Analysis of 686 expressed sequence tags (ESTs) from the intertidal harpacticoid copepod Tigriopus japonicus (Crustacea, Copepoda)

Allelopathic interactions between phytobenthos and meiofaunal community in an Adriatic benthic ecosystem: Understanding the role of aldehydes and macroalgal structural complexity

Macroalgae produce several allelopathic substances, including polyunsaturated aldehydes (PUAs), which may inhibit photosynthesis and growth rates of other algal species, and grazing. Additionally, macroalgal structural complexity is an important factor in determining abundance patterns and size structure of epiphytic organisms. In this study the PUAs production of two Mediterranean macroalgae, Dictyopteris polypodioides, (DP, Phaeophyceae, Dictyotales) and Cystoseira compressa (CC, Phaeophyceae, Fucales), was characterized to clarify the relationships between the meiobenthic and microphytobenthic communities. Results showed a higher PUAs production and a diverse qualitative profile for DP, which reported long-chain compounds (i.e. C14-C16) as main aldehydes, than CC, with the short-chain C6:2 as the main compound, as well as variability among sampling times. A clear separation of the meiofauna and microphytobenthos assemblages was found for the macroalgae, but with different temporal trends. Dissimilarities were due to five microalgal orders, namely Naviculales, Lyrellales, Gonyaulacales (i.e. Ostreopsis), Bacillariales, and Licmophorales, and to the meiofaunal groups nematodes, copepods, and copepod nauplii, which were more abundant on DP than on CC. Results indicate that macroalgal complexity is a major determinant of the meiofaunal community structure (accounting for 26% of the variation), rather than PUAs production itself (17%). PUAs effects seem species-specific, thus affecting some grazers instead of the entire community. Conversely, microphytobenthos affected the meiofauna assemblages, particularly harpacticoids, confirming the role of these organisms as the primary food source of all marine food chain producers. Since PUAs are produced also by several epiphytic diatoms, the understanding of their effects on the community structure and on the relationships among taxa in the field is complicated and requires further in-depth investigations in simplified systems (i.e. microcosms).

Instant taxonomy: choosing adequate characters for species delimitation and description through congruence between molecular data and quantitative shape analysis

The lack of university funding is one of the major impediments to taxonomy, partly because traditional taxonomic training takes longer than a PhD course. Understanding ranges of phenotypic variability for different morphological structures, and their use as characters for delimitation and description of taxa, is a tedious task. We argue that the advent of molecular barcoding and quantitative shape analysis makes it unnecessary. As an example, we tackle a problematic species-complex of marine copepods from Korea and Japan, approaching it as a starting taxonomist might. Samples were collected from 14 locations and the mitochondrial COI gene was sequenced from 42 specimens. Our phylogenetic analyses reveal four distinct clades in Korea and Japan, and an additional nine belonging to a closely related complex from other parts of the Northern Pacific. Twenty different morphological structures were analysed for one Japanese and two Korean clades using landmark-based two-dimensional geometric morphometrics. Although there is no single morphological character that can distinguish with absolute certainty all three cryptic species, most show statistically significant interspecific differences in shape and size. We use five characters to describe two new species from Korea and to re-describe Tigriopus japonicus Mori, 1938 from near its type locality.

Gene expression patterns and stress response in marine copepods

Aquatic organisms are constantly exposed to both physical (e.g. temperature and salinity variations) and chemical (e.g. endocrine disruptor chemicals, heavy metals, hydrocarbons, diatom toxins, and other toxicants) stressors which they react to by activating a series of defense mechanisms. This paper reviews the literature on the defense systems, including detoxification enzymes and proteins (e.g. glutathione S-transferases, heat shock proteins, superoxide dismutase and catalase), studied in copepods at the molecular level. The data indicate high inter- and intra-species variability in copepod response, depending on the type of stressor tested, the concentration and exposure time, and the enzyme isoform studied. Ongoing -omics approaches will allow the identification of new genes which will give a more comprehensive overview of how copepods respond to specific stressors in laboratory and/or field conditions and the effects of these responses on higher trophic levels.

A corticotropin-releasing hormone binding protein (CRH-BP) gene from the intertidal copepod, Tigriopus japonicus

The corticotropin-releasing hormone (CRH) plays a critical role in stress-response regulation in vertebrates. The activity of CRH depends on CRH-binding protein (CRH-BP). CRH-BP is considered to play a chaperoning role in stress. Limited information mainly from the insects is available on the molecular structure and functions of invertebrate CRH and CRH-BP. We cloned and sequenced a CRH-BP gene from the intertidal copepod, Tigriopus japonicus which was expressed at all the stages of development. Molecular phylogenetic analysis showed that T. japonicus CRH-BP was closely related to CRH-BP of honeybee and other insects. The highest level of CRH-BP transcripts was expressed in adult males followed by nauplius stage 1. The expression of CRH-BP was upregulated when T. japonicus was subjected to temperature or salinity stress. This study demonstrates that CRH-BP in T. japonicus might play a role in stress-response. However, establishing such a role demands further studies on CRH-BP from other invertebrates and their expression under stress.

Acute toxicities of trace metals and common xenobiotics to the marine copepod Tigriopus japonicus: Evaluation of its use as a benchmark species for routine ecotoxicity tests in Western Pacific coastal regions

Marine copepods have recently been recognized as important organisms in ecotoxicity testing for regulatory purposes. The harpacticoid copepod Tigriopus japonicus has a wide geographical distribution along the coast in the Western Pacific including Japan, South Korea, Taiwan, and Hong Kong. This study evaluated the acute toxicity sensitivity profile of Tigriopus japonicus against 12 common toxic substances including six endocrine disrupting chemicals (EDCs), three biocides and three trace metals. Through standard acute toxicity test procedures, toxicity endpoints LC(50), LC(10), and no observed effect concentration (NOEC) of each chemical were obtained. Although T. japonicus depicted different sensitivities towards different chemicals, a dose-response relationship was consistent in all cases. T. japonicus was particularly sensitive to most of the EDCs, but relatively less sensitive to molinate (a thiocarbate herbicide). Across all tested chemicals, tributyltin (TBT) was the most toxic to the copepod with the LC(50), LC(10), and NOEC of 0.05, 0.03, and 0.02 mg/L, respectively. A comparison made with available data on acute toxicities of these chemicals to other marine copepod species revealed that T. japonicus is generally more sensitive to EDCs and in particular to TBT. We, therefore, strongly advocate that T. japonicus shall be adopted as a benchmark marine species for routine ecotoxicity testing and ecotoxicological studies in Western Pacific coasts.

Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis

BACKGROUND

Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking.

METHODOLOGY/PRINCIPAL FINDINGS

We generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy.

CONCLUSIONS/SIGNIFICANCE

Despite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and can be browsed and searched at gmod.mbl.edu.

The copepod Tigriopus: a promising marine model organism for ecotoxicology and environmental genomics

There is an increasing body of evidence to support the significant role of invertebrates in assessing impacts of environmental contaminants on marine ecosystems. Therefore, in recent years massive efforts have been directed to identify viable and ecologically relevant invertebrate toxicity testing models. Tigriopus, a harpacticoid copepod has a number of promising characteristics which make it a candidate worth consideration in such efforts. Tigriopus and other copepods are widely distributed and ecologically important organisms. Their position in marine food chains is very prominent, especially with regard to the transfer of energy. Copepods also play an important role in the transportation of aquatic pollutants across the food chains. In recent years there has been a phenomenal increase in the knowledge base of Tigriopus spp., particularly in the areas of their ecology, geophylogeny, genomics and their behavioural, biochemical and molecular responses following exposure to environmental stressors and chemicals. Sequences of a number of important marker genes have been studied in various Tigriopus spp., notably T. californicus and T. japonicus. These genes belong to normal biophysiological functions (e.g. electron transport system enzymes) as well as stress and toxic chemical exposure responses (heat shock protein 20, glutathione reductase, glutathione S-transferase). Recently, 40,740 expressed sequenced tags (ESTs) from T. japonicus, have been sequenced and of them, 5,673 ESTs showed significant hits (E-value, >1.0E-05) to the red flour beetle Tribolium genome database. Metals and organic pollutants such as antifouling agents, pesticides, polycyclic aromatic hydrocarbons (PAH) and polychrlorinated biphenyls (PCB) have shown reproducible biological responses when tested in Tigriopus spp. Promising results have been obtained when Tigriopus was used for assessment of risk associated with exposure to endocrine-disrupting chemicals (EDCs). Application of environmental gene expression techniques has allowed evaluation of transcriptional changes in T. japonicus with the ultimate aim of understanding the mechanisms of action of environmental stressors. Through a better understanding of toxicological mechanisms, ecotoxicologists may use this ecologically relevant species in risk assessment studies in marine systems. The combination of uses as a whole-animal bioassay and gene expression studies indicate that Tigriopus may serve as an excellent tool to evaluate the impacts of marine pollution throughout the coastal region. The purpose of this review is to illustrate the potential of using Tigriopus to fulfill the niche as an important invertebrate marine model organism for ecotoxicology and environmental genomics. In addition, the knowledge gaps and areas for further studies have also been discussed.

Environmental stressors (salinity, heavy metals, H2O2) modulate expression of glutathione reductase (GR) gene from the intertidal copepod Tigriopus japonicus

Glutathione reductase (GR) plays an essential role in cell defense against reactive oxygen metabolites by sustaining the reduced status of an important antioxidant, glutathione. To address the effect of oxidative stresses on the intertidal copepod Tigriopus japonicus, we exposed specimens to hydrogen peroxide, heavy metals and different salinity levels, cloned and sequenced the oxidative stress-related GR gene. T. japonicus GR gene (Tigriopus GR) cDNA contained 1526 bp including an open reading frame (ORF) encoding 458 amino acids with a theoretical pI of 6.58 and a calculated molecular weight of 49.6 kDa. Tigriopus GR showed a high similarity to frog Xenopus laevis GR (identity 57%) and the filarial parasite, Onchocerca volvulus GR (identity 57%). Specific motifs such as flavin adenine dinucleotide-binding site (LVLGGGSGGIASARRAAEF), pyridine nucleotide-disulphide oxidoreductases class-I active site (GGTCVNVGCVP), and NADPH binding motif (GxGYIAx18Rx5R) were highly conserved in the deduced amino acid sequence of Tigriopus GR. Interestingly, its expression and enzyme characteristics were different from GR homologue of filarial parasite O. volvulus. To investigate the biochemical and enzymatic characteristics of Tigriopus GR protein, we constructed the expression vector, pCRT7/TOPO NT containing Tigriopus GR. Tigriopus pCRT7/TOPO NT/GR was expressed in Escherichia coli, and the soluble protein was purified by 6x His-tag chromatography. The recombinant Tigriopus GR enzyme was found to make homodimer complexes of approximately 108 kDa on 12% native gel electrophoresis and showed enzymatic activity with NADPH and oxidized glutathione (GSSG) as substrates. To analyze the gene expression of Tigriopus GR against different environmental stresses (hydrogen peroxide, salinity, and heavy metals), we performed real-time reverse transcriptase-polymerase chain reaction (real-time RT-PCR). Slight down-regulation in the expression of Tigriopus GR at the initial stage was observed upon exposure to hydrogen peroxide. The expression recovered in 2h, while there were significant changes upon heavy metal (Cu and Mn) exposures in a time-dependent manner. Also, Tigriopus GR expression was significantly increased with moderately high salt stress (24 and 40 ppt). In the case of low salt stress (0 and 12 ppt) the expression was found to be down-regulated. These findings provide a better understanding of cellular protection mechanisms in the intertidal copepod T. japonicus against the environmental stressors caused by non-optimal salt levels.

Cloning and characterization of glutathione S-transferase gene in the intertidal copepod Tigriopus japonicus and its expression after exposure to endocrine-disrupting chemicals

To investigate the impacts of marine pollution on aquatic organisms, we tested the intertidal copepod Tigriopus japonicus as a model species. To analyze the copepods' responses to endocrine-disrupting chemicals (EDCs), we exposed them to two different chemicals: 4,4'-octylphenol (4,4'-OP, 12.5-100 microg/L for 2 h) and polychlorinated biphenyl (PCB, 6.25-25 microg/L for two days). 4,4'-OP was toxic, although exposure time was limited to 2h. After extracting total RNA from the exposed T. japonicus, we performed reverse transcriptase-polymerase chain reaction (RT-PCR) to determine gene expression patterns following chemical exposure. To analyze the gene expression of T. japonicus, we used glutathione S-transferase with GAPDH as an internal control. Of the genes tested using EDC-exposed samples, 4,4'-OP induced upregulation of the glutathione S-transferase (GST) gene, while PCB caused downregulation of the GST gene. These results suggest that the two EDCs act in different manners in T. japonicus.

The intertidal copepod Tigriopus japonicus small heat shock protein 20 gene (Hsp20) enhances thermotolerance of transformed Escherichia coli

To understand the role of the Tigriopus japonicus Hsp20 gene, we isolated this gene from a whole body cDNA library and found two heat shock factor elements at the 5'-UTR. The transformed bacteria containing Tigriopus Hsp20 showed thermotolerance against heat shock (54 degrees C) with different ranges of time. The Tigriopus Hsp20 gene is comprised of 174 amino acid residues and shows similarity to Caenorhabditis elegans (27% identity), silkworm (24.1% identity), moth (24.1% identity), Mexican tetra (19.5% identity), zebrafish (19.5% identity), and spiny dogfish (17.2% identity) genes, but shows more similarity in the C-terminal region that contains an alpha-crystallin domain. Protein motifs such as an N-glycosylation site (67-70 NKSE) and a casein kinase II phosphorylation site were found in Tigriopus Hsp20. The genomic structure of the Tigriopus Hsp20 gene did not contain introns. To characterize the biochemical characteristics of the Tigriopus Hsp20 protein, we expressed Tigriopus Hsp20 in Escherichia coli and purified the soluble protein via 6x His-tag chromatography. To analyze the gene expression of Tigriopus Hsp20 against environmental stresses (e.g., water temperature and salinity), we performed a semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). On exposure to different salinities, significant change in the expression of Tigriopus Hsp20 was not observed. However, upon heat shock (30 degrees C), Tigriopus Hsp20 expression was significantly increased, but in the case of cold shock (4 or 10 degrees C), expression was likely downregulated. These findings provide a better understanding of cellular protection mechanisms against environmental stress such as heat shock.