0224 ppm, and 0.961 ± 0.408 ppm, respectively. This paper represents the first application of PCR and LC-MS/MS to study microcystins in small freshwater reservoirs in Tanzania. This study confirms the presence of toxin-producing strains of Microcystis aeruginosa in both dams and also provides evidence of the occurrence of microcystins from these strains. These findings contribute in improving the monitoring of HABs contamination and their potential impact on water quality in Tanzanian reservoirs.

A microcystin synthesis mcyE/ndaF gene assay enables early detection of microcystin production in a tropical wastewater pond

Cyanobacteria can dominate the algal community in wastewater ponds, which can lead to the production of cyanotoxins and their release into the environment. We applied traditional and molecular techniques to identify cyanotoxin hazards and high-risk periods in a tropical wastewater treatment system. Potentially toxic cyanobacteria were identified by microscopy and amplicon sequencing over the course of a year. Toxin gene levels were monitored and compared to toxin production to identify likely toxin producing species and high-risk periods. Cyanobacteria were persistent in the effluent year-round, with Planktothrix and Microcystis the most abundant genera; Microcystis could not be resolved beyond genus using amplicon sequencing, but M. flos-aquae was identified as a dominant species by microscopy. Microcystin toxin was detected for the first time in treated effluent at the beginning of the wet season (December 2018), which correlated with an increase in Microcystis amplicon sequence abundance and elevated microcystin toxin gene (mcyE/ndaF) levels. Concomitantly, microscopy data showed an increase in M. flos-aquae but not M. aeruginosa. These data informed a refined sampling campaign in 2019 and results showed a strong correlation between mcyE/ndaF gene abundance, microcystin toxin levels and Microcystis amplicon sequence abundance. Microscopy data showed that in addition to M. flos-aquae, M. aeruginosa was also abundant in February and March 2019, with highest levels coinciding with toxin detection and toxin gene levels. M. aeruginosa was the most abundant Microcystis species detected in selected treated effluent samples by metagenomics analysis, and elevated levels coincided with toxin production. All microcystin genes in the biosynthesis pathway were detected, but microcystin genes from Planktothrix agardhii were not detected. Gene toxin assays were successfully used to predict microcystin production in this wastewater system. Changes in amplicon sequence relative abundance were a useful indicator of changes in the cyanobacterial community. We found that metagenomics was useful not just for identifying the most abundant Microcystis species, but the detection of microcystin biosynthesis genes helped confirm this genus as the most likely toxin producer in this system. We recommend toxin gene testing for the early detection of potential toxin producing cyanobacteria to manage the risk of toxicity and allow the implementation of risk management strategies.

Chlorophyll f production in two new subaerial cyanobacteria of the family Oculatellaceae

Chlorophyll (Chl) f was recently identified in a few cyanobacteria as the fifth chlorophyll of oxygenic organisms. In this study, two Leptolyngbya-like strains of CCNU0012 and CCNU0013 were isolated from a dry ditch in Chongqing city and a brick wall in Mount Emei Scenic Area in China, respectively. These two strains were described as new species: Elainella chongqingensis sp. nov. (Oculatellaceae, Synechococcales) and Pegethrix sichuanica sp. nov. (Oculatellaceae, Synechococcales) by the polyphasic approach based on morphological features, phylogenetic analysis of 16S rRNA gene and secondary structure comparison of 16S-23S internal transcribed spacer domains. Both strains produced Chl a under white light (WL) but additionally induced Chl f synthesis under far-red light (FRL). Unexpectedly, the content of Chl f in P. sichuanica was nearly half that in most Chl f-producing cyanobacteria. Red-shifted phycobiliproteins were also induced in both strains under FRL conditions. Subsequently, additional absorption peak beyond 700 nm in the FRL spectral region appeared in these two strains. This is the first report of Chl f production induced by FRL in the family Oculatellaceae. This study not only extended the diversity of Chl f-producing cyanobacteria but also provided precious samples to elucidate the essential binding sites of Chl f within cyanobacterial photosystems.

Effect of hydrological modification on the potential toxicity of Microcystis aeruginosa complex in Salto Grande reservoir, Uruguay

It is widely known that the environmental conditions caused by the construction of reservoirs favor the proliferation of toxic cyanobacteria and the formation of blooms due to the high residence time of the water, low turbidity, temperature regimes, among others. Microcystin-producing cyanobacteria such as those from the Microcystis aeruginosa complex (MAC) are the most frequently found organisms in reservoirs worldwide, being the role of the environment on microcystin production poorly understood. Here, we addressed the community dynamics and potential toxicity of MAC cyanobacteria in a subtropical reservoir (Salto Grande) located in the low Uruguay river. Samples were taken from five different sites (upstream, inside the reservoir and downstream) during contrasting seasons (summer and winter) to analyze: (i) the MAC community structure by amplicon sequencing of the phycocyanin gene spacer, (ii) the genotype diversity of microcystin-producing MAC by high resolution melting analysis of the mcyJ gene, and (iii) the abundance and mcy transcription activity of the microcystin-producing (toxic) fraction. We found that MAC diversity decreased from summer to winter but, despite the observed changes in MAC community structure, the abundance of toxic organisms and the transcription of mcy genes were always higher inside the reservoir, regardless of the season. Two different genotypes of toxic MAC were detected inside the reservoir, one associated with low water temperature (15 °C) and one thriving at high water temperature (31 °C). These findings indicate that the environmental conditions inside the reservoir reduce community diversity while promoting the proliferation of toxic genotypes that actively transcribe mcy genes, whose relative abundance will depend on the water temperature.

Microcystis pangenome reveals cryptic diversity within and across morphospecies

Microcystis, a common harmful algal bloom (HAB) taxon, threatens water supplies and human health, yet species delimitation is contentious in this taxon, leading to challenges in research and management of this threat. Historical and common morphology-based classifications recognize multiple morphospecies, most with variable and diverse ecologies, while DNA sequence-based classifications indicate a single species with multiple ecotypes. To better delimit Microcystis species, we conducted a pangenome analysis of 122 genomes. Core- and non-core gene phylogenetic analyses placed 113 genomes into 23 monophyletic clusters containing at least two genomes. Overall, genome-related indices revealed that Microcystis contains at least 16 putative genospecies. Fifteen genospecies included at least one Microcystis aeruginosa morphospecies, and 10 genospecies included two or more morphospecies. This classification system will enable consistent taxonomic identification of Microcystis and thereby aid in resolving some of the complexities and controversies that have long characterized eco-evolutionary research and management of this important HAB taxon.

Phylogenetic analysis of Arthrospira strains from Ordos based on 16S rRNA

To study the growth rate of different Arthrospira strains, three species of Arthrospira from Ordos alkaline lake, labeled as sp.DD, sp.ER, sp.FB, one species of Arthrospira from Hasu Sea in Hohhot, labeled as sp.HS, another purified strain labeled as sp.QD donated by the Ocean University of China had been collected. The first four need to be further isolated and purified in culture. The growth curves of all strains were plotted. Subsequently, 16S rRNA sequences were amplified and sequenced in an attempt to study taxonomic relationships. The results showed that the growth rate was increased in the first 9 days, and sp.DD had the highest growth rate. Analysis of the sequencing results revealed that sp.HS had 99.79% homology with Arthrospira platensis strain Sp-2, sp.DD had 99.69% homology with Arthrospira platensis FACHB834, sp.QD had 99.54% homology with Arthrospira platensis F3S, sp.ER had 99.79% homology with Arthrospira erdosensis ‘Inner Mongolia’, sp.FB had 99.74% homology with Arthrospira erdosensis ‘Inner Mongolia’. Phylogenetic analysis indicated that sp.HS was closely related to Arthrospira platensis strain Sp-2; sp.DD and sp.QD had a close genetic relationship; sp.ER and sp.FB had a close genetic relationship. In conclusion, these findings provide a theoretical basis for the further development and reproduction of dominant algae species in Inner Mongolia through biological analysis of Arthrospira.

Kovacikia minuta sp. nov. (Leptolyngbyaceae, Cyanobacteria), a new freshwater chlorophyll f-producing cyanobacterium

A few groups of cyanobacteria have been characterized as having far-red light photoacclimation (FaRLiP) that results from chlorophyll f (Chl f) production. In this study, using a polyphasic approach, we taxonomically transferred the Cf. Leptolyngbya sp. CCNUW1 isolated from a shaded freshwater pond, which produces Chl f under far-red light, to the genus Kovacikia and named this taxon Kovacikia minuta sp. nov. This strain was morphologically similar to Leptolyngbya-like strains. The thin filaments were purplish-brown under white light but became grass green under far-red light. The 31-gene phylogeny grouped K. minuta CCNU0001 into order Synechococcales and family Leptolyngbyaceae. Phylogenetic analysis based on 16S rRNA gene sequences further showed that K. minuta CCNU0001 was clustered into Kovacikia with similarities of 97.2-97.4% to the recently reported type species of Kovacikia muscicola HA7619-LM3. Additionally, the internal transcribed spacer region between 16S-23S rRNA genes had a unique sequence and secondary structure compared with other Kovacikia strains and phylogenetically related taxa. Draft genome sequences of K. minuta CCNU0001 (8,564,336 bp) were assembled into one circular chromosome and two circular plasmids. A FaRLiP 20-gene cluster comprised two operons with the unique organization. In sum, K. minuta was established as a new species, and it is the first species reported to produce Chl f and for which a draft genome was produced in genus Kovacikia. This study expanded our knowledge regarding the diversity of Chl f-producing cyanobacteria in far-red light-enriched environments and provides important foundational information for future investigations of FaRLiP evolution in cyanobacteria.

Application of a newly recorded diazotrophic cyanobacterium in acidified and Cd contaminated paddy soil: Promotes rice yield and decreases Cd accumulation

Acidification caused by excessive fertilization and heavy metals contamination are two prominent problems of agricultural soils. Diazotrophic cyanobacteria play important role in nitrogen (N) input in agricultural ecosystem. However, the effects of diazotrophic cyanobacteria on the growth of rice and heavy metal uptake by rice grain in acidified and heavy metal contaminated paddy soil remain unknown. In this study, a newly recorded diazotrophic cyanobacterium Aliinostoc sp. YYLX235 was isolated from acidified paddy soil. The results of pot experiment and in situ field plot experiment demonstrated that Aliinostoc sp. YYLX235 could promote rice grain yield and decrease cadmium (Cd) accumulation in rice grain. Nitrogen input by N₂-fixation and increase of bio-available phosphorus (P) by promotion of activity of soil phosphatase may be the main mechanisms for growth-promoting effects of Aliinostoc sp. YYLX235 on rice. Binding and immobilization of Cd through hydroxyl, carboxyl, and amino groups may be the reason for decrease of Cd accumulation in rice grain by Aliinostoc sp. YYLX235 inoculation. The results presented in this study suggest that diazotrophic cyanobacteria have great potential in safe cropping in acidified and Cd contaminated paddy soils.

Occurrence of Mycosporine-like Amino Acids (MAAs) from the Bloom-Forming Cyanobacteria Aphanizomenon Strains

Mycosporine-like amino acids (MAAs) are widespread in various microbes and protect them against harsh environments. Here, four different Aphanizomenon species were isolated from severely eutrophic waterbodies, Lake Dianchi and the Guanqiao fishpond. Morphological characters and molecular phylogenetic analysis verified that the CHAB5919, 5921, and 5926 strains belonged to the Aphanizomenon flos-aquae clade while Guanqiao01 belonged to the Aphanizomenon gracile clade. Full wavelength scanning proved that there was obvious maximal absorption at 334 nm through purified methanol extraction, and these substances were further analyzed by HPLC and UPLC-MS-MS. The results showed that two kinds of MAAs were discovered in the cultured Aphanizomenon strains. One molecular weight was 333.28 and the other was 347.25, and the daughter fragment patterns were in accordance with the previously articles reported shinorine and porphyra-334 ion characters. The concentration of the MAAs was calibrated from semi-prepared MAAs standards from dry cells of Microcystis aeruginosa PCC7806 algal powder, and the purity of shinorine and porphyra-334 were 90.2% and 85.4%, respectively. The average concentrations of shinorine and porphyra-334 were 0.307−0.385 µg/mg and 0.111−0.136 µg/mg in Aphanizomenon flos-aquae species, respectively. And there was only one kind of MAAs (shinorine) in Aphanizomenon gracile species.,with a content of 0.003−0.049 µg/mg dry weight among all Aphanizomenon gracile strains. The shinorine concentration in Aphanizomenon flos-aquae was higher than that in Aphanizomenon gracile strains. The total MAAs production can be ranked as Aphanizomenon flos-aquae > Aphanizomenon gracile.

Preliminary evidence on the presence of cyanobacteria and cyanotoxins from culture enrichments followed by PCR analysis: new perspectives from Africa (Mali) and South Pacific (Fiji) countries

Cyanobacteria are a group of microorganisms that can be found in a diverse range of biogeographical areas and produce potent and damaging cyanotoxins, which reveal importance for continuous studies and surveillance efforts. In this study, we analyzed worldwide two-month culture-enriched water samples collected from 12 distinct countries (Costa Rica, Cuba, Fiji, France, Indonesia, Mali, Portugal, South Africa, Spain, Thailand, USA, Vietnam) including two undisclosed areas (Fiji and Mali). We performed a PCR-based molecular multi-step scheme that consisted in the detection of the main cyanobacterial species, genera, and cyanotoxins biosynthesis genes. Results from this study indicate that Microcystis aeruginosa followed by Planktothrix agardhii were the most prevalent species of all the 12 countries analyzed. Cylindrospermospis raciborskii was detected in Costa Rica, while P. agardhii was detected in Fiji and South Africa. M. aeruginosa was detected in Fiji and Mali. Regarding the main cyanotoxins biosynthesis genes, a cyrC gene fragment (cylindrospermopsins) was amplified in the African continent (South Africa), while anaC (anatoxin-a) was detected in two distinct locations, Mali and Vietnam. Saxitoxins biosynthesis gene was also detected in Fiji and Vietnam. Microcystins biosynthesis gene (mcyA) was co-detected with anatoxin-a biosynthesis gene in Mali and with saxitoxins biosynthesis gene (sxtI) in Portugal. This study therefore constitutes a major contribution to the global biogeography of cyanobacteria and its cyanotoxins and recommends continuous vigilance of toxic cyanobacteria particularly in the more undisclosed areas of the world. The PCR analysis data obtained in our 2-month culture-enriched water samples supports molecular methods as a preliminary tool in the environmental surveillance of cyanobacteria and cyanotoxins in undisclosed locations, particularly since the several positive amplifications detected may indicate that though samples were collected under non-bloom conditions, if environmental conditions change in the ecosystem, there is a risk that bloom-forming species may arose along with their detected cyanotoxicity.

Occurrence of Raphidiopsis raciborskii blooms in cool waters: Synergistic effects of nitrogen availability and ecotypes with adaptation to low temperature

Raphidiopsis raciborskii is a diazotrophic and potentially toxic cyanobacterium. To date, this species has successfully invaded many regions from the tropics to sub-tropical and temperate regions, typically forming blooms at temperatures greater than 25 °C. However, there have been a few cases in which R. raciborskii blooms have occurred at low temperatures (below 15 °C), but its cause and mechanisms remain unclear. In this study, field investigations revealed that R. raciborskii blooms occurred at 10-15 °C in Lake Xihu, Yunnan, China. The biomass of R. raciborskii was found to be positively related to nitrate concentrations in this lake. Three strains of R. raciborskii, two isolated from Lake Xihu (CHAB 6611 and CHAB 6612) and one from Lushui Reservoir in central China (CHAB 3409), were used for growth experiments at 15 °C. The three strains exhibited genotypic (16S rRNA and ITS-L genes) and physiological differences in response to nitrogen concentrations at low temperature. The growth rates of strains CHAB 6611 and CHAB 6612 increased with nitrogen concentration while CHAB 3409 could not grow at 15 °C. Furthermore, the growth and phenotypic responses of CHAB 6611 and CHAB 6612 to nitrogen concentrations were different, despite the closer genetic relationship shared by these two strains. Thus, increased nitrogen concentration in water may enhance the biological availability and utilization of nitrogen by R. raciborskii, which is the external promoter, leading to improving the resistance of R. raciborskii to low temperature. The internal cause is the presence of ecotypes in R. raciborskii populations with adaptation to low temperature. With increasing global eutrophication, the distribution range of R. raciborskii as well as the scale of its blooms will increase. As such, the risk of exposure of aquatic biota and humans to cylindrospermopsin is also expected to increase.

Water quality and human health: A simple monitoring model of toxic cyanobacteria growth in highly variable Mediterranean hot dry environments

Due to population growth, urbanization and economic development, demand for freshwater in urban areas is increasing throughout Europe. At the same time, climate change, eutrophication and pollution are affecting the availability of water supplies. Sicily, a big island in southern Italy, suffers from an increasing drought and consequently water shortage. In the last decades, in Sicilian freshwater reservoirs several Microcystis aeruginosa and more recently Planktothrix rubescens blooms were reported. The aims of the study were: (1) identify and quantify the occurring species of cyanobacteria (CB), (2) identify which parameters, among those investigated in the waters, could favor their growth, (3) set up a model to identify reservoirs that need continuous monitoring due to the presences, current or prospected, of cyanobacterial blooms and of microcystins, relevant for environmental and, consequentially, for human health. Fifteen artificial reservoirs among the large set of Sicilian artificial water bodies were selected and examined for physicochemical and microbiological characterization. Additional parameters were assessed, including the presence, identification and count of the cyanobacterial occurring species, the measurement of microcystins (MCs) levels and the search for the genes responsible for the toxins production. Principal Component Analysis (PCA) was used to relate environmental condition to cyanobacterial growth. Water quality was poor for very few parameters, suggesting common anthropic pressures, and PCA highlighted clusters of reservoirs vulnerable to hydrological conditions, related to semi-arid Mediterranean climate and to the use of the reservoir. In summer, bloom was detected in only one reservoir and different species was highlighted among the Cyanobacteria community. The only toxins detected were microcystins, although always well below the WHO reference value for drinking waters (1.0 μg/L). However, molecular analysis could not show the presence of potential cyanotoxins producers since a few numbers of cells among total could be sufficient to produce these low MCs levels but not enough high to be proved by the traditional molecular method applied. A simple environmental risk-based model, which accounts for the high variability of both cyanobacteria growth and cyanotoxins producing, is proposed as a cost-effective tool to evaluate the need for monitoring activities in reservoirs aimed to guarantee supplying waters safety.

Phylogeographic, toxicological and ecological evidence for the global distribution of Raphidiopsis raciborskii and its northernmost presence in Lake Nero, Central Western Russia

Raphidiopsis raciborskii is a freshwater, potentially toxigenic cyanobacterium, originally described as a tropical species that is spreading to northern regions over several decades. The ability of R. raciborskii to produce cyanotoxins - in particular the alkaloid cylindrospermopsin (CYN), which is toxic to humans and animals - is of serious concern. The first appearance of R. raciborskii in Russia was noted in Lake Nero in the summer of 2010. This is the northernmost (57°N) recorded case of the simultaneous presence of R. raciborskii and detection of CYN. In this study, the data from long-term monitoring of the R. raciborskii population, temperature and light conditions in Lake Nero were explored. CYN and cyr/aoa genes present in environmental samples were examined using HPLC/MS-MS and PCR analysis. A R. raciborskii strain (R104) was isolated and its morphology, toxigenicity and phylogeography were studied. It is supposed that the trigger factor for the strong development of R. raciborskii in Lake Nero in summer 2010 may have been the relatively high water temperature, reaching 29-30 °C. Strain R. raciborskii R104 has straight trichomes and can produce akinetes, making it morphologically similar to European strains. Phylogeographic analysis based on nifH gene and 16S-23S rRNA ITS1 sequences showed that the Russian strain R104 grouped together with R. raciborskii strains isolated from Portugal, France, Germany and Hungary. The Russian strain R104 does not contain cyrA and cyrB genes, meaning that it - like all European strains - cannot produce CYN. Thus, while recent invasion of R. raciborskii into Lake Nero has occurred, morphological, genetic, and toxicological data supported the spreading of this cyanobacterium from other European lakes. Detection of CYN and cyr/aoa genes in environmental samples indicated the cyanobacterium Aphanizomenon gracile as a likely producer of CYN in Lake Nero. The article also discusses data on the global biogeography of R. raciborskii. Genetic similarity between R. raciborskii strains isolated from very remote continents might be related to the ancient origin of the cyanobacterium inhabiting the united continents of Laurasia and Gondwana, rather than comparably recent transoceanic exchange between R. raciborskii populations.

Revealing Cryptic Changes of Cyanobacterial Community Structure in Two Eutrophic Lakes Using eDNA Sequencing

Harmful cyanobacterial blooms pose a risk to human health worldwide. To enhance understanding on the bloom-forming mechanism, the spatiotemporal changes in cyanobacterial diversity and composition in two eutrophic lakes (Erhai Lake and Lushui Reservoir) of China were investigated from 2010 to 2011 by high-throughput sequencing of environmental DNA. For each sample, 118 to 260 cpcBA-IGS operational taxonomic units (OTUs) were obtained. Fifty-two abundant OTUs were identified, which made up 95.2% of the total sequences and were clustered into nine cyanobacterial groups. Although the cyanobacterial communities of both lakes were mainly dominated by Microcystis, Erhai Lake had a higher cyanobacterial diversity. The abundance of mixed Nostocales species was lower than that of Microcystis, whereas Phormidium and Synechococcus were opportunistically dominant. The correlation between the occurrence frequency and relative abundance of OTUs was poorly fitted by the Sloan neutral model. Deterministic processes such as phosphorus availability were shown to have significant effects on the cyanobacterial community structure in Erhai Lake. In summary, the Microcystis-dominated cyanobacterial community was mainly affected by the deterministic process. Opportunistically dominant species have the potential to replace Microcystis and form blooms in eutrophic lakes, indicating the necessity to monitor these species for drinking water safety.

Cyanobacteria Phylogenetic Studies Reveal Evidence for Polyphyletic Genera from Thermal and Freshwater Habitats

Cyanobacteria are among the most diverse morphological microorganisms that inhabit a great variety of habitats. Their presence in the Azores, a volcanic archipelago of nine islands in the middle of the North Atlantic Ocean, has already been reported. However, due to the high diversity of cyanobacteria habitats, their biodiversity is still understudied, mainly in extreme environments. To address this, a total of 156 cyanobacteria strains from Azores lakes, streams, thermal and terrestrial habitats were isolated. Identification was made based on a polyphasic approach using classical taxonomy (morphological characteristics and environmental data) and phylogeny among 81 strains assessed by maximum likelihood and Bayesian analysis of 16S rDNA partial sequences. The 156 isolates showed a high genera diversity (38) belonging to the orders Chroococcales, Nostocales, Oscillatoriales, and Synechococcales. Eleven new genera for the Azores habitats are here reported, reinforcing that cyanobacteria biodiversity in these islands is still much understudied. Phylogenetic analysis showed 14 clusters associated with these cyanobacteria orders, with evidence for six new genera and valuable information towards Microchaete/Coleospermum taxonomic revision that better reflects species environmental distribution. These results emphasize the need for cyanobacteria taxonomy revisions, through polyphasic studies, mainly in Synechococcales order and in the Microchaete/Coleospermum, Nostoc, and Anabaena genera.

Utility of a PCR-based method for rapid and specific detection of toxigenic Microcystis spp. in farm ponds

Microcystis is a widespread freshwater cyanobacterium that can produce microcystin, a potent hepatotoxin harmful to animals and humans. Therefore, it is crucial to monitor for the presence of toxigenic Microcystis spp. to provide early warning of potential microcystin contamination. Microscopy, which has been used traditionally to identify Microcystis spp., cannot differentiate toxigenic from non-toxigenic Microcystis. We developed a PCR-based method to detect toxigenic Microcystis spp. based on detection of the microcystin synthetase C (mcyC) gene and 16S rRNA gene. Specificity was validated against toxic and nontoxic M. aeruginosa strains, as well as 4 intergeneric freshwater cyanobacterial strains. Analytical sensitivity was as low as 747 fg/µL genomic DNA (or 3 cells/µL) for toxic M. aeruginosa. Furthermore, we tested 60 water samples from 4 farm ponds providing drinking water to swine facilities in the midwestern United States using this method. Although all water samples were positive for Microcystis spp. (i.e., 16S rRNA gene), toxigenic Microcystis spp. were detected in only 34 samples (57%). Seventeen water samples contained microcystin (0.1-9.1 μg/L) determined with liquid chromatography-mass spectrometry, of which 14 samples (82%) were positive for mcyC. A significant correlation was found between the presence of toxigenic Microcystis spp. and microcystin in water samples (p = 0.0004). Our PCR method can be a low-cost molecular tool for rapid and specific identification of toxigenic Microcystis spp. in farm ponds, improving detection of microcystin contamination, and ensuring water safety for farm animals.

Blooms of Toxic Cyanobacterium Nodularia spumigena in Norwegian Fjords During Holocene Warm Periods

In paleoecological studies, molecular markers are being used increasingly often to reconstruct community structures, environmental conditions and ecosystem changes. In this work, nodularin, anabaenopeptins and selected DNA sequences were applied as Nodularia spumigena markers to reconstruct the history of the cyanobacterium in the Norwegian fjords. For the purpose of this study, three sediment cores collected in Oslofjorden, Trondheimsfjorden and Balsfjorden were analyzed. The lack of nodularin in most recent sediments is consistent with the fact that only one report on the sporadic occurrence and low amounts of the cyanobacterium in Norwegian Fjords in 1976 has been published. However, analyses of species-specific chemical markers in deep sediments showed that thousands of years ago, N. spumigena constituted an important component of the phytoplankton community. The content of the markers in the cores indicated that the biomass of the cyanobacterium increased during the warmer Holocene periods. The analyses of genetic markers were less conclusive; they showed the occurrence of microcystin/nodularin producing cyanobacteria of Nostocales order, but they did not allow for the identification of the organisms at a species level.

Factors related to aggravated Cylindrospermopsis (cyanobacteria) bloom following sediment dredging in an eutrophic shallow lake

In recent years, Cylindrospermopsis raciborskii blooms have been widely found worldwide. Topics dealing with the mitigation of C. raciborskii bloom is of great importance for toxins produced could threaten public health. The paper first investigated C. raciborskii dynamics over three years following sediment dredging in a shallow eutrophic Lake Dongqian (China). Based on rpoC1 gene copies, C. raciborskii bloom formed with average density of 1.30 × 10⁶ cells/L on July 2009. One year later after sediment dredging, C. raciborskii cell density decreased below 1.17 × 10⁵ cells/L or under detected limits during summer days on 2010. While two years later, the C. raciborskii bloom period was returned with markedly increased cell density reaching up to 4.15 × 10⁷ cells/L on October 2011, and the maximum peak density was shown at 20.3 °C that was much lower than reported optimal growth temperature. Inferred from Spearman correlation analysis, linear regression showed C. raciborskii density was significant and positive with pH and SD, whereas they were significant and negative with TP and DO. Multiple regression analysis further demonstrated that TN, TP, SRP, pH and DO provided the best model and explained 53.1% of the variance in C. raciborskii dynamics. The approaches managing nutrients reduction might not control C. raciborskii bloom as extremely low TN (avg. 0.18 mg/L) and TP concentrations (avg. 0.05 mg/L) resulted in the highest C. raciborskii cell density after sediment dredging.

Detection of Cyanotoxin-Producing Genes in a Eutrophic Reservoir (Billings Reservoir, São Paulo, Brazil)

CyanoHABs (cyanobacterial harmful algal blooms) are blooms of cyanobacteria capable of producing cyanotoxins, a large group of secondary metabolites that are toxic to most eukaryotes. In this work, the main aim was to evaluate the presence of multiple genes from each of the clusters responsible for biosynthesis of cyanotoxins (cylindrospermopsin, microcystin and saxitoxin) in total DNA obtained from sixteen environmental water samples by PCR. Microcystin gene mcyE was amplified in all analyzed samples. Among the cylindrospermopsin genes analyzed, only the cyrC gene was amplified from DNA obtained from three of sixteen samples. Of the three different saxitoxin genes analyzed, sxtB and sxtI were present in four and three of the sixteen samples studied, respectively, and sxtA did not show any positive result. Based on our results, we suggest caution when using only one gene from the full clusters responsible for biosynthesis of cyanotoxins, given that it may not be sufficient to confirm or exclude the toxigenic potential of a sample.

Phylogenetic relationships and genetic divergence of paralytic shellfish toxin- and cylindrospermopsin- producing Cylindrospermopsis and raphidiopsis

Cylindrospermopsis and Raphidiopsis (C/R group) are closely related species responsible for cyanobacterial blooms worldwide. Paralytic shellfish toxins (PSTs) and cylindrospermopsins (CYNs) have been identified in different C/R group strains. However, the evolutionary relationship between PST- and CYN-producing strains has not been systematically evaluated. In this study, C/R group strains and their toxin biosynthesis genes were evaluated by phylogenetic analysis and sequence comparison. None of the tested strains are able to produce PSTs and CYNs simultaneously. The C/R group strains were clustered into five clades, including two non-toxic, two CYN-producing and one PST-producing clades. A high degree of similarity was observed for rpoC1 (> 96%) and ITS-L (> 97%) sequences within each clade with the exception of the ITS-L (87% to 100%) region in CYN-producing R. curvata, which has been shown to contain variable sequence insertions. Genomic analysis revealed that sxtY and sxtZ could be found in both toxic and non-toxic strains. The transposase gene IS4 was only observed in strains from the PST-producing clade. The sxt and cyr gene clusters share five gene families with similar functions. The amino acid sequences of the adenylyl-sulfate kinase genes, sxtO and cyrN, are more similar (45% to 81%) than other pairs of genes (8.0% to 40%). SxtO and CyrN proteins from C/R group strains forms an independent clade on the phylogenetic tree with a high degree of sequence similarity (78% to 100%). In conclusion, PST- and CYN- producing C/R group species can be classified into different clades based on their phylogenetic profile. The sxtO and cyrN genes have probably diverged from a single ancestral adenylyl-sulfate kinase gene, and may be specifically used for toxin biosynthesis in C/R group species.

Distribution of the Harmful Bloom-Forming Cyanobacterium, Microcystis aeruginosa, in 88 Freshwater Environments across Japan

Microcystis aeruginosa was quantitatively surveyed in 88 freshwater environments across Japan within 3‍ ‍weeks in 2011. In order to clarify the distribution pattern of M. aeruginosa at the intra-species level, three major genotypes, which were defined by 16S-23S rRNA inter-transcribed-spacer (ITS) regions, were selectively detected using quantitative real-time PCR assays. Of the 68 sites at which the Microcystis intergenic-spacer region of the phycocyanin (IGS-PC) gene was detected, the M. aeruginosa morphotype-related genotype (MG1) dominated in 41 sites, followed by the non-toxic M. wesenbergii-related genotype (MG3). A correlation analysis showed that total nitrogen and phosphate positively correlated with the abundance of IGS-PC, which positively correlated with microcystin synthetase gene abundance. A redundancy analysis of genotype compositions showed that pH positively correlated with the dominance of MG3 and negatively correlated with MG1, i.e., both toxic and non-toxic genotypes. Our survey of Microcystis populations over a wide area revealed that MG1 is a dominant genotype in Japan.

Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses

Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the "omics" technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.

Intraspecific variability in response to phosphorus depleted conditions in the cyanobacteria Microcystis aeruginosa and Raphidiopsis raciborskii

Phosphorus loading plays an important role in the occurrence of cyanobacterial blooms and understanding how this nutrient affects the physiology of cyanobacteria is imperative to manage these phenomena. Microcystis aeruginosa and Raphidiopsis raciborskii are cyanobacterial species that form potentially toxic blooms in freshwater ecosystems worldwide. Blooms comprise numerous strains with high trait variability, which can contribute to the widespread distribution of these species. Here, we explored the intraspecific variability in response to phosphorus depleted conditions (P-) testing five strains of each species. Strains could be differentiated by cell volume or genetic profiles except for those of the same species, sampling location and date, though these presented differences in their response to (P-). Although differently affected by (P-) over 10 days, all strains were able to grow and maintain photosynthetic activity. For most M. aeruginosa and R. raciborskii strains growth rates were not significantly different comparing (P+) and (P-) conditions. After ten days in (P-), only one M. aeruginosa strain and two R. raciborskii strains showed reduction in biovolume yield as compared to (P+) but in most strains chlorophyll-a concentrations were lower in (P-) than in (P+). Reduced photosystem II efficiency was found for only one R. raciborskii strain while all M. aeruginosa strains were affected. Only two M. aeruginosa and one R. raciborskii strain increased alkaline phosphatase activity under (P-) as compared to (P+). Variation in P-uptake was also observed but comparison among strains yielded homogeneous groups comprised of representatives of both species. Comparing the response of each species as a whole, the (P-) condition affected growth rate, biovolume yield and chlorophyll yield. However, these parameters revealed variation among strains of the same species to the extent that differences between M. aeruginosa and R. raciborskii were not significant. Taken together, these results do not support the idea that R. raciborskii, as a species, can withstand phosphorus limitation better than M. aeruginosa and also point that the level of intraspecific variation may preclude generalizations based on studies that use only one or few strains.

Microcystis Chemotype Diversity in the Alimentary Tract of Bigheaded Carp

Most cyanobacterial organisms included in the genus Microcystis can produce a wide repertoire of secondary metabolites. In the mid-2010s, summer cyanobacterial blooms of Microcystis sp. occurred regularly in Lake Balaton. During this period, we investigated how the alimentary tract of filter-feeding bigheaded carps could deliver different chemotypes of viable cyanobacteria with specific peptide patterns. Twenty-five Microcystis strains were isolated from pelagic plankton samples (14 samples) and the hindguts of bigheaded carp (11 samples), and three bloom samples were collected from the scums of cyanobacterial blooms. An LC-MS/MS-based untargeted approach was used to analyze peptide patterns, which identified 36 anabaenopeptin, 17 microginin, and 13 microcystin variants. Heat map clustering visualization was used to compare the identified chemotypes. A lack of separation was observed in peptide patterns of Microcystis that originated from hindguts, water samples, and bloom-samples. Except for 13 peptides, all other congeners were detected from the viable and cultivated chemotypes of bigheaded carp. This finding suggests that the alimentary tract of bigheaded carps is not simply an extreme habitat, but may also supply the cyanobacterial strains that represent the pelagic chemotypes.

Spatial-temporal survey of Microcystis oligopeptide chemotypes in reservoirs with dissimilar waterbody features and their relation to genetic variation

The ability of cyanobacteria to produce toxins and other secondary metabolites is patchily distributed in natural populations, enabling the use of cellular oligopeptide compositions as markers to classify strains into ecologically-relevant chemotypical subpopulations. The composition and spatiotemporal distribution of Microcystis chemotypes within and among waterbodies was studied at different time scales by analyzing (i) Microcystis strains isolated between 1998 and 2007 from different Spanish reservoirs and (ii) individual Microcystis aeruginosa colonies collected from pelagic and littoral habitats in Valmayor reservoir (Spain) during a bloom. No agreement between chemotypes and both morphotypes and genotypes (based on cpcBA-IGS, 16S-23S rRNA ITS and mcyB genes) was found, suggesting that oligopeptide profiles in individual strains evolve independently across morphospecies and phylogenetic genotypes, and that the diversity of microcystin variants produced cannot be explained by mcyB gene variations alone. The presence of identical chemotypes in spatially-distant reservoirs with dissimilar trophic state, lithology or depth indicate that waterbody characteristics and geographical boundaries weakly affect chemotype composition and distribution. At smaller spatiotemporal scales (i.e. during bloom), M. aeruginosa populations showed high number of chemotypes, as well as marked differences in chemotype composition and relative abundance among the littoral and pelagic habitats. This indicates that the factors influencing chemotype composition, relative abundance and dynamics operate at short spatial and temporal scales, and supports emerging hypotheses about interactions with antagonistic microorganisms as possible drivers for widespread chemical polymorphisms in cyanobacteria.

Specific Chemical and Genetic Markers Revealed a Thousands-Year Presence of Toxic Nodularia spumigena in the Baltic Sea

In the Baltic Sea, diazotrophic cyanobacteria have been present for thousands of years, over the whole brackish water phase of the ecosystem. However, our knowledge about the species composition of the cyanobacterial community is limited to the last several decades. In the current study, the presence of species-specific chemical and genetic markers in deep sediments were analyzed to increase the existing knowledge on the history of toxic Nodularia spumigena blooms in the Baltic Sea. As chemical markers, three cyclic nonribosomal peptides were applied: the hepatotoxic nodularin, which in the sea was detected solely in N. spumigena, and two anabaenopeptins (AP827 and AP883a) characteristic of two different chemotypes of this species. From the same sediment samples, DNA was isolated and the gene involved in biosynthesis of nodularin, as well as the phycocyanin intergenic spacer region (PC-IGS), were amplified. The results of chemical and genetic analyses proved for the first time the thousands-year presence of toxic N. spumigena in the Baltic Sea. They also indicated that through all this time, the same two sub-populations of the species co-existed.

Targeted deep sequencing reveals high diversity and variable dominance of bloom-forming cyanobacteria in eutrophic lakes

Cyanobacterial blooms in eutrophic lakes are severe environmental problems worldwide. To characterize the spatiotemporal heterogeneity of cyanobacterial blooms, a high-throughput method is necessary for the specific detection of cyanobacteria. In this study, the cyanobacterial composition of three eutrophic waters in China (Taihu Lake, Dongqian Lake, and Dongzhen Reservoir) was determined by pyrosequencing the cpcBA intergenic spacer (cpcBA-IGS) of cyanobacteria. A total of 2585 OTUs were obtained from the normalized cpcBA-IGS sequence dataset at a distance of 0.05. The 238 most abundant OTUs contained 92% of the total sequences and were classified into six cyanobacterial groups. The water samples of Taihu Lake were dominated by Microcystis, mixed Nostocales species, Synechococcus, and unclassified cyanobacteria. Besides, all the samples from Taihu Lake were clustered together in the dendrogram based on shared abundant OTUs. The cyanobacterial diversity in Dongqian Lake was dramatically decreased after sediment dredging and Synechococcus became exclusively dominant in this lake. The genus Synechococcus was also dominant in the surface water of Dongzhen Reservoir, while phylogenetically diverse cyanobacteria coexisted at a depth of 10m in this reservoir. In summary, targeted deep sequencing based on cpcBA-IGS revealed a large diversity of bloom-forming cyanobacteria in eutrophic lakes and spatiotemporal changes in the composition of cyanobacterial communities. The genus Microcystis was the most abundant bloom-forming cyanobacteria in eutrophic lakes, while Synechococcus could be exclusively dominant under appropriate environmental conditions.

Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality

Next generation sequencing (NGS) has rapidly become an invaluable tool for the detection, identification and relative quantification of environmental microorganisms. Here, we demonstrate two new 16S rDNA primer sets, which are compatible with NGS approaches and are primarily for use in water quality studies. Compared to 16S rRNA gene based universal primers, in silico and experimental analyses demonstrated that the new primers showed increased specificity for the Cyanobacteria and Proteobacteria phyla, allowing increased sensitivity for the detection, identification and relative quantification of toxic bloom-forming microalgae, microbial water quality bioindicators and common pathogens. Significantly, Cyanobacterial and Proteobacterial sequences accounted for ca. 95% of all sequences obtained within NGS runs (when compared to ca. 50% with standard universal NGS primers), providing higher sensitivity and greater phylogenetic resolution of key water quality microbial groups. The increased selectivity of the new primers allow the parallel sequencing of more samples through reduced sequence retrieval levels required to detect target groups, potentially reducing NGS costs by 50% but still guaranteeing optimal coverage and species discrimination.

Genetic divergence among toxic and non-toxic cyanobacteria of the dry zone of Sri Lanka

Sri Lanka has rich cyanobacterial diversity, however, only few studies have been conducted to identify the potential toxin producers in water bodies used for human consumption. As the detection of cyanotoxin is vital in water quality management, a study was done by employing 16S rRNA gene to explore the genetic divergence, phylogenetic relationships and potential toxin producing cyanobacteria in reservoirs and well waters in the dry zone of Sri Lanka. Forty five, 16S rRNA gene sequences were assayed and phylogenetic tree was constructed. Among 45 isolates, 20 isolates were classified as unidentified cyanobacteria and considered as novel cyanobacterial genera. Of 25 identified isolates, seven isolates were identified up to species level. With 16S rRNA phylogeny, 20 unidentified cyanobacterial isolates were able to place on their taxonomic positions up to order level. Results revealed that water samples understudy had vast cyanobacterial diversity with potential microcystin (MC) and cylindrospermopsin (CYN) producers and eleven clusters clearly demonstrated five cyanobacterial orders with more than 90% similarity irrespective to their toxicity which showed the suitability of 16S rRNA gene for taxonomic differentiation. Sixteen isolates had the potential to produce MC and two isolates to produce CYN. Findings of the study confirm the rich cyanobacterial diversity and the divergence among the potential cyanotoxin producers in the dry zone water bodies of Sri Lanka.

Chemical and Genetic Diversity of Nodularia spumigena from the Baltic Sea

Nodularia spumigena is a toxic, filamentous cyanobacterium occurring in brackish waters worldwide, yet forms extensive recurrent blooms in the Baltic Sea. N. spumigena produces several classes of non-ribosomal peptides (NRPs) that are active against several key metabolic enzymes. Previously, strains from geographically distant regions showed distinct NRP metabolic profiles. In this work, conspecific diversity in N. spumigena was studied using chemical and genetic approaches. NRP profiles were determined in 25 N. spumigena strains isolated in different years and from different locations in the Baltic Sea using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genetic diversity was assessed by targeting the phycocyanin intergenic spacer and flanking regions (cpcBA-IGS). Overall, 14 spumigins, 5 aeruginosins, 2 pseudaeruginosins, 2 nodularins, 36 anabaenopeptins, and one new cyanopeptolin-like peptide were identified among the strains. Seven anabaenopeptins were new structures; one cyanopeptolin-like peptide was discovered in N. spumigena for the first time. Based on NRP profiles and cpcBA-IGS sequences, the strains were grouped into two main clusters without apparent influence of year and location, indicating persistent presence of these two subpopulations in the Baltic Sea. This study is a major step in using chemical profiling to explore conspecific diversity with a higher resolution than with a sole genetic approach.

Molecular separation of two long taxonomically debated cyanobacterial genera Cylindrospermopsis and Raphidiopsis (Nostocales) based on the ITS-L phylogeny

The cyanobacterial genera Raphidiopsis and Cylindrospermopsis morphologically resembled each other and are difficult to distinguish, especially when heterocytes do not form in Cylindrospermopsis species. The phylogeny based on multiple gene loci sequences in previous studies cannot divide the strains of these two genera into separate clusters. In the present study, four gene loci 16S rRNA, ITS-L, cpcBA-IGS and rpoC1, sequenced from many Chinese strains (44 Cylindrospermopsis strains and 16 Raphidiopsis strains), were analyzed to infer the phylogenetic relationship between the two genera. According to the 16S rRNA, cpcBA-IGS and rpoC1 gene phylogeny, Cylindrospermopsis and Raphidiopsis strains are intermixed and divide into two or three groups. By contrast, the ITS-L analysis implied that they respectively form two separate and unique clusters. A fragment of 7bp (RAGAAACT) in ITS-L was conserved for Raphidiopsis strains, which could be distinguished from Cylindrospermopsis strains. A pair of primers targeting the ITS-L fragment specific to Raphidiopsis strains were designed and further verified.

A review of the phylogeny, ecology and toxin production of bloom-forming Aphanizomenon spp. and related species within the Nostocales (cyanobacteria)

The traditional genus Aphanizomenon comprises a group of filamentous nitrogen-fixing cyanobacteria of which several memebers are able to develop blooms and to produce toxic metabolites (cyanotoxins), including hepatotoxins (microcystins), neurotoxins (anatoxins and saxitoxins) and cytotoxins (cylindrospermopsin). This genus, representing geographically widespread and extensively studied cyanobacteria, is in fact heterogeneous and composed of at least five phylogenetically distant groups (Aphanizomenon, Anabaena/Aphanizomenon like cluster A, Cuspidothrix, Sphaerospermopsis and Chrysosporum) whose taxonomy is still under revision. This review provides a thorough insight into the phylogeny, ecology, biogeography and toxicogenomics (cyr, sxt, and ana genes) of the five best documented "Aphanizomenon" species with special relevance for water risk assessment: Aphanizomenon flos-aquae, Aphanizomenon gracile, Cuspidothrix issatschenkoi, Sphaerospermopsis aphanizomenoides and Chrysosporum ovalisporum. Aph. flos-aquae, Aph. gracile and C. issatschenkoi have been reported from temperate areas only whereas S. aphanizomenoides shows the widest distribution from the tropics to temperate areas. Ch. ovalisporum is found in tropical, subtropical and Mediterranean areas. While all five species show moderate growth rates (0.1-0.4day^-1) within a wide range of temperatures (15-30°C), Aph. gracile and A. flos-aquae can grow from around (or below) 10°C, whereas Ch. ovalisporum and S. aphanizomenoides are much better competitors at high temperatures over 30°C or even close to 35°C. A. gracile has been confirmed as the producer of saxitoxins and cylindrospermopsin, C. issatschenkoi of anatoxins and saxitoxins and Ch. ovalisporum of cylindrospermopsin. The suspected cylindrospermopsin or anatoxin-a production of A. flos-aquae or microcystin production of S. aphanizomenoides is still uncertain. This review includes a critical discussion on the the reliability of toxicity reports and on the invasive potential of "Aphanizomenon" species in a climate change scenario, together with derived knowledge gaps and research needs. As a whole, this work is intended to represent a key reference for scientists and water managers involved in the major challenges of identifying, preventing and mitigating toxic Aphanizomenon blooms.

Distribution and population dynamics of potential anatoxin-a-producing cyanobacteria in Lake Dianchi, China

The occurrence of cyanobacterial blooms is often accompanied by a variety of toxic secondary metabolites known as cyanotoxins. Anatoxin-a (ATX-a) is a highly toxic cyanobacterial neurotoxin synthesized by numerous species (e.g., Aphanizomenon, Anabaena and Oscillatoria) that has received much public attention. In this study, we used molecular methods (PCR and qPCR) to track the presence and dynamics of ATX-a-producing cyanobacteria, Aphanizomenon and Anabaena in Lake Dianchi, China based on the anaC and cpcBA-IGS genes over a 23-month period (from June 2010 to April 2012). Results revealed that Aphanizomenon was the major potential ATX-a producer in Lake Dianchi and that they were most abundant in early spring and least abundant in summer, coinciding with observed Aphanizomenon blooms. It was found that the proportion of ATX-a toxigenic cells was lower in the northern part of the lake (2.1%) than the middle (16.7%) and southern parts (19.2%). The information on the spatio-temporal distributions of ATX-a-producing cyanobacteria obtained in this study will help to build management strategies to improve water quality for public health.

Ecological Specialization of Two Photobiont-Specific Maritime Cyanolichen Species of the Genus Lichina

All fungi in the class Lichinomycetes are lichen-forming and exclusively associate with cyanobacteria. Two closely related maritime species of the genus Lichina (L. confinis and L. pygmaea) show similar distribution ranges in the Northeast Atlantic, commonly co-occurring at the same rocky shores but occupying different littoral zones. By means of 16S rRNA and phycocyanin operon markers we studied a) the phylogenetic relationships of cyanobionts associated with these species, b) the match of divergence times between both symbionts, and c) whether Lichina species differ in photobiont association and in how geography and ecology affect selectivity. The cyanobionts studied are closely related to both marine and freshwater strains of the genus Rivularia. We found evidence of a high specificity to particular cyanobiont lineages in both species: Lichina pygmaea and L. confinis incorporate specific lineages of Rivularia that do not overlap at the haplotype nor the OTU levels. Dating divergences of the fungal and cyanobacterial partners revealed an asynchronous origin of both lineages. Within each fungal species, selectivity varied across the studied area, influenced by environmental conditions (both atmospheric and marine), although patterns were highly correlated between both lichen taxa. Ecological speciation due to the differential association of photobionts to each littoral zone is suspected to have occurred in marine Lichina.

Effects of linear alkylbenzene sulfonate on the growth and toxin production of Microcystis aeruginosa isolated from Lake Dianchi

The exogenous organic pollutant linear alkylbenzene sulfonate (LAS) pollution and Microcystis bloom are two common phenomena in eutrophic lakes, but the effects of LAS alone on Microcystis remain unclear. In the present study, we investigated the effects of LAS on the growth, photochemical efficiency, and microcystin production of Microcystis aeruginosa in the laboratory. Results showed that low LAS (≤10 mg/L) concentrations improved the growth of M. aeruginosa (12 days of exposure). High LAS (20 mg/L) concentrations inhibited the growth of M. aeruginosa on the first 8 days of exposure; afterward, growth progressed. After 12 days of exposure, the concentrations of chlorophyll a in algal cells were not significantly affected by any of LAS concentrations (0.05 to 20 mg/L) in the present study; by contrast, carotenoid and protein concentrations were significantly inhibited when LAS concentrations reached as high as 20 mg/L. After 6 and 12 days of exposure, low LAS (≤10 mg/L) concentrations enhanced the maximal photochemical efficiency (Fv/Fm) and the maximal electron transport rate (ETRmax) of M. aeruginosa. Furthermore, LAS increased the microcystin production of M. aeruginosa. Extracellular and intracellular microcystin contents were significantly increased after M. aeruginosa was exposed to high LAS concentrations. Our results indicated that LAS in eutrophic lakes may increase the risk of Microcystis bloom and microcystin production.