Miniprep DNA isolation from unicellular and filamentous cyanobacteria

A direct PCR approach with low-biomass insert opens new horizons for molecular sciences on cryptogam communities

Molecular sequence data have transformed research on cryptogams (e.g., lichens, microalgae, fungi, and symbionts thereof) but methods are still strongly hampered by the small size and intermingled growth of the target organisms, poor cultivability and detrimental effects of their secondary metabolites. Here, we aim to showcase examples on which a modified direct PCR approach for diverse aspects of molecular work on environmental samples concerning biocrusts, biofilms, and cryptogams gives new options for the research community. Unlike traditional approaches, this methodology only requires biomass equivalent to colonies and fragments of 0.2 mm in diameter, which can be picked directly from the environmental sample, and includes a quick DNA lysis followed by a standardized PCR cycle that allows co-cycling of various organisms/target regions in the same run. We demonstrate that this modified method can (i) amplify the most widely used taxonomic gene regions and those used for applied and environmental sciences from single colonies and filaments of free-living cyanobacteria, bryophytes, fungi, and lichens, including their mycobionts, chlorobionts, and cyanobionts from both isolates and in situ material during co-cycling; (ii) act as a tool to confirm that the dominant lichen photobiont was isolated from the original sample; and (iii) optionally remove inhibitory secondary lichen substances. Our results represent examples which highlight the method's potential for future applications covering mycology, phycology, biocrusts, and lichenology, in particular.IMPORTANCECyanobacteria, green algae, lichens, and other cryptogams play crucial roles in complex microbial systems such as biological soil crusts of arid biomes or biofilms in caves. Molecular investigations on environmental samples or isolates of these microorganisms are often hampered by their dense aggregation, small size, or metabolism products which complicate DNA extraction and subsequent PCRs. Our work presents various examples of how a direct DNA extraction and PCR method relying on low biomass inserts can overcome these common problems and discusses additional applications of the workflow including adaptations.

GlcNac produced by the gut microbiome enhances host influenza resistance by modulating NK cells

Microbiota are known to modulate the host response to influenza infection, but the mechanisms remain largely unknown. Gut metabolites are the key mediators through which gut microbes play anti-influenza effect. Transferring fecal metabolites from mice with high influenza resistance into antibiotic-treated recipient mice conferred resistance to influenza infections. By comparing the metabolites of different individuals with high or low influenza resistance, we identified and validated N-acetyl-D-glucosamine (GlcNAc) and adenosine showed strong positive correlations with influenza resistance and exerted anti-influenza effects in vivo or in vitro, respectively. Especially, GlcNAc mediated the anti-influenza effect by increasing the proportion and activity of NK cells. Several gut microbes, including Clostridium sp., Phocaeicola sartorii, and Akkermansia muciniphila, were positively correlated with influenza resistance, and can upregulate the level of GlcNAc in the mouse gut by exogenous supplementation. Subsequent studies confirmed that administering a combination of the three bacteria to mice via gavage resulted in similar modulation of NK cell responses as observed with GlcNAc. This study demonstrates that gut microbe-produced GlcNAc protects the host against influenza by regulating NK cells, facilitating the elucidation of the action mechanism of gut microbes mediating host influenza resistance.

Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems

Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.

Amazonocrinis nigriterrae gen. nov., sp. nov., Atlanticothrix silvestris gen. nov., sp. nov. and Dendronalium phyllosphericum gen. nov., sp. nov., nostocacean cyanobacteria from Brazilian environments

The cyanobacterial genus Nostoc is an important contributor to carbon and nitrogen bioavailability in terrestrial ecosystems and a frequent partner in symbiotic relationships with non-diazotrophic organisms. However, since this currently is a polyphyletic genus, the diversity of Nostoc-like cyanobacteria is considerably underestimated at this moment. While reviewing the phylogenetic placement of previously isolated Nostoc-like cyanobacteria originating from Brazilian Amazon, Caatinga and Atlantic forest samples, we detected 17 strains isolated from soil, freshwater, rock and tree surfaces presenting patterns that diverged significantly from related strains when ecological, morphological, molecular and genomic traits were also considered. These observations led to the identification of the evaluated strains as representative of three novel nostocacean genera and species: Amazonocrinis nigriterrae gen. nov., sp. nov.; Atlanticothrix silvestris gen. nov., sp. nov.; and Dendronalium phyllosphericum gen. nov., sp. nov., which are herein described according to the rules of the International Code of Nomenclature for algae, fungi and plants. This finding highlights the great importance of tropical and equatorial South American ecosystems for harbouring an unknown microbial diversity in the face of the anthropogenic threats with which they increasingly struggle.

Influence of Abiotic Factors on the Growth of Cyanobacteria Isolated from Nakdong River, South Korea1

Changes in physico-chemical factors due to natural climate variability and eutrophication could affect the cyanobacterial growth patterns in aquatic systems that may cause environmental health problems. Based on morphological and 16S rRNA gene analysis, three cyanobacterial species isolated for the first time from the Nakdong River water sample in South Korea were identified as Amazoninema brasiliense, Microcystis elabens, and Nododsilinea nodulosa. The variations in temperature, pH, nitrogen, or phosphorus levels significantly impacted the cyanobacterial growth patterns. The optimal temperature range for the growth of isolates was from 25-30°C. A neutral or weak alkaline environment favored growth; however, A. brasiliense resulted in 44.2-87.5% higher biomass (0.75 g · L^-1 as dry solids, DS) and growth rate (0.24 · d^-1 ) at pH 7 than the other isolates (0.4-0.52 g DS · L^-1 , 0.16-0.19 · d^-1 ). The increased nitrate-nitrogen (NO₃ -N) concentrations significantly (P < 0.05) favored biomass production and growth rate for A. brasiliense and M. elabens, respectively, and the maximum growth rate was observed for A. brasiliense at 3.5 mg NO₃ -N · L^-1 . The orthophosphate concentration (PO₄ -P) from 0.1 to 0.5 mg PO₄ -P · L^-1 increased the growth of the isolates. These observations suggest that isolate growth rates in water bodies can vary depending on different physico-chemical parameters. This study contributes to the further understanding of the growth of microalgae in natural freshwater bodies under fluctuating environmental conditions and aquatic ecosystem stability.

Dereplication of Natural Products with Antimicrobial and Anticancer Activity from Brazilian Cyanobacteria

Cyanobacteria are photosynthetic organisms that produce a large diversity of natural products with interesting bioactivities for biotechnological and pharmaceutical applications. Cyanobacterial extracts exhibit toxicity towards other microorganisms and cancer cells and, therefore, represent a source of potentially novel natural products for drug discovery. We tested 62 cyanobacterial strains isolated from various Brazilian biomes for antileukemic and antimicrobial activities. Extracts from 39 strains induced selective apoptosis in acute myeloid leukemia (AML) cancer cell lines. Five of these extracts also exhibited antifungal and antibacterial activities. Chemical and dereplication analyses revealed the production of nine known natural products. Natural products possibly responsible for the observed bioactivities and five unknown, chemically related chlorinated compounds present only in Brazilian cyanobacteria were illustrated in a molecular network. Our results provide new information on the vast biosynthetic potential of cyanobacteria isolated from Brazilian environments.

Physiological and thylakoid ultrastructural changes in cyanobacteria in response to toxic manganese concentrations

In this study, two cyanobacterial strains (morphologically identified as Microcystis novacekii BA005 and Nostoc paludosum BA033) were exposed to different Mn concentrations: 7.0, 10.5, 15.7, 23.6 and 35.4 mg L^-1 for BA005; and 15.0, 22.5, 33.7, 50.6, and 76.0 mg L^-1 for BA033. Manganese toxicity was assessed by growth rate inhibition (EC₅₀), chlorophyll a content, quantification of Mn accumulation in biomass and monitoring morphological and ultrastructural effects. The Mn EC₅₀ values were 16 mg L^-1 for BA005 and 39 mg L^-1 for BA033, respectively. Reduction of chlorophyll a contents and ultrastructural changes were observed in cells exposed to Mn concentrations greater than 23.6 and 33.7 mg L^-1 for BA005 and BA033. Damage to intrathylakoid spaces, increased amounts of polyphosphate granules and an increased number of carboxysomes were observed in both strains. In the context of the potential application of these strains in bioremediation approaches, BA005 was able to remove Mn almost completely from aqueous medium after 96 h exposure to an initial concentration of 10.5 mg L^-1, and BA033 was capable of removing 38% when exposed to initial Mn concentration of 22.5 mg L^-1. Our data shed light on how these cyanobacterial strains respond to Mn stress, as well as supporting their utility as organisms for monitoring Mn toxicity in industrial wastes and potential bioremediation application.

Cyanobacterial diversity in mat sample obtained from hypersaline desert, Rann of Kachchh

Rann of Kachchh (RoK) is a unique geoformation, which is exposed to dynamic environmental changes such as salinity, temperature, and nutrients throughout the year. In this study, the pooled mat sample was examined for the cyanobacterial community structure using culture-dependent and culture-independent approaches. Taxonomic profiling was studied using amplicon sequencing that revealed the enrichment of Pseudanabaenales and Oscillatoriales by QIIME and MG-RAST, respectively. Other abundant orders were represented by Chroococcales, Nostocales, and unclassified cyanobacteria by both approaches. Nine cyanobacterial cultures were isolated from mat samples showing 90-98% similarities with available sequences in GenBank. The culture-dependent study suggested that mat was dominated by cyanobacterial orders such as Oscillatoriales-filamentous and Chroococcales-unicellular. Our results from the culture-dependent approach also indicated that despite high similarities in gene sequences, six cyanobacteria fall into the separate clade in the phylogenetic analysis that could be signs of evolution due to an extreme environment. Cultured isolates are correlated well with abundant taxa from amplicon sequencing. Further, protein profiling was done specifically for phycobiliproteins which will be helpful to elucidate their roles in light harvesting and energy transfer mechanism in the unique environment of RoK.

Optimization of Light Intensity and NaNO3 Concentration in Amazon Cyanobacteria Cultivation to Produce Biodiesel

The objective of this study, for the first time, was to optimize Amazonian cyanobacterial culture conditions for improving cell productivity and lipid content, by analyzing the effect of light intensity and nitrogen concentration, for empirically evaluating biodiesel quality parameters. The strains Synechocystis sp. CACIAM05, Microcystis aeruginosa CACIAM08, Pantanalinema rosaneae CACIAM18, and Limnothrix sp. CACIAM25, were previously identified by morphological and molecular analysis (16S rRNA) and were selected based on their production of chlorophyll a and dry cell weight. Then, factorial planning (2²) with central points was applied, with light intensity and NaNO₃ concentration as independent variables. As response variables, cell productivity and lipid content were determined. Statistical analysis indicated that for all strains, the independent variables were statistically significant for cell productivity. Analysis of the fatty acid composition demonstrated diversity in the composition of the fatty acid profile from the experimental planning assays of each strain. The Biodiesel Analyzer software predicted the biodiesel quality parameters. CACIAM05 and CACIAM25 obtained better parameters with low levels of light intensity and NaNO₃ concentration, whereas CACIAM08 and CACIAM18 obtained better parameters with low NaNO₃ concentrations and high luminous intensity.

An efficient method for DNA extraction from cyanobacteria isolated from hypersaline and marine environments

Cyanobacteria are ancient organisms surviving on the earth due to their simple nutritional requirements and ability to produce distinct secondary metabolites that can combat detrimental environmental impacts. In order to understand these abilities of cyanobacteria at the molecular level, it is necessary to extract high-quality genomic DNA. However, the presence of secondary metabolites and exopolysaccharides hinders the DNA extraction from these organisms, especially from hypersaline environments. Here we have developed and compared a new method with two known methods of DNA extraction from environmental isolates. The results clearly indicate that the new optimized method yielded large amount of DNA with high purity. Additionally, the extracted DNA showed reduced degradation and excellent overall quality, which can be used directly for downstream purposes such as PCR and sequencing.

Genomic Features for Desiccation Tolerance and Sugar Biosynthesis in the Extremophile Gloeocapsopsis sp. UTEX B3054

For tolerating extreme desiccation, cyanobacteria are known to produce both compatible solutes at intracellular level and a copious amount of exopolysaccharides as a protective coat. However, these molecules make cyanobacterial cells refractory to a broad spectrum of cell disruption methods, hindering genome sequencing, and molecular studies. In fact, few genomes are already available from cyanobacteria from extremely desiccated environments such as deserts. In this work, we report the 5.4 Mbp draft genome (with 100% of completeness in 105 contigs) of Gloeocapsopsis sp. UTEX B3054 (subsection I; Order Chroococcales), a cultivable sugar-rich and hardly breakable hypolithic cyanobacterium from the Atacama Desert. Our in silico analyses focused on genomic features related to sugar-biosynthesis and adaptation to dryness. Among other findings, screening of Gloeocapsopsis genome revealed a unique genetic potential related to the biosynthesis and regulation of compatible solutes and polysaccharides. For instance, our findings showed for the first time a novel genomic arrangement exclusive of Chroococcaceae cyanobacteria associated with the recycling of trehalose, a compatible solute involved in desiccation tolerance. Additionally, we performed a comparative genome survey and analyses to entirely predict the highly diverse pool of glycosyltransferases enzymes, key players in polysaccharide biosynthesis and the formation of a protective coat to dryness. We expect that this work will set the fundamental genomic framework for further research on microbial tolerance to desiccation and to a wide range of other extreme environmental conditions. The study of microorganisms like Gloeocapsopsis sp. UTEX B3054 will contribute to expand our limited understanding regarding water optimization and molecular mechanisms allowing extremophiles to thrive in xeric environments such as the Atacama Desert.

Kryptousia macronema gen. nov., sp. nov. and Kryptousia microlepis sp. nov., nostocalean cyanobacteria isolated from phyllospheres

Tropical ecosystems worldwide host very diverse microbial communities, but are increasingly threatened by deforestation and climate change. Thus, characterization of biodiversity in these environments, and especially of microbial communities that show unique adaptations to their habitats, is a very urgent matter. Information about representatives of the phylum Cyanobacteria in tropical environments is scarce, even though they are fundamental primary producers that help other microbes to thrive in nutrient-depleted habitats, including phyllospheres. In order to increase our knowledge of cyanobacterial diversity, a study was conducted to characterize isolates from Avicennia schaueriana and Merostachys neesii leaves collected at a mangrove and an Atlantic forest reserve located at the littoral of São Paulo state, south-east Brazil. The morphological, ultrastructural, phylogenetic, molecular and ecological features of the strains led to the recognition of the new genus Kryptousia, comprising two new species, Kryptousiamacronema gen. nov., sp. nov. and Kryptousiamicrolepis sp. nov., described here according to the International Code of Nomenclature for algae, fungi and plants. The new genus and species were classified in the nostocalean family Tolypotrichaceae. This finding advances knowledge on the microbial diversity of South American ecosystems and sheds further light on the systematics of cyanobacteria.

Light influences cytokinin biosynthesis and sensing in Nostoc (cyanobacteria)

Cytokinins are an important group of plant hormones that are also found in other organisms, including cyanobacteria. While various aspects of cytokinin function and metabolism are well understood in plants, the information is limited for cyanobacteria. In this study, we first experimentally confirmed a prenylation of tRNA by recombinant isopentenyl transferase NoIPT2 from Nostoc sp. PCC 7120, whose encoding gene we previously identified in Nostoc genome along with the gene for adenylate isopentenyl transferase NoIPT1. In contrast to NoIPT2, the transcription of NoIPT1 was strongly activated during the dark period and was followed by an increase in the cytokinin content several hours later in the light period. Dominant cytokinin metabolites detected at all time points were free bases and monophosphates of isopentenyladenine and cis-zeatin, while N-glucosides were not detected at all. Whole transcriptome differential expression analysis of cultures of the above Nostoc strain treated by cytokinin compared to untreated controls indicated that cytokinin together with light trigger expression of several genes related to signal transduction, including two-component sensor histidine kinases and two-component hybrid sensors and regulators. One of the affected histidine kinases with a cyclase/histidine kinase-associated sensory extracellular domain similar to the cytokinin-binding domain in plant cytokinin receptors was able to modestly bind isopentenyladenine. The data show that the genetic disposition allows Nostoc not only to produce free cytokinins and prenylate tRNA but also modulate the cytokinin biosynthesis in response to light, triggering complex changes in sensing and regulation.

Biochemical Characterization of Putative Adenylate Dimethylallyltransferase and Cytokinin Dehydrogenase from Nostoc sp. PCC 7120

Cytokinins, a class of phytohormones, are adenine derivatives common to many different organisms. In plants, these play a crucial role as regulators of plant development and the reaction to abiotic and biotic stress. Key enzymes in the cytokinin synthesis and degradation in modern land plants are the isopentyl transferases and the cytokinin dehydrogenases, respectively. Their encoding genes have been probably introduced into the plant lineage during the primary endosymbiosis. To shed light on the evolution of these proteins, the genes homologous to plant adenylate isopentenyl transferase and cytokinin dehydrogenase were amplified from the genomic DNA of cyanobacterium Nostoc sp. PCC 7120 and expressed in Escherichia coli. The putative isopentenyl transferase was shown to be functional in a biochemical assay. In contrast, no enzymatic activity was detected for the putative cytokinin dehydrogenase, even though the principal domains necessary for its function are present. Several mutant variants, in which conserved amino acids in land plant cytokinin dehydrogenases had been restored, were inactive. A combination of experimental data with phylogenetic analysis indicates that adenylate-type isopentenyl transferases might have evolved several times independently. While the Nostoc genome contains a gene coding for protein with characteristics of cytokinin dehydrogenase, the organism is not able to break down cytokinins in the way shown for land plants.

Halotia gen. nov., a phylogenetically and physiologically coherent cyanobacterial genus isolated from marine coastal environments

Nostoc is a common and well-studied genus of cyanobacteria and, according to molecular phylogeny, is a polyphyletic group. Therefore, revisions of this genus are urged in an attempt to clarify its taxonomy. Novel strains isolated from underexplored environments and assigned morphologically to the genus Nostoc are not genetically related to the ‘true Nostoc’ group. In this study, four strains isolated from biofilms collected in Antarctica and five strains originated from Brazilian mangroves were evaluated. Despite their morphological similarities to other morphotypes of Nostoc , these nine strains differed from other morphotypes in ecological, physiological and genetic aspects. Based on the phylogeny of the 16S rRNA gene, the Antarctic sequences were grouped together with the sequences of the Brazilian mangrove isolates and Nostoc sp. Mollenhauer 1 : 1-067 in a well-supported cluster (74 % bootstrap value, maximum-likelihood). This novel cluster was separated phylogenetically from the ‘true Nostoc’ clade and from the clades of the morphologically similar genera Mojavia and Desmonostoc. The 16S rRNA gene sequences generated in this study exhibited 96 % similarity to sequences from the nostocacean genera mentioned above. Physiologically, these nine strains showed the capacity to grow in a salinity range of 1–10 % NaCl, indicating their tolerance of saline conditions. These results provide support for the description of a new genus, named Halotia gen. nov., which is related morphologically to the genera Nostoc , Mojavia and Desmonostoc. Within this new genus, three novel species were recognized and described based on morphology and internal transcribed spacer secondary structures: Halotia branconii sp. nov., Halotia longispora sp. nov. and Halotia wernerae sp. nov., under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants.

Pantanalinema gen. nov. and Alkalinema gen. nov.: novel pseudanabaenacean genera (Cyanobacteria) isolated from saline–alkaline lakes

The genus Leptolyngbya Anagnostidis & Komárek (1988) was described from a set of strains identified as ‘LPP-group B’. The morphology within this group is not particularly informative and underestimates the group’s genetic diversity. In the present study, two new pseudanabaenacean genera related to Leptolyngbya morphotypes, Pantanalinema gen. nov. and Alkalinema gen. nov., are described under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants, based on a polyphasic approach. Pantanalinema gen. nov. (type species Pantanalinema rosaneae sp. nov.) has sheaths and trichomes with slight gliding motility, which distinguish this genus from Alkalinema gen. nov. (type species Alkalinema pantanalense sp. nov.), which possesses trichomes arranged in an ornate (interwoven) pattern. 16S rRNA gene sequences of strains of Pantanalinema and Alkalinema exhibited low identity to each other (≤91.6 %) and to other sequences from known pseudanabaenacean genera (≤94.3 and 93.7 %, respectively). In a phylogenetic reconstruction, six sequences from strains of Pantanalinema and four from strains of Alkalinema formed two separate and robust clades (99 % bootstrap value), with the genera Oculatella and Phormidesmis, respectively, as the closest related groups. 16S–23S rRNA intergenic spacer sequences and secondary structures of strains of Pantanalinema and Alkalinema did not correspond to any previous descriptions. The strains of Pantanalinema and Alkalinema were able to survive and produce biomass at a range of pH (pH 4–11) and were also able to alter the culture medium to pH values ranging from pH 8.4 to 9.9. These data indicate that cyanobacterial communities in underexplored environments, such as the Pantanal wetlands, are promising sources of novel taxa.

Nonheterocytous cyanobacteria from Brazilian saline-alkaline lakes

Saline-alkaline lakes are extreme environments that limit the establishment and development of life. The Nhecolândia, a subregion of the Pantanal wetland in Brazil, is characterized by the existence of ~500 saline-alkaline lakes, which support an underexplored and rich diversity of microorganisms. In this study, unicellular and homocytous cyanobacteria from five saline-alkaline lakes were accessed by culture-dependent approaches. Morphological evaluation and analyses of near complete sequences (~1400 nt) of the 16S rRNA genes were applied for phylogenetic and taxonomic placement. This polyphasic approach allowed for the determination of the taxonomic position of the isolated strains into the following genera: Cyanobacterium, Geminocystis, Phormidium, Leptolyngbya, Limnothrix, and Nodosilinea. In addition, fourteen Pseudanabaenales and Oscillatoriales representatives of putative novel taxa were found. These sequences fell into five new clades that could correspond to new generic units of the Pseudanabaenaceae and Phormidiaceae families.

The use of fosmid metagenomic libraries in preliminary screening for various biological activities

BACKGROUND

It is generally believed that there are many natural sources of as yet unknown bioactive compounds with a high biotechnological potential. However, the common method based on the use of cell extracts in the preliminary screening for particular molecules or activities is problematic as amounts of obtained compounds may be low, and such experiments are hardly reproducible. Therefore, the aim of this work was to test whether a novel strategy to search for previously unknown biological activities can be efficient. This strategy is based on construction of metagenomic libraries and employment of Escherichia coli strains as cell factories producing compounds of properties potentially useful in biotechnology.

RESULTS

Three cyanobacterial metagenomic libraries were constructed in the fosmid system. The libraries were screened for various biological activities. Extracts from selected E. coli clones bearing constructs with fragments of cyanobacterial genomes revealed antimicrobial or anticancer activities. Interestingly, stimulation of growth of host bacteria bearing particular plasmids with certain cyanobacterial genes was detected, suggesting a potential possibility for improvement of E. coli cultivation during biotechnological production. The most interesting plasmids were sequenced, and putative mechanisms of biological effects caused by cyanobacterial gene products are discussed.

CONCLUSIONS

The strategy of exploring cyanobacteria as sources of bioactive compounds, based on E. coli cell factories producing compounds due to expression of genes from metagenomic libraries, appears to be effective.

Sequestration of CO2 by halotolerant algae

The potential of halotolerant algae isolated from natural resources was used to study CO2 fixation and algal lipid production. Biological fixation of CO2 in photobioreactor in presence of salinity is exploited. The CO2 concentration 1060 ppm gave the highest biomass yield (700 mg dry wt/l), the highest total lipid content (10.33%) with 80% of CO2 removal.

Phylogeny of culturable cyanobacteria from Brazilian mangroves

The cyanobacterial community from Brazilian mangrove ecosystems was examined using a culture-dependent method. Fifty cyanobacterial strains were isolated from soil, water and periphytic samples collected from Cardoso Island and Bertioga mangroves using specific cyanobacterial culture media. Unicellular, homocytous and heterocytous morphotypes were recovered, representing five orders, seven families and eight genera (Synechococcus, Cyanobium, Cyanobacterium, Chlorogloea, Leptolyngbya, Phormidium, Nostoc and Microchaete). All of these novel mangrove strains had their 16S rRNA gene sequenced and BLAST analysis revealed sequence identities ranging from 92.5 to 99.7% when they were compared with other strains available in GenBank. The results showed a high variability of the 16S rRNA gene sequences among the genotypes that was not associated with the morphologies observed. Phylogenetic analyses showed several branches formed exclusively by some of these novel 16S rRNA gene sequences. BLAST and phylogeny analyses allowed for the identification of Nodosilinea and Oxynema strains, genera already known to exhibit poor morphological diacritic traits. In addition, several Nostoc and Leptolyngbya morphotypes of the mangrove strains may represent new generic entities, as they were distantly affiliated with true genera clades. The presence of non-ribosomal peptide synthetase, polyketide synthase, microcystin and saxitoxin genes were detected in 20.5%, 100%, 37.5% and 33.3%, respectively, of the 44 tested isolates. A total of 134 organic extracts obtained from 44 strains were tested against microorganisms, and 26% of the extracts showed some antimicrobial activity. This is the first polyphasic study of cultured cyanobacteria from Brazilian mangrove ecosystems using morphological, genetic and biological approaches.

Characterization of freshwater benthic biofilm-forming Hydrocoryne (Cyanobacteria) isolates from Antarctica

The aims of this work were to study cyanobacterial isolates resembling the genus Hydrocoryne using a combination of morphology and phylogeny of 16S rRNA and nifH sequences and to investigate genes involved in cyanotoxin and protease inhibitor production. Four new cyanobacterial strains, isolated from biofilm samples collected from King George Island, Antarctica, were studied. In terms of morphology, these new strains share traits similar to true Anabaena morphotypes (benthic ones), whereas phylogenetic analysis of their 16S rRNA gene sequences grouped them with the sequence of the type species Hydrocoryne spongiosa (H. Schwabe ex Bornet and Flahault 1886-1888), but not with sequences of the type species from the genus Anabaena. This cluster is the sister group of Anabaena morphotypes isolated only from the Gulf of Finland. In addition, this cluster is related to two other clusters formed by sequences of Anabaena isolated from different sites. Partial nifH genes were sequenced from two strains and the phylogenetic tree revealed that the Antarctic nifH sequences clustered with sequences from Anabaena. Furthermore, two strains were tested, using PCR with specific primers, for the presence of genes involved in cyanotoxins (microcystin and saxitoxin) and protease inhibitor (aeruginosin, and cyanopeptolin). Only cyanopeptolin was amplified using PCR. These four Hydrocoryne strains are the first to be isolated and sequenced from Antarctica, which improves our knowledge on this poorly defined cyanobacterial genus.

Cylindrospermopsin and saxitoxin synthetase genes in Cylindrospermopsis raciborskii strains from Brazilian freshwater

The Cylindrospermopsis raciborskii population from Brazilian freshwater is known to produce saxitoxin derivatives (STX), while cylindrospermopsin (CYN), which is commonly detected in isolates from Australia and Asia continents, has thus far not been detected in South American strains. However, during the investigation for the presence of cyrA, cyrB, cyrC and cyrJ CYN synthetase genes in the genomes of four laboratory-cultured C. raciborskii Brazilian strains, the almost complete cyrA gene sequences were obtained for all strains, while cyrB and cyrC gene fragments were observed in two strains. These nucleotide sequences were translated into amino acids, and the predicted protein functions and domains confirmed their identity as CYN synthetase genes. Attempts to PCR amplify cyrJ gene fragments from the four strains were unsuccessful. Phylogenetic analysis grouped the nucleotide sequences together with their homologues found in known CYN synthetase clusters of C. raciborskii strains with high bootstrap support. In addition, fragments of sxtA, sxtB and sxtI genes involved in STX production were also obtained. Extensive LC-MS analyses were unable to detect CYN in the cultured strains, whereas the production of STX and its analogues was confirmed in CENA302, CENA305 and T3. To our knowledge, this is the first study reporting the presence of cyr genes in South American strains of C. raciborskii and the presence of sxt and cyr genes in a single C. raciborskii strain. This discovery suggests a shift in the type of cyanotoxin production over time of South American strains of C. raciborskii and contributes to the reconstruction of the evolutionary history and diversification of cyanobacterial toxins.

Metabolic regulation and chromosomal localization of carbaryl degradation pathway in Pseudomonas sp. strains C4, C5 and C6

Pseudomonas sp. strains C4, C5 and C6 degrade carbaryl (1-naphthyl N-methylcarbamate) via 1-naphthol, 1,2-dihydroxynaphthalene, salicylate and gentisate. Carbon source-dependent metabolic studies suggest that enzymes responsible for carbaryl degradation are probably organized into 'upper' (carbaryl to salicylate), 'middle' (salicylate to gentisate) and 'lower' (gentisate to TCA cycle) pathway. Carbaryl and 1-naphthol were found to induce all carbaryl pathway enzymes, while salicylate and gentisate induce middle and lower pathway enzymes. The strains were found to harbor plasmid(s), and carbaryl degradation property was found to be stable. Genes encoding enzymes of the degradative pathway such as 1-naphthol 2-hydroxylase, salicylaldehyde dehydrogenase, salicylate 5-hydroxylase and gentisate 1,2-dioxygenase were amplified from chromosomal DNA of these strains. The gene-specific PCR products were sequenced from strain C6, and phylogenetic tree was constructed. Southern hybridization and PCR analysis using gel eluted DNA as template supported the presence of pathway genes onto the chromosome and not on the plasmid(s).

Toxopsis calypsus gen. nov., sp. nov. (Cyanobacteria, Nostocales) from cave ‘Francthi’, Peloponnese, Greece: a morphological and molecular evaluation

Representatives of a new cyanobacterial genus, Toxopsis Lamprinou & Pantazidou gen. nov., were found in fresh material from Cave ‘Francthi’ (Peloponnese, Greece) and isolated in cultures. Ecological data relating to the environmental parameters of the sampling sites are provided, such as the photosynthetically active radiation (PAR), temperature and relative humidity. Morphological characteristics and the life cycle of the type species Toxopsis calypsus Lamprinou & Pantazidou sp. nov. were studied using light microscopy and scanning and transmission microscopy. Molecular analysis based on the 16S rRNA gene sequence was also conducted. Toxopsis calypsus sp. nov. is a false-branched nostocalean cyanobacterium with both isopolar and heteropolar filaments bearing mono-pored and bi-pored heterocysts, and also hormogonia and akinetes. Isopolar filaments adhere by the centre to the substrate and are found mainly in fresh material and in young cultures; heteropolar filaments bearing a basic mono-pore heterocyst are dominant in aged (more than one-year-old) cultures. According to the revised taxonomic classification system of Komárek & Anagnostidis (1989) [Komárek, J. & Anagnostidis, K. (1989). Algol Stud, 56, 247–345] based mainly on morphological data, the new genus described here shares morphological characters with both nostocalean families Scytonemataceae and Microchaetaceae, showing similarities in particular to Scytonematopsis contorta [Vaccarino, M. A. & Johansen, J. R. (2011). Fottea 11, 149–161], Microchaetaceae. Molecular data from the 16S rRNA sequence determined in this paper showed that Toxopsis calypsus sp. nov. is more related to the family Microchaetaceae, and the five phylotypes analysed by PCR showed that the closest nostocalean relatives are Tolypothrix distorta SAG 93.79 (GenBank accession no. GQ287651) and Coleodesmium sp. ANT.L52B.5 (AY493596) with 95–96 % and 96 % similarity, respectively. In contrast, the five phylotypes showed a distant similarity to Scytonematopsis contorta (<91 %). The phenotypic and genetic traits strongly supported the classification of the five phylotypes as a new taxon for which the name Toxopsis calypsus Lamprinou & Pantazidou gen. nov., sp. nov. is proposed.

l-Asparaginase Production by Moderate Halophilic Bacteria Isolated from Maharloo Salt Lake

l-Asparaginase is an anti-neoplastic drug used in lymphoblastic leukemia chemotherapy. Nowadays, this enzyme derived from bacterial sources, mostly l-asparaginase II from Escherichia coli and in lesser amount l-asparaginase of Erwinia sp. has medical utilization. The long-term usage of these agents leads to allergic reactions and new asparaginase with new immunological characteristics is required. Halophilic bacteria might contain l-asparaginase with novel immunological properties that can be used in hypersensitive patients. In this experiment, we have screened moderate Halophilic bacteria for l-asparaginase production ability and showed that Halophilic bacteria produce intra- and extracellular l-asparaginase. Bacillus sp. BCCS 034 was found to produce the highest l-asparaginase (1.64 IU/ml supernatant) extracellularly.

A method for rapid isolation of total RNA of high purity and yield from Arthrospira platensis

Arthrospira (Spirulina) platensis is widely used as a food supplement and has been an economically important species for centuries. However, the genetic aspect of studies of this particular organism has always been neglected, mainly because of the nonavailability of suitable methods for isolation of nucleic acids and the difficulties faced during further manipulations. Although total RNA has been isolated using commercially available kits, we present a method optimized to obtain DNA-free total RNA of higher yields and higher purity in less time than is required by other methods (<2 h). It involves hot phenol - chloroform - IAA extraction using an aqueous to organic phase ratio of 1:2 followed by lithium chloride precipitation and 70% ethanol wash. This method, optimized for the cyanobacterium Arthrospira (Spirulina) platensis, eliminates the need for DNase treatment and produces high-quality RNA, as validated by bioanalyzer, RT-PCR, and cloning. With the recent release of the Arthrospira genome, the current method will be of great value for carrying out high-throughput studies like microarray and real-time PCR.

An efficient DNA isolation protocol for filamentous cyanobacteria of the genus Arthrospira

Thanks to their photosynthetic and nutritive properties, cyanobacteria of the Arthrospira genus are of interest as food supplements, as efficient oxygen producing life support system organisms for manned space flight, and for the production of biofuels. Despite these potential valuable applications, full genome sequences and genetic information in general on Arthrospira remain scarce. This is mainly due to the difficulty to extract sufficient high molecular weight nucleic acids from these filamentous cyanobacteria. In this article, an efficient and reproducible DNA extraction procedure for cyanobacteria of the genus Arthrospira was developed. The method is based on the combination of a soft mechanical lysis with enzymatic disruption of the cell wall. The comparison with other extraction protocols clearly indicates that this optimised method allows the recovery of a larger amount of DNA. Furthermore, the extracted DNA presents a high molecular weight, a reduced degradation and an excellent overall quality. It can be directly used for molecular biology purposes such as PCR, and clone library construction.

IMPROVED METHODS FOR THE ISOLATION OF CYANOBACTERIAL DNA FROM ENVIRONMENTAL SAMPLES(1)

DNA isolated from environmental samples often contains enzyme inhibitors disruptive to downstream molecular applications. Most of the existing methods of cyanobacterial DNA isolation do not effectively eliminate these inhibitors from sediment samples or cells collected from freshwater ecosystems. We describe improved methods based on the xanthogenate-SDS nucleic acid isolation (XS) method of Tillett and Neilan (2000). Our improved methods provided high-quality cyanobacterial DNA that could be amplified in PCR and digested with a restriction enzyme. Results were superior to several commercial kits. The DNA yield was also similar to that obtained via the standard XS method. These methods should provide valuable new tools for the expanded application of molecular genetics to limnological and oceanographic research.

A NOVEL EPIPHYTIC CYANOBACTERIAL SPECIES FROM THE GENUS BRASILONEMA CAUSING DAMAGE TO EUCALYPTUS LEAVES(1)

A cyanobacterial mat colonizing the leaves of Eucalyptus grandis was determined to be responsible for serious damage affecting the growth and development of whole plants under the clonal hybrid nursery conditions. The dominant cyanobacterial species was isolated in BG-11 medium lacking a source of combined nitrogen and identified by cell morphology characters and molecular phylogenetic analysis (16S rRNA gene and cpcBA-IGS sequences). The isolated strain represents a novel species of the genus Brasilonema and is designated Brasilonema octagenarum strain UFV-E1. Thin sections of E. grandis leaves analyzed by light and electron microscopy showed that the B. octagenarum UFV-E1 filaments penetrate into the leaf mesophyll. The depth of infection and the mechanism by which the cyanobacterium invades leaf tissue were not determined. A major consequence of colonization by this cyanobacterium is a reduction in photosynthesis in the host since the cyanobacterial mats decrease the amount of light incident on leaf surfaces. Moreover, the cyanobacteria also interfere with stomatal gas exchange, decreasing CO2 assimilation. To our knowledge, this is the first report of an epiphytic cyanobacterial species causing damage to E. grandis leaves.

Characterization of nitrogen-fixing cyanobacteria in the Brazilian Amazon floodplain

The diversity of the free-living nitrogen-fixing cyanobacterial community in the floodplain sediments along the Solimões and Amazon Rivers and some of their tributaries (Japurá, Negro and Madeira) was investigated. Five cyanobacterial genera were morphologically identified, four of which (Nostoc, Calothrix, Cylindrospermum and Fischerella) have not previously been isolated from the Brazilian Amazon floodplain. Nostoc strains were the most commonly found heterocyst-forming cyanobacteria. Five strains (N. muscorum CENA18 and CENA61, N. piscinale CENA21, Cylindrospermum sp. CENA33 and Fischerella sp. CENA19) were selected for growth measurement, ability to fix N2 and phylogenetic analysis, based on their widespread distribution and morphological distinction. Molecular analyses employing 16S rRNA sequences indicated that some of the isolates may represent novel cyanobacterial species. Dinitrogen fixed by these strains was measured indirectly as acetylene reduction activity and ranged from 11.5 to 22.2 nmol C2H4 microg Chl a(-1) h(-1). These results provide evidence of widespread and importance of nitrogen-fixing cyanobacteria as a source of N inputs in the Amazonian ecosystem.

Characterization and transcriptional analysis of hupSLW in Gloeothece sp. ATCC 27152: an uptake hydrogenase from a unicellular cyanobacterium

The structural genes (hupSL) encoding an uptake hydrogenase in the unicellular cyanobacterium Gloeothece sp. ATCC 27152, a strain capable of aerobic N(2) fixation, were identified and sequenced. 3'-RACE experiments uncovered the presence of an additional ORF 184 bp downstream of hupL, showing a high degree of sequence identity with a gene encoding an uptake-hydrogenase-specific endopeptidase (hupW) in other cyanobacteria. In addition, the transcription start point was identified 238 bp upstream of the hupS translational start. RT-PCR experiments revealed that hupW is co-transcribed with the uptake hydrogenase structural genes in Gloeothece sp. ATCC 27152. In addition, Northern hybridizations clearly showed that hupSLW are transcribed under nitrogen fixing conditions, but not in the presence of combined nitrogen. A putative NtcA binding site was identified in the promoter region upstream of hupS, centred at -41.5 bp with respect to the transcription start point. Electrophoretic retardation of a labelled DNA fragment (harbouring the putative NtcA-binding motif) was significantly affected by an Escherichia coli cell-free extract containing overexpressed NtcA, suggesting that NtcA is involved in the transcriptional regulation of hupSLW.