sm80n1-4292

Identification of Chattonella (Raphidophyceae) species in long-term phytoplankton samples from Santa Giusta Lagoon, Italy

Daniela Stacca 1, Cecilia Teodora Satta 1, Silvia Casabianca 2, Antonella Penna 2,
Bachisio Mario Padedda 1, Nicola Sechi 1, Antonella Lugliè 1

1 Dipartimento di Architettura, Design e Urbanistica, University of Sassari, Via Piandanna 4, 07100 Sassari, Italy. E-mail: dstacca@uniss.it
2 Dipartimento di Scienze Biomolecolari, University of Urbino, Viale Trieste 296, 61100 Pesaro, Italy.

Abstract: Chattonella species in a Mediterranean lagoon (Santa Giusta Lagoon, Sardinia, Italy) were identified by applying a molecular approach to fixed natural phytoplankton samples collected over the last two decades. Like the other raphidophytes, Chattonella cells are naked and lose their shape when fixed, making species identification difficult on the basis of their morphological characteristics. Employing species-specific primers (oBTG-005-F, oBTG-027-R, oBTG-028-R) for the amplification of the ITS-5.8S rDNA region, we established the occurrence of C. subsalsa in fixed natural phytoplankton samples collected in coincidence with fish death events. Additionally, we established the presence of the recently discovered C. cf. subsalsa Adriatic genotype by analysing cellular cultures obtained from the same lagoon in 2013. This is the second worldwide record of C. cf. subsalsa Adriatic genotype. Our results revealed that the species-specific primers oBTG-005-F and oBTG-028-R distinguished this new genotype only when present singularly. This study provides valuable data that increase knowledge of C. subsalsa genotypes and of the long-term occurrence of Chattonella blooms in a transitional ecosystem through the use of samples up to 20 years old.

Keywords: Chattonella subsalsa genotypes; transitional ecosystems; harmful algal blooms; LTER-Italy; ITS-5.8S rDNA; LSU rDNA.

Identificación de especies de Chattonella (Raphidophyceae) presentes en muestras de fitoplancton recogidas durante un monitoreo de larga duración en la Laguna de Santa Giusta (Cerdeña, Italia)

Resumen: Se identificaron especies de Chattonella mediante la aplicación de técnicas moleculares en muestras naturales de fitoplancton. Las muestras fueron recogidas y fijadas durante las últimas dos décadas en una laguna litoral mediterránea (Laguna de Santa Giusta, Cerdeña, Italia). Al igual que otras rafidoficeas , las células de Chattonella no poseen teca y, por lo tanto, pierden su forma cuando se fijan lo que dificulta la identificación basada en características morfológicas. Con el uso de cebadores específicos a nivel de especie (OBTG-005-F, OBTG-027-R, OBTG-028-R) diseñados para la amplificación de la región ITS- 5.8S rDNA, se detectó la presencia de C. subsalsa en las muestras recogidas en periodos coincidentes con eventos de muerte de peces. A través del análisis de los cultivos celulares obtenidos de la misma laguna en el año 2013, se identificó la presencia, por segunda vez a nivel mundial, del recientemente descubierto genotipo Adriático de C. cf. subsalsa. Los resultados revelaron que los cebadores oBTG-005-F y oBTG-028-R amplifican este nuevo genotipo sólo cuando está presente individualmente. En este estudio se presentan datos relevantes para el conocimiento de los genotipos de C. subsalsa y sobre la presencia recurrente de proliferaciones de especies de Chatonella en un ecosistema de transición a través de la utilización de muestras recogidas durante los últimos veinte años y analizadas hoy en día.

Palabras clave: genotipos de Chattonella subsalsa; ecosistemas de transición; proliferaciones algales nocivas; LTER-Italia; ITS-5.8S rDNA; LSU rDNA.

Citation/Como citar este artículo: Stacca D., Satta C.T., Casabianca S., Penna A., Padedda B.M., Sechi N., Lugliè A. 2016. Identification of Chattonella (Raphidophyceae) species in long-term phytoplankton samples from Santa Giusta Lagoon, Italy. Sci. Mar. 80(1): 17-25. doi: http://dx.doi.org/10.3989/scimar.04292.09A

Editor: E. Garcés.

Received: June 15, 2015. Accepted: September 8, 2015. Published: December 11, 2015.

Copyright: © 2016 CSIC. This is an open-access article distributed under the Creative Commons Attribution-Non Commercial Lisence (by-nc) Spain 3.0.

Contents

Summary
Resumen
Introduction
Materials and methods
Results
Discussion
Acknowledgements
References

INTRODUCTIONTop

Chattonella Biecheler (Raphidophyceae) exhibits a worldwide distribution and includes deleterious species causing fish kills in natural environments and aquaculture systems (Imai and Yamaguchi 2012Imai I., Yamaguchi M. 2012. Life cycle, physiology, ecology and red tide occurrences of the fish-killing raphidophyte Chattonella. Harmful Algae 14: 46-70. and references therein). The existing Chattonella taxonomy is still debated. Imai and Yamaguchi (2012)Imai I., Yamaguchi M. 2012. Life cycle, physiology, ecology and red tide occurrences of the fish-killing raphidophyte Chattonella. Harmful Algae 14: 46-70., in their review, recognized five species: Chattonella antiqua (Hada) Ono, C. marina (Subrahmanyan) Hara et Chihara, C. minima Hara et Chihara, C. ovata Hara et Chihara, and C. subsalsa Biecheler. Previously, Demura et al. (2009)Demura M., Noël M.H., Kasai F., et al. 2009. Taxonomic revision of Chattonella antiqua, C. marina and C. ovata (Raphidophyceae) based on their morphological characteristics and genetic diversity. Phycologia 48(6): 518-535. had proposed three species, determining that C. antiqua and C. ovata were varieties of C. marina. Recently, a new C. cf. subsalsa genotype was discovered in the Mediterranean Sea (Adriatic Sea; Klöpper et al. 2013Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92.), and a distinct species was recognized and related to C. subsalsa in the Oman Sea, along the southeast coast of Iran (Attaran-Fariman and Bolch 2014Attaran-Fariman G., Bolch C.J.S. 2014. Morphology and genetic affinities of a novel Chattonella isolate (Raphidophyceae) isolated from Iran’s south coast (Oman Sea). Turk. J. Bot. 38: 156-168.).

Like the other raphidophytes, Chattonella species lack rigid cell walls. Consequently, their cellular shape and morphology are lost with fixation (Band-Schmidt et al. 2004Band-Schmidt C.J., Morquecho L., Hernandez-Becerril D.U., et al. 2004. Raphidophyceans on the coasts of Mexico. Hydrobiologia 515: 79-89., Zingone et al. 2006Zingone A., Siano R., D’Alelio D., et al. 2006. Potentially toxic and harmful microalgae from coastal waters of the Campania region (Tyrrhenian Sea, Mediterranean Sea). Harmful Algae 5: 321-337.), making their identification particularly difficult. Instead, molecular techniques enable the identification of Chattonella species, similarly to other raphidophytes, in fixed samples. Moreover, species identification by the molecular approach can be used in retrospective studies (Bowers et al. 2006Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348.).

On this basis, the first of our objectives was to identify which Chattonella species had been responsible for past blooms, in a part of the cases (four on five occasions) that coincided with fish kills in a Mediterranean lagoon (Santa Giusta Lagoon, Sardinia). In fact, although Bowers et al. (2006)Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348. have already reported C. subsalsa in Santa Giusta Lagoon (Oristano Lagoon Sardinia), we hypothesized that another species, C. marina, might also have been present, due to its morphological similarity to C. subsalsa and its overt harmfulness for fish (Imai and Yamaguchi 2012Imai I., Yamaguchi M. 2012. Life cycle, physiology, ecology and red tide occurrences of the fish-killing raphidophyte Chattonella. Harmful Algae 14: 46-70. and references therein). Other mass fish and invertebrate mortalities have been attributed to a C. antiqua monospecific bloom in the Mediterranean Sea (Alexandria, Egypt; Mikhail 2007Mikhail S.K. 2007. First monospecific bloom of the harmful raphidophyte Chattonella antiqua (Hada) Ono in Alexandria waters related to water quality and copepod grazing. Chem. Ecol. 23(5): 393-407.).

To achieve our objective, we used a qualitative polymerase chain reaction on archived fixed natural phytoplankton samples (hereinafter named archived samples) up to twenty-years old that were collected during past summer blooms in 1994, 1998, 1999, 2010 and 2013.

Until 2013, as stated above, all strains of C. subsalsa appeared to form a globally homogenous group (hereinafter named Global genotype, Bowers et al. 2006Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348.). Clear differences have been reported only recently among strains of the Global genotype and strains from the Adriatic Sea (hereinafter named the Adriatic genotype, Klöpper et al. 2013Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92.) and Oman Sea (Attaran-Fariman and Bolch 2014Attaran-Fariman G., Bolch C.J.S. 2014. Morphology and genetic affinities of a novel Chattonella isolate (Raphidophyceae) isolated from Iran’s south coast (Oman Sea). Turk. J. Bot. 38: 156-168.). Since Bowers et al. (2006)Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348. identified in Santa Giusta Lagoon C. subsalsa sequences coinciding with the Global genotype and we established the presence of the Adriatic genotype in the same lagoon in 2013, our hypothesis was that both C. subsalsa genotypes might have been present in the analysed archived samples. As a second objective of this study, we wanted to verify whether the same PCR-based assay could discriminate the two genotypes.

MATERIALS AND METHODSTop

Study area

Santa Giusta Lagoon (Italy, western Mediterranean Sea) is located along the west central coast of Sardinia Island (Fig. 1). It is a research station in part of the site “14 Sardinian marine ecosystems” of the LTER-Italy network (www.lteritalia.it). Santa Giusta Lagoon has an area of 8 km2 and a mean depth of 1 m. The two primary freshwater inputs are located on the lagoon’s east side and sea exchanges are on the western side. Santa Giusta underwent substantial human modification during the last century, resulting in profound ecosystem alterations (Sechi et al. 2001Sechi N., Fiocca F., Sannio A., et al. 2001. Santa Giusta Lagoon (Sardinia): phytoplankton and nutrients before and after waste water diversion. J. Limnol. 60(2): 194-200., Lugliè et al. 2002Lugliè A., Sechi N., Oggiano G., et al. 2002. Ecological assessment of Santa Giusta Lagoon (Sardinia, Italy). Ann. Chim-Rome 92: 239-247.). Sechi et al. (2001)Sechi N., Fiocca F., Sannio A., et al. 2001. Santa Giusta Lagoon (Sardinia): phytoplankton and nutrients before and after waste water diversion. J. Limnol. 60(2): 194-200. signalled its hypertrophy and reported several fish kill events associated with harmful algal blooms. Moreover, Satta et al. (2014)Satta C.T., Anglès S., Garcès E., et al. 2014. Dinoflagellate cyst assemblages in surface sediments from three shallow Mediterranean Lagoons (Sardinia, North Western Mediterranean Sea). Estuar Coasts 37: 646-663. reported the presence of harmful dinoflagellate cysts in the sediments.

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Fig. 1. – Santa Giusta Lagoon and sampling stations.

Sampling and phytoplankton analysis

The 27 archived samples analysed in this study (Table 1) belong to the LTER phytoplankton samples collection maintained at the Dipartimento di Architettura, Design e Urbanistica of the University of Sassari. They were collected from the water surface layer (–30 cm), from 3 to 5 stations (Fig. 1) during Chattonella blooms in the summers of 1994, 1998, 1999, 2010 and 2013, the first four coinciding with extensive fish mortalities. All samples were immediately fixed with Lugol’s iodine solution and analysed within ten days from sampling to assess Chattonella cell densities, following the Utermöhl method (Utermöhl 1958Utermöhl H. 1958. Zur vervollkommung der quantitativen phytoplankton-methodik. Verkandlungen der Internationalen Vereinigung für Theoretische und Angewandte, Limnol 9: 1-39.) and using an inverted Axiovert Zeiss 25 microscope. Further, within a few hours from the collection, live samples were always observed under the microscope for species identification.

Table 1. – List of analysed samples, Chattonella densities and PCR amplification assay results. +, positive amplification; –, negative amplification. * BLD, below the detection limit of <10 cells L–1.

Sampling date Station Chattonella density (cells 103 L–1) PCR amplifications
Chattonella subsalsa Chattonella marina
Undiluted DNA Diluted DNA Undiluted DNA Diluted DNA
03/08/1994 1 12,927 - - - + + + - - - - - -
3 30,243 - - - + + - - - - - - -
25/08/1994 5 187 + + - + + - - - - - - -
06/09/1994 3 831 + + - + + - - - - - - -
5 256 + + - + - - - - - - - -
03/09/1998 1 179 + + + + - - - - - - - -
5 3,249 + + + + + - - - - - - -
26/08/1999 2 3,692 + + - + + - - - - - - -
3 11,931 + + - + + - - - - - - -
07/09/1999 1 1,278 - - - + + - - - - - - -
2 1,315 + - - + - - - - - - - -
19/07/2010 3 399 + + - + + - - - - - - -
5 390 + + - + - - - - - - - -
17/07/2010 6 BLD* + + - - - - - - - - - -
3 BLD* - - - - - - - - - - - -
4 BLD* - - - - - - - - - - - -
22/07/2010 2 474 + + + + + - - - - - - -
3 2,191 + + - + + + - - - - - -
4 584 + + - + - - - - - - - -
24/07/2010 1 1,600 + + + + + + - - - - - -
3 1,827 + + - + + + - - - - - -
04/08/2010 2 898 + - - + + - - - - - - -
3 2,511 + + - - - - - - - - - -
05/04/2012 3 BLD* - - - - - - - - - - - -
30/07/2013 3 15 + + + + + + - - - - - -
5 34 + + + + + + - - - - - -
07/08/2013 3 65 + + + + + + - - - - - -

Cellular cultures

Five clonal cultures of C. cf. subsalsa (Adriatic genotype) were established from samples collected from Santa Giusta Lagoon in July 2013 (UNISS7, UNISS8, UNISS9, UNISS10, UNISS11). Vegetative cells were isolated with glass micropipettes and transferred into IWAKI tissue culture multiplates. Plates were filled with L1 medium (Guillard and Hargraves 1993Guillard R.R.L., Hargraves P.E. 1993. Stichochrysis immobilis is a diatom, not a chrysophyte. Phycologia 32(3): 234-236.) prepared with filtered seawater adjusted to a salinity of 35, and maintained at 20±1°C with a 12:12 light:dark cycle. Illumination was provided by a photon irradiance of 100 µmol m–2 s–1.

Reference cultures of C. subsalsa (CCMP217; Global genotype) from the Scandinavian Culture Collection of Algae & Protozoa (SCCAP) and C. antiqua (C. marina var. antiqua, NIES 1) (fixed with Lugol’s iodine solution) from the Provasoli-Guillard National Centre for Marine Algae and Micobiota (NCMA, formerly CCMP) were also acquired.

Artificial samples and DNA tests

Three artificial phytoplankton samples (Lugol-fixed, hereinafter named artificial samples) were used to create controlled conditions of presence of Global and Adriatic C. subsalsa genotypes and other algae, as could happen in natural conditions. The first sample contained CCMP217 and UNISS8 strains (sample A; i.e. both Global and Adriatic genotypes), the others only one of the two genotypes, respectively sample B the Global genotype (CCMP217) and sample C the Adriatic genotype (UNISS8; Table 2).

Table 2. – Species composition and cell abundances (cells 103 L–1) of the analysed artificial samples.

Sample A Sample B Sample C
C. subsalsa CCMP217 816 816 0
C. cf. subsalsa Adriatic Genotype 764 0 764
Alexandrium minutum Halim 304 304 304
Amphidinium carterae Hulburt 550 550 550
Scrippsiella sp. 694 694 694
Cylindrotheca sp. 490 490 490

Further, we mixed in different proportions the DNA extracted from two different cultures of C. subsalsa genotypes (CCMP217 and UNISS8, respectively) by performing six tests (hereinafter named DNA tests, Table 3) to verify whether different DNA concentrations might affect the ITS-5.8S rDNA amplification region.

Table 3. – List of tests carried out using the two C. subsalsa genotypes with different DNA concentrations (ng µL–1).

C. subsalsa CCMP217 C. cf. subsalsa UNISS8 Concentration ratio
TEST 1 5.65 11.29 1:2
TEST 2 2.26 11.29 1:5
TEST 3 1.13 11.29 1:10
TEST 4 0.45 11.29 1:25
TEST 5 0.26 11.29 1:50
TEST 6 0.11 11.29 1:100

Molecular analyses

DNA was extracted with the DNeasy Plant Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions from 50 mL of archived samples, artificial samples and from 15 mL of fixed cultures (Fig. 2).

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Fig. 2. – Scheme of the protocol used; in the first passage, 50 mL of archived samples, 15 mL of artificial samples or 15 mL of cultures were used.

PCR analyses were performed on archived samples from at least two of the sampled stations for each sampling date (Table 1). An archived sample with C. subsalsa abundance below the detection limit (<10 cells L–1) and from a season not favourable to C. subsalsa growth (Station 3 of 5/4/2012) was used as a negative control. A first PCR was performed with 1 µL of extracted DNA (Fig. 2) in a total of 40.5 µL reaction mixture containing the following: 0.25 mM of each dNTP; 0.1µM of each primer; 2.5 mM MgCl2; 1x HotMaster Taq Buffer (PRIME, Hamburg, Germany); and 2.5 U Taq DNA polymerase (PRIME). ITSA and ITSB primers (Adachi et al. 1994Adachi M., Sako Y., Ishida Y. 1994. Restriction fragment length polymorphism of ribosomal DNA internal transcribed spacer and 5.8S regions in Japanese Alexandrium species (Dinophyceae). J. Phycol. 30: 857-863.) were used to amplify the internal transcribed spacer (ITS) regions and 5.8S rDNA. PCR conditions were as follows: an initial denaturation step at 94°C for 5 min, followed by 35 cycles at 94°C for 20 s, 57°C for 10 s, and 70°C for 30 s; and a final elongation step at 70°C for 5 min. Six PCR replicates for each sample were performed, three with undiluted DNA and three with 1:10 diluted DNA (Fig. 2). Subsequently, 1 µL of each PCR product was used in two distinct nested PCR amplifications (Fig. 2), with the same mixture condition as above. These two different nested PCRs were carried out with specific primers: oBTG-005-F (CTGGGGAAGGATCATTACC) and oBTG-027-R (GCCGATTGCTTCCAGAGA) for C. marina, and oBTG-005-F and oBTG-028-R(CGCCACTCGTTGCCCAGT) for C. subsalsa (Connell 2002Connell L. 2002. Rapid identification of marine algae (Raphidophyceae) using three-primer PCR amplification of nuclear internal transcribed spacer (ITS) regions from fresh and archived material. Phycologia 41(1): 15-21.). Nested PCR conditions were as follows: an initial denaturation step at 95°C for 5 min; then 35 cycles at 95°C for 30 s, 55°C for 10 s (using species-specific primers for C. marina) or 45°C for 10 s (using species-specific primers for C. subsalsa), and 72°C for 30 s; and a final elongation step at 72°C for 10 min. The DNA extracted from the cultures C. subsalsa CCMP217 and C. antiqua (C. marina var. antiqua) NIES 1 were used as a positive control in each PCR on the analysed archived samples.

Genetic analyses were also conducted to confirm species and genotype identification of the five C. cf. subsalsa UNISS7, UNISS8, UNISS9, UNISS10, UNISS11 cultures. For the ITS-5.8S rDNA sequences, the first PCR was performed using ITSA and ITSB primers (Adachi et al. 1994Adachi M., Sako Y., Ishida Y. 1994. Restriction fragment length polymorphism of ribosomal DNA internal transcribed spacer and 5.8S regions in Japanese Alexandrium species (Dinophyceae). J. Phycol. 30: 857-863.) and the nested PCR with primers oBTG-005-F and oBTG-028-R (Connell 2002Connell L. 2002. Rapid identification of marine algae (Raphidophyceae) using three-primer PCR amplification of nuclear internal transcribed spacer (ITS) regions from fresh and archived material. Phycologia 41(1): 15-21.), with the same PCR protocol as that described above. PCR primers D1R and D2C (Scholin et al. 1994Scholin C.A., Herzog M., Sogin M., et al. 1994. Identification of group and strain-specific genetic markers for globally distributed Alexandrium (Dinophyceae). 2. Sequence analysis of a fragment of the LSU rRNA gene. J. Phycol. 30(6): 999-1011.) were used to amplify the LSU rDNA. PCR was carried out in 50-μL reactions containing 1 μL of DNA extract, 0.8 µM of each primer, 200 µM of dNTPs (Qiagen mix), PCR Buffer 1X (Qiagen) containing 1.5 mM of MgCl2, and 1.25 U of Taq DNA polymerase. Thermocycling included one initial step at 95°C for 5 min followed by 40 cycles at 95°C for 20 s, 55°C and at 72°C for 1 min, followed by a final extension at 72°C for 10 min.

The whole protocol applied on archived samples was also tested on the three artificial samples (Fig. 2, Table 2). The same PCR-based assay was also applied on the six DNA tests (Table 3). The DNA concentration was evaluated with the SmartSpecTM Plus Spectrophotometer (Bio-rad) following the manufacturer’s instruction.

All PCR amplifications were performed in a DNA Engine® Thermal Cycler.

All PCR products were resolved on a 1.8% (80v) agarose gel. All nested PCR products were purified and sequenced by an external service (Macrogen Inc., Europe) using both primers, and a 3730XL DNA sequencer.

Phylogenetic analyses

Sequences obtained in this study were compared with sequences in the NCBI Nucleotide Collection (BLAST Algorithm; http://www.ncbi.nlm.-nih.gov) to determine the closest known sequences. Sequences were also aligned with those obtained from GenBank (Table 4 and 5) using the MAFFT v.6 program (Katoh et al. 2002Katoh K., Misawa K., Kuma K., et al. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14): 3059-3066.) under FFT-NS-i (slow; iterative refinement method). Alignments were manually checked with BioEdit v. 7.0.5 (Hall 1999Hall T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acid. S. 41: 95-98.). Phylogenetic relationships, based on the LSU rDNA data (Table 5), were inferred using maximum likelihood (ML) method and the GTRGAMMA evolution model on Randomized Axelerated Maximum Likelihood v. 7.0.4 (RA×ML) (Stamatakis 2006Stamatakis A. 2006. RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models. Bioinformatics 22(21): 2688-2690.). All model parameters were estimated by RA×ML, using Pseudochattonella verruculosa strains from public databases as an outgroup. The tree with the best topology (the one with the greatest likelihood of 1000 alternative trees) was selected by repeated runs on distinct starting trees. Bootstrap ML analysis was done with 1000 pseudo-replicates and the consensus tree was computed with the RA×ML software.

Table 4. – ITS-5.8S rDNA sequences obtained in this study and the sequences deposited at GenBank which showed a strong similarity with ours in the BLAST analysis.

Accession number Geographical origin Strain code or source References
AB334367 Gulf of Mexico, USA CCMP 217 Demura et al. 2009Demura M., Noël M.H., Kasai F., et al. 2009. Taxonomic revision of Chattonella antiqua, C. marina and C. ovata (Raphidophyceae) based on their morphological characteristics and genetic diversity. Phycologia 48(6): 518-535.
AB334368 Indian River Bay, USA CCMP 2191 Demura et al. 2009Demura M., Noël M.H., Kasai F., et al. 2009. Taxonomic revision of Chattonella antiqua, C. marina and C. ovata (Raphidophyceae) based on their morphological characteristics and genetic diversity. Phycologia 48(6): 518-535.
AF153196 Gulf of Mexico, USA CCMP 217 Connell 2000Connell L.B. 2000. Nuclear ITS region of the alga Heterosigma akashiwo (Chromophyta: Raphidophyceae) is identical in isolates from Atlantic and Pacific basins. Mar. Biol. 136: 953-960.
AF409126 / / Ben Ali et al. 2002Ben Ali A., De Baere R., De Wachter R., et al. 2002. Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA. Protist 153(2): 123-132.
AY858864 Seto Island Sea, Japan CMSTAC J04 C. Tomas Japan Bowers et al. 2006Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348.
AY858866 Salton Sea, California, USA CMSTAC SS 4 C. Tomas California Bowers et al. 2006Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348.
AY858868 New River, North Carolina, USA CMSTAC NR 22 C. Tomas North Carolina Bowers et al. 2006Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348.
AY858869 Santa Giusta Lagoon, Sardinia, Italy CMSTAC OL 4 C. Tomas Sardinia Bowers et al. 2006Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348.
DQ191680 Delaware Inland Bays, USA CCMP 2191 Zhang et al. 2006Zhang Y., Fu F.-X., Whereat E., Coyne K.J., Hutchins D.A. 2006. Bottom-up controls on a mixed-species HAB assemblage: A comparison of sympatric Chattonella subsalsa and Heterosigma akashiwo (Raphidophyceae) isolates from the Delaware Inland Bays. Harmful Algae 5: 310-320.
JF896101 Iran CHPI36 Attaran-Fariman and Bolch 2014 Attaran-Fariman G., Bolch C.J.S. 2014. Morphology and genetic affinities of a novel Chattonella isolate (Raphidophyceae) isolated from Iran’s south coast (Oman Sea). Turk. J. Bot. 38: 156-168.
JF907041 Bahia de Navachiste, Sinaloa, Mexico CSNAV-1 Band-Schmidt et al. 2012 Band-Schmidt C.J., Martínez-López A., Bustillos-Guzmán J.J., et al. 2012. Morphology, biochemistry, and growth of raphidophyte strains from the Gulf of California. Hydrobiologia 693: 81-97.
JX067584 Adriatic Sea, Rimini, Italy CRIM_F Klöpper et al. 2013Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92.
JX067585 Adriatic Sea, Rimini, Italy CRIM_E Klöpper et al. 2013Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92.
KR709213 Santa Giusta Lagoon, Italy UNISS7 This study
KR709214 Santa Giusta Lagoon, Italy UNISS8 This study
KR709215 Santa Giusta Lagoon, Italy UNISS9 This study
KR709216 Santa Giusta Lagoon, Italy UNISS10 This study
KR709217 Santa Giusta Lagoon, Italy UNISS11 This study
KR709218 Gulf of Mexico, USA CCMP217 This study

Table 5. – List of the species, strains, geographical origin and GenBank accession numbers of species used in the LSU rDNA phylogenetic tree. * obtained in this study.

Species Strain code or source Geographical origin Accession Number
Fibrocapsa cf. japonica FRIM_A Adriatic Sea, Rimini, Italy JX067577
FRIM_B Adriatic Sea, Rimini, Italy JX067578
FRIM_C Adriatic Sea, Rimini, Italy JX067574
FRIM_D Adriatic Sea, Rimini, Italy JX067575
FRIM_E Adriatic Sea, Rimini, Italy JX067576
F. japonica Toriumi et Takano  CCMP1661 Port Phillip Bay, Australia JX067580
Fibjap_JG North Sea, Germany: JX067579
LB2162 / AF086949
Haramonas dimorpha Horiguchi 1996 CCMP2053 Queensland, Australia JX067581
Heterosigma akashiwo (Hada) Hada ex Hara et Chihara  NIES-145 Kagoshima, Japan AB217645
893 / AB217646
OS-11 / AB217647
/ Korea JX067554
CCMP2274 California, USA JX067555
C. subsalsa Biecheler / / AF409126
CCMP217 Gulf of Mexico, USA JX067559
CCMP217 Gulf of Mexico, USA AF210736
CCMP217 Gulf of Mexico, USA KR709212*
C. cf. subsalsa CHPI36 Iran JF896100
C. cf. subsalsa Adriatic R281 Gulf of Naples, Italy JN390438
CRIM_A Rimini, Adriatic, Italy JX067560
CRIM_B Rimini, Adriatic, Italy JX067562
CRIM_C Rimini, Adriatic, Italy JX067568
CRIM_D Rimini, Adriatic, Italy JX067564
CRIM_E Rimini, Adriatic, Italy JX067567
CRIM_F Rimini, Adriatic, Italy JX067563
CRIM_G Rimini, Adriatic, Italy JX067572
CRIM_H Rimini, Adriatic, Italy JX067561
CRIM_I Rimini, Adriatic, Italy JX067571
CRIM_J Rimini, Adriatic, Italy JX067570
CRIM_K Rimini, Adriatic, Italy JX067565
CRIM_L Rimini, Adriatic, Italy JX067566
CRIM_M Rimini, Adriatic, Italy JX067569
CRIM_N Rimini, Adriatic, Italy JX067573
UNISS7 Santa Giusta Lagoon, Italy KR709207*
UNISS8 Santa Giusta Lagoon, Italy KR709208*
UNISS9 Santa Giusta Lagoon, Italy KR709209*
UNISS10 Santa Giusta Lagoon, Italy KR709210*
UNISS11 Santa Giusta Lagoon, Italy KR709211*
Chattonella marina var. antiqua (Hada) Demura & Kawachi, comb et stat. nov. CCMP2052 Aichi, Japan JX067556
G8 / AB217634
NIES-1 Harima-Nada, Japan AB217631
NIES-1 Harima-Nada, Japan AF210737
NIES-558 Mikawa Bay, Japan AB217632
NIES-86 Uranouchi Bay, Japan AB217868
OA-3 / AB217633
C. marina var. marina (Subrahmanyan) Hara et Chihara  S-11 / AB217637
NIES-559 Maizuru Bay, Japan AB217636
G-12 / AB217638
MS-3-P / AB217639
NIES-121 Kagoshima Bay, Japan AB217635
/ Hong Kong AY704162
CCMP-217 / AF210739
CCMP2049 Kagoshima, Japan JX067557
Chattonella marina var. ovata (Y. Hara & Chihara)
Demura & Kawachi, comb. et stat. nov.
NIES-603 Harima-Nada, Japan AB217640
ovata-P / AB217641
/ Hong Kong AY704163
NIES-603 Harima-Nada, Japan AF210738
Pseudochattonella verruculosa Hosoi-Tanabe 2007 NIES 670 Harima-Nada, Japan AM040504
NIES-670 Harima-Nada, Japan AB217642
ver-P / AB217643

RESULTSTop

Archived samples

Through the sequencing and BLAST analysis of the nested PCR products, C. subsalsa was detected in all archived samples, which resulted positive also for microscope analysis (Table 1). The only exception was a sample taken before the beginning of the bloom in 2010 (17/7/2010), for which PCR results were positive and microscope analysis negative, and the sample was assumed as negative (Station 3 of 5/4/2012).

All PCR products unequivocally belonged to C. subsalsa, with control DNA of 380 bp length for C. subsalsa CCMP217 (Fig 3a, GenBank accession number KR709218) and 181 bp for C. antiqua (C. marina var. antiqua) NIES 1 (Fig 3b).

sm4292fig3.jpg

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Fig. 3. – Nested PCR amplification products using an EasyLadder I - Bioline (L) for C. subsalsa and C. antiqua (C. marina var. antiqua) NIES 1: a) C. subsalsa, six replicates of 22-7-2010 (station 2) sample with five positive PCR amplifications (2-6), the positive control using CCMP217 culture (+), and the negative control (–); b) C. marina, six replicates of 22-7-2010 (station 3) sample with six negative PCR amplifications (1-6), three replicates of C. antiqua (C. marina var. antiqua) NIES 1 culture as positive controls (+), and the negative control (–).

ITS-5.8S rDNA sequences comparison among sequences from the 24 archived samples and those of C. subsalsa deposited in GenBank (Table 4) yielded a BLAST analysis with a 99%-100% similarity with the Global genotype sequences, 96%-97% sequence identity with the C. cf. subsalsa strains CRIM E and CRIM F (i.e. Adriatic genotype) and 98%-99% sequence identity with the C. cf. subsalsa strain CHPI36.

Cellular cultures

The nested PCR on cellular cultures produced six ITS-5.8S rDNA sequences (Table 4), four of which were of 573 bp (UNISS7, UNISS8, UNISS9, UNISS10 strains) and one of 576 pb (UNISS11 strain). These five sequences were longer than the nested PCR product of CCMP217 strain (380 pb) (Fig. 4).

sm4292fig4.jpg

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Fig. 4. – Nested PCR amplification products using an EasyLadder I - Bioline (L) for C. cf. subsalsa Adriatic genotype (where C1AS, C1DS are the UNISS7 strain and C7AS, C7DS are the UNISS11 strain), C. subsalsa CCMP217 culture (+S), and two negative controls (=, –).

The MAFT alignment among the oBTG-028-R primer and the ITS-5.8S rDNA sequences of C. subsalsa strains (UNISS7, UNISS9, CCMP217, CRIM E and C. Tomas Sardinia) indicated seven differences for UNISS7, UNISS9, CRIM E strains (i.e. Adriatic genotype) with respect to the CCMP217 and C. Tomas Sardinia strains (i.e. Global genotype). The BLAST analysis of 5.8S-ITS rDNA sequences showed a 99%-100% similarity of UNISS7, UNISS8, UNISS9, UNISS10 and UNISS11 strains with C. cf. subsalsa CRIM E and CRIM F strains and 94%-96% sequence identity with all C. subsalsa Global sequences (Table 4).

The six LSU rDNA partial sequences were long 652 pb for UNISS7, 650 pb for UNISS8, UNISS10 and UNISS11, 651 pb for UNISS9 and 643 pb for CCMP217. The ML phylogenetic tree obtained for LSU rDNA sequences showed that C. subsalsa strains divided into two distinct groups (Fig. 5). The first group showed a branch with the only C. cf. subsalsa CHPI36 and another with C. subsalsa CCMP217 and C. subsalsa AF409126. The second group included all C. cf. subsalsa Adriatic genotype (Klöpper et al. 2013Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92.) and UNISS7, UNISS8, UNISS9, UNISS10, UNISS11 strains, with a bootstrap value of 100%. All strains of C. marina var. marina, C. marina var. ovata, and C. marina var. antiqua grouped together with a 100% bootstrap support.

sm4292fig5.jpg

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Fig. 5. – Maximum likelihood (ML) phylogenetic tree of LSU rDNA sequences among Chattonella-like species. C. subsalsa CCMP217_UNISS12 is the sequence obtained in this study for the C. subsalsa Global genotype (KR709212), Pseudochattonella verruculosa strains from public databases were used as an outgroup. Bootstrap values (>70%) are shown respectively at each node.

Artificial samples and DNA tests

The nested PCR of the samples A and B produced sequences with a length of 380 pb belonging to C. subsalsa CCMP217. The nested PCR of sample C produced a sequence with a length of 573 pb belonging to C. cf. subsalsa UNISS8.

The nested PCR of DNA tests produced sequences with a length of 380 pb belonging to the CCMP217 strain even when C. cf. subsalsa UNISS8 had a concentration one hundred times higher.

DISCUSSIONTop

Chattonella is one of the raphidophyte genera which includes species associated with fish kills (Hallegraeff and Hara 2003Hallegraeff G.M., Hara Y. 2003. Taxonomy of harmful marine raphidophytes. In: Hallegraeff G.M., Anderson D.M., Cembella A.D. (eds), Manual on harmful marine microalgae. Monographs on Oceanographic Methodology. Methodology 11, Unesco Paris, pp. 511-522.). The searching out of these taxa in recent investigations and in time series data has been very difficult due to the loss of necessary morphological characteristics in fixed samples (Klöpper et al. 2013Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92.), and presumably due to low cell abundance in coastal areas (Imai et al. 2006Imai I., Yamaguchi M., Hori Y. 2006. Eutrophication and occurrences of harmful algal blooms in the Seto Inland Sea. Plank. Benth. Res. 1: 71-84.). Consequently, Chattonella species often become evident only when harmful events occur. Further, whereas harmful Chattonella blooms have been well documented on East Asian coasts, i.e. those of Japan, Korea (Kim et al. 2007Kim S.Y., Seo K.S., Lee C.K., et al. 2007. Diurnal modification of a red tide causing organisms, Chattonella antiqua (Raphidophyceae) from Korea. Algae 22: 95-106.), China (Tseng et al. 1993Tseng C.K., Zhou M.J., Zou J.Z. 1993. Toxic phytoplankton studies in China. In: Smayda T.J., Shimizu Y. (eds), Toxic Phytoplankton Blooms in the Sea. Elsevier, New York, pp. 347-352.), India (Subrahmanyan 1954Subrahmanyan R. 1954. On the life-history and ecology of Hornellia marina gen. et sp. nov., (Chloromonadineae), causing green discoloration of the sea and mortality among marine organisms off the Malabar Coast. Indian J. Fish. 1: 182-203., Jugnu and Kripa 2009Jugnu R., Kripa V. 2009. Effect of Chattonella marina [(Subrahmanyan) Hara et Chihara 1982] bloom on the coastal fishery resources along Kerala coast, India. Indian J. Mar. Sci. 38: 77-88.), South Australia (Hallegraeff et al. 1998Hallegraeff G.M., Munday B., Baden D., et al. 1998. Chattonella marina (Raphidophyte) bloom associated with mortality of cultured bluefin tuna (Thunnus maccoyii) in south Australia. In: Reguera B., Blanco J., Fernandez M.L., et al. (eds), Harmful Algae. Xunta de Galicia and IOC-UNESCO, Vigo, Paris, pp. 93-96.), and southeast USA (California, Tomas 1998Tomas C. 1998. Blooms of potentially harmful raphidophycean flagellates in Florida coastal waters. In: Reguera B., Blanco J., Fernandez M.L., et al. (eds), Harmful Algae. Xunta de Galicia and IOC-UNESCO, pp. 101-103., Lewitus et al. 2008Lewitus A.J., Brock L.M., Burke M.K., et al. 2008. Lagoonal stormwater detention ponds as promoters of harmful algal blooms and eutrophication along the South Carolina coast. Harmful Algae 8: 60-65.), in the last few decades (Imai and Yamaguchi 2012Imai I., Yamaguchi M. 2012. Life cycle, physiology, ecology and red tide occurrences of the fish-killing raphidophyte Chattonella. Harmful Algae 14: 46-70.) they have been less frequently reported from Mediterranean coastal areas, including lagoons and other transitional ecosystems (Mikhail 2007Mikhail S.K. 2007. First monospecific bloom of the harmful raphidophyte Chattonella antiqua (Hada) Ono in Alexandria waters related to water quality and copepod grazing. Chem. Ecol. 23(5): 393-407.). The use of molecular methods to detect the presence of Chattonella species is a viable alternative approach to expedite and facilitate identification in fixed natural samples (Connell 2002Connell L. 2002. Rapid identification of marine algae (Raphidophyceae) using three-primer PCR amplification of nuclear internal transcribed spacer (ITS) regions from fresh and archived material. Phycologia 41(1): 15-21., Bowers et al. 2006Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348.; Marin and Scholin 2010Marin III R., Scholin C. 2010. Sandwich Hybridization. In: Karlson B., Cusack C., Bresnan E. (eds), Microscopic and molecular methods for quantitative phytoplankton analysis. IOC Man Guides 55, Unesco Paris, pp 87-110.), as has been experienced for other harmful species (Penna et al. 2007Penna A., Bertozzini E., Battocchi C., et al. 2007. Monitoring of HAB species in the Mediterranean Sea through molecular techniques. J. Plankton Res. 29: 19-38.).

Between C. marina and C. subsalsa, the former is the most notorious fish-killing species and has caused severe damage to fish farming and wild fish populations, with great economic losses (Imai and Yamaguchi 2012Imai I., Yamaguchi M. 2012. Life cycle, physiology, ecology and red tide occurrences of the fish-killing raphidophyte Chattonella. Harmful Algae 14: 46-70.). C. subsalsa has exhibited relatively more recent history as a deleterious species, and data on this species is scarce (Imai and Yamaguchi 2012Imai I., Yamaguchi M. 2012. Life cycle, physiology, ecology and red tide occurrences of the fish-killing raphidophyte Chattonella. Harmful Algae 14: 46-70.). Cell morphology shows overlapping characters between C. subsalsa and C. marina, as emphasized by Hallegraeff and Hara (2003)Hallegraeff G.M., Hara Y. 2003. Taxonomy of harmful marine raphidophytes. In: Hallegraeff G.M., Anderson D.M., Cembella A.D. (eds), Manual on harmful marine microalgae. Monographs on Oceanographic Methodology. Methodology 11, Unesco Paris, pp. 511-522.. Consequently, species identification with microscopic methods is uncertain, especially on fixed samples, whereas molecular techniques appear useful for obtaining valuable results.

Bowers et al. (2006)Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348. have already reported C. subsalsa in Santa Giusta Lagoon, analysing a strain obtained from a non-bloom sample (Lugliè A., personal communication). Our study considered a longer and more detailed temporal scale in the same Mediterranean lagoon and documented the presence of C. subsalsa also during four past harmful events coinciding with fish kills (1994, 1998, 1999, 2010), and a bloom in 2013 (cells density up to 65 103 L–1). The use of molecular investigative techniques on archived samples collected over time up to 20 years old allowed us to identify unequivocally the species and helped increase knowledge of C. subsalsa in the Mediterranean Sea. Indeed, this geographical area is not yet well documented for this species, though its type locality is a Mediterranean lagoon (Thau Lagoon, Salins de Villeroy, Sète; Biecheler 1936Biecheler B. 1936. Sur une Chloromonadine nouvelle d’eau saumatre Chattonella subsalsa n. gen., n. sp. Arch. Zool. Exp. Gen. 78: 79-83.). Although we cannot support a cause-effect relationship between C. subsalsa blooms and fish kills, which have been observed concurrently over the years, our results can confirm that when harmful events occurred, C. subsalsa was present. On-going studies integrating our long-term ecological data will offer further detailed scenarios on the environmental conditions accompanying these events.

A further new knowledge that emerged from our results was the presence of the C. cf. subsalsa Adriatic genotype in the Santa Giusta Lagoon, thanks to the analyses on the cultures obtained in 2013. This is the first unequivocal evidence of this genotype in a Mediterranean lagoon and in a different place to those of its first ascertainment (Klöpper et al. 2013Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92.). The analyses performed to assess whether both genotypes had been present in the archived samples could not resolve the question. In fact, the positive results of the PCR only for C. subsalsa Global genotype in the archived samples, artificial samples A and B and DNA tests could be explained because of the differences in the DNA bases of the two C. subsalsa genotypes where the oBTG-028-R primer binds. This is a specific primer constructed by Connell (2002)Connell L. 2002. Rapid identification of marine algae (Raphidophyceae) using three-primer PCR amplification of nuclear internal transcribed spacer (ITS) regions from fresh and archived material. Phycologia 41(1): 15-21. for C. subsalsa CCMP217 Global genotype. The length of C. subsalsa Global genotype sequences obtained in this study was in accordance with Connell (2002)Connell L. 2002. Rapid identification of marine algae (Raphidophyceae) using three-primer PCR amplification of nuclear internal transcribed spacer (ITS) regions from fresh and archived material. Phycologia 41(1): 15-21., whereas C. cf. subsalsa Adriatic genotype sequences were longer, indicating a different primer response. Therefore, this primer cannot discriminate the two C. subsalsa genotypes when they are present at the same time. On this basis, because of the positivity of C. subsalsa Global genotype in all archived samples, we cannot state whether the blooms were due to the contemporaneous presence of both the genotypes. However, for the same reason, we can state that none of them was due only to the C. cf. subsalsa Adriatic genotype.

In conclusion, our results support the recent studies of Klöpper et al. (2013)Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92. and Attaran-Fariman and Bolch (2014)Attaran-Fariman G., Bolch C.J.S. 2014. Morphology and genetic affinities of a novel Chattonella isolate (Raphidophyceae) isolated from Iran’s south coast (Oman Sea). Turk. J. Bot. 38: 156-168., highlighting the existence of clearly distinct strains of C. subsalsa. We also support the “overlapping hypothesis” of the two genotypes, Adriatic and Global, in the same geographical area (Klöpper et al. 2013Klöpper S., John U., Zingone A., et al. 2013. Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Eur. J. Phycol. 48(1):79-92.). In fact, in addition to our assessment of the C. cf. subsalsa Adriatic genotype in Santa Giusta Lagoon and the previous record of the C. subsalsa Global genotype at the same site (Bowers et al. 2006Bowers H., Tomas C., Tengs T., et al. 2006. Raphidophyceae [Chadefaud ex Silva] systematics and rapid identification: sequence analyses and real-time PCR assays. J. Phycol. 42: 1333-1348.), we also confirm the presence of the Global genotype along the western Sardinian coasts (Bosa beach; data not published).

The need for further studies is evident, using a plurality of markers on strains from additional Mediterranean and world sites, in order to ascertain the possibility of different new species.

ACKNOWLEDGEMENTSTop

This study was produced as part of the PhD dissertation in Environmental Biology from the University of Sassari, Academic year 2010-2011 – 26th cycle, with the support of a grant funded with resources from the POR SARDINIA F.S.E. 2007-2013 – Objective Regional Competitiveness and Employment, Human Capital Priority IV, Line Operation l.3.1. The authors thank Adriana Zingone of the Laboratory of Marine Botany, Stazione Zoologica “A. Dohrn”, Napoli, Italy for her support and advice on the analyses.

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