Journal articles: 'Phytoplankton – Phylogeny'

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Sal, Sofía, Laura Alonso-Sáez, Juan Bueno, Francisca C. García, and Ángel López-Urrutia. "Thermal adaptation, phylogeny, and the unimodal size scaling of marine phytoplankton growth." Limnology and Oceanography 60, no. 4 (April 23, 2015): 1212–21. http://dx.doi.org/10.1002/lno.10094.

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Kang, Ilnam, Hyun-Myung Oh, Kevin L. Vergin, Stephen J. Giovannoni, and Jang-Cheon Cho. "Genome Sequence of the Marine Alphaproteobacterium HTCC2150, Assigned to the Roseobacter Clade." Journal of Bacteriology 192, no. 23 (October 1, 2010): 6315–16. http://dx.doi.org/10.1128/jb.01088-10.

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ABSTRACT Here we announce the genome sequence of a marine bacterium, HTCC2150, that was isolated off the Oregon coast using dilution-to-extinction culturing and that is affiliated with the Roseobacter clade. The 16S rRNA phylogeny showed that the strain was closely related to members of the RCA clade. The genome sequence suggests that strain HTCC2150 is an organoheterotroph carrying diverse metabolic potential, including a close relationship with phytoplankton.

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Galloway, Aaron W. E., and Monika Winder. "Partitioning the Relative Importance of Phylogeny and Environmental Conditions on Phytoplankton Fatty Acids." PLOS ONE 10, no. 6 (June 15, 2015): e0130053. http://dx.doi.org/10.1371/journal.pone.0130053.

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LIU, XUDONG, HUAN ZHU, BENWEN LIU, GUOXIANG LIU, and ZHENGYU HU. "Phylogeny and morphology of genus Nephrocytium (Sphaeropleales, Chlorophyceae, Chlorophyta) from China." Phytotaxa 319, no. 1 (August 29, 2017): 84. http://dx.doi.org/10.11646/phytotaxa.319.1.4.

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The genus Nephrocytium Nägeli is a common member of phytoplankton communities that has a distinctive morphology. Its taxonomic position is traditionally considered to be within the family Oocystaceae (Trebouxiophyceae). However, research on its ultrastructure is rare, and the phylogenetic position has not yet been determined. In this study, two strains of Nephrocytium, N. agardhianum Nägeli and N. limneticum (G.M.Smith) G.M.Smith, were identified and successfully cultured in the laboratory. Morphological inspection by light and electron microscopy and molecular phylogenetic analyses were performed to explore the taxonomic position. Ultrastructure implied a likely irregular network of dense and fine ribs on the surface of the daughter cell wall that resembled that of the genus Chromochloris Kol & Chodat (Chromochloridaceae). Phylogenetic analyses revealed that Nephrocytium formed an independent lineage in the order Sphaeropleales (Chlorophyceae) with high support values and a close phylogenetic relationship with Chromochloris. Based on combined morphological, ultrastructural and phylogenetic data, we propose a re-classification of Nephrocytium into Sphaeropleales, sharing a close relationship with Chromochloris.

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Gianuca, Andros T., Jelena H. Pantel, and Luc De Meester. "Disentangling the effect of body size and phylogenetic distances on zooplankton top-down control of algae." Proceedings of the Royal Society B: Biological Sciences 283, no. 1828 (April 13, 2016): 20160487. http://dx.doi.org/10.1098/rspb.2016.0487.

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A negative consequence of biodiversity loss is reduced rates of ecosystem functions. Phylogenetic-based biodiversity indices have been claimed to provide more accurate predictions of ecosystem functioning than species diversity alone. This approach assumes that the most relevant traits for ecosystem functioning present a phylogenetic signal. Yet, traits-mediating niche partitioning and resource uptake efficiency in animals can be labile. To assess the relative power of a key trait (body size) and phylogeny to predict zooplankton top-down control on phytoplankton, we manipulated trait and phylogenetic distances independently in microcosms while holding species richness constant. We found that body size provided strong predictions of top-down control. In contrast, phylogeny was a poor predictor of grazing rates. Size-related grazing efficiency asymmetry was mechanistically more important than niche differences in mediating ecosystem function in our experimental settings. Our study demonstrates a strong link between a single functional trait (i.e. body size) in zooplankton and trophic interactions, and urges for a cautionary use of phylogenetic information and taxonomic diversity as substitutes for trait information to predict and understand ecosystem functions.

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Endo, H., K. Sugie, T. Yoshimura, and K. Suzuki. "Effects of CO2 and iron availability on rbcL gene expression in Bering Sea diatoms." Biogeosciences Discussions 11, no. 12 (December 20, 2014): 18105–43. http://dx.doi.org/10.5194/bgd-11-18105-2014.

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Abstract. Iron (Fe) can limit phytoplankton productivity in approximately 40% of the global ocean, including high-nutrient, low-chlorophyll (HNLC) waters. However, there is little information available on the impact of CO2-induced seawater acidification on natural phytoplankton assemblages in HNLC regions. We therefore conducted an on-deck experiment manipulating CO2 and Fe using Fe-deficient Bering Sea waters during the summer of 2009. The concentrations of CO2 in the incubation bottles were set at 380 and 600 ppm in the non-Fe-added (control) bottles and 180, 380, 600, and 1000 ppm in the Fe-added bottles. The phytoplankton assemblages were primarily composed of diatoms followed by haptophytes in all incubation bottles as estimated by pigment signatures throughout the 7 day incubation period. At the end of incubation, the relative contributions of diatoms to chlorophyll a biomass decreased significantly with increased CO2 levels in the controls, whereas minimal changes were found in the Fe-added treatments. These results indicate that, under Fe-deficient conditions, the growth of diatoms was negatively affected by the increase in CO2 availability. To confirm this, we estimated the expression and phylogeny of rbcL (which encodes the large subunit of RubisCO) mRNA in diatoms by quantitative reverse transcription PCR and clone library techniques, respectively. Interestingly, regardless of Fe availability, the expression and diversity of rbcL cDNA decreased in the high CO2 treatments (600 and 1000 ppm). The present study suggests that the projected future increase in seawater pCO2 could reduce the RubisCO activity of diatoms, resulting in a decrease in primary productivity and a shift in the food web structure of the Bering Sea.

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Endo, H., K. Sugie, T. Yoshimura, and K. Suzuki. "Effects of CO2 and iron availability on rbcL gene expression in Bering Sea diatoms." Biogeosciences 12, no. 7 (April 15, 2015): 2247–59. http://dx.doi.org/10.5194/bg-12-2247-2015.

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Abstract. Iron (Fe) can limit phytoplankton productivity in approximately 40% of the global ocean, including in high-nutrient, low-chlorophyll (HNLC) waters. However, there is little information available on the impact of CO2-induced seawater acidification on natural phytoplankton assemblages in HNLC regions. We therefore conducted an on-deck experiment manipulating CO2 and Fe using Fe-deficient Bering Sea water during the summer of 2009. The concentrations of CO2 in the incubation bottles were set at 380 and 600 ppm in the non-Fe-added (control) bottles and 180, 380, 600, and 1000 ppm in the Fe-added bottles. The phytoplankton assemblages were primarily composed of diatoms followed by haptophytes in all incubation bottles as estimated by pigment signatures throughout the 5-day (control) or 6-day (Fe-added treatment) incubation period. At the end of incubation, the relative contribution of diatoms to chlorophyll a biomass was significantly higher in the 380 ppm CO2 treatment than in the 600 ppm treatment in the controls, whereas minimal changes were found in the Fe-added treatments. These results indicate that, under Fe-deficient conditions, the growth of diatoms could be negatively affected by the increase in CO2 availability. To further support this finding, we estimated the expression and phylogeny of rbcL (which encodes the large subunit of RuBisCO) mRNA in diatoms by quantitative reverse transcription polymerase chain reaction (PCR) and clone library techniques, respectively. Interestingly, regardless of Fe availability, the transcript abundance of rbcL decreased in the high CO2 treatments (600 and 1000 ppm). The present study suggests that the projected future increase in seawater pCO2 could reduce the RuBisCO transcription of diatoms, resulting in a decrease in primary productivity and a shift in the food web structure of the Bering Sea.

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Kim, Hyun Jung, Zhun Li, Nam Seon Kang, Haifeng Gu, Daekyung Kim, Min Ho Seo, Sang Deuk Lee, Suk Min Yun, Seok-Jin Oh, and Hyeon Ho Shin. "Morphology and Phylogeny of Scrippsiella precaria Montresor & Zingone (Thoracosphaerales, Dinophyceae) from Korean Coastal Waters." Journal of Marine Science and Engineering 9, no. 2 (February 3, 2021): 154. http://dx.doi.org/10.3390/jmse9020154.

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The dinoflagellate genus Scrippsiella is a common member of phytoplankton and their cysts are also frequently reported in coastal sediments worldwide. However, the diversity of Scrippsiella in Korean waters has not been fully investigated. Here, several isolates of Scrippsiella precaria collected from Korean waters and germinated from resting cysts were examined using light and scanning electron microscopy. The resting cysts were characterized by pointed calcareous spines and one or two red accumulation bodies, and the archeopyle was mesoepicystal, representing the loss of 2–4′ and 1–3a paraplates. Rounded resting cysts were found in culture, and an increase in spine length was observed until 8 days of development. Korean isolates of S. precaria had the plate formula of Po, X, 4′, 3a, 7″, 6C, 4S, 5‴, 2⁗. There were differences in the cell size and location of the red body between Korean isolates and previously described cells of S. precaria. In addition, the Korean isolates of S. precaria had two types of the 5″ plate that either contacted the 2a plate or not. Molecular phylogeny based on internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequences revealed that the Korean isolates were nested within the subclade of PRE (S. precaria and related species) in the clade of Scrippsiella sensu lato, and that the PRE subclade had two ribotypes: ribotype 1 consisting of the isolates from Korea, China, and Australia, and ribotype 2 consisting of the isolates from Italy and Greece. Lineages between isolates of ribotype 1 were likely to be related to the dispersal by ocean currents and ballast waters from international shipping, and the two types of spine shapes and locations of the 5″ plates may be a distinct feature for ribotype 1.

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Gómez, Fernando, Luis F. Artigas, and Rebecca J. Gast. "Phylogeny and Synonymy of Gyrodinium heterostriatum comb. nov. (Dinophyceae), a Common Unarmored Dinoflagellate in the World Oceans [plus supplementary materials]." Acta Protozoologica 59, no. 2 (2020): 77–87. http://dx.doi.org/10.4467/16890027ap.20.007.12675.

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The North Sea and the English Channel are regions with a long tradition of plankton studies, where the colony-forming haptophyte Phaeocystis globosa dominates the spring phytoplankton blooms. Among its predators, we investigated an abundant unarmored dinoflagellate (~3000 cells per liter) in the North Sea in May 2019. It has been reported in the literature as Gymnodinium heterostriatum or G. striatissimum, and often identified as Gyrodinium spirale. Phylogenetic analyses using the small-, large subunit- and Internal Transcriber Spacers of the ribosomal RNA (SSU-, LSU-, ITS rRNA) gene sequences indicate that our isolates clustered within the Gyrodinium clade. The new sequences formed a sister group with sequences of the freshwater taxon Gyrodinium helveticum, being one of the infrequent marine-freshwater transitions in the microbial world. This isolate is the first characterized member of a clade of numerous environmental sequences widely distributed from cold to tropical seas. This common and abundant taxon has received several names due to its morphological plasticity (changes of size and shape, often deformed after engulfing prey) and the difficulty in discerning surface striation. We conclude that the priority is for the species name Gymnodinium heterostriatum Kofoid & Swezy 1921, a new name that was proposed for Gymnodinium spirale var. obtusum sensu Dogiel 1906. The species Gyrodinium striatissimum (Hulburt 1957) Gert Hansen & Moestrup 2000 and Gymnodinium lucidum D. Ballantine in Parke & Dixon 1964 (=G. hyalinum M. Lebour 1925) are posterior synonyms. We propose Gyrodinium heterostriatum comb. nov. for Gymnodinium heterostriatum.

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Gómez, Fernando, Luis F. Artigas, and Rebecca J. Gast. "Phylogeny and Synonymy of Gyrodinium heterostriatum comb. nov. (Dinophyceae), a Common Unarmored Dinoflagellate in the World Oceans [plus supplementary materials]." Acta Protozoologica 59, no. 2 (2020): 77–87. http://dx.doi.org/10.4467/16890027ap.20.007.12675.

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The North Sea and the English Channel are regions with a long tradition of plankton studies, where the colony-forming haptophyte Phaeocystis globosa dominates the spring phytoplankton blooms. Among its predators, we investigated an abundant unarmored dinoflagellate (~3000 cells per liter) in the North Sea in May 2019. It has been reported in the literature as Gymnodinium heterostriatum or G. striatissimum, and often identified as Gyrodinium spirale. Phylogenetic analyses using the small-, large subunit- and Internal Transcriber Spacers of the ribosomal RNA (SSU-, LSU-, ITS rRNA) gene sequences indicate that our isolates clustered within the Gyrodinium clade. The new sequences formed a sister group with sequences of the freshwater taxon Gyrodinium helveticum, being one of the infrequent marine-freshwater transitions in the microbial world. This isolate is the first characterized member of a clade of numerous environmental sequences widely distributed from cold to tropical seas. This common and abundant taxon has received several names due to its morphological plasticity (changes of size and shape, often deformed after engulfing prey) and the difficulty in discerning surface striation. We conclude that the priority is for the species name Gymnodinium heterostriatum Kofoid & Swezy 1921, a new name that was proposed for Gymnodinium spirale var. obtusum sensu Dogiel 1906. The species Gyrodinium striatissimum (Hulburt 1957) Gert Hansen & Moestrup 2000 and Gymnodinium lucidum D. Ballantine in Parke & Dixon 1964 (=G. hyalinum M. Lebour 1925) are posterior synonyms. We propose Gyrodinium heterostriatum comb. nov. for Gymnodinium heterostriatum.

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Vancaester, Emmelien, Thomas Depuydt, Cristina Maria Osuna-Cruz, and Klaas Vandepoele. "Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms." Molecular Biology and Evolution 37, no. 11 (July 16, 2020): 3243–57. http://dx.doi.org/10.1093/molbev/msaa182.

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Abstract Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favorable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3–5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes was detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.

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Masseret, Estelle, Daniel Grzebyk, Satoshi Nagai, Benjamin Genovesi, Bernard Lasserre, Mohamed Laabir, Yves Collos, André Vaquer, and Patrick Berrebi. "Unexpected Genetic Diversity among and within Populations of the Toxic Dinoflagellate Alexandrium catenella as Revealed by Nuclear Microsatellite Markers." Applied and Environmental Microbiology 75, no. 7 (February 5, 2009): 2037–45. http://dx.doi.org/10.1128/aem.01686-08.

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ABSTRACT Since 1998, blooms of Alexandrium catenella associated with paralytic shellfish poisoning have been repeatedly reported for Thau Lagoon (French Mediterranean coast). Based on data obtained for rRNA gene markers, it has been suggested that the strains involved could be closely related to the Japanese temperate Asian ribotype of the temperate Asian clade. In order to gain more insight into the origin of these organisms, we carried out a genetic analysis of 61 Mediterranean and 23 Japanese strains using both ribosomal and microsatellite markers. Whereas the phylogeny based on ribosomal markers tended to confirm the previous findings, the analysis of microsatellite sequences revealed an unexpected distinction between the French and Japanese populations. This analysis also highlighted great intraspecific diversity that was not detected with the classical rRNA gene markers. The Japanese strains are divided into two differentiated A. catenella lineages: the Sea of Japan lineage and the east coast lineage, which includes populations from the Inland Sea and the Pacific Ocean. A. catenella strains isolated from Thau Lagoon belong to another lineage. These findings indicate that microsatellite markers are probably better suited to investigations of the population genetics of this species that is distributed worldwide. Finally, application of the population genetics concepts available for macroorganisms could support new paradigms for speciation and migration in phytoplankton assemblages.

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Samanta, Brajogopal, and Punyasloke Bhadury. "A comprehensive framework for functional diversity patterns of marine chromophytic phytoplankton using rbcL phylogeny." Scientific Reports 6, no. 1 (February 10, 2016). http://dx.doi.org/10.1038/srep20783.

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Comeau, André M., Marcos G. Lagunas, Karen Scarcella, Diana E. Varela, and Connie Lovejoy. "Nitrate Consumers in Arctic Marine Eukaryotic Communities: Comparative Diversities of 18S rRNA, 18S rRNA Genes, and Nitrate Reductase Genes." Applied and Environmental Microbiology 85, no. 14 (May 3, 2019). http://dx.doi.org/10.1128/aem.00247-19.

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ABSTRACT For photosynthetic microbial eukaryotes, the rate-limiting step in NO3− assimilation is its reduction to nitrite (NO2−), which is catalyzed by assimilatory nitrate reductase (NR). Oceanic productivity is primarily limited by available nitrogen and, although nitrate is the most abundant form of available nitrogen in oceanic waters, little is known about the identity of microbial eukaryotes that take up nitrate. This lack of knowledge is especially severe for ice-covered seas that are being profoundly affected by climate change. To address this, we examined the distribution and diversity of NR genes in the Arctic region by way of clone libraries and data mining of available metagenomes (total of 4.24 billion reads). We directly compared NR clone phylogenies with the V4 region of the 18S rRNA gene (DNA pool) and 18S rRNA (RNA pool) at two ice-influenced stations in the Canada Basin (Beaufort Sea). The communities from the two nucleic acid templates were similar at the level of major groups, and species identified by way of NR gene phylogeny and microscopy were a subset of the 18S results. Most NR genes from arctic clone libraries matched diatoms and chromist nanoflagellates, including novel clades, while the NR genes in arctic eukaryote metagenomes were dominated by chlorophyte NR, in keeping with the ubiquitous occurrence of Mamiellophyceae in the Arctic Ocean. Overall, these data suggest that a dynamic and mixed eukaryotic community utilizes nitrate across the Arctic region, and they show the potential utility of NR as a tool to identify ongoing changes in arctic photosynthetic communities. IMPORTANCE To better understand the diversity of primary producers in the Arctic Ocean, we targeted a nitrogen cycle gene, NR, which is required for phytoplankton to assimilate nitrate into organic forms of nitrogen macromolecules. We compared this to the more detailed taxonomy from ice-influenced stations using a general taxonomic gene (18S rRNA). NR genes were ubiquitous and could be classified as belonging to diatoms, dinoflagellates, other flagellates, chlorophytes, and unknown microbial eukaryotes, suggesting novel diversity of both species and metabolism in arctic phytoplankton.

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Wolter, Laura A., Maximilian Mitulla, Jovan Kalem, Rolf Daniel, Meinhard Simon, and Matthias Wietz. "CAZymes in Maribacter dokdonensis 62–1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain." Frontiers in Microbiology 12 (April 12, 2021). http://dx.doi.org/10.3389/fmicb.2021.628055.

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Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62–1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62–1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain “polysaccharide niches.” Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.

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Journal articles on the topic 'Phytoplankton – Phylogeny'

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