High-level congruence of Myrionecta rubra prey and Dinophysis species plastid identities as revealed by genetic analyses of isolates from Japanese coastal waters

A novel parasite strain of Amoebophrya sp. infecting the toxic dinoflagellate Alexandrium catenella (Group I) and its effect on the host bloom in Osaka Bay, Japan

The endoparasitic dinoflagellates belonging to the genus Amoebophrya can infect a broad range of free-living marine dinoflagellates, including harmful/toxic species. The parasite kills its host; the high prevalence of the parasite has been suggested to be a significant factor for the termination of dinoflagellate blooms in marine systems. The issues involved in culturing host-parasite systems have greatly restricted further research on Amoebophrya biology. Here, we established the culture of a novel strain of Amoebophrya sp. ex Alexandrium catenella (Group I) from Osaka Bay, Japan, and studied its genetic diversity, host specificity, and prevalence in the field. Genetic analysis established that the strain we isolated was a novel culture strain infecting A. catenella. Among the host species tested, the Amoebophrya sp. could infect the genera Alexandrium and Prorocentrum in culture, and the infection was also confirmed in the genus Tripos in a field sample. A maximum prevalence of 73% was recorded during the Alexandrium bloom period in Osaka Bay, after which the host cell density rapidly declined. Our results indicated that the existence of the parasite had a significant effect on the dynamics of A. catenella, especially on the termination of the blooms.

Genomic Insights into Plastid Evolution

The origin of plastids (chloroplasts) by endosymbiosis stands as one of the most important events in the history of eukaryotic life. The genetic, biochemical, and cell biological integration of a cyanobacterial endosymbiont into a heterotrophic host eukaryote approximately a billion years ago paved the way for the evolution of diverse algal groups in a wide range of aquatic and, eventually, terrestrial environments. Plastids have on multiple occasions also moved horizontally from eukaryote to eukaryote by secondary and tertiary endosymbiotic events. The overall picture of extant photosynthetic diversity can best be described as “patchy”: Plastid-bearing lineages are spread far and wide across the eukaryotic tree of life, nested within heterotrophic groups. The algae do not constitute a monophyletic entity, and understanding how, and how often, plastids have moved from branch to branch on the eukaryotic tree remains one of the most fundamental unsolved problems in the field of cell evolution. In this review, we provide an overview of recent advances in our understanding of the origin and spread of plastids from the perspective of comparative genomics. Recent years have seen significant improvements in genomic sampling from photosynthetic and nonphotosynthetic lineages, both of which have added important pieces to the puzzle of plastid evolution. Comparative genomics has also allowed us to better understand how endosymbionts become organelles.

Dinophysis Ehrenberg (Dinophyceae) in Southern Chile harbours red cryptophyte plastids from Rhodomonas/Storeatula clade

Photosynthetic species of the dinoflagellate genus Dinophysis are known to retain temporary cryptophyte plastids of the Teleaulax/Plagioselmis/Geminigera clade after feeding the ciliate Mesodinium rubrum. In the present study, partial plastid 23S rDNA sequences were retrieved in Southern Chilean waters from oceanic (Los Lagos region), and fjord systems (Aysén region), in single cells of Dinophysis and accompanying organisms (the heliozoan Actinophrys cf. sol and tintinnid ciliates), identified by means of morphological discrimination under the light microscope. All plastid 23S rDNA sequences (n = 23) from Dinophysis spp. (Dinophysis acuta, D. caudata, D. tripos and D. subcircularis) belonged to cryptophytes from clade V (Rhinomonas, Rhodomonas and Storeatula), although they could not be identified at genus level. Moreover, five plastid sequences obtained from heliozoans (Actinophryida, tentatively identified as Actinophrys cf. sol), and tintinnid ciliates, grouped together with those cryptophyte sequences. In contrast, two additional sequences from tintinnids belonged to other taxa (chlorophytes and cyanobacteria). Overall, the present study represents the first time that red cryptophyte plastids outside of the Teleaulax/Plagioselmis/Geminigera clade dominate in wild photosynthetic Dinophysis spp. These findings suggest that either Dinophysis spp. are able to feed on other ciliate prey than Mesodinium and/or that cryptophyte plastids from clade V prevail in members of the M. rubrum species complex in the studied area.

Dimorphism in the Antarctic cryptophyte Geminigera cryophila (Cryptophyceae)

A pink to red-pigmented cryptophyte of undetermined taxonomic affinity was isolated and cloned from two seasonally ice-covered. meromictic, saline Antarctic aquatic environments: Bayly Bay (BB) and Ace Lake (AL). The clones shared a number of morphological and ultrastructural similarities with other cryptomonad genera, which confounded identification by light and electron microscopy. Cellular pigments extracted from the AL clone showed an absorption maximum corresponding to the biliprotein Cr-phycoerythrin 545, thus narrowing its potential taxonomic affinities. Partial 18S SSU ribosomal gene sequences were isolated from both the AL and the BB cryptomonads' nuclear rDNA, whereas PCR-amplified and their molecular phylogenies inferred from the subject sequences. Our results, and the results of another study that used our prepublished sequence data, invariably resolved both clones as very close matches with the Antarctic cryptophyte, Geminigera cryophila. When combined, the morphological, chemical, and molecular evidence suggested that both of our cryptophyte clones were a cryptomorph of the G. cryophila campylomorph. Slight differences between the AL and BB nuclear tree reconstructions suggested divergent microevolution following long-term isolation of the AL population from the surrounding marine ecosystem. This study provides further compelling evidence that certain Cryptophyceae engage in a life-history strategy, which includes alternating morphologically distinct cell-types (dimorphism); cell-types which without molecular analyses could be mistaken as novel taxa.

Unveiling the hidden genetic diversity and chloroplast type of marine benthic ciliate Mesodinium species

Ciliate Mesodinium species are commonly distributed in diverse aquatic systems worldwide. Among Mesodinium species, M. rubrum is closely associated with microbial food webs and red tide formation and is known to acquire chloroplasts from its cryptophyte prey for use in photosynthesis. For these reasons, Mesodinium has long received much attention in terms of ecophysiology and chloroplast evolution. Mesodinium cells are easily identifiable from other organisms owing to their unique morphology comprising two hemispheres, but a clear distinction among species is difficult under a microscope. Recent taxonomic studies of Mesodinium have been conducted largely in parallel with molecular sequence analysis, and the results have shown that the best-known planktonic M. rubrum in fact comprises eight genetic clades of a M. rubrum/M. major complex. However, unlike the planktonic Mesodinium species, little is known of the genetic diversity of benthic Mesodinium species, and to our knowledge, the present study is the first to explore this. A total of ten genetic clades, including two clades composed of M. chamaeleon and M. coatsi, were found in marine sandy sediments, eight of which were clades newly discovered through this study. We report the updated phylogenetic relationship within the genus Mesodinium comprising heterotrophic/mixotrophic as well as planktonic/benthic species. Furthermore, we unveiled the wide variety of chloroplasts of benthic Mesodinium, which were related to the green cryptophyte Chroomonas/Hemiselmis and the red cryptophyte Rhodomonas/Storeatula/Teleaulax groups.

Growth and Chloroplast Replacement of the Benthic Mixotrophic Ciliate Mesodinium coatsi

While the ecophysiology of planktonic Mesodinium rubrum species complex has been relatively well studied, very little is known about that of benthic Mesodinium species. In this study, we examined the growth response of the benthic ciliate Mesodinium coatsi to different cryptophyte prey using an established culture of this species. M. coatsi was able to ingest all of the offered cryptophyte prey types, but not all cryptophytes supported its positive, sustained growth. While M. coatsi achieved sustained growth on all of the phycocyanin‐containing Chroomonas spp. it was offered, it showed different growth responses to the phycoerythrin‐containing cryptophytes Rhodomonas spp., Storeatula sp., and Teleaulax amphioxeia. M. coatsi was able to easily replace previously ingested prey chloroplasts with newly ingested ones within 4 d, irrespective of prey type, if cryptophyte prey were available. Once retained, the ingested prey chloroplasts seemed to be photosynthetically active. When fed, M. coatsi was capable of heterotrophic growth in darkness, but its growth was enhanced significantly in the light (14:10 h light:dark cycle), suggesting that photosynthesis by ingested prey chloroplast leads to a significant increase in the growth of M. coatsi. Our results expand the knowledge of autecology and ecophysiology of the benthic M. coatsi.

Seasonal succession of ciliate Mesodinium spp. with red, green, or mixed plastids and their association with cryptophyte prey

Mesodinium spp. are commonly found in marine and brackish waters, and several species are known to contain red, green, or both plastids that originate from cryptophyte prey. We observed the seasonal succession of Mesodinium spp. in a Japanese brackish lake, and we analysed the origin and diversity of the various coloured plastids within the cells of Mesodinium spp. using a newly developed primer set that specifically targets the cryptophyte nuclear 18S rRNA gene. Mesodinium rubrum isolated from the lake contained only red plastids originating from cryptophyte Teleaulax amphioxeia. We identified novel Mesodinium sp. that contained only green plastids or both red and green plastids originating from cryptophytes Hemiselmis sp. and Teleaulax acuta. Although the morphology of the newly identified Mesodinium sp. was indistinguishable from that of M. rubrum under normal light microscopy, phylogenetic analysis placed this species between the M. rubrum/major species complex and a well-supported lineage of M. chamaeleon and M. coatsi. Close associations were observed in cryptophyte species composition within cells of Mesodinium spp. and in ambient water samples. The appearance of suitable cryptophyte prey is probably a trigger for succession of Mesodinium spp., and the subsequent abundance of Mesodinium spp. appears to be influenced by water temperature and dissolved inorganic nutrients.

Metabolomic Profiles of Dinophysis acuminata and Dinophysis acuta Using Non-Targeted High-Resolution Mass Spectrometry: Effect of Nutritional Status and Prey

Photosynthetic species of the genus Dinophysis are obligate mixotrophs with temporary plastids (kleptoplastids) that are acquired from the ciliate Mesodinium rubrum, which feeds on cryptophytes of the Teleaulax-Plagioselmis-Geminigera clade. A metabolomic study of the three-species food chain Dinophysis-Mesodinium-Teleaulax was carried out using mass spectrometric analysis of extracts of batch-cultured cells of each level of that food chain. The main goal was to compare the metabolomic expression of Galician strains of Dinophysis acuminata and D. acuta that were subjected to different feeding regimes (well-fed and prey-limited) and feeding on two Mesodinium (Spanish and Danish) strains. Both Dinophysis species were able to grow while feeding on both Mesodinium strains, although differences in growth rates were observed. Toxin and metabolomic profiles of the two Dinophysis species were significantly different, and also varied between different feeding regimes and different prey organisms. Furthermore, significantly different metabolomes were expressed by a strain of D. acuminata that was feeding on different strains of the ciliate Mesodinium rubrum. Both species-specific metabolites and those common to D. acuminata and D. acuta were tentatively identified by screening of METLIN and Marine Natural Products Dictionary databases. This first metabolomic study applied to Dinophysis acuminata and D.acuta in culture establishes a basis for the chemical inventory of these species.

The Genetic Diversity of Mesodinium and Associated Cryptophytes

Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.

Gut content microbiota of introduced bigheaded carps (Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Studying the microbiota in the alimentary tract of bigheaded carps (Hypophthalmichthys spp.) gained special interest recently, as these types of investigations on non-native fish species may lead to a better understanding of their ecological role and feeding habits in an invaded habitat. For microbiological examinations, bigheaded carp gut contents and water column samples from Lake Balaton (Hungary) were collected from spring to autumn in 2013. Denaturing Gradient Gel Electrophoresis (DGGE) and pyrosequencing of the 16S rRNA gene were performed to reveal the composition. According to the DGGE patterns, bacterial communities of water samples separated clearly from that of the intestines. Moreover, the bacterial communities in the foreguts and hindguts were also strikingly dissimilar. Based on pyrosequencing, both foregut and hindgut samples were predominated by the fermentative genus Cetobacterium (Fusobacteria). The presence of some phytoplankton taxa and the high relative abundance of cellulose-degrading bacteria in the guts suggest that intestinal microbes may have an important role in digesting algae and making them utilizable for bigheaded carps that lack cellulase enzyme. In turn, the complete absence of typical heterotrophic freshwater bacteria in all studied sections of the intestines indicated that bacterioplankton probably has a negligible role in the nutrition of bigheaded carps.

Mercury concentration in phytoplankton in response to warming of an autumn - winter season

Among other climate changes in the southern Baltic, there is a tendency towards warming, especially in autumn-winter. As a result, the ice cover on the coastal zone often fails to occur. This is conducive to the thriving of phytoplankton, in which metals, including mercury, can be accumulated. The dry deposition of atmospheric Hg during heating seasons is more intense than in non-heating seasons, owing to the combustion of fossil fuels for heating purposes. This has resulted in studies into the role of phytoplankton in the introduction of Hg into the first link of trophic chain, as a function of autumn and winter warming in the coastal zone of the lagoon. The studies were conducted at two stations in the coastal zone of the southern Baltic, in the Puck Lagoon, between December 2011 and May 2013. The obtained results show that, in the estuary region, the lack of ice cover can lead to a 30% increase and during an "extremely warm" autumn and winter an increase of up to three-fold in the mean annual Hg pool in phytoplankton (mass of Hg in phytoplankton per liter of seawater). The Hg content in phytoplankton was higher when Mesodinium rubrum was prevalent in the biomass, while the proportion of dinoflagellates was small.

Molecular diversity of endosymbiotic Nephroselmis (Nephroselmidophyceae) in Hatena arenicola (Katablepharidophycota)

Hatena arenicola (Katablepharidophycota) is a single-celled eukaryote that temporarily possesses a chlorophyte alga of the genus Nephroselmis as an intracellular symbiont. In the present study, we investigated the molecular diversity of the endosymbiont Nephroselmis in a natural population of the host H. arenicola. We sequenced the host's 18S rRNA gene and the endosymbiont's plastid-encoded 16S rRNA gene. The results indicated that almost identical strains of the host harbored at least three distinct strains of the algal endosymbiont affiliated to the clade Nephroselmis rotunda. This finding supports our previous hypothesis that H. arenicola and its symbiotic alga are in an early stage of secondary endosymbiosis.

DINOPHYSIS CAUDATA (DINOPHYCEAE) SEQUESTERS AND RETAINS PLASTIDS FROM THE MIXOTROPHIC CILIATE PREY MESODINIUM RUBRUM(1)

"Phototrophic"Dinophysis Ehrenberg species are well known to have chloroplasts of a cryptophyte origin, more specifically of the cryptophyte genus complex Teleaulax/Geminigera. Nonetheless, whether chloroplasts of "phototrophic"Dinophysis are permanent plastids or periodically derived kleptoplastids (stolen chloroplasts) has not been confirmed. Indeed, molecular sequence data and ultrastructural data lead to contradictory interpretations about the status of Dinophysis plastids. Here, we used established cultures of D. caudata strain DC-LOHABE01 and M. rubrum strain MR-MAL01 to address the status of Dinophysis plastids. Our approach was to experimentally generate D. caudata with "green" plastids and then follow the ingestion and fate of "reddish-brown" prey plastids using light microscopy, time-lapse videography, and single-cell TEM. Our results for D. caudata resolve the apparent discrepancy between morphological and molecular data by showing that plastids acquired when feeding on M. rubrum are structurally modified and retained as stellate compound chloroplasts characteristic of Dinophysis species.

Nuclear, mitochondrial and plastid gene phylogenies of Dinophysis miles (Dinophyceae): evidence of variable types of chloroplasts

The Dinophysis genus is an ecologically and evolutionarily important group of marine dinoflagellates, yet their molecular phylogenetic positions and ecological characteristics such as trophic modes remain poorly understood. Here, a population of Dinophysis miles var. indica was sampled from South China Sea in March 2010. Nuclear ribosomal RNA gene (rDNA) SSU, ITS1-5.8S-ITS2 and LSU, mitochondrial genes encoding cytochrome B (cob) and cytochrome C oxidase subunit I (cox1), and plastid rDNA SSU were PCR amplified and sequenced. Phylogenetic analyses based on cob, cox1, and the nuclear rRNA regions showed that D. miles was closely related to D. tripos and D. caudata while distinct from D. acuminata. Along with morphology the LSU and ITS1-5.8S-ITS2 molecular data confirmed that this population was D. miles var. indica. Furthermore, the result demonstrated that ITS1-5.8S-ITS2 fragment was the most effective region to distinguish D. miles from other Dinophysis species. Three distinct types of plastid rDNA sequences were detected, belonging to plastids of a cryptophyte, a haptophyte, and a cyanobacterium, respectively. This is the first documentation of three photosynthetic entities associated with a Dinophysis species. While the cyanobacterial sequence likely represented an ectosymbiont of the D. miles cells, the detection of the cryptophyte and haptophyte plastid sequences indicates that the natural assemblage of D. miles likely retain more than one type of plastids from its prey algae for temporary use in photosynthesis. The result, together with recent findings of plastid types in other Dinophysis species, suggests that more systematic research is required to understand the complex nutritional physiology of this genus of dinoflagellates.

Multiple plastids collected by the dinoflagellate Dinophysis mitra through kleptoplastidy

Kleptoplastidy is the retention of plastids obtained from ingested algal prey, which may remain temporarily functional and be used for photosynthesis by the predator. We showed that the marine dinoflagellate Dinophysis mitra has great kleptoplastid diversity. We obtained 308 plastid rbcL sequences by gene cloning from 14 D. mitra cells and 102 operational taxonomic units (OTUs). Most sequences were new in the genetic database and positioned within Haptophyceae (227 sequences [73.7%], 80 OTUs [78.4%]), particularly within the genus Chrysochromulina. Others were closely related to Prasinophyceae (16 sequences [5.2%], 5 OTUs [4.9%]), Dictyochophyceae (14 sequences [4.5%], 5 OTUs [4.9%]), Pelagophyceae (14 sequences [4.5%], 1 OTU [1.0%]), Bolidophyceae (3 sequences [1.0%], 1 OTU [1.0%]), and Bacillariophyceae (1 sequence [0.3%], 1 OTU [1.0%]); however, 33 sequences (10.8%) as 9 OTUs (8.8%) were not closely clustered with any particular group. Only six sequences were identical to those of Chrysochromulina simplex, Chrysochromulina hirta, Chrysochromulina sp. TKB8936, Micromonas pusilla NEPCC29, Micromonas pusilla CCMP491, and an unidentified diatom. Thus, we detected >100 different plastid sequences from 14 D. mitra cells, strongly suggesting kleptoplastidy and the need for mixotrophic prey such as Laboea, Tontonia, and Strombidium-like ciliates, which retain numerous symbiotic plastids from different origins, for propagation and plastid sequestration.