Eukaryotic Plankton Research Articles

Dynamic genetic features of eukaryotic plankton diversity in the Nakdong River estuary of Korea

Estuaries are environments where freshwater and seawater mix and they display various salinity profiles. The construction of river barrages and dams has rapidly changed these environments and has had a wide range of impacts on plankton communities. To understand the dynamics of such communities, researchers need accurate and rapid techniques for detecting plankton species. We evaluated the diversity of eukaryotic plankton over a salinity gradient by applying a metagenomics tool at the Nakdong River estuary in Korea. Environmental samples were collected on three dates during summer and autumn of 2011 at the Eulsukdo Bridge at the mouth of that river. Amplifying the 18S rDNA allowed us to analyze 456 clones and 122 phylotypes. Metagenomic sequences revealed various taxonomic groups and cryptic genetic variations at the intra- and inter-specific levels. By analyzing the same station at each sampling date, we observed that the phylotypes presented a salinity-related pattern of diversity in assemblages. The variety of species within freshwater samples reflected the rapid environmental changes caused by freshwater inputs. Dinophyceae phylotypes accounted for the highest proportion of overall diversity in the seawater samples. Euryhaline diatoms and dinoflagellates were observed in the freshwater, brackish and seawater samples. The biological data for species composition demonstrate the transitional state between freshwater and seawater. Therefore, this metagenomics information can serve as a biological indicator for tracking changes in aquatic environments.

Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea.

Microbial plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities sampled in summer along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. In contrast, no clear trends in alpha-diversity for bacterial or eukaryotic communities could be detected along the transect. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but groups novel to the Baltic Sea were also identified, such as relatives to the coccolithophore Emiliana huxleyi detected in the northern Baltic Sea. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.

Environmental carbonate chemistry selects for phenotype of recently isolated strains of Emiliania huxleyi

Coccolithophorid algae, particularly Emiliania huxleyi, are prolific biomineralisers that, under many conditions, dominate communities of marine eukaryotic plankton. Their ability to photosynthesise and form calcified scales (coccoliths) has placed them in a unique position in the global carbon cycle. Contrasting reports have been made with regards to the response of E. huxleyi to ocean acidification. Therefore, there is a pressing need to further determine the fate of this key organism in a rising CO2 world. In this paper, we investigate the phenotype of newly isolated, genetically diverse, strains of E. huxleyi from UK Ocean Acidification Research Programme (UKOA) cruises around the British Isles, the Arctic, and the Southern Ocean. We find a continuum of diversity amongst the physiological and photosynthetic parameters of different strains of E. huxleyi morphotype A under uniform, ambient conditions imposed in the laboratory. This physiology is best explained by adaptation to carbonate chemistry in the former habitat rather than being prescribed by genetic fingerprints such as the coccolithophore morphology motif (CMM). To a first order, the photosynthetic capacity of each strain is a function of both aqueous CO2 availability, and calcification rate, suggestive of a link between carbon concentrating ability and calcification. The calcification rate of each strain is related linearly to the natural environmental [CO32−] at the site of isolation, but a few exceptional strains display low calcification rates at the highest [CO32−] when calcification is limited by low CO2 availability and/or a lack of a carbon concentrating mechanism. We present O2-electrode measurements alongside coccolith oxygen isotopic composition and the uronic acid content (UAC) of the coccolith associated polysaccharide (CAP), that act as indirect tools to show the differing carbon concentrating ability of the strains. The environmental selection revealed amongst our recently isolated strain collection points to the future outcompetition of the slow growing morphotypes B/C and R (which also lack a carbon concentrating mechanism) by more rapidly photosynthesising, and lightly calcified strains of morphotype A but with their rate of calcification highly dependent on the surface ocean saturation state. The mechanism of E. huxleyi response to carbonate chemistry in the modern ocean appears to be selection from a continuum of phenotype.

Nutrient Limitation in Surface Waters of the Oligotrophic Eastern Mediterranean Sea: an Enrichment Microcosm Experiment.

The growth rates of planktonic microbes in the pelagic zone of the Eastern Mediterranean Sea are nutrient limited, but the type of limitation is still uncertain. During this study, we investigated the occurrence of N and P limitation among different groups of the prokaryotic and eukaryotic (pico-, nano-, and micro-) plankton using a microcosm experiment during stratified water column conditions in the Cretan Sea (Eastern Mediterranean). Microcosms were enriched with N and P (either solely or simultaneously), and the PO4 turnover time, prokaryotic heterotrophic activity, primary production, and the abundance of the different microbial components were measured. Flow cytometric and molecular fingerprint analyses showed that different heterotrophic prokaryotic groups were limited by different nutrients; total heterotrophic prokaryotic growth was limited by P, but only when both N and P were added, changes in community structure and cell size were detected. Phytoplankton were N and P co-limited, with autotrophic pico-eukaryotes being the exception as they increased even when only P was added after a 2-day time lag. The populations of Synechococcus and Prochlorococcus were highly competitive with each other; Prochlorococcus abundance increased during the first 2 days of P addition but kept increasing only when both N and P were added, whereas Synechococcus exhibited higher pigment content and increased in abundance 3 days after simultaneous N and P additions. Dinoflagellates also showed opportunistic behavior at simultaneous N and P additions, in contrast to diatoms and coccolithophores, which diminished in all incubations. High DNA content viruses, selective grazing, and the exhaustion of N sources probably controlled the populations of diatoms and coccolithophores.

A new approach to ancient microorganisms: taxonomy, paleoecology, and biostratigraphy of the Lower Cambrian Berkuta and Chulaktau microbiotas of South Kazakhstan

AbstractPeritidal cherts and silicified phosphorites of the Early Cambrian Kyrshabakta (Berkuta Member) and Chulaktau formations of South Kazakhstan contain diverse assemblages of cellularly permineralized microorganisms that like other microbiotas of similar age and setting are dominated by cyanobacteria, both filamentous (oscillatoriacean trichomes and empty sheaths) and coccoidal (chroococcaceans). Although these near-shore assemblages contain sphaeromorph acritarchs, they differ from Neoproterozoic and Early Cambrian microbiotas of more open-marine environments by lacking morphologically complex planktonic eukaryotes such as the acanthomorphic acritarchs that are abundant in the Chulaktau-overlying Shabakta Formation. In general composition, the Berkuta and Chulaktau assemblages are similar both to microfossil assemblages of the pre-trilobite Rovno and Lontova Regional Stages of the East European Platform and to Early Cambrian microbiotas known from chert-phosphorite deposits worldwide.The studies reported here are based on use of optical microscopy combined with techniques recently introduced to paleobiology: confocal laser scanning microscopy, and Raman and fluorescence spectroscopy and imagery. Taken together, these provide information in situ, in three dimensions and at high spatial resolution, about the organismal morphology; cellular anatomy; chemical composition; and mode, fidelity, and environment of preservation of the permineralized microfossils. Data are presented suggesting that the substitution of samarium for calcium in fossil-preserving apatite may provide evidence of its oxic or anoxic paleoenvironment of formation.We interpret the Berkuta and Chulaktau assemblages to be composed of 27 taxa assigned to 17 genera of microscopic prokaryotes and eukaryotes that include one new genus and species, Berkutaphycus elongatus.

N2-fixation, ammonium release and N-transfer to the microbial and classical food web within a plankton community.

We investigated the role of N2-fixation by the colony-forming cyanobacterium, Aphanizomenon spp., for the plankton community and N-budget of the N-limited Baltic Sea during summer by using stable isotope tracers combined with novel secondary ion mass spectrometry, conventional mass spectrometry and nutrient analysis. When incubated with (15)N2, Aphanizomenon spp. showed a strong (15)N-enrichment implying substantial (15)N2-fixation. Intriguingly, Aphanizomenon did not assimilate tracers of (15)NH4(+) from the surrounding water. These findings are in line with model calculations that confirmed a negligible N-source by diffusion-limited NH4(+) fluxes to Aphanizomenon colonies at low bulk concentrations (<250 nm) as compared with N2-fixation within colonies. No N2-fixation was detected in autotrophic microorganisms <5 μm, which relied on NH4(+) uptake from the surrounding water. Aphanizomenon released about 50% of its newly fixed N2 as NH4(+). However, NH4(+) did not accumulate in the water but was transferred to heterotrophic and autotrophic microorganisms as well as to diatoms (Chaetoceros sp.) and copepods with a turnover time of ~5 h. We provide direct quantitative evidence that colony-forming Aphanizomenon releases about half of its recently fixed N2 as NH4(+), which is transferred to the prokaryotic and eukaryotic plankton forming the basis of the food web in the plankton community. Transfer of newly fixed nitrogen to diatoms and copepods furthermore implies a fast export to shallow sediments via fast-sinking fecal pellets and aggregates. Hence, N2-fixing colony-forming cyanobacteria can have profound impact on ecosystem productivity and biogeochemical processes at shorter time scales (hours to days) than previously thought.

Genetic data from algae sedimentary DNA reflect the influence of environment over geography.

Genetic investigations on eukaryotic plankton confirmed the existence of modern biogeographic patterns, but analyses of palaeoecological data exploring the temporal variability of these patterns have rarely been presented. Ancient sedimentary DNA proved suitable for investigations of past assemblage turnover in the course of environmental change, but genetic relatedness of the identified lineages has not yet been undertaken. Here, we investigate the relatedness of diatom lineages in Siberian lakes along environmental gradients (i.e. across treeline transects), over geographic distance and through time (i.e. the last 7000 years) using modern and ancient sedimentary DNA. Our results indicate that closely-related Staurosira lineages occur in similar environments and less-related lineages in dissimilar environments, in our case different vegetation and co-varying climatic and limnic variables across treeline transects. Thus our study reveals that environmental conditions rather than geographic distance is reflected by diatom-relatedness patterns in space and time. We tentatively speculate that the detected relatedness pattern in Staurosira across the treeline could be a result of adaptation to diverse environmental conditions across the arctic boreal treeline, however, a geographically-driven divergence and subsequent repopulation of ecologically different habitats might also be a potential explanation for the observed pattern.

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies.

BackgroundCost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture.ResultsThe 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene.ConclusionHigh coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.

High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

Going ballistic in the plankton: Anisotropic swimming behavior of marine protists

Lay AbstractPlankton are a critically important group of oceanic organisms, comprising the base of marine food webs and accounting for half of all biological carbon fixation on Earth. Although plankton have traditionally been thought of as passive drifters in the ocean, many of these organisms have the ability to move of their own accord. The twisting paths that swimming protists (single‐cell eukaryotic plankton) traced out in previous laboratory studies have frequently been compared with the paths that a molecule follows as it moves randomly through space due to thermal energy in a process called diffusion. However, it is also well known that many protists in the ocean undergo large vertical migrations of several meters or more, which can be explained only if the cells were able to swim in essentially straight vertical lines, known as ballistic motion. Although there have been a few direct observations of ballistic motion of protists in the laboratory, little quantitative proof has been accumulated thus far. We assembled a large data set of relatively long‐duration, three‐dimensional swimming paths for several protist species, both plant‐ and animal‐like, and calculated how long they tended to swim straight before turning. Since almost all the cells moved primarily in the vertical direction, we separated the horizontal dimensions from the vertical in this analysis. All the protist species observed here did make frequent horizontal (left/right) turns, matching a diffusion model at scales greater than a few seconds or fractions of a millimeter. However, turns in the vertical direction were extremely rare for almost all species, indicating vertical ballistic motion (i.e., moving either up or down without switching direction) at swimming speeds that match the large‐scale field observations of migratory behavior. Our observations show ballistic swimming for much longer than in several previous studies—up to 120 s or 6 mm for organisms sized about the diameter of a human hair. The habitat and biogeochemical footprint of these planktonic protists are therefore much larger than one might expect based on their microscopic size.

The role of mixotrophic protists in the biological carbon pump

Abstract. The traditional view of the planktonic food web describes consumption of inorganic nutrients by photoautotrophic phytoplankton, which in turn supports zooplankton and ultimately higher trophic levels. Pathways centred on bacteria provide mechanisms for nutrient recycling. This structure lies at the foundation of most models used to explore biogeochemical cycling, functioning of the biological pump, and the impact of climate change on these processes. We suggest an alternative new paradigm, which sees the bulk of the base of this food web supported by protist plankton communities that are mixotrophic – combining phototrophy and phagotrophy within a single cell. The photoautotrophic eukaryotic plankton and their heterotrophic microzooplankton grazers dominate only during the developmental phases of ecosystems (e.g. spring bloom in temperate systems). With their flexible nutrition, mixotrophic protists dominate in more-mature systems (e.g. temperate summer, established eutrophic systems and oligotrophic systems); the more-stable water columns suggested under climate change may also be expected to favour these mixotrophs. We explore how such a predominantly mixotrophic structure affects microbial trophic dynamics and the biological pump. The mixotroph-dominated structure differs fundamentally in its flow of energy and nutrients, with a shortened and potentially more efficient chain from nutrient regeneration to primary production. Furthermore, mixotrophy enables a direct conduit for the support of primary production from bacterial production. We show how the exclusion of an explicit mixotrophic component in studies of the pelagic microbial communities leads to a failure to capture the true dynamics of the carbon flow. In order to prevent a misinterpretation of the full implications of climate change upon biogeochemical cycling and the functioning of the biological pump, we recommend inclusion of multi-nutrient mixotroph models within ecosystem studies.

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton

How reproducibly microbial populations assemble in the wild remains poorly understood. Here, we assess evidence for ecological specialization and predictability of fine-scale population structure and habitat association in coastal ocean Vibrionaceae across years. We compare Vibrionaceae lifestyles in the bacterioplankton (combinations of free-living, particle, or zooplankton associations) measured using the same sampling scheme in 2006 and 2009 to assess whether the same groups show the same environmental association year after year. This reveals complex dynamics with populations falling primarily into two categories: (i) nearly equally represented in each of the two samplings and (ii) highly skewed, often to an extent that they appear exclusive to one or the other sampling times. Importantly, populations recovered at the same abundance in both samplings occupied highly similar habitats suggesting predictable and robust environmental association while skewed abundances of some populations may be triggered by shifts in ecological conditions. The latter is supported by difference in the composition of large eukaryotic plankton between years, with samples in 2006 being dominated by copepods, and those in 2009 by diatoms. Overall, the comparison supports highly predictable population-habitat linkage but highlights the fact that complex, and often unmeasured, environmental dynamics in habitat occurrence may have strong effects on population dynamics.

Flow cytometric identification ofMamiellalesclade II in the Southern Atlantic Ocean

Flow cytometric sorting, based on cellular optical properties and macromolecule content, has been successfully employed to taxonomically affiliate bacterioplankton. However, this approach has not been much used for eukaryotic plankton. To redress this imbalance, we identified a conspicuous group of red autofluorescent picoplankton in surface waters of the South Atlantic Ocean. Using catalysed reporter deposition fluorescence in situ hybridization, virtually, all cells sorted from that group were affiliated with the Mamiellales clade II (84 ± 4%, division Chlorophyta) with a size of 1.6 ± 0.03 μm. Based on electron microscopy, the Mamiellales clade II-sorted cells have a simple morphology with apparently no scales, flagella or surface features. Their latitudinal distribution resembled the distribution of Synechococcus with very low concentrations in the surface waters of the Southern subtropical gyre (0.6-1.6 × 10(3) cells mL(-1)) and increased concentrations in the Southern temperate waters 8.3 × 10(3) cells mL(-1). Identification of the flow cytometric group as Mamiellales clade II allowed us to characterize the morphology of these enigmatic uncultured picoplanktonic cells by electron microscopy and to determine their apparent preference for temperate rather than subtropical oceanic photic waters.

Hidden diversity of eukaryotic plankton in the soda lake Nakuru, Kenya, during a phase of low salinity revealed by a SSU rRNA gene clone library

A SSU rRNA gene clone library was constructed to establish the diversity of eukaryotic plankton in the African soda lake Nakuru during a phase of low salinity (9.7 ppt = hyposaline). Normally, the lake is mesosaline (up to 50 ppt) and its phytoplankton is dominated by few species of cyanobacteria, in particular Arthrospira fusiformis, which is the main food resource of Lesser Flamingos. Our study recovered a unique phytoplankton species composition characterized by a high diversity of monadoid and coccoid green algae. Out of 77 clones detected, 52 belonged to Chlorophyta. Many of the chlorophytes were transported from the catchment area into the lake through small seasonal rivers and an outflow of the Nakuru town sewage treatment plant. Other phylogenetic groups detected were Fungi, Cryptophyta, Jakobida, Alveolata, Stramenopiles, and Metazoa. Our findings reveal a hidden diversity, which would not have been detected by traditional observations.

낙동강 하류 물금과 을숙도 수환경의 진핵 플랑크톤 종조성에 대한 분자모니터링

We have studied the eukaryotic plankton species diversity to compare the community structure of fresh and brackish waters in the lower reaches of the Nakdong River using metagenomic methods. We constructed 18S rDNA clone libraries of total DNAs extracted from environmental water samples collected at Mulgeum (MG100929, fresh) and Eulsukdo bridge (ES, brackish). Through the steps of colony PCR, PCR-RFLP, sequencing and similarity analysis, we discovered the diverse species composition of eukaryotic plankton. Total 338 clones (170 at MG100929 and 168 at ES) were analyzed, and then we found 74 phylotypes (49 for MG100929 and 25 for ES). From the phylogenetic analysis, we confirmed various eukaryotic plankton of broad range of taxonomic groups, including Stramenopiles, Cryptophyta, Viridiplantae, Alveolata, Rhizaria, Metazoa, and Fungi. We also found several unreported species in Korea and candidates of new taxonomic entities at levels higher than genus. Especially, the cryptic species diversity including unreported phylotypes of Pirsonia (Stramenopiles) and Perkinsea (Alveolata) suggests that the molecular monitoring method can produce new informative biological data in monitoring the changes in the Nakdong River Mouth ecosystem.

Metagenomic examination of diversity within eukaryotic plankton from the ulleung basin in the East Sea of Korea

We constructed planktonic 18S rDNA clone libraries for micro-organisms in the euphotic zone of the Ulleung Basin in the East Sea of Korea. They revealed the cryptic biodiversity of eukaryotic planktons and demonstrated specific phylogenetic affiliations at certain water depths. Dinoflagellate clones dominated at the surface and 75-m depth. Members of the Syndiniales order (Groups I and II), containing wellknown parasitic dinoflagellates, as well as one their prominent hosts, Polycystinea, were found exclusively at 75 m. These observations suggest that the presence of species from Groups I and II is closely related to the specific water mass. Therefore, their metagenomics information might be useful for delineating both water-mass and physico-chemical properties.

Genetic diversity of planktonic eukaryotes in high mountain lakes (Central Pyrenees, Spain)

The genetic diversity of planktonic eukaryotic microorganisms (size range 3-40 µm) inhabiting 11 alpine lakes of the Central Pyrenees (Spain) was analysed by cloning and sequencing of the 18S rRNA gene. The selected lakes covered a wide range of environmental conditions representative of the regional landscape heterogeneity. Overall, we obtained 953 sequences (averaged length 750 bp) that were grouped in 343 representative OTUs (98% identity). The genetic richness was high, and the 18S rRNA gene sequences spread within nine high-rank taxonomic groups and grouped in 26 eukaryal classes. Most of the sequences affiliated with Stramenopiles (> 55% of total sequences, mostly Chrysophyceae), Cryptophyta and Alveolata (15% each). Three groups had relative abundance < 5%, i.e. Opisthokonta (mostly Fungi), Viridiplantae (mostly Chlorophyceae) and Rhizaria (cercomonads). Finally, minor groups were related to Katablepharidophyta, Euglenozoa and Telonemida. The lakes showed a different community structure being pH, and phosphorous and Chl a concentrations the main environmental drivers. The novelty level was high, and a quarter of the retrieved OTUs were notably divergent (< 97% identity) from any previously known sequence, mainly for Rhizaria and Opisthokonta. More than 50% of the sequences affiliated with clusters exclusively formed by uncultured protists. Cryptophyta and Viridiplantae showed the largest number of sequences closely related to cultured counterparts. This work is the first description of the genetic diversity of eukaryotic assemblages in ultraoligotrophic high mountain lakes, and the study unveils alpine environments as an important reservoir of microbial eukaryotic biodiversity.

부산 연안역의 진핵플랑크톤 종다양성에 대한 메타게놈 분석 연구

The species composition of plankton is essential to understand the material and energy cycling within marine ecosystem. It also provides the useful information for understanding the properties of marine environments due to its sensitivity to the physicochemical characteristics and variability of water masses. In this study we adopted metagenomics to evaluate eukaryotic plankton species diversity from coastal waters off Busan. Characteristics of water masses at sampling sites is expected to be very complex due to the mixing of various water masses; Nakdong River runoff, Changjiang diluted water (CDW), South Sea coastal water, and Tsushima warm current. 18S rDNA clone libraries were constructed from surface waters at the three sites off Busan. Clone libraries revealed 94 unique phylotypes from 370 clones; Dinophyceae(42 phylotypes), Ciliophora(15 phylotypes), Bacillariophyta(7 phylotypes), Chlorophyta(2 phylotypes), Haptophyceae(1 phylotype), Metazoa(Arthropoda( 17 phylotypes), Chaetognatha(1 phylotypes), Cnidaria(2 phylotypes), Chordata(1 phylotype)), Rhizaria (Acantharea(2 phylotypes), Polycystinea(1 phylotype)), Telonemida(1 phylotype), Fungi(2 phylotypes). The difference in species diversity at the closely located three sites off Busan may be attributed to the various physicochemical properties of water masses at these sites by the mixture of water masses of various origins. Metagenomic study of species composition may provide useful information for understanding marine ecosystem of coastal waters with various physicochemical properties in the near feature.

The distinct nitrogen isotopic compositions of low and high molecular weight marine DON

To constrain the sources and cycling of bulk and size-fractionated marine dissolved organic nitrogen (DON), samples were collected for concentration and isotopic (δ15N) analysis from the western tropical North Atlantic Ocean as well as over the North Australian shelf. Bulk DON concentrations are typically between 4 and 6μM, with low molecular weight (LMW, i.e., <1000Da) DON accounting for 60 to 70% of total DON. The δ15N of both bulk and high molecular weight (HMW, i.e., >1000Da to <0.2μm) DON from the western tropical North Atlantic is similar to previous measurements, as well as to bulk and HMW DON collected off the North Australian Shelf, ~4‰. Here we report the first measurement of marine LMW DON δ15N, and a coherent pattern emerges where LMW DON δ15N<HMW DON δ15N. An analytical concern is that the bulk DON δ15N as calculated from our coupled HMW and LMW measurements is often lower than that measured directly for the bulk DON. Despite this discrepancy, the self-consistency of the data in other regards argues for the robustness of the basic observation of lower δ15N in LMW relative to HMW DON. One explanation for this isotopic difference is considered most likely, based on the model that DON δ15N elevation relative to PON is fundamentally due to DON production from PON without isotopic fractionation, coupled with DON destruction occurring with fractionation. In this model, HMW DON loss must occur predominantly through the breakage of N-containing bonds, for which isotope fractionation should be substantial, whereas LMW DON loss is partly due to direct assimilation by phytoplankton and other microbes, which appears to occur with only minor isotopic fractionation. However, an alternative hypothesis exists: LMW and HMW DON may have distinct sources, for example, prokaryotic and eukaryotic plankton, respectively. In either case, it appears that most LMW DON has not passed through the HMW DON pool, as this would require an unrealistically large isotope fractionation at the HMW to LMW conversion. Finally, neither the concentration nor the δ15N of the bulk or either size fraction of DON varies with in situ N2 fixation rates measured at the time of sample collection. However, the δ15N of both bulk and LMW DON from the western tropical North Atlantic shows significant differences between samples collected six months apart, which may be due to seasonally variable stimulation of primary production by the Amazon River.

Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation

BackgroundSmall size eukaryotes play a fundamental role in the functioning of coastal ecosystems, however, the way in which these micro-organisms respond to combined effects of water temperature, UVB radiations (UVBR) and nutrient availability is still poorly investigated.ResultsWe coupled molecular tools (18S rRNA gene sequencing and fingerprinting) with microscope-based identification and counting to experimentally investigate the short-term responses of small eukaryotes (<6 μm; from a coastal Mediterranean lagoon) to a warming treatment (+3°C) and UVB radiation increases (+20%) at two different nutrient levels. Interestingly, the increase in temperature resulted in higher pigmented eukaryotes abundances and in community structure changes clearly illustrated by molecular analyses. For most of the phylogenetic groups, some rearrangements occurred at the OTUs level even when their relative proportion (microscope counting) did not change significantly. Temperature explained almost 20% of the total variance of the small eukaryote community structure (while UVB explained only 8.4%). However, complex cumulative effects were detected. Some antagonistic or non additive effects were detected between temperature and nutrients, especially for Dinophyceae and Cryptophyceae.ConclusionsThis multifactorial experiment highlights the potential impacts, over short time scales, of changing environmental factors on the structure of various functional groups like small primary producers, parasites and saprotrophs which, in response, can modify energy flow in the planktonic food webs.