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1.
BMC Evol Biol ; 19(1): 145, 2019 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311504

RESUMO

BACKGROUND: China is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distribution. Therefore, many biogeographical studies have focused on the organisms of the region, especially zooplankton, which is essential in the formation of biogeographical principles. Moreover, the generality of endemism also reinforces the need for detailed regional studies of zooplankton. Bosmina, a group of cosmopolitan zooplankton, is difficult to identify by morphology, and no genetic data are available to date to assess this species complex in China. In this study, 48 waterbodies were sampled covering a large geographical and ecological range in China, the goal of this research is to explore the species distribution of Bosmina across China and to reveal the genetic information of this species complex, based on two genetic markers (a mtDNA 16S and a nuclear ITS). The diversity of taxa in the Bosmina across China was investigated using molecular tools for the first time. RESULTS: Two main species were detected in 35 waterbodies: an endemic east Asia B. fatalis, and the B. longirostris that has a Holarctic distribution. B. fatalis had lower genetic polymorphism and population differentiation than B. longirostris. B. fatalis was preponderant in central and eastern China, whereas B. longirostris was dominated in western China. The third lineage (B. hagmanni) was only detected in a reservoir (CJR) of eastern China (Guangdong province). Bosmina had limited distribution on the Tibetan plateau. CONCLUSIONS: This study revealed that the biogeography of Bosmina appear to be affected by historical events (Pleistocene glaciations) and contemporary environment (such as altitude, eutrophication and isolated habitat).


Assuntos
Cladóceros/genética , DNA Intergênico/genética , DNA Mitocondrial/genética , Variação Genética , Animais , Núcleo Celular/genética , China , Ecossistema , Marcadores Genéticos , Geografia , Haplótipos/genética , Funções Verossimilhança , Mitocôndrias/genética , Filogenia , Polimorfismo Genético , Zooplâncton/genética
2.
PLoS Genet ; 15(2): e1007943, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30735490

RESUMO

Marine ecosystems are changing rapidly as the oceans warm and become more acidic. The physical factors and the changes to ocean chemistry that they drive can all be measured with great precision. Changes in the biological composition of communities in different ocean regions are far more challenging to measure because most biological monitoring methods focus on a limited taxonomic or size range. Environmental DNA (eDNA) analysis has the potential to solve this problem in biological oceanography, as it is capable of identifying a huge phylogenetic range of organisms to species level. Here we develop and apply a novel multi-gene molecular toolkit to eDNA isolated from bulk plankton samples collected over a five-year period from a single site. This temporal scale and level of detail is unprecedented in eDNA studies. We identified consistent seasonal assemblages of zooplankton species, which demonstrates the ability of our toolkit to audit community composition. We were also able to detect clear departures from the regular seasonal patterns that occurred during an extreme marine heatwave. The integration of eDNA analyses with existing biotic and abiotic surveys delivers a powerful new long-term approach to monitoring the health of our world's oceans in the context of a rapidly changing climate.


Assuntos
Organismos Aquáticos/genética , Biodiversidade , Mudança Climática , Ecossistema , Animais , Organismos Aquáticos/classificação , DNA/genética , DNA/isolamento & purificação , Código de Barras de DNA Taxonômico , Monitoramento Ambiental , Oceanos e Mares , Filogenia , Estações do Ano , Austrália Ocidental , Zooplâncton/classificação , Zooplâncton/genética
3.
Mitochondrial DNA A DNA Mapp Seq Anal ; 30(1): 118-125, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-29671658

RESUMO

Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology. Here, by analysing the mitochondrial COI gene, we explore the taxa across the SCA using molecular tools for the first time. Our results show that sequence divergence among species varies within a large range, from 12.93% to 35.82%. Sixteen of the taxonomic units recovered by DNA taxonomy agree well with morphology, but Paraconchoecia oblonga, Conchoecia magna and Halocypris brevirostris split into two clades each, each of which contains cryptic species.


Assuntos
Biodiversidade , Crustáceos/genética , Código de Barras de DNA Taxonômico/métodos , Filogenia , Zooplâncton/genética , Animais , Crustáceos/classificação , Código de Barras de DNA Taxonômico/normas , Complexo IV da Cadeia de Transporte de Elétrons/genética , Zooplâncton/classificação
4.
Mol Ecol ; 28(2): 176-189, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30403421

RESUMO

Gelatinous zooplankton play a crucial role in marine planktonic food webs. However, primarily due to methodological challenges, the in situ diet of zooplankton remains poorly investigated and little is known about their trophic interactions including feeding behaviour, prey selection and in situ feeding rates. This is particularly true for gelatinous zooplankton including the marine pelagic tunicate, Dolioletta gegenbauri. In this study, we applied an 18S rRNA amplicon metabarcoding approach to identify the diet of captive-fed and wild-caught D. gegenbauri on the midcontinental shelf of the South Atlantic Bight, USA. Sequencing-based approaches were complimented with targeted quantitative real-time polymerase chain reaction (PCR) analyses. Captive-fed D. gegenbauri gut content was dominated by pico-, nano- and micro-plankton including pico-dinoflagellates (picozoa) and diatoms. These results suggested that diatoms were concentrated by D. gegenbauri relative to their concentration in the water column. Analysis of wild-caught doliolids by quantitative real-time PCR utilizing a group-specific diatom primer set confirmed that diatoms were concentrated by D. gegenbauri, particularly by the gonozooid life stage associated with actively developing blooms. Sequences derived from larger metazoans were frequently observed in wild-caught animals but not in captive-fed animals suggesting experimental bias associated with captive feeding. These studies revealed that the diet of D. gegenbauri is considerably more diverse than previously described, that parasites are common in wild populations, and that prey quality, quantity and parasites are likely all important factors in regulating doliolid population dynamics in continental shelf environments.


Assuntos
Código de Barras de DNA Taxonômico , Diatomáceas/genética , Zooplâncton/genética , Animais , Diatomáceas/fisiologia , Comportamento Alimentar/fisiologia , Cadeia Alimentar , RNA Ribossômico 18S/genética , Análise de Sequência de DNA , Zooplâncton/fisiologia
5.
Microb Ecol ; 77(2): 277-287, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29951743

RESUMO

Bacterioplankton are both primary producers and primary consumers in aquatic ecosystems, which were commonly investigated to reflect environmental changes, evaluate primary productivity, and assess biogeochemical cycles. However, there is relatively less understanding of their responses to anthropogenic disturbances such as constructions of dams/tunnels/roads that may significantly affect the aquatic ecosystem. To fill such gap, this study focused on the bacterioplankton communities' diversity and turnover during a tunnel construction across an urban lake (Lake Donghu, Wuhan, China), and five batches of samples were collected within 2 months according to the tunnel construction progress. Results indicated that both resources and predator factors contributed significant to the variations of bacterioplankton communities, but the closed area and open areas showed different diversity patterns due to the impacts of tunnel construction. Briefly, the phytoplankton, TN, and TP in water were still significantly correlated with the bacterioplankton composition and diversity like that in normal conditions. Additionally, the organic matter, TN, and NH4-N in sediments also showed clear effects on the bacterioplankton. However, the predator effects on the bacterioplankton in the closed-off construction area mainly derived from large zooplankton (i.e., cladocerans), while small zooplankton such as protozoa and rotifers are only responsible for weak predator effects on the bacterioplankton in the open areas. Further analysis about the ecological driving forces indicated that the bacterioplankton communities' turnover during the tunnel construction was mainly governed by the homogeneous selection due to similar environments within the closed area or the open areas at two different stages. This finding suggests that bacterioplankton communities can quickly adapt to the environmental modifications resulting from tunnel construction activities. This study can also give references to enhance our understanding on bacterioplankton communities' response to ecological and environmental changes due to intensification of construction and urbanization in and around lake ecosystems.


Assuntos
Bactérias/isolamento & purificação , Lagos/microbiologia , Plâncton/isolamento & purificação , Animais , Bactérias/classificação , Bactérias/genética , Biodiversidade , China , Sedimentos Geológicos/microbiologia , Sedimentos Geológicos/parasitologia , Lagos/parasitologia , Filogenia , Plâncton/classificação , Plâncton/genética , Zooplâncton/classificação , Zooplâncton/genética , Zooplâncton/isolamento & purificação
6.
BMC Evol Biol ; 18(1): 130, 2018 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-30176793

RESUMO

BACKGROUND: The zooplanktonic cladocerans Daphnia, present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing eggs carried by waterfowl, Daphnia often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species, D. galeata, we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci. RESULTS: Mitochondrial DNA demonstrated relatively shallow divergence within D. galeata, with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European D. galeata populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for D. galeata populations in China but not in Europe. CONCLUSIONS: Our results indicate relatively recent spread of D. galeata across wide expanses of the Palaearctic, with one mtDNA lineage of D. galeata successfully establishing over large distances. Despite a clear differentiation of Chinese and European D. galeata at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.


Assuntos
Núcleo Celular/genética , Daphnia/genética , Variação Genética , Haplótipos/genética , Mitocôndrias/genética , Alelos , Animais , Teorema de Bayes , China , DNA/genética , DNA Mitocondrial/genética , Europa (Continente) , Genes Mitocondriais , Genética Populacional , Geografia , Repetições de Microssatélites/genética , Filogenia , Zooplâncton/genética
7.
Sci Rep ; 8(1): 12085, 2018 08 14.
Artigo em Inglês | MEDLINE | ID: mdl-30108256

RESUMO

Zooplankton plays a pivotal role in marine ecosystems and the characterisation of its biodiversity still represents a challenge for marine ecologists. In this study, mesozooplankton composition from 46 samples collected in summer along the western Adriatic Sea, was retrieved by DNA metabarcoding analysis. For the first time, the highly variable fragments of the mtDNA COI and the V9 region of 18S rRNA genes were used in a combined matrix to compile an inventory of mesozooplankton at basin scale. The number of sequences retrieved after quality filtering were 824,148 and 223,273 for COI and 18S (V9), respectively. The taxonomical assignment against reference sequences, using 95% (for COI) and 97% (for 18S) similarity thresholds, recovered 234 taxa. NMDS plots and cluster analysis divided coastal from offshore samples and the most representative species of these clusters were distributed according to the dominant surface current pattern of the Adriatic for the summer period. For selected sampling sites, mesozooplankton species were also identified under a stereo microscope providing insights on the strength and weakness of the two approaches. In addition, DNA metabarcoding was shown to be helpful for the monitoring of non-indigenous marine metazoans and spawning areas of commercial fish species. We defined pros and cons of applying this approach at basin scale and the benefits of combining the datasets from two genetic markers.


Assuntos
Biodiversidade , Código de Barras de DNA Taxonômico/métodos , Monitorização de Parâmetros Ecológicos/métodos , Metagenômica/métodos , Zooplâncton/genética , Animais , DNA Mitocondrial/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Espécies Introduzidas , Biologia Marinha/métodos , Metagenoma/genética , Oceanos e Mares , RNA Ribossômico 18S/genética , Análise de Sequência de DNA/métodos , Zooplâncton/classificação
8.
J Phycol ; 54(4): 557-570, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29908074

RESUMO

Some diatoms are able to colonize as epibionts on their potential zooplankton predators. Here, we report Pseudohimantidium pacificum living on the copepod Corycaeus giesbrechti and as a new finding on Oithona nana, Protoraphis atlantica living on the copepod Pontellopsis brevis, Protoraphis hustedtiana on the cypris larvae of barnacles, and Falcula hyalina on the copepod Acartia lilljeborgii. The epizoic diatoms were able to grow as free-living forms under culture conditions. Pseudohimantidium pacificum and P. atlantica appeared as the most derived species from their benthic diatom ancestors. The mucilage pad or stalk of the strains of these species showed important morphological distinction when compared with their epizoic forms. Barnacle larvae explore benthic habitats before settlement, and epibiosis on them is an example where P. hustedtiana profits from the host behavior for dispersal of its benthic populations. Molecular phylogenies based on the SSU rRNA and RuBisCO large subunit (rbcL) gene sequences revealed F. hyalina as an independent lineage within the Fragilariales (Tabularia, Catacombas, and others), consistent with its morphological distinction in the low number of rows (≤6) in the ocellulimbus, among other features. We propose the transfer of F. hyalina to the genus Pseudofalcula gen. nov. Molecular phylogeny suggests a single order for the members of the Cyclophorales and the Protoraphidales, and that the epibioses of araphid diatoms on marine zooplankton have been independently acquired several times. These clades are constituted of both epizoic and epiphytic/epilithic forms that evidence a recent acquisition of the epizoic modus vivendi.


Assuntos
Diatomáceas/classificação , Zooplâncton/classificação , Animais , DNA Ribossômico/análise , Diatomáceas/citologia , Diatomáceas/genética , Diatomáceas/ultraestrutura , Microscopia Eletrônica de Varredura , Filogenia , Fitoplâncton/classificação , Fitoplâncton/citologia , Fitoplâncton/genética , Fitoplâncton/ultraestrutura , Ribulose-Bifosfato Carboxilase/análise , Zooplâncton/citologia , Zooplâncton/genética , Zooplâncton/ultraestrutura
9.
Mol Ecol ; 27(11): 2544-2559, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29691934

RESUMO

Local adaptation and phenotypic plasticity are main mechanisms of organisms' resilience in changing environments. Both are affected by gene flow and are expected to be weak in zooplankton populations inhabiting large continuous water bodies and strongly affected by currents. Lake Baikal, the deepest and one of the coldest lakes on Earth, experienced epilimnion temperature increase during the last 100 years, exposing Baikal's zooplankton to novel selective pressures. We obtained a partial transcriptome of Epischura baikalensis (Copepoda: Calanoida), the dominant component of Baikal's zooplankton, and estimated SNP allele frequencies and transcript abundances in samples from regions of Baikal that differ in multiyear average surface temperatures. The strongest signal in both SNP and transcript abundance differentiation is the SW-NE gradient along the 600+ km long axis of the lake, suggesting isolation by distance. SNP differentiation is stronger for nonsynonymous than synonymous SNPs and is paralleled by differential survival during a laboratory exposure to increased temperature, indicating directional selection operating on the temperature gradient. Transcript abundance, generally collinear with the SNP differentiation, shows samples from the warmest, less deep location clustering together with the southernmost samples. Differential expression is more frequent among transcripts orthologous to candidate thermal response genes previously identified in model arthropods, including genes encoding cytoskeleton proteins, heat-shock proteins, proteases, enzymes of central energy metabolism, lipid and antioxidant pathways. We conclude that the pivotal endemic zooplankton species in Lake Baikal exists under temperature-mediated selection and possesses both genetic variation and plasticity to respond to novel temperature-related environmental pressures.


Assuntos
Expressão Gênica/genética , Frequência do Gene/genética , Polimorfismo de Nucleotídeo Único/genética , Zooplâncton/genética , Adaptação Fisiológica/genética , Animais , Artrópodes/genética , Copépodes/genética , Lagos , Especificidade da Espécie , Temperatura Ambiente
10.
Nat Commun ; 9(1): 373, 2018 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-29371626

RESUMO

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.


Assuntos
Organismos Aquáticos , Eucariotos/genética , Células Eucarióticas/metabolismo , Metagenoma , Filogenia , Zooplâncton/genética , Sequência de Aminoácidos , Animais , Atlas como Assunto , Bactérias/classificação , Bactérias/genética , Biodiversidade , Ecossistema , Eucariotos/classificação , Células Eucarióticas/citologia , Metagenômica/métodos , Oceanos e Mares , Fitoplâncton/classificação , Fitoplâncton/genética , Água do Mar , Vírus/classificação , Vírus/genética , Zooplâncton/classificação
11.
Microb Ecol ; 75(2): 293-302, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-28866755

RESUMO

The increasing proliferation of cyanobacterial blooms prolongs the impact of cyanobacteria on aquatic fauna, potentially altering trophic relationships. We hypothesized that any effect of dissolved microcystins (toxins produced by cyanobacteria) on plankton assemblages would be more evident in artificial reservoirs and ponds than in natural ones. The concentrations of dissolved microcystins in the waters we studied ranged widely from 0.07 to 0.81 µg/L. We showed that the artificial ponds were subjected to more frequent and longer-lasting harmful algal blooms. The plankton occurring in them were exposed to significantly higher concentrations of dissolved microcystins than those in natural oxbow lakes. Using a general linear model (GLM) regression, our study identified a significant relationship between dissolved microcystins and both the density and biomass of particular zooplankton groups (ciliates, rotifers, cladocerans, copepods). The density, biomass, and richness of the animal plankton were significantly lower in the artificial ponds than in the natural oxbow lakes. The impact of microcystins and the length of time that they remained in the water caused structural homogenization of the plankton.


Assuntos
Cianobactérias/metabolismo , Lagos/química , Microcistinas/análise , Zooplâncton/crescimento & desenvolvimento , Animais , Biomassa , Cianobactérias/genética , Cianobactérias/crescimento & desenvolvimento , Ecossistema , Proliferação Nociva de Algas , Lagos/microbiologia , Lagos/parasitologia , Microcistinas/metabolismo , Zooplâncton/classificação , Zooplâncton/efeitos dos fármacos , Zooplâncton/genética
12.
Nat Commun ; 8(1): 1608, 2017 11 20.
Artigo em Inglês | MEDLINE | ID: mdl-29151571

RESUMO

The gut microbiota impacts many aspects of its host's biology, and is increasingly considered as a key factor mediating performance of host individuals in continuously changing environments. Here we use gut microbiota transplants to show that both host genotype and gut microbiota mediate tolerance to toxic cyanobacteria in the freshwater crustacean Daphnia magna. Interclonal variation in tolerance to cyanobacteria disappears when Daphnia are made germ-free and inoculated with an identical microbial inoculum. Instead, variation in tolerance among recipient Daphnia mirrors that of the microbiota donors. Metagenetic analyses point to host genotype and external microbial source as important determinants of gut microbiota assembly, and reveal strong differences in gut microbiota composition between tolerant and susceptible genotypes. Together, these results show that both environmentally and host genotype-induced variations in gut microbiota structure mediate Daphnia tolerance to toxic cyanobacteria, pointing to the gut microbiota as a driver of adaptation and acclimatization to cyanobacterial harmful algal blooms in zooplankton.


Assuntos
Cianobactérias/fisiologia , Daphnia/genética , Daphnia/microbiologia , Microbioma Gastrointestinal , Zooplâncton/genética , Zooplâncton/microbiologia , Animais , Cadeia Alimentar , Água Doce/análise , Genótipo , Proliferação Nociva de Algas
13.
Sci Rep ; 7(1): 13702, 2017 10 20.
Artigo em Inglês | MEDLINE | ID: mdl-29057900

RESUMO

We determined the nearly complete mitochondrial genomes of the Arctic Calanus glacialis and its North Atlantic sibling Calanus finmarchicus, which are key zooplankton components in marine ecosystems. The sequenced part of C. glacialis mitogenome is 27,342 bp long and consists of two contigs, while for C. finmarchicus it is 29,462 bp and six contigs, what makes them the longest reported copepod mitogenomes. The typical set of metazoan mitochondrial genes is present in these mitogenomes, although the non-coding regions (NCRs) are unusually long and complex. The mitogenomes of the closest species C. glacialis and C. finmarchicus, followed by the North Pacific C. sinicus, are structurally similar and differ from the much more typical of deep-water, Arctic C. hyperboreus. This evolutionary trend for the expansion of NCRs within the Calanus mitogenomes increases mitochondrial DNA density, what resulted in its similar density to the nuclear genome. Given large differences in the length and structure of C. glacialis and C. finmarchicus mitogenomes, we conclude that the species are genetically distinct and thus cannot hybridize. The molecular resources presented here: the mitogenomic and rDNA sequences, and the database of repetitive elements should facilitate the development of genetic markers suitable in pursuing evolutionary research in copepods.


Assuntos
Copépodes/genética , Genoma Mitocondrial , Zooplâncton/genética , Animais , Regiões Árticas , Evolução Molecular
14.
PLoS One ; 12(10): e0185697, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28977035

RESUMO

Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here mitochondrial cytochrome c oxidase I (COI) fragment barcodes from 910 freshwater zooplankton specimens (87 morphospecies) were recovered by a high-throughput sequencing platform, Ion Torrent PGM. Intraspecific divergence of most zooplanktons was < 5%, except Branchionus leydign (Rotifer, 14.3%), Trichocerca elongate (Rotifer, 11.5%), Lecane bulla (Rotifer, 15.9%), Synchaeta oblonga (Rotifer, 5.95%) and Schmackeria forbesi (Copepod, 6.5%). Metabarcoding data of 28 environmental samples from Lake Tai were annotated by both an indigenous database and NCBI Genbank database. The indigenous database improved the taxonomic assignment of metabarcoding of zooplankton. Most zooplankton (81%) with barcode sequences in the indigenous database were identified by metabarcoding monitoring. Furthermore, the frequency and distribution of zooplankton were also consistent between metabarcoding and morphology identification. Overall, the indigenous database improved the taxonomic assignment of zooplankton.


Assuntos
Código de Barras de DNA Taxonômico , Bases de Dados Genéticas , Zooplâncton/genética , Animais , Reação em Cadeia da Polimerase
15.
Sci Rep ; 7(1): 1773, 2017 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-28496194

RESUMO

Communities of zooplankton, a critical portion of aquatic ecosystems, can be adversely affected by contamination resulting from human activities. Understanding the influence of environmental change on zooplankton communities under field-conditions is hindered by traditional labor-intensive approaches that are prone to taxonomic and enumeration mistakes. Here, metabarcoding of cytochrome c oxidase I (COI) region of mitochondrial DNA was used to characterize the genetic diversity of zooplankton. The species composition of zooplankton communities determined by metabarcoding was consistent with the results based on the traditional morphological approach. The spatial distribution of common species (frequency of occurrence >10 samples) by metabarcoding exhibited good agreement with morphological data. Furthermore, metabarcoding can clearly distinguish the composition of the zooplankton community between lake and river ecosystems. In general, rotifers were more abundant in riverine environments than lakes and reservoirs. Finally, the sequence read number of different taxonomic groups using metabarcoding was positively correlated with the zooplankton biomass inferred by density and body length of zooplankton. Overall, the utility of metabarcoding for taxonomic profiling of zooplankton communities was validated by the morphology-based method on a large ecological scale. Metabarcoding of COI could be a powerful and efficient biomonitoring tool to protect local aquatic ecosystems.


Assuntos
Biodiversidade , Código de Barras de DNA Taxonômico , Lagos , Zooplâncton/classificação , Zooplâncton/genética , Animais , Metaboloma , Metabolômica/métodos , Filogenia , Rios , Zooplâncton/metabolismo
16.
Environ Microbiol Rep ; 9(4): 383-388, 2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-28429584

RESUMO

Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. Here we tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. Significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a 3-month period in spring were found. Patterns followed the same trend as plankton estimates measured using traditional microscopic methods. The bloom of a conditionally rare bacterial taxon belonging to Arcicella was characterized, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. The data demonstrate the potential of universal DNA metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.


Assuntos
Bactérias/isolamento & purificação , Eucariotos/isolamento & purificação , Lagos/microbiologia , Lagos/parasitologia , Fitoplâncton/isolamento & purificação , Zooplâncton/isolamento & purificação , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Biodiversidade , Código de Barras de DNA Taxonômico , Ecossistema , Eucariotos/classificação , Eucariotos/genética , Lagos/química , Filogenia , Fitoplâncton/classificação , Fitoplâncton/genética , Estações do Ano , Zooplâncton/classificação , Zooplâncton/genética
17.
Sci Rep ; 7: 43983, 2017 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-28276459

RESUMO

Understanding the colonisation process in zooplankton is crucial for successful restoration of aquatic ecosystems. Here, we analyzed the clonal and genetic structure of the cyclical parthenogenetic rotifer Brachionus plicatilis by following populations established in new temporary ponds during the first three hydroperiods. Rotifer populations established rapidly after first flooding, although colonisation was ongoing throughout the study. Multilocus genotypes from 7 microsatellite loci suggested that most populations (10 of 14) were founded by few clones. The exception was one of the four populations that persisted throughout the studied hydroperiods, where high genetic diversity in the first hydroperiod suggested colonisation from a historical egg bank, and no increase in allelic diversity was detected with time. In contrast, in another of these four populations, we observed a progressive increase of allelic diversity. This population became less differentiated from the other populations suggesting effective gene flow soon after its foundation. Allelic diversity and richness remained low in the remaining two, more isolated, populations, suggesting little gene flow. Our results highlight the complexity of colonisation dynamics, with evidence for persistent founder effects in some ponds, but not in others, and with early immigration both from external source populations, and from residual, historical diapausing egg banks.


Assuntos
Efeito Fundador , Tanques/microbiologia , Zooplâncton/genética , Alelos , Animais , Variação Genética , Genética Populacional , Rotíferos/genética
18.
Artigo em Inglês | MEDLINE | ID: mdl-27920375

RESUMO

Urbanization causes both changes in community composition and evolutionary responses, but most studies focus on these responses in isolation. We performed an integrated analysis assessing the relative contribution of intra- and interspecific trait turnover to the observed change in zooplankton community body size in 83 cladoceran communities along urbanization gradients quantified at seven spatial scales (50-3200 m radii). We also performed a quantitative genetic analysis on 12 Daphnia magna populations along the same urbanization gradient. Body size in zooplankton communities generally declined with increasing urbanization, but the opposite was observed for communities dominated by large species. The contribution of intraspecific trait variation to community body size turnover with urbanization strongly varied with the spatial scale considered, and was highest for communities dominated by large cladoceran species and at intermediate spatial scales. Genotypic size at maturity was smaller for urban than for rural D. magna populations and for animals cultured at 24°C compared with 20°C. While local genetic adaptation likely contributed to the persistence of D. magna in the urban heat islands, buffering for the phenotypic shift to larger body sizes with increasing urbanization, community body size turnover was mainly driven by non-genetic intraspecific trait change.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.


Assuntos
Evolução Biológica , Cladóceros/fisiologia , Daphnia/genética , Zooplâncton/fisiologia , Animais , Biodiversidade , Tamanho Corporal , Cladóceros/genética , Daphnia/fisiologia , Urbanização , Zooplâncton/genética
19.
Protist ; 167(6): 568-583, 2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27816811

RESUMO

The genus Amphidiniopsis is a benthic (sand-dwelling) lineage of thecate dinoflagellates, containing 19 morphologically diverse species. Past work has shown that some Amphidiniopsis species form a clade with the sand-dwelling Herdmania litoralis as well as some planktonic species in the family Protoperidiniaceae (i.e. the Monovela group). Still, our contemporary knowledge regarding Amphidiniopsis is limited, compared to the Protoperidiniaceae. To this end, we obtained 18S rDNA data from seven Amphidiniopsis species and a part of the 28S rDNA from four Amphidiniopsis species, with the goal of improving our understanding of phylogenetic relationships among Amphidiniopsis and the Monovela group. Results from the molecular phylogenetic analyses showed that Amphidiniopsis spp., with the exception of A. cf. arenaria, H. litoralis, and members within the Monovela group formed a single clade. Within the clade, relationships among Amphidiniopsis spp. and the Monovela group were more complicated - some subclades contained both representatives of Amphidiniopsis and the Monovela group. Our study suggests that habitat (benthic or planktonic), as well as traditionally used, general morphological characteristics, do not reflect molecular phylogenetic relationships, and that the taxonomy of the sand-dwelling genus Amphidiniopsis, and the planktonic family Protoperidiniaceae, should be reconsidered simultaneously.


Assuntos
Dinoflagelados/classificação , Filogenia , Zooplâncton/classificação , Animais , Dinoflagelados/genética , Ecossistema , RNA de Protozoário/genética , RNA Ribossômico 18S/genética , Análise de Sequência de RNA , Zooplâncton/genética
20.
PLoS One ; 11(7): e0157307, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27383475

RESUMO

Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis-Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae-Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica-Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica-Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.


Assuntos
Copépodes/genética , Código de Barras de DNA Taxonômico , Complexo IV da Cadeia de Transporte de Elétrons/genética , Zooplâncton/genética , Animais , Genes Mitocondriais , Variação Genética , Geografia , Filogenia , República da Coreia , Análise de Sequência de DNA , Especificidade da Espécie
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