Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection

Cyanobacterial diversity held in microbial biological resource centers as a biotechnological... Cyanobacteria are a well-known source of bioproducts which renders culturable strains a valuable resource for biotechnology purposes. We describe here the establishment of a cyanobacterial culture collection (CC) and present the first version of the strain catalog and its online database (http://lege.ciimar.up.pt/). The LEGE CC holds 386 strains, mainly collected in coastal (48%), estuarine (11%), and fresh (34%) water bodies, for the most part from Portugal (84%). By following the most recent taxonomic classification, LEGE CC strains were classified into at least 46 genera from six orders (41% belong to the Synechococcales), several of them are unique among the phylogenetic diversity of the cyanobacteria. For all strains, primary data were obtained and secondary data were surveyed and reviewed, which can be reached through the strain sheets either in the catalog or in the online database. An overview on the notable biodiversity of LEGE CC strains is showcased, including a searchable phylogenetic tree and images for all strains. With this work, 80% of the LEGE CC strains have now their 16S rRNA gene sequences deposited in GenBank. Also, based in primary data, it is demonstrated that several LEGE CC strains are a promising source of extracellular polymeric substances (EPS). Through a review of previously published data, it is exposed that LEGE CC strains have the potential or actual capacity to produce a variety of biotechnologically interesting compounds, including common cyanotoxins or unprecedented bioactive molecules. Phylogenetic diversity of LEGE CC strains does not entirely reflect chemodiversity. Further bioprospecting should, therefore, account for strain specificity of the valuable cyanobacterial holdings of LEGE CC. Vitor Ramos, João Morais, and Raquel Castelo-Branco contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10811-017-1369-y) contains supplementary material, which is available to authorized users. * Vitor M. Vasconcelos ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade vmvascon@fc.up.pt do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal Interdisciplinary Centre of Marine and Environmental Research Master 2 Biotechnologie, Université de Bretagne-Sud, BP 92116, (CIIMAR/CIMAR), Terminal de Cruzeiros do Porto de Leixões, 56000 Lorient/Vannes, France University of Porto, 4450-208 Matosinhos, Portugal 2 Laboratory of Algae Cultivation and Bioprospection, Federal Amapá Faculdade de Ciências, Universidade do Porto, Rua do Campo University (UNIFAP), Rodovia JK, km 2, Macapá, Amapá, Brazil Alegre, Edifício FC4, 4169-007 Porto, Portugal Health and Environment Research Centre, School of Health, Nanotechnology and Functional Materials, Department of Polytechnic Institute of Porto, Rua Dr. António Bernardino de Engineering Sciences, Uppsala University, Box 534, 751 Almeida, 400, 4200-072 Porto, Portugal 21 Uppsala, Sweden 4 9 IPMA-Portuguese Institute of Sea and Atmosphere, Rua Alfredo Alpha Environmental Solutions, P.O. Box 37977, Dubai, United Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal Arab Emirates 1438 J Appl Phycol (2018) 30:1437–1451 . . . . . Keywords Cyanobacteria Strains Biodiversity Chemodiversity Culture collection Biological resource centers Introduction by revealing (4) their phylogenetic diversity. Cyanobacterial strains in LEGE CC were (re-)identified using an approach com- Microbial biological resource centers (mBRCs) are quality- bining morphological and phylogenetic data, as recommended managed culture collections that ensure the ex situ preservation by Komárek (2016), which confers added value to the collection. of microorganisms, while providing public access to their mi- Likewise, based on some novel and existing data, we reviewed crobial diversity (i.e., to live strains or to genomic DNA from (5) biotechnologically relevant information from the strains, and these strains), to relevant data related to it (e.g., taxonomic iden- make some (6) considerations on the relation between biodiver- sity and chemodiversity for the discovery of natural compounds tification, culture conditions, ecophysiological features, etc.), and also to expertise services such as training or consulting from cyanobacterial strains. Altogether, the disclosed data from (Antunes et al. 2016). mBRCs are pivotal in underpinning the the strains makes LEGE CC a valuable resource for further bioeconomy derived from microbial resources (Smith et al. bioprospecting, toxicological, and/or taxonomic studies. 2014). In this particular case, cyanobacteria have been pointed out in the past few decades as one of the most promising groups of microorganisms for the discovery of natural compounds with Materials and methods pharmacological and other biotechnological applications (Margesin and Schinner 2001;Abedetal. 2009; Singh et al. Strain codes for all strains at BBE were standardized by using the 2011; Wijffels et al. 2013). For oncology drugs only, the phar- acronym LEGE followed by a five-digit number. The workflow maceutical value of the estimated marine cyanobacteria diversity followed during the establishment of the culture collection is was evaluated in US$37.5–181.5 billion, in 2010 dollars (Erwin depicted in Fig. 1. The figure shows the processes and methods et al. 2010). One other relevant property of cyanobacteria with used for researching and collecting secondary data (e.g., infor- biotechnological interest is the production of extracellular poly- mation on secondary metabolite production; some nucleotide meric substances (EPSs) (Abed et al. 2009; Pereira et al. 2011). sequences) and for generating primary data from the strains The Blue Biotechnology and Ecotoxicology (BBE) group, at (e.g., morphometry, microphotographs, most of the 16S rRNA CIIMAR, Portugal, has recently undertaken a process of orga- gene sequences, and evaluation of EPS production). It also indi- nizing its cyanobacterial strains into a culture collection (acro- cates the main outputs of these processes, which are presented in nym LEGE). It began as an in-house collection in 1991, when a this study. number of strains from the colonial toxic cyanobacterium Microcystis aeruginosa were isolated from freshwater water bod- Literature and data survey ies in Portugal (Vasconcelos et al. 1995). Since then, a good number of strains have been isolated and assessed in ecotoxico- Eighty-three strains had been previously published using other logical studies or used for the discovery of biologically active strain names/codes or identifications. For that reason, all existing compounds, the main research lines of the group. As a conse- synonyms for a same strain were considered during the literature quence, a considerable body of research (e.g., Vasconcelos et al. search and data survey. Strain synonyms and references where 1995; Martins et al. 2005, 2013;Leãoetal. 2013b; Brito et al. they appear are provided in the catalog, in Online Resource 3. 2015) emphasizes that several strains now deposited at the LEGE Strains having any type of data on natural products were culture collection (CC) have the potential or actual capacity to recorded. produce a myriad of chemical compounds, including toxins or newly discovered bioactive molecules. Yet, most of the strains at Light microscopy and morphological characterization BBE were kept independently by their isolators along these years, and were poorly characterized, named inconsistently or Morphological characteristics of LEGE CC strains were exam- even unidentified. ined and microphotographed using a Leica DMLB light micro- For these reasons, a decision was made to characterize and scope coupled to a Leica ICC50 HD digital camera (Leica organize all the strains (and their associated data) at BBE, and Microsystems, Germany). Morphometric measurements were make publicly available this bioresource by establishing a culture then performed using the image analysis software Leica collection in accordance to the Organisation for Economic Co- Application Suite version 4.2.0 (Leica Microsystems). Strains operation and Development (OECD 2007) and World Federation were analyzed during the exponential phase of growth (i.e., 2- for culture collections (WFCC 2010) guidelines. In this work, we to 3-week old cultures, depending on the strain; culture condi- illustrate (1) the process followed to establish LEGE CC, and tions for each strain can be found in the catalog (Online Resource give an overview of the collection by presenting (2) the catalog 3). Each quantifiable morphological character was measured at of strains, (3) the online database (http://lege.ciimar.up.pt/), and least 20 times, along different positions of the slide preparation. J Appl Phycol (2018) 30:1437–1451 1439 Fig. 1 The workflow followed during the data gathering on the LEGE CC strains, the completed and expected outputs of the process and the planned updates (standard flowchart symbols were used). The LEGE CC website can be accessed at http://lege.ciimar.up.pt These include size of vegetative, specialized, or dormant cells, et al. 2008) were used for the amplification of a portion of and of filaments or colonies. the 16S rRNA gene. PCR reactions were performed in a final Additionally, to evaluate the production of EPSs by the volume of 20 μL containing 1× Green GoTaq Flexi Buffer, strains, early stationary-phase cultures (i.e., 3- to 5-week old 2.5 mM MgCl , 125.0 mM of each deoxynucleotide triphos- cultures, depending on the strain) were stained with 0.5% phate, 1.0 μM of each primer, 0.5 U of GoTaq Flexi DNA −1 Alcian Blue solutions (Sigma A-3157), prepared either in Polymerase (Promega, USA), 10 mg mL of bovine serum 50% ethanol (v/v)orin1%acetic acid(v/v) (Di Pippo et al. albumin (BSA), and 10–30 ng of template DNA, on a 2013). Cultures were also negatively stained using India ink TProfessional Standard thermal cycler (Biometra, Germany). (Micheletti et al. 2008). Images were acquired using the The PCR conditions were as follows: initial denaturation at abovementioned equipment and software. 94 °C for 4 min, followed by 35 cycles of denaturation at When relevant, other qualitative morphological features 94 °C for 30 s, annealing at 52 °C for 30 s, and extension at and distinguishing traits were recorded (e.g., the shape and 72 °C for 45 s, with a final extension step at 72 °C for 6 min. arrangement of cells or filaments, the color of the cultures, PCR products were separated with a 1.5% (w/v) agarose gel the presence or absence of sheaths, motility, the existence of stained with GelRed (Biotium, USA) and DNA fragments constrictions at the cross-wall of filaments, and the formation with the expected size were excised from the gel and purified of hormogonia and necridial cells). using the NucleoSpin Gel and PCR Clean-up Kit (Macherey- Nagel, Germany), according to the manufacturer’s instruc- DNA extraction, PCR, and sequencing tions. Sequences were obtained by either directly sequencing the purified amplicons at GATC Biotech (Germany) or after Cells were harvested from log-phase cultures, and total geno- cloning these into pGEM-T Easy vector (Promega, USA). In mic DNA (gDNA) of each strain was extracted using the the latter case, vectors containing inserts were then trans- commercial PureLink Genomic DNA Mini Kit (Invitrogen, formed into Escherichia coli TOP10 chemically competent USA), according the to the manufacturer’s instructions pro- cells (Invitrogen, San Diego, CA). Plasmid DNA was isolated vided for Gram-negative bacteria. The DNA integrity was using NZY Miniprep kit (NYZtech, Portugal) and sequenced confirmed with agarose gel electrophoresis using GelRed at GATC Biotech using M13 primers. All nucleotide se- (Biotium, USA) staining. Cyanobacteria-specific primers quences were manually inspected for quality and assembled for each strain using the Geneious (v8.1.8) software package CYA-106F and CYA-785R (Nübel et al. 1997; Muhling 1440 J Appl Phycol (2018) 30:1437–1451 (Biomatters Limited, New Zealand). Two hundred and standard identification keys were used for the twenty-four novel sequences associated with this study were morphological-based identification of the strains (Komárek deposited in the GenBank database under the accession num- and Anagnostidis 1998, 2005; Komárek 2013). Then, each bers KU951663–KU951886. strain identification was compared with its phylogenetic placement (namely, assessing if the LEGE strain is closely Phylogenetic analyses related to any Type strain) and with the recent taxonomic classification proposed by Komárek et al. (2014), at low Molecular-based analyses were conducted using the bioinfor- (i.e., genus) and high (i.e., order) taxonomic levels. If existing, matics software package MEGA7 (Kumar et al. 2016). Two taxonomic notes for a strain (e.g., incongruities between clas- phylogenetic analyses based on 16S rRNA gene sequences sification schemes) were added to the correspondent catalog were performed, one that reflects the overall cyanobacterial sheet (Online Resource 3). diversity present at LEGE CC and a second analysis that high- lights the connection between such biodiversity and its asso- ciated chemodiversity. In both cases, sequences were aligned Results and discussion using the ClustalW algorithm (Thompson et al. 1994) and phylogenies were inferred by using the Maximum Three hundred and eighty-six cyanobacterial strains are in- Likelihood (ML) method (Felsenstein 1981) based on the cluded in the first version of the catalog of LEGE CC (see General Time Reversible model (Rodriguez et al. 1990), Fig. 2 for a morphological overview). For each particular which was the nucleotide substitution model that best fitted strain, primary and secondary data collected in this study the alignments data as evaluated by the corrected Akaike (Fig. 1), such as species identification, origin, morphometric Information Criterion (Sugiura 1978). For both analyses also, information, morphological description, and ecophysiological a discrete Gamma distribution (+G) was used to model evo- properties of the strain, microphotographs, literature refer- lutionary rate differences among sites, while the rate variation ences, synonyms for the strain, accession numbers for se- model allowed for some sites to be evolutionarily invariable quences, etc., can be retrieved in the corresponding catalog (+I). In the first case, the analysis involved 457 nucleotide sheet (Online Resource 3) or be searched in the website data- sequences from LEGE CC strains and from relevant strains base of the culture collection at http://lege.ciimar.up.pt. included in CyanoType v.1 (see Ramos et al. 2017). These include: (1) Type strains (T) of Type species (i.e. LEGE CC conditions cyanobacterial strains that were used to describe a new genus); (2) strains known to have the same phylogenetic placement as The LEGE CC is hosted in a new building, with modern the Type species (t), when the sequence from the latter is not facilities at CIIMAR, Matosinhos, Portugal. It includes available; (3) Reference strains (R) from the Bergey’sManual cyanobacterial strains collected since 1991. LEGE CC strains −2 −1 of Systematic Bacteriology (Castenholz et al. 2001); and, (4) are normally kept at 10–30 μmol photons m s under 12/ strains known to be included in the same phylogenetic cluster 12 h or 14/10 h light/dark cycles. The range of controlled as the Reference strain (r), as mentioned in the Bergey’s temperature conditions at LEGE CC are 14, 19 (for most Manual (Castenholz et al. 2001). There were a total of 563 strains), and 25 °C. Strains are maintained by subculturing positions in the final dataset. The tree was rooted with the transfers (held every 6 months for most of the strains), but outgroup Chloroflexus aurantiacus J-10-fl (NR_074263). In soon, a stock comprising the full collection will be cryopre- the second case, the phylogenetic analysis involved 165 nu- served and stored at − 150 °C (some strains are cryopreserved cleotide sequences from LEGE CC strains only and there were at − 80 °C; see also Rastoll et al. 2013). Despite the fact that a total of 252 positions in the final dataset. axenicization of LEGE CC strains will be attempted in the future, currently, all are xenic, unicyanobacterial, and clonal. Strain identification General statistics of holdings By using data generated in this study, the taxonomic assign- ments of previously identified strains were reevaluated by an LEGE CC strains were isolated from samples mainly collected approach combining morphological and phylogenetic data. in Portugal (84%), including Madeira and Azores Islands. The most recent classification, recommendations and advice There are also strains from South (5%) and North (2%) for the identification of cyanobacteria (Komárek et al. 2014; America, Africa (3%), other European countries (1%), Dvořák et al. 2015; Komárek 2016) were followed, namely Oceania (1%), Antarctica (1%), and Asia (one strain). In rela- the adoption of a conservative approach (Dvořák et al. 2015; tion to the habitat, LEGE CC strains were mainly collected Komárek 2016). Previously unidentified strains were identi- from aquatic environments, including marine (46%), freshwa- fied following the same procedures and principles. First, ter (34%), brackish (11%), and hypersaline (2%) J Appl Phycol (2018) 30:1437–1451 1441 Fig. 2 Example of morphological diversity among cyanobacterial strains 07179; h Chroococcopsis sp. LEGE 07187; i Chroococcidiopsis sp. from LEGE CC. Strains belong to the orders: a–b Synechococcales, c–e LEGE 06174; j cf. Oxynema acuminatum LEGE 06072; k Phormidium Chroococcales, f Chroococcidiopsidales, g–i Pleurocapsales, j–l sp. LEGE 00064; l cf. Spirulina sp. LEGE 11439; m Rivularia sp. LEGE Oscillatoriales, and m–t Nostocales. Identifications are as follows: a 07159; n Calothrix sp. LEGE 06100; o Plectonema cf. radiosum LEGE Cyanobium sp. LEGE 06127; b Nodosilinea sp. LEGE 06069; c 06114; p Tolypothrix sp. LEGE 11397; q Nodularia sp. LEGE 06071; r Synechocystis salina LEGE 06099; d Microcystis aeruginosa LEGE Nostoc sp. LEGE 07365; s Dolichospermum flosaquae LEGE 04289, an 91094, a microcystin producer strain highly used in the literature (see anatoxin-a producer strain; t Cylindrospermopsis raciborskii LEGE also Fig. 3); e unidentified filamentous Chroococcales LEGE 11427; f 95046, a non-cylindrospermopsin producer often used in the literature Gloeocapsopsis crepidinum LEGE 06123; g Hyella patelloides LEGE (see also Fig. 3). Scale bars represent 10 μm environments, while some strains are of terrestrial origin (3%). the species level, 205 at the genus, while 70 strains remain Concerning taxonomy, LEGE CC strains are distributed by unidentified at the genus level. Of course, the ever-changing the orders Synechococcales (41%), Chroococcales (17%), nature of taxonomy causes identification to change over time, Nostocales (17%), Oscillatoriales (8%), Pleurocapsales and thus, these numbers are expected to change in the next (2%), and Chroococcidiopsidales (2%) (see also Fig. 3). versions of the catalog. Three-hundred and seven LEGE CC One-hundred and eleven LEGE CC strains are identified at strains (80% of the entire collection) have now their 16S 1442 J Appl Phycol (2018) 30:1437–1451 Fig. 3 Circular ML tree (− lnl = 25,944.6863) of 16S rRNA gene strains producing the following cyanotoxins, as demonstrated by analyt- sequences illustrating the phylogenetic diversity of LEGE CC strains ical chemistry methods: A anatoxin-a, e.g., Osswald et al. (2009); B (in gray), their placement at the order level, and some traits or BMAA (Cianca et al. 2012); C cylindrospermopsin, e.g., Saker and information relevant for biotechnological purposes. One hundred and Eaglesham (1999); and M microcystin, e.g., Vasconcelos et al. (1995). fifty-two sequences from reference material (Ramos et al. 2017)were Arrows point to strains used to isolate and elucidate the structure of the included to disclose the cyanobacterial BTree of Life^ (T or t stand for following secondary metabolites: 1 hierridin B (Leão et al. 2013b), 2 type strains designated as representing type species, R or r for reference portoamides (Leão et al. 2010), 3 bartolosides (Leão et al. 2015; strains sensu Bergey’s Manual (Castenholz et al. 2001); and G for ge- Afonso et al. 2016), and 4 dehydroabietic acid (Costa et al. 2016). nome sequences available; see also Material and methods section for Black stars indicate strains having (or soon will have) their genome se- details). Accession numbers for all sequences are shown. Only bootstrap quenced, and the white star stands for a strain that has a submitted patent support values over 50% are given. Black arrowheads indicate strains application. Black circles and numbers within refer to highly used strains capable of producing good amounts of EPSs. White arrowheads denote and to the number of times they appear in the literature, respectively rRNA gene sequences deposited in GenBank, which contrast Several LEGE CC strains have been used in academia, with the 110 (28%) sequences from LEGE CC strains that most of them in research related to cyanobacterial natural existed before this study (see Online Resource 1). products, as underlined by data available in the literature. J Appl Phycol (2018) 30:1437–1451 1443 Such information was found to be disseminated through 98 and shows visible sheaths and double false-branching (Brito different journal articles (for a reference list, see Online et al. 2012), is phylogenetically placed within the Nostocales Resource 3). In December 2016, 171 strains (44% of the total) (Fig. 3). Plectonema is traditionally classified in the had some sort of data available in published journal articles, Oscillatoriales as it lacks specialized cells (Komárek and from which 165 (43%) concerned natural products, including Anagnostidis 2005; Komárek et al. 2014), but its taxonomy toxins (see also Figs. 3 and 4 and Online Resource 3). The is debatable and requires revision (Komárek and Anagnostidis three most frequently reported LEGE CC strains were found 2005). For instance, as observed with Plectonema cf. to be included in ten or more journal articles (Fig. 3 and radiosum LEGE 06114, some Plectonema species exhibit Online Resource 3). These are the microcystin-producing double false-branching similar to those found in Nostocales (MC) strain Microcystis aeruginosa LEGE 91094 (Fig. 2d), genera (e.g., Scytonema,(Komárek 2013)) and could be trans- the cylindrospermopsin-producing (CYN) strain ferred to this order according to Komárek and Anagnostidis Cylindrospermopsis raciborskii LEGE 97047, and (2005). Information on these and other (apparent) taxonomic Cylindrospermopsis raciborskii LEGE 95046, a non-CYN incongruities, peculiarities, or doubts that may have arisen producer (Fig. 2t). after the identification of LEGE CC strains were included in the catalog sheet of the corresponding strain, as taxonomic Strain characterization and identification notes (Online Resource 3). The so-called modern approach currently recommended The morphological and molecular-based characterization ex- for identification of cyanobacteria (e.g., Komárek 2016)has posed the wide diversity of LEGE CC strains (Figs. 2 and 3), cause and will continue to result in important changes for the being included in six orders (Fig. 3) and 46 genera (Table 1). taxonomy of cyanobacteria (Komárek et al. 2014). Traditional Komárek et al. (2014) haverecentlyproposedanew taxono- genera or species, especially those with little phenotypic dif- my classification for cyanobacteria. Based on phylogenetic ferentiation, very often exhibit polyphyly in phylogenetic systematics, these authors have either erected new studies (see Dvořák et al. (2015) for a review). Such findings cyanobacterial orders or redefined the classical ones. For in- suggest that extensive taxonomic revisions of those taxa are in stance, unicellular or colonial cyanobacteria formerly includ- need (Komárek et al. 2014; Dvořák et al. 2015, Komárek ed in the classical order Chroococcales (Komárek and 2016). As a consequence, the number of new genera that are Anagnostidis 1998) are now distributed in the new order being described using combined taxonomy of morphology Synechococcales and/or in the revisited Pleurocapsales and molecular phylogeny is growing rapidly, being that sev- (Komárek et al. 2014). The same is true to filamentous non- eral of these genera represent earlier entangled, cryptic taxa heterocytous cyanobacteria, which were traditionally included that have emerged from traditional genera (Dvořák et al. 2015; in the Oscillatoriales (Komárek and Anagnostidis 2005)and Komárek 2016). Given the current status of taxonomy, and as are now distributed in the redefined orders Chroococcales or implicitly recommended by Dvořák et al. (2015), we have Oscillatoriales (Komárek et al. 2014). Accordingly, several adopted a conservative approach for the identification of LEGE CC strains that were previously assigned to those clas- LEGE CC strains at low taxonomic levels. The availability sical orders (e.g., Brito et al. 2012; Lopes et al. 2012)were and inclusion of sequences from Type strains (Ramos et al. now re-classified by using this new classification scheme 2017) in the phylogenetic analysis (Fig. 3) was essential to (Komárek et al. 2014) and by assessing their phylogenetic accurately identify the strains, namely to ascertain if they position, as depicted in Fig. 3 (also provided in a scalable, could belong to recently proposed genera not covered by the high quality vector format in Online Resource 1). For this classification keys used (Komárek and Anagnostidis 1998, purpose, sequences from the same reference strains included 2005;Komárek 2013). Therefore, previous morphology- in the phylogeny performed by Komárek et al. (2014)were based identifications of the strains were not considered if the used in our analysis, which has permitted to map out the or- phylogeny indicated that the strains belong to such recent ders in the phylogenetic tree (Fig. 3). genera, or if they were phylogenetically placed away from The abovementioned grouping of unicellular and filamen- the holotypeinquestion(i.e.,Typestrainusedtodescribea tous non-heterocytous forms into new orders is illustrated by a genus) (Fig. 3). Applying these criteria resulted in 70 LEGE selection of LEGE CC strains included in Fig. 2. Colonial CC strains remaining unidentified since it was not possible to forms that were divided by multiple fission (Fig. 2g–i) and achieve an unequivocal identification at the genus level, even heterocytous strains (Fig. 2m–t) from the LEGE CC were if in most cases it was possible to achieve an assignment at the found to be part of the Pleurocapsales and Nostocales clades, order level (Table 1). On the other hand, 86 strains were iden- respectively (Fig. 3). tified as belonging to 18 recently described genera by means Interestingly, the filamentous cyanobacterium Plectonema of modern taxonomy (see Table 1). cf. radiosum LEGE 06114 (Fig. 2o), which lacks heterocytes Well represented genera at LEGE CC include the and akinetes, exhibits discoid cells and rounded apical cells, picocyanobacterium Cyanobium (48 strains; Fig. 2a), the 1444 J Appl Phycol (2018) 30:1437–1451 filamentous non-heterocytous Nodosilinea (44; Fig. 2b), the Fig. 4 ML cladogram (− lnl = 3431.5512) for 165 LEGE CC strains having available data related to natural products. Capital letters in the bloom forming Microcystis (37, including both microcystin tree highlight clades encompassing close-related strains for which the and non-microcystin producers; Fig. 2d), the unicellular production of some of the following specific metabolites were detected Synechocystis (21), and the filamentous non-heterocytous (+)ornot (−): Cyanotoxins: ANA-a anatoxin-a, BMAA β- Tychonema (21). Methylamino-L-alanine, CYN cylindrospermopsin, and MC microcystin. Bioactive compounds: 1 portoamides, 2 bartolosides, 3 LEGE CC aims to value its cyanobacterial diversity in a dehydroabietic acid, 4 abietic acid, 5 hierridin B, and 6 anabaenopeptins way that can be perceived by others, namely by stakeholders A and D. Notice that the production (+) or absence of production (−)of from the biotechnology sector. As such, strains are character- the different compounds were confirmed by analytical techniques such ized in order to highlight features that may have interest from as HPLC, LC-MS, or NMR. Metabolites between parentheses and sym- bols in gray indicate unpublished data. Symbols indicate the existence of an applied point of view. As depicted from the qualitative data (either for the detection or non-detection) on: toxicity, bioactivity, or evaluation made by different staining techniques (see as an allelopathy assays (▲); screening of metabolites by MALDI-TOF Mass example Online Resource 2), several LEGE CC strains pro- Spectrometry or by LC–MS analysis coupled with molecular networking duce considerable amounts of EPSs (Fig. 3), a feature that [13] (■); cyanotoxins (� , first column); other than cyanotoxins nonribosomal peptide synthetases, polyketide synthases, or hybrid may have biotechnological applications. For instance, NRPS-PKS (� , second column); ribosomally synthesized and post- cyanobacterial EPSs can be used for heavy metal removal translationally modified peptides (Martins et al. 2013)(� ,third column); from contaminated waters (Pereira et al. 2011), as was already and other family of compounds such as terpenes, glycolipids, etc. (� , demonstrated for one of our strains, Synechocystis sp. LEGE fourth column). To get at the data on a particular strain, please find the literature references in the corresponding catalog sheet (Online Resource 00032 (Ribeiro et al. 2008). Also, six strains (Fig. 3) have had 3) their genomes sequenced and these will be made publicly available, following curation. One such strain, Cyanobium sp. LEGE 06113, has been included on a submitted patent application for a promising anti-malarial compound. Some strains. Indeed, some LEGE CC strains were used (Leão strains held in LEGE CC have an earthy odor, something that et al. 2010, 2013a, 2015; Costa et al. 2016) to isolate novel may indicate the presence of odiferous metabolites such as 2- and known bioactive metabolites (Fig. 3). methlyisoborneol or geosmin (Giglio et al. 2010), two volatile Currently, 165 cyanobacterial LEGE CC strains, organic compounds that pose problems in drinking water sup- representing 43% of the total number of strains, have some ply systems. This qualitative data was included in the catalog associated data (mostly published) concerning the production of strains (Online Resource 3). of natural products or information on biological activity of their constituents (Fig. 4). The phylogenetic relationships LEGE CC strains and their (potential) chemodiversity among these strains and associated data are depicted in the unrooted tree shown in Fig. 4. If available, data can be reached Since the main research lines of BBE are ecotoxicology and through the publications mentioned in the catalog sheet for a the discovery of new natural products, in particular, those with particular strain, whereas the full references are listed at the biotechnological potential, it is not surprising that a consider- end of the catalog (Online Resource 3). able fraction of LEGE CC strains (43%) have been studied LEGE CC strains have the potential (e.g., presence of and/or used for their potential production of bioactive second- genes involved in the biosynthesis of secondary metabolites) ary metabolites (see Fig. 4). or the effective capacity to produce different chemical com- In total, there are 37 strains in LEGE CC known to produce pounds (Fig. 4, see also Leão et al. 2013b; Martins et al. 2013; common cyanotoxins (Fig. 3). Details and information related Brito et al. 2015). Several of those compounds being produced to shipment, handling, and disposal of toxic strains, verifica- by LEGE CC strains exhibit anti-cancer (e.g., portoamides tion of toxin production by LEGE CC, expertise services, etc. and hierridin B; Leão et al. 2010, 2013a), anti-viral (crude are included in the catalog (Online Resource 3). Nine out of 32 extract; Lopes et al. 2011), anti-microbial (fractions; Costa Microcystis aeruginosa strains included in LEGE CC are MC et al. 2014, 2015; Leão et al. 2013a), or anti-biofouling producers. Other toxin-producing strains include the anatoxin- (crude extract; Almeida et al. 2015) properties. Dittmann a (ANA-a) producers Dolichospermum spp. LEGE 00240, et al. (2015) claim that more than 1100 secondary metabolites 00241, and 04289, and Limnothrix sp. LEGE 00237, the already known to be produced by cyanobacteria are just a CYN producer Cylindrospermopsis raciborskii LEGE fraction of the true metabolic potential of these microorgan- 97047, as well as several strains, belonging to different taxa, isms. As an example, some LEGE CC strains were used to that produce β-methylamino-L-alanine (BMAA), a toxin isolate unprecedented bioactive secondary metabolites (Figs. shown to be widespread among cyanobacteria (Cox et al. 3 and 4, compounds 1 and 2), the lipopeptides portoamides 2005;Cianca etal. 2012)(see also Fig. 3). Besides toxins, (Phormidium sp. LEGE 05292) (Leão et al. 2010) and the other secondary metabolites (e.g., hierridin B, portoamides, dialkylresorcinol glycolipids bartolosides (Synechocystis and bartolosides) are known to be produced by LEGE CC salina LEGE 06155 and Nodosilinea nodulosa LEGE J Appl Phycol (2018) 30:1437–1451 1445 1446 J Appl Phycol (2018) 30:1437–1451 Fig. 4 (continued) 06102) (Leão et al. 2015). The diterpenoid dehydroabietic the diterpenoid-producing cyanobacteria. The same pattern acid, isolated from Plectonema cf. radiosum LEGE 06105 can be observed in different cyanobacterial clades (A-E) and the unidentified colonial Synechococcales LEGE 10388 highlighted in Fig. 4, for different metabolites studied by an- (Figs. 3 and 4), was for the first time detected in an organism alytical methods. For instance, regarding toxins, there are other than gymnosperms (Costa et al. 2016). By screening 15 closely related LEGE CC strains assigned as ANA-a pro- LEGE CC strains, Costa et al. (2016) soon demonstrated that ducers and non-producers, in clade A and B, CYN producers this and one other terpenoid, the abietic acid, are present in a and non-producers in clade C, and MC producers and non- wide range of cyanobacteria (Fig. 4, compounds 3 and 4). In producers in clade D. Closely related strains that produce or the same study, it was also shown that in some cases the two did not produce the diterpenoids are included in clade E. Of compounds could not be detected in strains closely related to course, a metabolite can remain undetected if it is being J Appl Phycol (2018) 30:1437–1451 1447 Table 1 Number of cyanobacterial strains, by taxa, in LEGE CC (386 strains in total) Order Genus (reference) Number of strains Origin Ecology Chroococcales Cyanobacterium 1 Por f Geminobacterium (Brito et al. 2017)1* Por m Microcystis 37 (9) Bra, Gre, Mex, Mor, Por f Synechocystis 21 (3) Por b, f, and m unidentified Chroococcales 4 Por m Chroococcidiopsidales Gloeocapsa-like 1 Por m Gloeocapsopsis 4 Por m unidentified Chroococcidiopsidales 3 unknown unknown Nostocales Anabaena 3(1) Fin f Calothrix 2 Por m Chrysosporum (Zapomělová et al. 2009)1(1) Isr f Cuspidothrix (Rajaniemi et al. 2005)4(1) Por f Cylindrospermopsis 6(1) Aus, Por f Desmonostoc (Hrouzek et al. 2013)1 Por t Dolichospermum (Wacklin et al. 2009)11(4) Por f Fortiea 1 unknown unknown Nodularia 2(1) Por b, f Nostoc 14 (1) Mor, Por b, m, and t Plectonema 2 Por m Rivularia 3 Por m Roholtiella (Bohunická et al. 2015)1 Por f Scytonema 2 Por m Sphaerospermopsis (Zapomělová et al. 2009)4 Mex, Por f Tolypothrix 1 Por f unidentified Nostocales 9 Col, Por f, m, and t Oscillatoriales Coleofasciculus (Siegesmund et al. 2008)2(1) Por b Limnoraphis (Komárek et al. 2013) 1 unknown f Lusitaniella (Brito et al. 2017)4* Por m Microcoleus 1(1) Por b Oxynema (Chatchawan et al. 2012)2(2) Por b, m Phormidium 5 Mor, Por f, m Planktothrix 10 Por f Spirulina 1 Por m Tychonema 21 Col, Por f unidentified Oscillatoriales 4 Mor, Por f, m Pleurocapsales Chroococcidiopsis 1 Por m Chroococcopsis 2 Por m Hyella 1 Por m Myxosarcina 1 Por m unidentified Pleurocapsales 2 Por m Synechococcales Alkalinema (Vaz et al. 2015)1 Bra f Calenema (Brito et al. 2017)1* Por m Cyanobium 48 (1) Chi, Mor, Por b, f, and m Geitlerinema 4 Bra h Halomicronema (Abed et al. 2002)1 Por m Jaaginema 1 Por m Leptolyngbya 13 Bra, Por f, h, and m Limnothrix 1(1) Por f 1448 J Appl Phycol (2018) 30:1437–1451 Table 1 (continued) Order Genus (reference) Number of strains Origin Ecology Nodosilinea (Perkerson 3rd et al. 2011)44(5) Ant, Por b, f, m, and t Oculatella (Zammit et al. 2012)1 Por m Phormidesmis (Turicchia et al. 2009)5 Por m Pseudanabaena 3 Por f, m Romeria 4 Por b, m Schizothrix 1 Por m Synechococcus 12 Bra, Por b, h, and m Toxifilum (Zimba et al. 2017)1 Por m unidentified Synechococcales 32 (3) Chi, Mex, Mor, Por b, f, h, and m Unclear taxa unidentified cyanobacterium 16 Bra, Chi, Mor, Por f, h, and m Ant, Antarctica; Aus, Australia; Bra,Brazil; Chi, Chile; Col,Colombia; Fin,Finland; Gre,Greece; Isr,Israel; Mex,Mexico; Mor, Morocco; Por, Portugal; b, brackish water; f,freshwater; h, hypersaline; m,marine; t, terrestrial Recently described taxa; references only to these genera In parentheses indicated the number of strains known to produce common cyanotoxins (including BMAA) The inconsistency between genus and order assignments (as in Komárek et al. 2014) seems to indicate that taxonomic revision of these taxa is in need (the order placement was defined by phylogeny; see Fig. 3 or Online Resource 1) *Including the strain used to describe the genus (see Brito et al. 2017) produced at low levels, below the limit of detection of the potential of these microorganisms as a source of natural prod- analytical technique. It is also possible that some of the bio- ucts, bioprospection should be ideally conducted strain-by- logical activities observed are related to the microbiota asso- strain rather than taxonomically or phylogenetically guided ciated with the cyanobacteria and not to the cyanobacteria (Dittmann et al. 2015). themselves; however, in light of the well-recognized ability of cyanobacteria to produce bioactive compounds and to the low densities of heterotrophic bacteria in these unicyanobacterial cultures, we find that this is rather unlikely. Conclusions It can also happen that, under some conditions (e.g., lack of environmental stimuli), a cyanobacterium does not produce a Acting as repositories of strains and of their genetic material, particular metabolite despite possessing the biosynthetic path- mBRCs facilitate the access to their diversity, their (meta)data way to produce it (Watanabe and Oishi 1985;Boopathiand Ki and their associated natural compounds, being able to satisfy 2014). It is also possible that the biosynthetic machinery is the needs of academia or the industry. With this in mind, we inactive (e.g., due to gene mutation events) (Leikoski et al. decided to organize our cyanobacterial strains into a publicly 2012; Vestola et al. 2014). Comparative genomics studies on available culture collection. The cyanobacterial diversity that diverse cyanobacterial taxa have demonstrated that closely currently makes up the LEGE CC is an increasingly important related strains (i.e., at the subspecies level) may present high bioresource, either from the taxonomic point of view (e.g. levels of genome divergence (Rocap et al. 2003;Shihet al. Ramos et al. 2010 in Komárek et al. 2014; Brito et al. 2017) 2013; Bombar et al. 2014; Calteau et al. 2014). For instance, or from a biotechnological perspective (e.g., Brito et al. 2015). some of those phylogenetically highly related strains may LEGE CC is now a member of the WFCC (WDCM #1089), possess functionally active genes (or gene clusters) linked to also part of EMBRC.PT, the Portuguese node of the research the production of natural products, while others do not (Shih infrastructure European Marine Biological Resource Centre. et al. 2013; Sinha et al. 2014; Calteau et al. 2014;Dittmann Possible biotechnological applications for LEGE CC strains et al. 2015). On the other hand, it reinforces the importance of and their bioproducts were described in several studies, syn- the clonal status of strains for securing reproducibility of re- opsized here, and are related to their anti-cancer, anti-viral, sults, since strains from the same population may exhibit very anti-microbial, or anti-biofouling properties. Even though different biosynthetic potential as depicted from the study of using phylogenetic diversity data is a valid strategy for Shih et al. (2013). All these issues have important implications directing strain selection for natural product screening, this for the discovery of natural compounds from cyanobacteria. In study illustrates that natural product discovery programs particular, it indicates that, for an exploration of the full should consider a strain-by-strain assessment. J Appl Phycol (2018) 30:1437–1451 1449 Acknowledgements VR gratefully acknowledges financial support from new genera and species of marine cyanobacteria from the a Fundação para a Ciência e a Tecnologia (FCT) fellowship SFRH/BD/ Portuguese Atlantic coast. Mol Phylog Evol 111:18–34 80153/2011. The Project NOMORFILM has received funding from the Calteau A, Fewer DP, Latifi A, Coursin T, Laurent T, Jokela J, Kerfeld European Union’s Horizon 2020 Research and Innovation Programme CA, Sivonen K, Piel J, Gugger M (2014) Phylum-wide comparative under grant agreement No. 634588. Structured Program of R&D&I genomics unravel the diversity of secondary metabolism in INNOVMAR-Innovation and Sustainability in the Management and Cyanobacteria. BMC Genomics 15:977 Exploitation of Marine Resources (reference NORTE-01-0145-FEDER- Castenholz RW, Wilmotte A, Herdman M, Rippka R, Waterbury JB, 000035, Research Line NOVELMAR), funded by the Northern Regional Iteman I, Hoffmann L (2001) Phylum BX. Cyanobacteria. In: Operational Program (NORTE2020) through the European Regional Boone DR, Castenholz RW, Garrity GM (eds) Bergey’smanual of Development Fund (ERDF). PNL acknowledges funding from FCT systematic bacteriology, volume one: the archaea and the deeply through contract (IF/01358/2014). branching and phototrophic bacteria. Springer, New York, pp 473– Chatchawan T, Komarek J, Strunecký O, Šmarda J, Peerapornpisal Y (2012) Oxynema, a new genus separated from the genus Phormidium (Cyanophyta). Cryptogam Algol 33:41–59 Cianca RCC, Baptista MS, Lopes VR, Vasconcelos VM (2012) The non- Open Access This article is distributed under the terms of the Creative protein amino acid beta-N-methylamino-L-alanine in Portuguese Commons Attribution 4.0 International License (http:// cyanobacterial isolates. 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Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection

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Life Sciences; Plant Sciences; Freshwater & Marine Ecology; Plant Physiology; Ecology
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Abstract

Cyanobacteria are a well-known source of bioproducts which renders culturable strains a valuable resource for biotechnology purposes. We describe here the establishment of a cyanobacterial culture collection (CC) and present the first version of the strain catalog and its online database (http://lege.ciimar.up.pt/). The LEGE CC holds 386 strains, mainly collected in coastal (48%), estuarine (11%), and fresh (34%) water bodies, for the most part from Portugal (84%). By following the most recent taxonomic classification, LEGE CC strains were classified into at least 46 genera from six orders (41% belong to the Synechococcales), several of them are unique among the phylogenetic diversity of the cyanobacteria. For all strains, primary data were obtained and secondary data were surveyed and reviewed, which can be reached through the strain sheets either in the catalog or in the online database. An overview on the notable biodiversity of LEGE CC strains is showcased, including a searchable phylogenetic tree and images for all strains. With this work, 80% of the LEGE CC strains have now their 16S rRNA gene sequences deposited in GenBank. Also, based in primary data, it is demonstrated that several LEGE CC strains are a promising source of extracellular polymeric substances (EPS). Through a review of previously published data, it is exposed that LEGE CC strains have the potential or actual capacity to produce a variety of biotechnologically interesting compounds, including common cyanotoxins or unprecedented bioactive molecules. Phylogenetic diversity of LEGE CC strains does not entirely reflect chemodiversity. Further bioprospecting should, therefore, account for strain specificity of the valuable cyanobacterial holdings of LEGE CC. Vitor Ramos, João Morais, and Raquel Castelo-Branco contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10811-017-1369-y) contains supplementary material, which is available to authorized users. * Vitor M. Vasconcelos ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade vmvascon@fc.up.pt do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal Interdisciplinary Centre of Marine and Environmental Research Master 2 Biotechnologie, Université de Bretagne-Sud, BP 92116, (CIIMAR/CIMAR), Terminal de Cruzeiros do Porto de Leixões, 56000 Lorient/Vannes, France University of Porto, 4450-208 Matosinhos, Portugal 2 Laboratory of Algae Cultivation and Bioprospection, Federal Amapá Faculdade de Ciências, Universidade do Porto, Rua do Campo University (UNIFAP), Rodovia JK, km 2, Macapá, Amapá, Brazil Alegre, Edifício FC4, 4169-007 Porto, Portugal Health and Environment Research Centre, School of Health, Nanotechnology and Functional Materials, Department of Polytechnic Institute of Porto, Rua Dr. António Bernardino de Engineering Sciences, Uppsala University, Box 534, 751 Almeida, 400, 4200-072 Porto, Portugal 21 Uppsala, Sweden 4 9 IPMA-Portuguese Institute of Sea and Atmosphere, Rua Alfredo Alpha Environmental Solutions, P.O. Box 37977, Dubai, United Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal Arab Emirates 1438 J Appl Phycol (2018) 30:1437–1451 . . . . . Keywords Cyanobacteria Strains Biodiversity Chemodiversity Culture collection Biological resource centers Introduction by revealing (4) their phylogenetic diversity. Cyanobacterial strains in LEGE CC were (re-)identified using an approach com- Microbial biological resource centers (mBRCs) are quality- bining morphological and phylogenetic data, as recommended managed culture collections that ensure the ex situ preservation by Komárek (2016), which confers added value to the collection. of microorganisms, while providing public access to their mi- Likewise, based on some novel and existing data, we reviewed crobial diversity (i.e., to live strains or to genomic DNA from (5) biotechnologically relevant information from the strains, and these strains), to relevant data related to it (e.g., taxonomic iden- make some (6) considerations on the relation between biodiver- sity and chemodiversity for the discovery of natural compounds tification, culture conditions, ecophysiological features, etc.), and also to expertise services such as training or consulting from cyanobacterial strains. Altogether, the disclosed data from (Antunes et al. 2016). mBRCs are pivotal in underpinning the the strains makes LEGE CC a valuable resource for further bioeconomy derived from microbial resources (Smith et al. bioprospecting, toxicological, and/or taxonomic studies. 2014). In this particular case, cyanobacteria have been pointed out in the past few decades as one of the most promising groups of microorganisms for the discovery of natural compounds with Materials and methods pharmacological and other biotechnological applications (Margesin and Schinner 2001;Abedetal. 2009; Singh et al. Strain codes for all strains at BBE were standardized by using the 2011; Wijffels et al. 2013). For oncology drugs only, the phar- acronym LEGE followed by a five-digit number. The workflow maceutical value of the estimated marine cyanobacteria diversity followed during the establishment of the culture collection is was evaluated in US$37.5–181.5 billion, in 2010 dollars (Erwin depicted in Fig. 1. The figure shows the processes and methods et al. 2010). One other relevant property of cyanobacteria with used for researching and collecting secondary data (e.g., infor- biotechnological interest is the production of extracellular poly- mation on secondary metabolite production; some nucleotide meric substances (EPSs) (Abed et al. 2009; Pereira et al. 2011). sequences) and for generating primary data from the strains The Blue Biotechnology and Ecotoxicology (BBE) group, at (e.g., morphometry, microphotographs, most of the 16S rRNA CIIMAR, Portugal, has recently undertaken a process of orga- gene sequences, and evaluation of EPS production). It also indi- nizing its cyanobacterial strains into a culture collection (acro- cates the main outputs of these processes, which are presented in nym LEGE). It began as an in-house collection in 1991, when a this study. number of strains from the colonial toxic cyanobacterium Microcystis aeruginosa were isolated from freshwater water bod- Literature and data survey ies in Portugal (Vasconcelos et al. 1995). Since then, a good number of strains have been isolated and assessed in ecotoxico- Eighty-three strains had been previously published using other logical studies or used for the discovery of biologically active strain names/codes or identifications. For that reason, all existing compounds, the main research lines of the group. As a conse- synonyms for a same strain were considered during the literature quence, a considerable body of research (e.g., Vasconcelos et al. search and data survey. Strain synonyms and references where 1995; Martins et al. 2005, 2013;Leãoetal. 2013b; Brito et al. they appear are provided in the catalog, in Online Resource 3. 2015) emphasizes that several strains now deposited at the LEGE Strains having any type of data on natural products were culture collection (CC) have the potential or actual capacity to recorded. produce a myriad of chemical compounds, including toxins or newly discovered bioactive molecules. Yet, most of the strains at Light microscopy and morphological characterization BBE were kept independently by their isolators along these years, and were poorly characterized, named inconsistently or Morphological characteristics of LEGE CC strains were exam- even unidentified. ined and microphotographed using a Leica DMLB light micro- For these reasons, a decision was made to characterize and scope coupled to a Leica ICC50 HD digital camera (Leica organize all the strains (and their associated data) at BBE, and Microsystems, Germany). Morphometric measurements were make publicly available this bioresource by establishing a culture then performed using the image analysis software Leica collection in accordance to the Organisation for Economic Co- Application Suite version 4.2.0 (Leica Microsystems). Strains operation and Development (OECD 2007) and World Federation were analyzed during the exponential phase of growth (i.e., 2- for culture collections (WFCC 2010) guidelines. In this work, we to 3-week old cultures, depending on the strain; culture condi- illustrate (1) the process followed to establish LEGE CC, and tions for each strain can be found in the catalog (Online Resource give an overview of the collection by presenting (2) the catalog 3). Each quantifiable morphological character was measured at of strains, (3) the online database (http://lege.ciimar.up.pt/), and least 20 times, along different positions of the slide preparation. J Appl Phycol (2018) 30:1437–1451 1439 Fig. 1 The workflow followed during the data gathering on the LEGE CC strains, the completed and expected outputs of the process and the planned updates (standard flowchart symbols were used). The LEGE CC website can be accessed at http://lege.ciimar.up.pt These include size of vegetative, specialized, or dormant cells, et al. 2008) were used for the amplification of a portion of and of filaments or colonies. the 16S rRNA gene. PCR reactions were performed in a final Additionally, to evaluate the production of EPSs by the volume of 20 μL containing 1× Green GoTaq Flexi Buffer, strains, early stationary-phase cultures (i.e., 3- to 5-week old 2.5 mM MgCl , 125.0 mM of each deoxynucleotide triphos- cultures, depending on the strain) were stained with 0.5% phate, 1.0 μM of each primer, 0.5 U of GoTaq Flexi DNA −1 Alcian Blue solutions (Sigma A-3157), prepared either in Polymerase (Promega, USA), 10 mg mL of bovine serum 50% ethanol (v/v)orin1%acetic acid(v/v) (Di Pippo et al. albumin (BSA), and 10–30 ng of template DNA, on a 2013). Cultures were also negatively stained using India ink TProfessional Standard thermal cycler (Biometra, Germany). (Micheletti et al. 2008). Images were acquired using the The PCR conditions were as follows: initial denaturation at abovementioned equipment and software. 94 °C for 4 min, followed by 35 cycles of denaturation at When relevant, other qualitative morphological features 94 °C for 30 s, annealing at 52 °C for 30 s, and extension at and distinguishing traits were recorded (e.g., the shape and 72 °C for 45 s, with a final extension step at 72 °C for 6 min. arrangement of cells or filaments, the color of the cultures, PCR products were separated with a 1.5% (w/v) agarose gel the presence or absence of sheaths, motility, the existence of stained with GelRed (Biotium, USA) and DNA fragments constrictions at the cross-wall of filaments, and the formation with the expected size were excised from the gel and purified of hormogonia and necridial cells). using the NucleoSpin Gel and PCR Clean-up Kit (Macherey- Nagel, Germany), according to the manufacturer’s instruc- DNA extraction, PCR, and sequencing tions. Sequences were obtained by either directly sequencing the purified amplicons at GATC Biotech (Germany) or after Cells were harvested from log-phase cultures, and total geno- cloning these into pGEM-T Easy vector (Promega, USA). In mic DNA (gDNA) of each strain was extracted using the the latter case, vectors containing inserts were then trans- commercial PureLink Genomic DNA Mini Kit (Invitrogen, formed into Escherichia coli TOP10 chemically competent USA), according the to the manufacturer’s instructions pro- cells (Invitrogen, San Diego, CA). Plasmid DNA was isolated vided for Gram-negative bacteria. The DNA integrity was using NZY Miniprep kit (NYZtech, Portugal) and sequenced confirmed with agarose gel electrophoresis using GelRed at GATC Biotech using M13 primers. All nucleotide se- (Biotium, USA) staining. Cyanobacteria-specific primers quences were manually inspected for quality and assembled for each strain using the Geneious (v8.1.8) software package CYA-106F and CYA-785R (Nübel et al. 1997; Muhling 1440 J Appl Phycol (2018) 30:1437–1451 (Biomatters Limited, New Zealand). Two hundred and standard identification keys were used for the twenty-four novel sequences associated with this study were morphological-based identification of the strains (Komárek deposited in the GenBank database under the accession num- and Anagnostidis 1998, 2005; Komárek 2013). Then, each bers KU951663–KU951886. strain identification was compared with its phylogenetic placement (namely, assessing if the LEGE strain is closely Phylogenetic analyses related to any Type strain) and with the recent taxonomic classification proposed by Komárek et al. (2014), at low Molecular-based analyses were conducted using the bioinfor- (i.e., genus) and high (i.e., order) taxonomic levels. If existing, matics software package MEGA7 (Kumar et al. 2016). Two taxonomic notes for a strain (e.g., incongruities between clas- phylogenetic analyses based on 16S rRNA gene sequences sification schemes) were added to the correspondent catalog were performed, one that reflects the overall cyanobacterial sheet (Online Resource 3). diversity present at LEGE CC and a second analysis that high- lights the connection between such biodiversity and its asso- ciated chemodiversity. In both cases, sequences were aligned Results and discussion using the ClustalW algorithm (Thompson et al. 1994) and phylogenies were inferred by using the Maximum Three hundred and eighty-six cyanobacterial strains are in- Likelihood (ML) method (Felsenstein 1981) based on the cluded in the first version of the catalog of LEGE CC (see General Time Reversible model (Rodriguez et al. 1990), Fig. 2 for a morphological overview). For each particular which was the nucleotide substitution model that best fitted strain, primary and secondary data collected in this study the alignments data as evaluated by the corrected Akaike (Fig. 1), such as species identification, origin, morphometric Information Criterion (Sugiura 1978). For both analyses also, information, morphological description, and ecophysiological a discrete Gamma distribution (+G) was used to model evo- properties of the strain, microphotographs, literature refer- lutionary rate differences among sites, while the rate variation ences, synonyms for the strain, accession numbers for se- model allowed for some sites to be evolutionarily invariable quences, etc., can be retrieved in the corresponding catalog (+I). In the first case, the analysis involved 457 nucleotide sheet (Online Resource 3) or be searched in the website data- sequences from LEGE CC strains and from relevant strains base of the culture collection at http://lege.ciimar.up.pt. included in CyanoType v.1 (see Ramos et al. 2017). These include: (1) Type strains (T) of Type species (i.e. LEGE CC conditions cyanobacterial strains that were used to describe a new genus); (2) strains known to have the same phylogenetic placement as The LEGE CC is hosted in a new building, with modern the Type species (t), when the sequence from the latter is not facilities at CIIMAR, Matosinhos, Portugal. It includes available; (3) Reference strains (R) from the Bergey’sManual cyanobacterial strains collected since 1991. LEGE CC strains −2 −1 of Systematic Bacteriology (Castenholz et al. 2001); and, (4) are normally kept at 10–30 μmol photons m s under 12/ strains known to be included in the same phylogenetic cluster 12 h or 14/10 h light/dark cycles. The range of controlled as the Reference strain (r), as mentioned in the Bergey’s temperature conditions at LEGE CC are 14, 19 (for most Manual (Castenholz et al. 2001). There were a total of 563 strains), and 25 °C. Strains are maintained by subculturing positions in the final dataset. The tree was rooted with the transfers (held every 6 months for most of the strains), but outgroup Chloroflexus aurantiacus J-10-fl (NR_074263). In soon, a stock comprising the full collection will be cryopre- the second case, the phylogenetic analysis involved 165 nu- served and stored at − 150 °C (some strains are cryopreserved cleotide sequences from LEGE CC strains only and there were at − 80 °C; see also Rastoll et al. 2013). Despite the fact that a total of 252 positions in the final dataset. axenicization of LEGE CC strains will be attempted in the future, currently, all are xenic, unicyanobacterial, and clonal. Strain identification General statistics of holdings By using data generated in this study, the taxonomic assign- ments of previously identified strains were reevaluated by an LEGE CC strains were isolated from samples mainly collected approach combining morphological and phylogenetic data. in Portugal (84%), including Madeira and Azores Islands. The most recent classification, recommendations and advice There are also strains from South (5%) and North (2%) for the identification of cyanobacteria (Komárek et al. 2014; America, Africa (3%), other European countries (1%), Dvořák et al. 2015; Komárek 2016) were followed, namely Oceania (1%), Antarctica (1%), and Asia (one strain). In rela- the adoption of a conservative approach (Dvořák et al. 2015; tion to the habitat, LEGE CC strains were mainly collected Komárek 2016). Previously unidentified strains were identi- from aquatic environments, including marine (46%), freshwa- fied following the same procedures and principles. First, ter (34%), brackish (11%), and hypersaline (2%) J Appl Phycol (2018) 30:1437–1451 1441 Fig. 2 Example of morphological diversity among cyanobacterial strains 07179; h Chroococcopsis sp. LEGE 07187; i Chroococcidiopsis sp. from LEGE CC. Strains belong to the orders: a–b Synechococcales, c–e LEGE 06174; j cf. Oxynema acuminatum LEGE 06072; k Phormidium Chroococcales, f Chroococcidiopsidales, g–i Pleurocapsales, j–l sp. LEGE 00064; l cf. Spirulina sp. LEGE 11439; m Rivularia sp. LEGE Oscillatoriales, and m–t Nostocales. Identifications are as follows: a 07159; n Calothrix sp. LEGE 06100; o Plectonema cf. radiosum LEGE Cyanobium sp. LEGE 06127; b Nodosilinea sp. LEGE 06069; c 06114; p Tolypothrix sp. LEGE 11397; q Nodularia sp. LEGE 06071; r Synechocystis salina LEGE 06099; d Microcystis aeruginosa LEGE Nostoc sp. LEGE 07365; s Dolichospermum flosaquae LEGE 04289, an 91094, a microcystin producer strain highly used in the literature (see anatoxin-a producer strain; t Cylindrospermopsis raciborskii LEGE also Fig. 3); e unidentified filamentous Chroococcales LEGE 11427; f 95046, a non-cylindrospermopsin producer often used in the literature Gloeocapsopsis crepidinum LEGE 06123; g Hyella patelloides LEGE (see also Fig. 3). Scale bars represent 10 μm environments, while some strains are of terrestrial origin (3%). the species level, 205 at the genus, while 70 strains remain Concerning taxonomy, LEGE CC strains are distributed by unidentified at the genus level. Of course, the ever-changing the orders Synechococcales (41%), Chroococcales (17%), nature of taxonomy causes identification to change over time, Nostocales (17%), Oscillatoriales (8%), Pleurocapsales and thus, these numbers are expected to change in the next (2%), and Chroococcidiopsidales (2%) (see also Fig. 3). versions of the catalog. Three-hundred and seven LEGE CC One-hundred and eleven LEGE CC strains are identified at strains (80% of the entire collection) have now their 16S 1442 J Appl Phycol (2018) 30:1437–1451 Fig. 3 Circular ML tree (− lnl = 25,944.6863) of 16S rRNA gene strains producing the following cyanotoxins, as demonstrated by analyt- sequences illustrating the phylogenetic diversity of LEGE CC strains ical chemistry methods: A anatoxin-a, e.g., Osswald et al. (2009); B (in gray), their placement at the order level, and some traits or BMAA (Cianca et al. 2012); C cylindrospermopsin, e.g., Saker and information relevant for biotechnological purposes. One hundred and Eaglesham (1999); and M microcystin, e.g., Vasconcelos et al. (1995). fifty-two sequences from reference material (Ramos et al. 2017)were Arrows point to strains used to isolate and elucidate the structure of the included to disclose the cyanobacterial BTree of Life^ (T or t stand for following secondary metabolites: 1 hierridin B (Leão et al. 2013b), 2 type strains designated as representing type species, R or r for reference portoamides (Leão et al. 2010), 3 bartolosides (Leão et al. 2015; strains sensu Bergey’s Manual (Castenholz et al. 2001); and G for ge- Afonso et al. 2016), and 4 dehydroabietic acid (Costa et al. 2016). nome sequences available; see also Material and methods section for Black stars indicate strains having (or soon will have) their genome se- details). Accession numbers for all sequences are shown. Only bootstrap quenced, and the white star stands for a strain that has a submitted patent support values over 50% are given. Black arrowheads indicate strains application. Black circles and numbers within refer to highly used strains capable of producing good amounts of EPSs. White arrowheads denote and to the number of times they appear in the literature, respectively rRNA gene sequences deposited in GenBank, which contrast Several LEGE CC strains have been used in academia, with the 110 (28%) sequences from LEGE CC strains that most of them in research related to cyanobacterial natural existed before this study (see Online Resource 1). products, as underlined by data available in the literature. J Appl Phycol (2018) 30:1437–1451 1443 Such information was found to be disseminated through 98 and shows visible sheaths and double false-branching (Brito different journal articles (for a reference list, see Online et al. 2012), is phylogenetically placed within the Nostocales Resource 3). In December 2016, 171 strains (44% of the total) (Fig. 3). Plectonema is traditionally classified in the had some sort of data available in published journal articles, Oscillatoriales as it lacks specialized cells (Komárek and from which 165 (43%) concerned natural products, including Anagnostidis 2005; Komárek et al. 2014), but its taxonomy toxins (see also Figs. 3 and 4 and Online Resource 3). The is debatable and requires revision (Komárek and Anagnostidis three most frequently reported LEGE CC strains were found 2005). For instance, as observed with Plectonema cf. to be included in ten or more journal articles (Fig. 3 and radiosum LEGE 06114, some Plectonema species exhibit Online Resource 3). These are the microcystin-producing double false-branching similar to those found in Nostocales (MC) strain Microcystis aeruginosa LEGE 91094 (Fig. 2d), genera (e.g., Scytonema,(Komárek 2013)) and could be trans- the cylindrospermopsin-producing (CYN) strain ferred to this order according to Komárek and Anagnostidis Cylindrospermopsis raciborskii LEGE 97047, and (2005). Information on these and other (apparent) taxonomic Cylindrospermopsis raciborskii LEGE 95046, a non-CYN incongruities, peculiarities, or doubts that may have arisen producer (Fig. 2t). after the identification of LEGE CC strains were included in the catalog sheet of the corresponding strain, as taxonomic Strain characterization and identification notes (Online Resource 3). The so-called modern approach currently recommended The morphological and molecular-based characterization ex- for identification of cyanobacteria (e.g., Komárek 2016)has posed the wide diversity of LEGE CC strains (Figs. 2 and 3), cause and will continue to result in important changes for the being included in six orders (Fig. 3) and 46 genera (Table 1). taxonomy of cyanobacteria (Komárek et al. 2014). Traditional Komárek et al. (2014) haverecentlyproposedanew taxono- genera or species, especially those with little phenotypic dif- my classification for cyanobacteria. Based on phylogenetic ferentiation, very often exhibit polyphyly in phylogenetic systematics, these authors have either erected new studies (see Dvořák et al. (2015) for a review). Such findings cyanobacterial orders or redefined the classical ones. For in- suggest that extensive taxonomic revisions of those taxa are in stance, unicellular or colonial cyanobacteria formerly includ- need (Komárek et al. 2014; Dvořák et al. 2015, Komárek ed in the classical order Chroococcales (Komárek and 2016). As a consequence, the number of new genera that are Anagnostidis 1998) are now distributed in the new order being described using combined taxonomy of morphology Synechococcales and/or in the revisited Pleurocapsales and molecular phylogeny is growing rapidly, being that sev- (Komárek et al. 2014). The same is true to filamentous non- eral of these genera represent earlier entangled, cryptic taxa heterocytous cyanobacteria, which were traditionally included that have emerged from traditional genera (Dvořák et al. 2015; in the Oscillatoriales (Komárek and Anagnostidis 2005)and Komárek 2016). Given the current status of taxonomy, and as are now distributed in the redefined orders Chroococcales or implicitly recommended by Dvořák et al. (2015), we have Oscillatoriales (Komárek et al. 2014). Accordingly, several adopted a conservative approach for the identification of LEGE CC strains that were previously assigned to those clas- LEGE CC strains at low taxonomic levels. The availability sical orders (e.g., Brito et al. 2012; Lopes et al. 2012)were and inclusion of sequences from Type strains (Ramos et al. now re-classified by using this new classification scheme 2017) in the phylogenetic analysis (Fig. 3) was essential to (Komárek et al. 2014) and by assessing their phylogenetic accurately identify the strains, namely to ascertain if they position, as depicted in Fig. 3 (also provided in a scalable, could belong to recently proposed genera not covered by the high quality vector format in Online Resource 1). For this classification keys used (Komárek and Anagnostidis 1998, purpose, sequences from the same reference strains included 2005;Komárek 2013). Therefore, previous morphology- in the phylogeny performed by Komárek et al. (2014)were based identifications of the strains were not considered if the used in our analysis, which has permitted to map out the or- phylogeny indicated that the strains belong to such recent ders in the phylogenetic tree (Fig. 3). genera, or if they were phylogenetically placed away from The abovementioned grouping of unicellular and filamen- the holotypeinquestion(i.e.,Typestrainusedtodescribea tous non-heterocytous forms into new orders is illustrated by a genus) (Fig. 3). Applying these criteria resulted in 70 LEGE selection of LEGE CC strains included in Fig. 2. Colonial CC strains remaining unidentified since it was not possible to forms that were divided by multiple fission (Fig. 2g–i) and achieve an unequivocal identification at the genus level, even heterocytous strains (Fig. 2m–t) from the LEGE CC were if in most cases it was possible to achieve an assignment at the found to be part of the Pleurocapsales and Nostocales clades, order level (Table 1). On the other hand, 86 strains were iden- respectively (Fig. 3). tified as belonging to 18 recently described genera by means Interestingly, the filamentous cyanobacterium Plectonema of modern taxonomy (see Table 1). cf. radiosum LEGE 06114 (Fig. 2o), which lacks heterocytes Well represented genera at LEGE CC include the and akinetes, exhibits discoid cells and rounded apical cells, picocyanobacterium Cyanobium (48 strains; Fig. 2a), the 1444 J Appl Phycol (2018) 30:1437–1451 filamentous non-heterocytous Nodosilinea (44; Fig. 2b), the Fig. 4 ML cladogram (− lnl = 3431.5512) for 165 LEGE CC strains having available data related to natural products. Capital letters in the bloom forming Microcystis (37, including both microcystin tree highlight clades encompassing close-related strains for which the and non-microcystin producers; Fig. 2d), the unicellular production of some of the following specific metabolites were detected Synechocystis (21), and the filamentous non-heterocytous (+)ornot (−): Cyanotoxins: ANA-a anatoxin-a, BMAA β- Tychonema (21). Methylamino-L-alanine, CYN cylindrospermopsin, and MC microcystin. Bioactive compounds: 1 portoamides, 2 bartolosides, 3 LEGE CC aims to value its cyanobacterial diversity in a dehydroabietic acid, 4 abietic acid, 5 hierridin B, and 6 anabaenopeptins way that can be perceived by others, namely by stakeholders A and D. Notice that the production (+) or absence of production (−)of from the biotechnology sector. As such, strains are character- the different compounds were confirmed by analytical techniques such ized in order to highlight features that may have interest from as HPLC, LC-MS, or NMR. Metabolites between parentheses and sym- bols in gray indicate unpublished data. Symbols indicate the existence of an applied point of view. As depicted from the qualitative data (either for the detection or non-detection) on: toxicity, bioactivity, or evaluation made by different staining techniques (see as an allelopathy assays (▲); screening of metabolites by MALDI-TOF Mass example Online Resource 2), several LEGE CC strains pro- Spectrometry or by LC–MS analysis coupled with molecular networking duce considerable amounts of EPSs (Fig. 3), a feature that [13] (■); cyanotoxins (� , first column); other than cyanotoxins nonribosomal peptide synthetases, polyketide synthases, or hybrid may have biotechnological applications. For instance, NRPS-PKS (� , second column); ribosomally synthesized and post- cyanobacterial EPSs can be used for heavy metal removal translationally modified peptides (Martins et al. 2013)(� ,third column); from contaminated waters (Pereira et al. 2011), as was already and other family of compounds such as terpenes, glycolipids, etc. (� , demonstrated for one of our strains, Synechocystis sp. LEGE fourth column). To get at the data on a particular strain, please find the literature references in the corresponding catalog sheet (Online Resource 00032 (Ribeiro et al. 2008). Also, six strains (Fig. 3) have had 3) their genomes sequenced and these will be made publicly available, following curation. One such strain, Cyanobium sp. LEGE 06113, has been included on a submitted patent application for a promising anti-malarial compound. Some strains. Indeed, some LEGE CC strains were used (Leão strains held in LEGE CC have an earthy odor, something that et al. 2010, 2013a, 2015; Costa et al. 2016) to isolate novel may indicate the presence of odiferous metabolites such as 2- and known bioactive metabolites (Fig. 3). methlyisoborneol or geosmin (Giglio et al. 2010), two volatile Currently, 165 cyanobacterial LEGE CC strains, organic compounds that pose problems in drinking water sup- representing 43% of the total number of strains, have some ply systems. This qualitative data was included in the catalog associated data (mostly published) concerning the production of strains (Online Resource 3). of natural products or information on biological activity of their constituents (Fig. 4). The phylogenetic relationships LEGE CC strains and their (potential) chemodiversity among these strains and associated data are depicted in the unrooted tree shown in Fig. 4. If available, data can be reached Since the main research lines of BBE are ecotoxicology and through the publications mentioned in the catalog sheet for a the discovery of new natural products, in particular, those with particular strain, whereas the full references are listed at the biotechnological potential, it is not surprising that a consider- end of the catalog (Online Resource 3). able fraction of LEGE CC strains (43%) have been studied LEGE CC strains have the potential (e.g., presence of and/or used for their potential production of bioactive second- genes involved in the biosynthesis of secondary metabolites) ary metabolites (see Fig. 4). or the effective capacity to produce different chemical com- In total, there are 37 strains in LEGE CC known to produce pounds (Fig. 4, see also Leão et al. 2013b; Martins et al. 2013; common cyanotoxins (Fig. 3). Details and information related Brito et al. 2015). Several of those compounds being produced to shipment, handling, and disposal of toxic strains, verifica- by LEGE CC strains exhibit anti-cancer (e.g., portoamides tion of toxin production by LEGE CC, expertise services, etc. and hierridin B; Leão et al. 2010, 2013a), anti-viral (crude are included in the catalog (Online Resource 3). Nine out of 32 extract; Lopes et al. 2011), anti-microbial (fractions; Costa Microcystis aeruginosa strains included in LEGE CC are MC et al. 2014, 2015; Leão et al. 2013a), or anti-biofouling producers. Other toxin-producing strains include the anatoxin- (crude extract; Almeida et al. 2015) properties. Dittmann a (ANA-a) producers Dolichospermum spp. LEGE 00240, et al. (2015) claim that more than 1100 secondary metabolites 00241, and 04289, and Limnothrix sp. LEGE 00237, the already known to be produced by cyanobacteria are just a CYN producer Cylindrospermopsis raciborskii LEGE fraction of the true metabolic potential of these microorgan- 97047, as well as several strains, belonging to different taxa, isms. As an example, some LEGE CC strains were used to that produce β-methylamino-L-alanine (BMAA), a toxin isolate unprecedented bioactive secondary metabolites (Figs. shown to be widespread among cyanobacteria (Cox et al. 3 and 4, compounds 1 and 2), the lipopeptides portoamides 2005;Cianca etal. 2012)(see also Fig. 3). Besides toxins, (Phormidium sp. LEGE 05292) (Leão et al. 2010) and the other secondary metabolites (e.g., hierridin B, portoamides, dialkylresorcinol glycolipids bartolosides (Synechocystis and bartolosides) are known to be produced by LEGE CC salina LEGE 06155 and Nodosilinea nodulosa LEGE J Appl Phycol (2018) 30:1437–1451 1445 1446 J Appl Phycol (2018) 30:1437–1451 Fig. 4 (continued) 06102) (Leão et al. 2015). The diterpenoid dehydroabietic the diterpenoid-producing cyanobacteria. The same pattern acid, isolated from Plectonema cf. radiosum LEGE 06105 can be observed in different cyanobacterial clades (A-E) and the unidentified colonial Synechococcales LEGE 10388 highlighted in Fig. 4, for different metabolites studied by an- (Figs. 3 and 4), was for the first time detected in an organism alytical methods. For instance, regarding toxins, there are other than gymnosperms (Costa et al. 2016). By screening 15 closely related LEGE CC strains assigned as ANA-a pro- LEGE CC strains, Costa et al. (2016) soon demonstrated that ducers and non-producers, in clade A and B, CYN producers this and one other terpenoid, the abietic acid, are present in a and non-producers in clade C, and MC producers and non- wide range of cyanobacteria (Fig. 4, compounds 3 and 4). In producers in clade D. Closely related strains that produce or the same study, it was also shown that in some cases the two did not produce the diterpenoids are included in clade E. Of compounds could not be detected in strains closely related to course, a metabolite can remain undetected if it is being J Appl Phycol (2018) 30:1437–1451 1447 Table 1 Number of cyanobacterial strains, by taxa, in LEGE CC (386 strains in total) Order Genus (reference) Number of strains Origin Ecology Chroococcales Cyanobacterium 1 Por f Geminobacterium (Brito et al. 2017)1* Por m Microcystis 37 (9) Bra, Gre, Mex, Mor, Por f Synechocystis 21 (3) Por b, f, and m unidentified Chroococcales 4 Por m Chroococcidiopsidales Gloeocapsa-like 1 Por m Gloeocapsopsis 4 Por m unidentified Chroococcidiopsidales 3 unknown unknown Nostocales Anabaena 3(1) Fin f Calothrix 2 Por m Chrysosporum (Zapomělová et al. 2009)1(1) Isr f Cuspidothrix (Rajaniemi et al. 2005)4(1) Por f Cylindrospermopsis 6(1) Aus, Por f Desmonostoc (Hrouzek et al. 2013)1 Por t Dolichospermum (Wacklin et al. 2009)11(4) Por f Fortiea 1 unknown unknown Nodularia 2(1) Por b, f Nostoc 14 (1) Mor, Por b, m, and t Plectonema 2 Por m Rivularia 3 Por m Roholtiella (Bohunická et al. 2015)1 Por f Scytonema 2 Por m Sphaerospermopsis (Zapomělová et al. 2009)4 Mex, Por f Tolypothrix 1 Por f unidentified Nostocales 9 Col, Por f, m, and t Oscillatoriales Coleofasciculus (Siegesmund et al. 2008)2(1) Por b Limnoraphis (Komárek et al. 2013) 1 unknown f Lusitaniella (Brito et al. 2017)4* Por m Microcoleus 1(1) Por b Oxynema (Chatchawan et al. 2012)2(2) Por b, m Phormidium 5 Mor, Por f, m Planktothrix 10 Por f Spirulina 1 Por m Tychonema 21 Col, Por f unidentified Oscillatoriales 4 Mor, Por f, m Pleurocapsales Chroococcidiopsis 1 Por m Chroococcopsis 2 Por m Hyella 1 Por m Myxosarcina 1 Por m unidentified Pleurocapsales 2 Por m Synechococcales Alkalinema (Vaz et al. 2015)1 Bra f Calenema (Brito et al. 2017)1* Por m Cyanobium 48 (1) Chi, Mor, Por b, f, and m Geitlerinema 4 Bra h Halomicronema (Abed et al. 2002)1 Por m Jaaginema 1 Por m Leptolyngbya 13 Bra, Por f, h, and m Limnothrix 1(1) Por f 1448 J Appl Phycol (2018) 30:1437–1451 Table 1 (continued) Order Genus (reference) Number of strains Origin Ecology Nodosilinea (Perkerson 3rd et al. 2011)44(5) Ant, Por b, f, m, and t Oculatella (Zammit et al. 2012)1 Por m Phormidesmis (Turicchia et al. 2009)5 Por m Pseudanabaena 3 Por f, m Romeria 4 Por b, m Schizothrix 1 Por m Synechococcus 12 Bra, Por b, h, and m Toxifilum (Zimba et al. 2017)1 Por m unidentified Synechococcales 32 (3) Chi, Mex, Mor, Por b, f, h, and m Unclear taxa unidentified cyanobacterium 16 Bra, Chi, Mor, Por f, h, and m Ant, Antarctica; Aus, Australia; Bra,Brazil; Chi, Chile; Col,Colombia; Fin,Finland; Gre,Greece; Isr,Israel; Mex,Mexico; Mor, Morocco; Por, Portugal; b, brackish water; f,freshwater; h, hypersaline; m,marine; t, terrestrial Recently described taxa; references only to these genera In parentheses indicated the number of strains known to produce common cyanotoxins (including BMAA) The inconsistency between genus and order assignments (as in Komárek et al. 2014) seems to indicate that taxonomic revision of these taxa is in need (the order placement was defined by phylogeny; see Fig. 3 or Online Resource 1) *Including the strain used to describe the genus (see Brito et al. 2017) produced at low levels, below the limit of detection of the potential of these microorganisms as a source of natural prod- analytical technique. It is also possible that some of the bio- ucts, bioprospection should be ideally conducted strain-by- logical activities observed are related to the microbiota asso- strain rather than taxonomically or phylogenetically guided ciated with the cyanobacteria and not to the cyanobacteria (Dittmann et al. 2015). themselves; however, in light of the well-recognized ability of cyanobacteria to produce bioactive compounds and to the low densities of heterotrophic bacteria in these unicyanobacterial cultures, we find that this is rather unlikely. Conclusions It can also happen that, under some conditions (e.g., lack of environmental stimuli), a cyanobacterium does not produce a Acting as repositories of strains and of their genetic material, particular metabolite despite possessing the biosynthetic path- mBRCs facilitate the access to their diversity, their (meta)data way to produce it (Watanabe and Oishi 1985;Boopathiand Ki and their associated natural compounds, being able to satisfy 2014). It is also possible that the biosynthetic machinery is the needs of academia or the industry. With this in mind, we inactive (e.g., due to gene mutation events) (Leikoski et al. decided to organize our cyanobacterial strains into a publicly 2012; Vestola et al. 2014). Comparative genomics studies on available culture collection. The cyanobacterial diversity that diverse cyanobacterial taxa have demonstrated that closely currently makes up the LEGE CC is an increasingly important related strains (i.e., at the subspecies level) may present high bioresource, either from the taxonomic point of view (e.g. levels of genome divergence (Rocap et al. 2003;Shihet al. Ramos et al. 2010 in Komárek et al. 2014; Brito et al. 2017) 2013; Bombar et al. 2014; Calteau et al. 2014). For instance, or from a biotechnological perspective (e.g., Brito et al. 2015). some of those phylogenetically highly related strains may LEGE CC is now a member of the WFCC (WDCM #1089), possess functionally active genes (or gene clusters) linked to also part of EMBRC.PT, the Portuguese node of the research the production of natural products, while others do not (Shih infrastructure European Marine Biological Resource Centre. et al. 2013; Sinha et al. 2014; Calteau et al. 2014;Dittmann Possible biotechnological applications for LEGE CC strains et al. 2015). On the other hand, it reinforces the importance of and their bioproducts were described in several studies, syn- the clonal status of strains for securing reproducibility of re- opsized here, and are related to their anti-cancer, anti-viral, sults, since strains from the same population may exhibit very anti-microbial, or anti-biofouling properties. Even though different biosynthetic potential as depicted from the study of using phylogenetic diversity data is a valid strategy for Shih et al. (2013). All these issues have important implications directing strain selection for natural product screening, this for the discovery of natural compounds from cyanobacteria. In study illustrates that natural product discovery programs particular, it indicates that, for an exploration of the full should consider a strain-by-strain assessment. J Appl Phycol (2018) 30:1437–1451 1449 Acknowledgements VR gratefully acknowledges financial support from new genera and species of marine cyanobacteria from the a Fundação para a Ciência e a Tecnologia (FCT) fellowship SFRH/BD/ Portuguese Atlantic coast. Mol Phylog Evol 111:18–34 80153/2011. The Project NOMORFILM has received funding from the Calteau A, Fewer DP, Latifi A, Coursin T, Laurent T, Jokela J, Kerfeld European Union’s Horizon 2020 Research and Innovation Programme CA, Sivonen K, Piel J, Gugger M (2014) Phylum-wide comparative under grant agreement No. 634588. Structured Program of R&D&I genomics unravel the diversity of secondary metabolism in INNOVMAR-Innovation and Sustainability in the Management and Cyanobacteria. BMC Genomics 15:977 Exploitation of Marine Resources (reference NORTE-01-0145-FEDER- Castenholz RW, Wilmotte A, Herdman M, Rippka R, Waterbury JB, 000035, Research Line NOVELMAR), funded by the Northern Regional Iteman I, Hoffmann L (2001) Phylum BX. Cyanobacteria. In: Operational Program (NORTE2020) through the European Regional Boone DR, Castenholz RW, Garrity GM (eds) Bergey’smanual of Development Fund (ERDF). PNL acknowledges funding from FCT systematic bacteriology, volume one: the archaea and the deeply through contract (IF/01358/2014). branching and phototrophic bacteria. Springer, New York, pp 473– Chatchawan T, Komarek J, Strunecký O, Šmarda J, Peerapornpisal Y (2012) Oxynema, a new genus separated from the genus Phormidium (Cyanophyta). Cryptogam Algol 33:41–59 Cianca RCC, Baptista MS, Lopes VR, Vasconcelos VM (2012) The non- Open Access This article is distributed under the terms of the Creative protein amino acid beta-N-methylamino-L-alanine in Portuguese Commons Attribution 4.0 International License (http:// cyanobacterial isolates. 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Journal of Applied PhycologySpringer Journals

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