Cryptic speciation in Protoceratium reticulatum (Dinophyceae): Evidence from morphological, molecular and ecophysiological data

High-resolution DNA metabarcoding of modern surface sediments uncovers a diverse assemblage of dinoflagellate cysts in the Pacific and Arctic Oceans

Resting cysts of dinoflagellates can persist in sediments, seeding harmful algal blooms (HABs). A DNA metabarcoding approach was employed, targeting the large subunit ribosomal (LSU D1-D2) and the internal transcribed spacer (ITS1) to investigate the diversity and biogeography of dinoflagellate cysts from the South China Sea to the Chukchi Sea. The LSU and ITS1 datasets identified 196 and 118 species, respectively, with only 59 dinoflagellate cyst species revealed by both approaches. Eleven cyst species of potentially toxic dinoflagellates and 82 species previously unknown as cyst producers were detected. Cysts of Heterocapsa cf. horiguchii, Heterocapsa minima, Heterocapsa iwatakii, Heterocapsa rotundata, and Heterocapsa steinii were documented through germination for the first time, with the latter three species also detected via metabarcoding. This study provides critical insights into the diversity and biogeography of dinoflagellate cysts by highlighting the complementary detection capabilities of LSU and ITS1 molecular markers and their trans-latitudinal distribution patterns. The identification of potentially toxic cysts and their ecological distributions offers crucial information on the ecology of harmful dinoflagellates. These findings underscore the importance of molecular techniques in monitoring dinoflagellate cysts.

Seasonal monitoring of dissolved and particulate algal biotoxins in the northern Salish Sea using high performance liquid chromatography and tandem mass spectrometry

Harmful algae are present in the coastal waters of British Columbia, Canada yet little is known about the spatial and temporal distributions of the biotoxins produced by these organisms. We describe a method for profiling dissolved and particulate algal biotoxins in sea water including those associated with amnesic, paralytic, and diarrhetic shellfish poisoning (ASP, PSP and DSP). Surface sea water was filtered and biotoxins recovered from filters and filtrate using solvent extraction and solid phase extraction, respectively. Extracts were analyzed by high-performance liquid chromatography and tandem mass spectrometry using hydrophilic interaction liquid chromatography for ASP and PSP toxins and reversed-phased liquid chromatography for DSP and other lipophilic toxins. The method was applied to samples collected in the northern Salish Sea in April, June and October 2022. Highest total concentrations of domoic acid and saxitoxin were found above a shallow sill in the eastern Juan de Fuca Strait whereas those of dinophysistoxin 1, pectenotoxin 2, yessotoxin, and PSP toxins C1 and C2 were measured near the southern end of Malaspina Strait. These maximum concentrations were observed in June when surface salinity was lowest, temperature highest, and harmful algae most abundant, as reflected in the relative high proportion of particulate biotoxins. In contrast, the high proportion of dissolved biotoxins observed in April when temperature and algal abundance were relatively low suggests that certain biotoxins may persist in surface waters and that the risk of biotoxin exposure does not necessarily correlate with the abundance of harmful algae.

Cryptic diversity within the Gonyaulax spinifera species complex, its relation to the cyst-defined species Spiniferites bentorii, S. mirabilis and S. membranaceus, with the description of Gonyaulax carbonell-mooreae sp. nov. (Gonyaulacales, Dinophyceae)

The fossil dinoflagellates Spiniferites bentorii, S. mirabilis, and S. membranaceus are known to inhabit recent sediments and are often used to reconstruct past sea-surface conditions. However, information on their corresponding motile cells has been rare. We isolated single cysts resembling these fossil species from China and France to yield Gonyaulax spinifera-like cells. Gonyaulax strains were also established from Viet Nam and South Korea by isolating single cells. Both cysts and cells were examined by light and scanning electron microscopy, and their LSU rRNA genes were sequenced. A new Gonyaulax species, G. carbonell-mooreae, was obtained from S. bentorii-like cysts and considered the equivalent of Spiniferites bullatus, dating back to the Campanian. Gonyaulax kunsanensis was related to S. mirabilis-like cysts. A typical S. membranaceus cyst from France yielded cells resembling G. lewisiae but shared only 75% similarity in LSU rRNA gene sequence with those from South Korea. Molecular phylogeny revealed that the pronounced apical boss is systematically significant, whereas the presence of intergonal processes is insignificant. Two ASVs of 18S rRNA V4 region were respectively identified as G. kunsanensis and G. lewisiae from the Tara Oceans metabarcoding data. Gonyaulax kunsanensis has a wide distribution in the Pacific, Indian, and Atlantic Oceans, but G. lewisiae has a restricted distribution. One strain of G. kunsanensis was examined for yessotoxin content using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), but no detectable amounts of toxins were observed. Our results uncover the hidden diversity within the G. spinifera species complex and stress the significance of cyst morphology in the taxonomy of Gonyaulax.

Toxic effects of combined exposure to homoyessotoxin and nitrite on the survival, antioxidative responses, and apoptosis of the abalone Haliotis discus hannai

Homoyessotoxin (homo-YTX) and nitrite (NO2-N), released during harmful dinoflagellate cell lysis adversely affect abalones. However, their toxicity mechanisms in shellfish remain unclear. This study investigated the economic abalone species Haliotis discus hannai exposed to varying concentrations of homo-YTX (0, 2, 5, and 10 µg L-1) and NO2-N (0, 3, and 6 mg L-1) on the basis of their 12 h LC50 values (5.05 µg L-1 and 4.25 mg L-1, respectively) and the environmentally relevant dissolved concentrations during severe dinoflagellate blooms, including mixtures. The test abalones were exposed to homo-YTX and NO2-N for 12 h. The mortality rate (D), reactive oxygen species (ROS) levels, antioxidant defense capabilities, and expression levels of antioxidant-related, Hsp-related, and apoptosis-related genes in abalone gills were assessed. Results showed that the combined exposure to homo-YTX and NO2-N increased the D and ROS levels and upregulated B-cell lymphoma-2 (BCL2)-associated X (BAX) and caspase3 (CASP3) expression levels while reducing glutathione peroxidase (GPx) activity and GPx, CuZnSOD, and BCL2 expression levels. High concentrations of homo-YTX (10 µg L-1) and NO2-N (6 mg L-1) solutions and the combinations of these toxicants inhibited the activities of superoxide dismutase (SOD) and catalase (CAT) and downregulated the expression levels of MnSOD, CAT, Hsp70, and Hsp90. The ROS levels were negatively correlated with the activities of SOD, CAT, and GPx and the expression levels of MnSOD, CuZnSOD, CAT, GPx, Hsp70, Hsp90, and BCL2. These results suggest that homo-YTX, in conjunction with NO2-N, induces oxidative stress, disrupts antioxidant defense systems, and triggers caspase-dependent apoptosis in the gills of abalone. ROS-mediated antioxidative and heat-shock responses and apoptosis emerge as potential toxicity mechanisms affecting the survival of H. discus hannai due to homo-YTX and NO2-N exposure.

Effect of temperature on growth and yessotoxin production of Protoceratium reticulatum and Lingulodinium polyedra (Dinophyceae) isolates from the Portuguese coast (NE Atlantic)

The dinoflagellates Protoceratium reticulatum and Lingulodinium polyedra are potential yessotoxin (YTX) producers, which have been associated with blooms responsible for economic, social, and ecological impacts around the world. They occur in Iberian waters, but in this region, little is known of their ecophysiology and toxin profiles. This study investigated the growth and toxin production of two strains of each species, from the Portuguese coast, at 15 °C, 19 °C, and 23 °C. Growth curves showed higher growth rates at 19 °C, for both species. YTX and three analogs (homo YTX; 45-OH YTX; 45-OH homo YTX) were investigated by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS), and the presence of other analogs was investigated by Liquid Chromatography-High-Resolution Mass Spectrometry (LC-HRMS). No evidence of toxin production was found in L. polyedra. By contrast, YTX and 45,55-diOH-YTX were detected in both strains of P. reticulatum. These results confirm P. reticulatum as a source of yessotoxins along the Portuguese coast and add to the observed high intraspecific variability on YTX production of both species, at a global scale.

ROS-mediated physiological activities and apoptotic effect on the survival of abalone (Haliotis discus hannai) under homoyessotoxin and ammonia stresses

Serious dinoflagellate blooms produce homoyessotoxin (homo-YTX) and ammonia (NH3-N) in eutrophic seawaters, posing threats to the healthy development of the mariculture industry. This study aimed to explore the toxicity mechanism of homo-YTX and NH3-N on the survival of abalone, which is important for the ecotoxicological research and cultivation of shellfish. The economy abalone Haliotis discus hannai was placed in homo-YTX (0, 2, 5, and 10 μg L-1) and NH3-N (0, 1.08, and 3.16 mg L-1) and a mixture of the two compounds to determine the survival rate (S), antioxidative responses, physiological activities, and apoptosis of abalone. Results show that the combination of homo-YTX and NH3-N increased the reactive oxygen species level, the malondialdehyde content, and the expression level of BCL2-associated X but decreased S; the activities of superoxide dismutase, catalase, adenosine triphosphatase, glutamic-pyruvic transaminase, xanthine oxidase, lactate dehydrogenase, and lysozyme; and the expression level of B-cell lymphoma-2. The activities of alkaline phosphatase and acid phosphatase in 10 μg L-1 of homo-YTX and 3.16 mg L-1 of NH3-N solutions and in the mixture of the two toxicants decreased. The caspase3 expression level was downregulated in 10 μg L-1 of homo-YTX. These results suggest that homo-YTX and NH3-N enhanced the oxidative stress and lipid peroxidation reactions, inhibited the energy supply, disrupted the metabolic and immune physiological functions, and activated apoptosis in the gills of abalone. ROS-mediated physiological activities and apoptosis were among the potential toxicity mechanisms of the interactive effects of homo-YTX and NH3-N on abalone.

New Knowledge on Distribution and Abundance of Toxic Microalgal Species and Related Toxins in the Northwestern Black Sea

Numerous potentially toxic plankton species commonly occur in the Black Sea, and phycotoxins have been reported. However, the taxonomy, phycotoxin profiles, and distribution of harmful microalgae in the basin are still understudied. An integrated microscopic (light microscopy) and molecular (18S rRNA gene metabarcoding and qPCR) approach complemented with toxin analysis was applied at 41 stations in the northwestern part of the Black Sea for better taxonomic coverage and toxin profiling in natural populations. The combined dataset included 20 potentially toxic species, some of which (Dinophysis acuminata, Dinophysis acuta, Gonyaulax spinifera, and Karlodinium veneficum) were detected in over 95% of the stations. In parallel, pectenotoxins (PTX-2 as a major toxin) were registered in all samples, and yessotoxins were present at most of the sampling points. PTX-1 and PTX-13, as well as some YTX variants, were recorded for the first time in the basin. A positive correlation was found between the cell abundance of Dinophysis acuta and pectenotoxins, and between Lingulodinium polyedra and Protoceratium reticulatum and yessotoxins. Toxic microalgae and toxin variant abundance and spatial distribution was associated with environmental parameters. Despite the low levels of the identified phycotoxins and their low oral toxicity, chronic toxic exposure could represent an ecosystem and human health hazard.

Changes in physiological activities are responsible for homoyessotoxin-induced toxicity in abalone Haliotis discus hannai

Homoyessotoxin (homo-YTX) is a lipid-soluble toxin produced by toxic dinoflagellates. It is widely distributed in marine ecosystems worldwide, and it poses a threat to the survival of aquatic animals. The tissues of the abalone Haliotis discus hannai are easily damaged by homo-YTX during harmful algal blooms. In this study, H. discus hannai was exposed to homo-YTX (0, 2, 5, and 10 µg L^-1) to evaluate the rates of survival (S) and death (D) and the antioxidative, metabolic, and digestive physiological responses in the gills and digestive gland of abalone. Homo-YTX decreased S and the activities of Na⁺/K⁺-adenosine triphosphatase, Ca²⁺/Mg²⁺-adenosine triphosphatase, superoxide dismutase, catalase, alkaline phosphatase, xanthine oxidase, lactate dehydrogenase, amylase, protease, and lipase. Meanwhile, D, the reactive oxygen species level, and the malondialdehyde content increased with increasing concentrations of homo-YTX. In addition, homo-YTX induced oxidative stress, enhanced the lipid peroxidation reaction, reduced the energy supply, and inhibited the metabolic and digestive physiological activities in the gills and digestive gland of abalone. Oxidative stress-mediated insufficient energy supply and physiological activity reduction caused the death of abalone.

Unraveling the Gonyaulax baltica Species Complex: Cyst-theca Relationship of Impagidinium variaseptum, Spiniferites pseudodelicatus sp. nov. and S. ristingensis (Gonyaulacaceae, Dinophyceae), With Descriptions of Gonyaulax bohaiensis sp. nov, G. amoyensis sp. nov. and G. portimonensis sp. nov

The taxonomy of the extant dinoflagellate genus Gonyaulax is challenging since its thecate morphology is rather conservative. In contrast, cysts of Gonyaulax are varied in morphology and have been related with the fossil-based genera Spiniferites and Impagidinium. To better understand the systematics of Gonyaulax species, we performed germination experiments on cysts that can be identified as S. ristingensis, an unidentified Spiniferites with petaloid processes here described as Spiniferites pseudodelicatus sp. nov. and Impagidinium variaseptum from Chinese and Portuguese waters. Despite marked differences in cyst morphology, motile cells of S. pseudodelicatus and I. variaseptum are indistinguishable from Gonyaulax baltica. Motile cells hatched from S. ristingensis are morphologically similar to G. baltica as well but differ in the presence of one pronounced antapical spine. Three new species, Gonyaulax amoyensis (cyst equivalent S. pseudodelicatus), Gonyaulax bohaiensis (cyst equivalent I. variaseptum), and Gonyaulax portimonensis (cyst equivalent S. ristingensis), were erected. In addition, a new ribotype (B) of G. baltica was reported from South Korea and a bloom of G. baltica ribotype B is reported from New Zealand. Molecular phylogeny based on LSU and SSU rRNA gene sequences revealed that Gonyaulax species with minute or short antapical spines formed a well-resolved clade, whereas species with two pronounced antapical spines or lack of antapical spines formed the sister clade. Six strains of four above species were examined for yessotoxin production by liquid chromatography coupled with tandem mass spectrometry, and very low concentrations of yessotoxin were detected for one G. bohaiensis strain.

Using RDNA sequences to define dinoflagellate species

Dinoflagellate species are traditionally defined using morphological characters, but molecular evidence accumulated over the past several decades indicates many morphologically-based descriptions are inaccurate. This recognition led to an increasing reliance on DNA sequence data, particularly rDNA gene segments, in defining species. The validity of this approach assumes the divergence in rDNA or other selected genes parallels speciation events. Another concern is whether single gene rDNA phylogenies by themselves are adequate for delineating species or if multigene phylogenies are required instead. Currently, few studies have directly assessed the relative utility of multigene versus rDNA-based phylogenies for distinguishing species. To address this, the current study examined D1-D3 and ITS/5.8S rDNA gene regions, a multi-gene phylogeny, and morphological characters in Gambierdiscus and other related dinoflagellate genera to determine if they produce congruent phylogenies and identify the same species. Data for the analyses were obtained from previous sequencing efforts and publicly available dinoflagellate transcriptomic libraries as well from the additional nine well-characterized Gambierdiscus species transcriptomic libraries generated in this study. The D1-D3 and ITS/5.8S phylogenies successfully identified the described Gambierdiscus and Alexandrium species. Additionally, the data showed that the D1-D3 and multigene phylogenies were equally capable of identifying the same species. The multigene phylogenies, however, showed different relationships among species and are likely to prove more accurate at determining phylogenetic relationships above the species level. These data indicated that D1-D3 and ITS/5.8S rDNA region phylogenies are generally successful for identifying species of Gambierdiscus, and likely those of other dinoflagellates. To assess how broadly general this finding is likely to be, rDNA molecular phylogenies from over 473 manuscripts representing 232 genera and 863 described species of dinoflagellates were reviewed. Results showed the D1-D3 rDNA and ITS phylogenies in combination are capable of identifying 97% of dinoflagellate species including all the species belonging to the genera Alexandrium, Ostreopsis and Gambierdiscus, although it should be noted that multi-gene phylogenies are preferred for inferring relationships among these species. A protocol is presented for determining when D1-D3, confirmed by ITS/5.8S rDNA sequence data, would take precedence over morphological features when describing new dinoflagellate species. This protocol addresses situations such as: a) when a new species is both morphologically and molecularly distinct from other known species; b) when a new species and closely related species are morphologically indistinguishable, but genetically distinct; and c) how to handle potentially cryptic species and cases where morphotypes are clearly distinct but have the same rDNA sequence. The protocol also addresses other molecular, morphological, and genetic approaches required to resolve species boundaries in the small minority of species where the D1-D3/ITS region phylogenies fail.

Emerging harmful algal bloom species over the last four decades in China

The first recorded micro-algae bloom in Chinese coastal waters dates back to 1933 and was caused by a mixture of Noctiluca scintillans and Skeletonema costatum sensu lato along the Zhejiang coast (the East China Sea). While well-documented harmful algal blooms (HABs) appeared to be extremely scarce from the 1950s to 1990, both the frequency and intensity have been reportedly increasing since 1990. Among them, the fish-killing HABs, mainly caused by Karenia mikimotoi, Karlodinium digitatum, Karlodinium veneficum, Margalefidinium polykrikoides, and Heterocapsa spp., have intensified. Karenia mikimotoi was responsible for at least two extremely serious events in the Pearl River Estuary in 1998 and the Taiwan Strait (in the East China Sea) in 2012, which appeared to be associated with abnormal climate conditions and excessive nutrients loading. Other major toxic algal blooms have been caused by the species responsible for paralytic shellfish poisoning (including Alexandrium catenella, Alexandrium pacificum, Gymnodinium catenatum) and diarrhetic shellfish poisoning (including Dinophysis spp., and a couple of benthic dinoflagellates). Consequent closures of shellfish farms have resulted in enormous economic losses, while consumption of contaminated shellfish has led to occasional human mortality in the Bohai Sea and the East China Sea. Expansions of these HABs species along the coastline of China have occurred over the last four decades and, due to the projected global changes in the climate and marine environments and other anthropological activities, there is potential for the emergence of new types of HABs in China in the future. This literature review aimed to present an updated overview of HABs species over the last four decades in China.

Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy

Contemporary delimitation of species and populations in the microbial domain relies on an integrative approach combining molecular and morphological techniques. In case of the dinophyte Peridinium volzii, a considerable number of infraspecific taxonomic entities have been reported, but it is unclear at present whether the corresponding traits are stable within reproductively isolated units or refer to intraspecific variability. We established 26 monoclonal strains from Central Europe with a morphology that is consistent for P. volzii and characterised them by sequences gained from the rRNA operon. Ten of such strains, representative for the entire diversity observed, were investigated in detail morphologically using light and electron microscopy. In the molecular tree, P. volzii was monophyletic, sister group of Peridinium willei, and three ITS ribotypes could be distinguished. Some traits corresponding to previously described varieties and forms were found in individual cells across the strains under investigation, but not as stable characters correlating to certain ribotypes. We also observed new morphological variability (e.g., unusual shape of plate 4″). Cell size and displacement of the cingulum were significantly different between certain ribotypes but in turn, such diagnostic traits are impossible to assign to already described taxa due to their ambiguity. Based on the small first apical plate as diagnostic trait and putative apomorphy, P. volzii is a characteristic species but the present data given, we are reserved to accept more than a single reproductive unit. Thus, more research is necessary, including a focus on species delimitation to putative close relatives such as Peridinium maeandricum.

Paleoceanography and dinoflagellate cyst stratigraphy across the Lower-Middle Pleistocene Subseries (Calabrian-Chibanian Stage) boundary at the Chiba composite section, Japan

A dinoflagellate cyst record from the highly resolved Chiba composite section in Japan has been used to reconstruct sea-surface paleoceanographic changes across the Lower-Middle Pleistocene Subseries (Calabrian-Chibanian Stage) boundary at the global stratotype, constituting the first detailed study of this microfossil group from the Pleistocene of the Japanese Pacific margin. Cold, subarctic water masses from 794.2 ka gave way to warming and rapid retreat of the Subpolar Front at 789.3 ka, ~ 2000 years before the end of Marine Isotope Stage (MIS) 20. Throughout the fully interglacial conditions of MIS 19c, assemblages are consistent with warm sea surface temperatures but also reveal instability and latitudinal shifts in the Kuroshio Extension system. The abrupt dominance of Protoceratium reticulatum cysts between 772.9 and 770.4 ka (MIS 19b) registers the influence of cooler, mixed, nutrient-rich waters of the Kuroshio-Oyashio Interfrontal Zone resulting from a southward shift of the Kuroshio Extension. Its onset at 772.9 ka serves as a local ecostratigraphic marker for the Chibanian Stage Global Boundary Stratotype Section and Point (GSSP) which occurs just 1.15 m (= 1300 years) below it. An interval from 770.1 ka to the top of the examined succession at 765.8 ka (MIS 19a) represents warm, presumably stratified but still nutrient-elevated surface waters, indicating a northward shift of the Kuroshio Extension ~ 5 kyrs after the termination of full interglacial conditions on land.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s40645-021-00438-3.

Diversity and distribution of harmful microalgae in the Gulf of Thailand assessed by DNA metabarcoding

Information on the diversity and distribution of harmful microalgae in the Gulf of Thailand is very limited and mainly based on microscopic observations. Here, we collected 44 water samples from the Gulf of Thailand and its adjacent water (Perhentian Island, Malaysia) for comparison in 2018. DNA metabarcoding was performed targeting the partial large subunit ribosomal RNA gene (LSU rDNA D1-D3) and the internal transcribed spacers (ITS1 and ITS2). A total of 50 dinoflagellate genera (made up of 72 species) were identified based on the LSU rDNA dataset, while the results of ITS1 and ITS2 datasets revealed 33 and 32 dinoflagellate genera comprising 69 and 64 species, respectively. Five potentially toxic Pseudo-nitzschia (Bacillariophyceae) species were detected, with four as newly recorded species in the water (Pseudo-nitzschia americana/brasilliana, Pseudo-nitzschia simulans/delicatissima, P. galaxiae and P. multistriata). The highest relative abundances of P. galaxiae and P. multistriata were found in Trat Bay and Chumphon (accounting for 0.20% and 0.06% of total ASVs abundance, respectively). Three paralytic shellfish toxin producing dinoflagellate species were detected: Alexandrium tamiyavanichii, Alexandrium fragae, and Gymnodinium catenatum. The highest abundance of A. tamiyavanichii was found in the surface sample of Chumphon (CHO7 station), accounting for 1.95% of total ASVs abundance. Two azaspiracid producing dinoflagellate species, Azadinium poporum ribotype B, Azadinium spinosum ribotype A, and a pinnatoxin producing dinoflagellate species Vulcanodinium rugosum, with two ribotypes B and C, were revealed from the datasets although with very low abundances. Six fish killing dinoflagellate species, including Margalefidinium polykrikoides group IV, Margalefidinium fulvescens, Karenia mikimotoi, Karenia selliformis ribotype B, Karlodinium australe, and Karlodinium digitatum were detected and all representing new records in this area. The findings of numerous harmful microalgal species in the Gulf of Thailand highlight the potential risk of human intoxication and fish killing events.

An assessment on the intrapopulational and intraindividual genetic diversity in LSU rDNA in the harmful algal blooms-forming dinoflagellate Margalefidinium (= Cochlodinium) fulvescens based on clonal cultures and bloom samples from Jiaozhou Bay, China

Large subunit ribosomal DNA (LSU rDNA) sequences have been increasingly used to infer the phylogeny and species identity of organisms, a few previous studies, however, have observed high intraspecific and even intraindividual variability in LSU rDNA in some dinoflagellate species due to, assumably, large copy numbers of rDNA in dinoflagellates. Since the copy number of LSU rDNA varies tremendously among dinoflagellate species, the intraspecific and intraindividual diversity for a species of particular interest thus needs to be investigated individually. As a toxic and HABs-forming dinoflagellate, Margalefidinium (= Cochlodinium) fulvescens has been observed to approach blooming density in Jiaozhou Bay, China since 2015 after numerous blooms having been reported from other countries. In trying to identify the source of this newly observed HABs-forming species in China by sequencing the LSU rDNA for both field samples and clonal cultures, we noticed and thus further investigated high intrapopulational and intraindividual genetic diversities of the dinoflagellate. The D1-D6 region of the LSU rDNA (1,435 bases) was amplified from 7 field samples (pooled cells) and 11 clonal cultures, cloned, sequenced, and analyzed phylogenetically for 2,341 sequences obtained. All the numbers of sequences obtained from each clonal culture were far less than the estimated rDNA copy number in M. fulvescens. In the clone library, only one unique sequence was contained in all samples as the most dominant sequence. We found high intrapopulational and intraindividual genetic diversity in M. fulvescens as reflected in the number of polymorphic sites and unique sequences in the clone library for different field samples and clonal cultures in comparison to other species. The mean number of nucleotide differences of each sequence from different field samples and clonal cultures were 6.43 and 4.42 bases, respectively, with the highest being 132 bases, nearly 10%. The sequences with highest variability may be easily annotated as different species if they were obtained from environmental genomic studies because sequence-based species identification in meta-barcoding studies often use "97% identity" threshold. Based on that the mean and overall intrapopulational genetic diversity calculated for 7 field samples was equivalent to the mean and overall intraindividual variability for 11 clonal cultures in indices of genetic diversity, together with the result of AMOVA analysis, we infer that the variability within individual cells (i.e. variability among LSU rDNA polymorphic copies) caused both the intraindividual and intrapopulational genetic diversities observed in the M. fulvescens population, and a higher interpopulational diversity may exist among different geographic populations. The results provide an insightful basis for such a comprehensive interpopulational comparison and important implications for identifying species and establishing new taxa based on the similarity comparison to reference sequences deposited in databases.