The sequencing of 200 clones from the forward (individuals incubated at 10°C versus individuals exposed at 20°C) SSH library, as well as from the reverse library (individuals incubated at 20°C versus individuals exposed at 10°C), allowed the identification of 78 unique sequences for B. thermophilus (19% of the whole sequencing effort: other sequences are redundant). Table 1 shows the unique sequences obtained in both SSH libraries with the best E-values for the sequences when identified after Blast analysis. The identified sequences indicate that temperature regulates genes involved in various cell functions: (1) cell cycle regulation, DNA repair, protein regulation and transcription (8.5%), (2) mitochondrial respiratory chain (4%), (3) metabolism (6.4%), (4) stress response and detoxification (0.5%), (5) cell communication, membrane receptors and immune system (10.2%), (6) cytoskeleton production and maintenance (7.5%), (7) ribosomal proteins (10%), (8) proteins of unknown function (0.5%) and (9) unknown sequences (52%). A higher proportion (60%) of the genes identified in our libraries were expressed in mussel exposed to 10°C and were mainly involved in metabolism, stress response, transcription and cytoskeleton.

The sequencing of 200 clones from the forward (individuals incubated at 10°C versus individuals exposed at 20°C) SSH library, as well as from the reverse library (individuals incubated at 20°C versus individuals exposed at 10°C) allowed the identification of 83 different gene sequences for P. pandorae (20% of the whole sequencing effort: the other sequences are redundant). Table 2 shows the unique sequences obtained in both SSH libraries with the best E-values for the sequences when identified after Blast analysis. The identified sequences indicate that temperature regulates the expression of genes involved in various cell functions: (1) respiratory chain (9.6%), (2) sulfur and oxygen transport (8.4%), (3) metabolism (2.4%), (4) cell communication, membrane receptors and immune system (4.8%), (5) cytoskeleton production and maintenance (3.6%), (6) ribosomal proteins (8.4%), (7) proteins of unknown function (2.4%) and (8) unknown sequences (60.4%). Interestingly, most transcripts identified in the reverse subtractive library correspond to genes involved in the respiratory chain and in oxygen transport. A high proportion of unknown sequences were also obtained limiting the identification of new temperature-regulated putative candidate gene.

Levels of expression of 20 transcripts obtained in the B. thermophilus library and 14 transcripts identified in the P. pandorae library were quantified from pools of individuals of each thermal condition by using real-time PCR. For all the genes, we showed that the differential expression observed for the genes corresponds to the library they came from. In addition, stronger differential expressions were observed in B. thermophilus for metabolic genes such as S-adenosylhomocysteinase-hydrolase, arginine kinase or Δ5-desaturase, and some genes such as secreted protein acidic rich in cystein (SPARC, a basal membrane component), elongation factor beta, actin and proteins related to mussel mobility (foot protein and adhesive plaque matrix protein) (Table 3). While it was identified in the reverse library, the gene encoding the kalicludine did not display a clear differential expression between the two experimental conditions. In P. pandorae, differences between levels of expression of the two sets of experimented individuals were higher than those observed in mussels. Some genes also showed a very high level of expression in samples exposed to 10°C as compared to those exposed at 20°C, especially for the secreted nidogen domain protein, Rab7, the intracellular hemoglobin and the ribosomal protein S16 that were strongly inhibited in annelids exposed to 20°C. Almost all genes encoding subunits of hemoglobins (except linker L2) displayed a coherent expression pattern of up-regulation in annelids exposed to 20°C (Table 4).

Over 50% of the sequences for each species could not be identified based on homologies. This may be due to the limited amount of data available for invertebrates, or to the SSH protocol itself that requires the use of a restriction enzyme, possibly leaving only the UTRs for cloning. This may explain that we did not obtain typical heat stress proteins such as the inducible heat shock protein 70 (HSP70). This could also be due to the long term acclimation (about 2 days) offered to the animals leading to an attenuation of the stress machinery with time. None of the SSH libraries (mussel and annelid) indeed contained mRNA coding for any HSP70s, that are involved in the protection of other proteins from denaturation caused by a variety of stressors [32,33]. Available data dealing with HSP70 in hydrothermal species were only obtained from polychaetes, mussels and shrimps exposed to brief heat shocks [21,22,34]. In previous studies, a positive correlation between the levels of DNA strand breakage and HSP70 expression in response to decompression stress were also found by Pruski and Dixon [35]. In the shrimp Rimicaris exoculata, regulation of HSP70 in response to temperature was detected at the protein level [21], but no data related to HSP70 gene regulation is available so far.

Metabolic adjustments in response to thermal challenges are essential for aquatic ectotherms, whose body temperature fluctuates over the full range of temperature in their habitat [36]. Temperature can also influence metabolic regulation, eliciting transition to anaerobiosis even in oxygenated waters [37]. A high thermal sensitivity of metabolism over the environmental range is associated to increased long-term metabolic costs and with a lower tolerance to extreme temperatures. Classically, lowering metabolic rate and, thus energy saving is also considered as one of the most important adaptations for hypoxia endurance [38,39]. Adaptation to these conditions has resulted in reduced growth rates, as well as reduced development and metabolism [40]. Previous studies conducted on the marine gastropod Littorina saxatilis showed that an acute long-term temperature increase could disturb metabolism, leading to progressive metabolic depression and adverse changes in the cellular energy status due to its transition to partial anaerobiosis [41]. Antarctic marine species are also much less capable to survive elevated temperatures [42] and calculated temperature envelopes for these organisms were 2–4 times smaller than those for temperate species [43]. Studies on the Mediterranean mussel Mytilus galloprovincialis showed that a long acclimation of up to 30 days at high temperatures (18 to 30°C) leads to behavioral (increase of duration of valve closure), metabolic (metabolic depression with a shift from aerobic to anaerobic metabolism) and molecular (increase in HSPs protein levels) responses [44]. Interestingly, the deep-sea mussel B. thermophilus seems to share some general features with organisms living in polar oceans that are characterized by very stable low temperatures, below 5°C. We first hypothesized that annelids were able to cope with a larger range of temperature compared to the mussels, because they were described as early colonizers of new chimneys at hydrothermal vents [45], and thus able to sustain highest temperatures, at least over short periods of time. While few genes seem to be regulated similarly between the two species (actin, mitochondrial cytochrome oxydase, S-adenosylhomocysteine hydrolase), most cell functions are very dissimilar, suggesting a different response of these organisms to temperature. The genes that were identified in the mussel libraries could indicate that this species tends to react as a stenoecious species rather than an euryecious species (as could be expected for organisms living in a highly fluctuating environment). A general depression is indeed observed in expression of Bathymodiolus genes involved in transcription/translation, mobility, energetic metabolism, and oxidative stress in response to temperature increase. Conversely, genes involved in cell disorder and immune system (ie myc-homolog, kalicludin...) are up-regulated at the highest temperature. No similar pattern is observed in P. pandorae, leading to the hypothesis that this species could better adapt to high temperatures.

A long exposure at a temperature of 20°C (43 hours) clearly appears to be a thermal physiological limit for B. thermophilus that lives in colder habitats. As mussels encounter short pulses of hot water under in situ conditions, it seems that the duration of the heat exposure is critical and probably more important than the temperature value itself. According to the experimental conditions used for this study, it remains difficult to evaluate how long B. thermophilus is really able to withstand a temperature of 20°C without severe physiological damage. Complementary experiments such as the determination of differential mortality kinetic in longer-term exposures and at different ranges of temperatures have to be performed in further studies to better understand the thermal resistance/response/adaptation of this species. As all individuals survived for about 2 days (43-hour experiment), B. thermophilus can deal with thermal stress for at least few days but it is not clear whether they can then recover from such stress.

The hypothesized limited adaptation of B. thermophilus to high temperature is also supported by a decrease of expression of nearly all genes identified in the mussels exposed to 20°C, a pattern indicative of global metabolic depression. Among these genes, there were many ribosomal proteins and some elongation factors, indicating that the protein synthesis pathway was clearly involved in response to temperature. However, different ribosomal proteins are identified in both reverse and forward libraries showing a complex regulatory process (or the absence of regulation) in intra-molecular interactions in ribosomes. This result is commonly observed in transcriptomic studies in mollusks in response to various environmental parameters [46-49]. A higher number of ribosomal proteins were however identified in the mussel forward libraries suggesting a possible metabolic depression in samples exposed to 20°C when compared to those exposed at 10°C. In P. pandorae libraries, similar pattern of down regulation at 20°C of 5 ribosomal proteins among the 7 identified is observed.

More specifically, it is noteworthy that several genes of the mussel energetic pathways were down-regulated. Among them, arginine kinase (ArgK) and cytosolic malate dehydrogenase (cMDH) are found to be down regulated in mussels exposed to 20°C. ArgK catalyzes the transfer of phosphate between ATP and arginine (arginine phosphate + MgADP^- + H⁺ ↔ arginine + MgATP^2-), and plays a critical role in cellular energy metabolism in invertebrates [50]. It also serves as an energy reserve because it can readily transfer phosphor-arginine to ATP when energy is needed [51,52]. However, it was never found associated with thermal stress. To our knowledge, no data on the thermal regulation of mRNA expression of ArgK has been reported to date. Its regulation has mostly been studied at a protein level and this is the only phosphagen kinase known in crustaceans and mollusks. ArgK is indeed regulated in crustaceans and mollusks under hypoxia [53,54]. In the crustacean Marsupenaeus japonicus, the up-regulation of ArgK under hypoxia may represent a provision for oxygen recovery after a short period of hypoxia [54]. The second metabolic enzyme is the cytosolic malate dehydrogenase, which catalyzes the dehydrogenation of malate (malate + NADP⁺ ↔ oxaloacetate + NADPH + H⁺). It plays a major role in a number of metabolic pathways, including the malate-aspartate (or NADH) shuttle and the acetate shuttle active in lipogenesis, amino acid synthesis and gluconeogenesis. cMDH is an interesting candidate gene to study adaptation to temperature as this enzyme showed differences in the effects of temperature on kinetic properties in shallow water species [7,55,56]. Even though no cMDH mRNA expression has been reported in these studies, differences in protein properties strongly suggest a clear involvement of this key gene in response to temperature. The down-regulation of both ArgK and cMDH in B. thermophilus could lead to a decrease of mitochondrial respiration, leading to a lower ATP production, and resulting in the establishment of a global metabolic depression in response to temperature.

The cDNA coding for a HSP90 was found in the mussel SSH libraries. However, HSP90 displayed a down-regulation at 20°C when compared to 10°C suggesting that the process of protein re-naturation was probably over. HSP90 proteins have key roles in signal transduction, protein folding, protein degradation, and morphological evolution [57-59]. HSP90 is up-regulated in response to heat stress in Drosophila subobscura [60], the whitefly Bemisia argentifoli [61], and the flesh fly, Sarcophaga crassipalpis [62]. It is induced by thermal stress in the Goby fish but could also decrease in expression to a normal level during the acclimatization process [63]. In M. galloprovincialis, both HSP70 and HSP90 protein expression were shown to increase in response to long-term thermal challenge [44].

We identified several genes that are classically expressed in response to oxidative stress in the mussel libraries but not in the annelid libraries, suggesting a differential behavior of both species. Two main hypotheses can explain the presence of an oxidative stress: (1) a direct effect of temperature changes on lipid composition or (2) variations of the oxygen concentration during experiments. In the first hypothesis, temperature directly affects cells by modifying membrane composition through replacement of unsaturated fatty acids at low temperatures towards saturated fatty acids at high temperatures [64], and secondly by inducing apoptosis via activation of the sphingomyelin pathway that leads to the process of lipid peroxidation [65]. Many biological structures, such as enzymes and lipid bilayer membranes, depend on a particular degree of molecular instability or fluidity, which is directly affected by temperature. In the particular case of our experimented hydrothermal species, lipids of cell membrane bilayers must be both fluid and structurally coherent to form a functional membrane, a characteristic very sensitive to temperature change [2]. Lipid peroxyl radicals (LPO) are the result of a reaction between lipid and oxygen and are known to damage cells by changing the fluidity and permeability of the membrane and/or by directly damaging DNA and other intracellular molecules, such as proteins [66]. As a consequence of the lipid peroxidation process, superoxide anion radicals can be produced. Lipid peroxidation has been studied in hydrothermal vent mussels and high levels of LPO were detected in B. azoricus in response to a strong effect of environmental heavy metal concentrations [67]. Recently, heavy metal stresses, such as copper exposure, or changes in hydrostatic pressure were also shown to produce LPO in B. azoricus [68]. Fatty acid desaturases are very important during the process of fatty acid metabolism that contributes to the structural and functional maintenance of biological membranes in living organisms. The down-regulation of Δ5-desaturase mRNA expression of B. thermophilus exposed to 20°C is consistent with a modification of membrane lipid content. We also identified a gene encoding SPARC, which is more expressed in mussels incubated at 10°C when compared to those exposed to 20°C. SPARC is classically known to modulate cellular interaction with the extracellular matrix through interactions with proteins such as laminins and collagen [69,70]. SPARC was also shown to be up-regulated in response to heat-shock and other stresses [71,72]. SPARC also possesses a chaperone-like activity in vitro suggesting its involvement in stress response [73]. Its down-regulation at 20°C is coherent with results observed by previous authors and could reflect a strong disorder in membrane composition due to the high temperature.

In the second hypothesis, the generation of reactive oxygen species (ROS) as side products of electron transfer during aerobic metabolism [74] can explain the regulation of genes encoding protective proteins in mussels. Here, oxidative stress can be due to the experimental conditions used where sea-water was at a low-oxygen concentration (below 120 μM) associated with a consumption by animals and the effect of temperature. In the presence of low oxygen concentration or anoxic conditions, organisms use anaerobic metabolism and annelids and mollusks are able to use more efficient mitochondrial pathways of fermentation [75-77]. Under normal physiological conditions, anaerobic metabolism produces free radicals, and cells tend to maintain a balance between generation and neutralization of ROS. When organisms are subjected to xenobiotics, temperature increase or anoxia events, the generation of ROS can exceed the scavenging capacity [78]. All organisms possess their own cellular antioxidant defense system, composed of both enzymatic (superoxide dismutase, catalase and glutathione peroxidases) and non-enzymatic (glutathione, vitamins...) components. Glutathione peroxidases (GPx), that have protective roles against oxidative stress, have been identified in B. thermophilus libraries suggesting an oxidative stress as a direct or indirect result of temperature challenge. Surprisingly, GPx expression is lower in mussels exposed to 20°C than those exposed to 10°C despite the fact that oxidative stress is supposed to be stronger at 20°C, supporting the idea that B. thermophilus is no longer able to regulate expression of oxidative stress related genes. We also identified a gene encoding a myc homolog which is up-regulated at 20°C compared to 10°C-exposed mussels. This protein belongs to a transcription factor family and is involved in the cell division control. Myc and its binding partners regulate the expression of a large number of genes that regulate diverse functions, including protein synthesis, apoptosis, and DNA and energy metabolism [79-81]. Generally speaking, over-expression of a myc-homolog enhances apoptosis by acting as a transcription repressor [82,83]. In bivalves, c-myc has previously been shown to be up-regulated by hypoxia [49] and hydrocarbon stresses [46]. Identification of c-myc in mussel exposed to 20°C seems to be indicative of the very poor biological condition of the 20°C-exposed individuals and thus in accordance with the hypothesis of a low tolerance of B. thermophilus to extended exposure to high temperature.

A gene that is involved in adenosine metabolism, and that has previously been shown to be regulated in response to hypoxia, has also been found in both mussel and annelid libraries. This enzyme called S-adenosylhomocysteinase hydrolase (SAHH, EC 3.3.1.1) catalyses the reversible hydrolysis of S-adenosylhomocysteine to form homocysteine and adenosine [84]. AdenosineMethionine/AdenosineHomocysteine turnover is believed to play a critical role in methionine metabolism and the regulation of biological methylation processes. Tissue hypoxia induces a variety of functional changes, including enhanced transcriptional activity associated with high transmethylation activity (e.g. mRNA cap methylation) in the nucleus. Disturbance in DNA methylation pattern has previously been observed in response to various stressors, such as heavy metals, as a consequence of toxicity [85,86]. In both our species, the mRNA expression of this gene is lower in animals exposed to 20°C than to 10°C. This regulation of SAHH mRNA expression supports the hypothesis of a response to a direct or indirect oxidative stress. Presence of SAHH in response to temperature also illustrates the importance of methylation processes as a response to temperature increase. Generally speaking, a strong DNA methylation leads to a decrease or an inactivation of gene expression. Methylation processes regulation could be an interesting type of response to temperature in hydrothermal species.

In the mussel libraries, we interestingly identified three down-regulated genes at 20°C that are involved in foot activity (foot protein and pedal retractor muscle myosin) and byssus activity (adhesive plaque matrix protein). These results are in sharp contrast with previous studies performed on the brackish-water mussel, Mytilopsis leucophaeata that showed an increase in foot activity index and byssus thread production in response to thermal challenge [87]. Authors demonstrated that both foot activity and byssus production were higher when temperature increased from 4 to 20°C, remained stable between 20 and 28°C, and then strongly decreased beyond 28°C. This species commonly lives in a range of temperatures comprised between 4°C (winter) and 20°C (summer). Mussels of the genus Bathymodiolus are able to change location when the conditions are not adequate [88]. This can be viewed as an escape response in the presence of stress factors. They also probably use this mobility to optimize their position in the hydrothermal fluid in order to acquire the sulfide (and/or methane for some species) they need to feed their symbionts. The decrease of the expression of genes encoding proteins related to mobility in mussels exposed at 20°C, again reflects the poor physiological condition of these individuals, since mussels usually live in colder waters (4 to 14°C).

In the annelid SSH libraries, we identified several genes encoding various extracellular globin chains (B1, A2 and B2), one intracellular globin and also three linkers called linker L1, linker L2 and linker LY. These results illustrate a strong involvement of respiratory pigment in general and in particular of the hexagonal bilayer hemoglobin (HBL-Hb) in response to temperature in this species. In Alvinellidae, respiratory gas transport is performed by the blood and the coelomic fluid, and three main types of globins are present: non-circulating in the cytoplasm, circulating and intracellular in the coelom, and extracellular in the vascular system [24]. Earlier work reported the temperature effect on both the function and the stability of Hbs in the annelid Alvinella pompejana, under atmospheric pressure and for temperatures ranging from 10°C to 40°C. These Hbs are able to maintain a capacity to reversibly bind oxygen in vitro over this range. At 50°C, the Hbs are oxidized and aggregated during the de-oxygenation and the re-oxygenation [89]. These results are in agreement with the hypothesis that annelids, even if they are able to withstand a strong thermal stress [25], are nonetheless unable to sustain high temperature for a long time [24]. Because P. pandorae lives in a relatively cold environment compared to other Paralvinella species, such as P. sulfincola, and probably do not experience very high temperatures, the involvement of Hbs in temperature response could be the result of several processes and not only driven by Hb thermostability properties. We observed a strong increase of mRNA encoding extracellular Hb subunits in individuals exposed to 20°C and conversely, a decrease of intracellular subunit mRNA expression. It has been suggested that extracellular Hbs were preferentially involved in oxygen uptake and transport, while intracellular Hbs acted as an oxygen reserve for the worm and potentially returned oxygen to the extracellular Hb [90]. Because oxygen availability decreases with temperature, Paralvinella increased their extracellular Hb production to optimize the oxygen uptake and transport. At the same time the intracellular Hb was down-regulated, possibly to avoid the release of O₂ to the tissue since the worms experienced hot temperature but not hypoxia). We also observed an opposite regulation in the expression of linkers L1 and L2 in P. pandorae in response to thermal stress suggesting a possible rearrangement of the linker composition of the HBL-Hb molecule under temperature-induced oxidative stress. Very few studies have dealt with the linker function and regulation at a transcriptional level. In the Earthworm Lumbricus terrestris, linkers have been shown to exhibit a superoxide dismutase activity conferring a protection against superoxide ions for HBL-Hb molecules [91]. Linkers of the thermally-stressed alvinellids may therefore have been mobilized as an active defense against newly-produced ROS.

In the P. pandorae library, we also identified one gene encoding a secreted nidogen domain protein that showed a strong down-regulation at 20°C. Secreted nidogen domain protein, also known as entactin, belongs to basement membrane proteins. These membranes are made of type IV collagens and laminins, both of which exist as various isoforms in animals [92,93]. These proteins are cell-adhesive and form networks that confer mechanical stability to the basement membranes. Other ubiquitous basement membrane components are the proteoglycan perlecan and nidogen/entactin. Previous in vitro experiments showed that recombinant nidogen-1 interacted through different binding sites with the three main basement membrane components (laminin, collagen IV, and perlecan), and mediated the formation of ternary complexes between laminin and collagen IV [94]. These results therefore suggest that secreted nidogen domain protein is a key component of alvinellid basement membranes assembly, connecting the laminin and collagen networks, and integrating other basement membrane components as previously reported by Timpl and Brown [93]. We suggest that temperature (and/or pressure) above normal could induce strong changes in the membrane composition of the worms and therefore increase interactions between secreted nidogen domain protein, collagen and other membrane protein in order to readjust porosity/permeability. Other proteins that are thought to partially play a role in membrane component modeling have also been characterized. We identified a Ras-associated binding 7 (Rab 7) protein belonging to the Rab family. These are small GTPases of the Ras superfamily that continuously cycle between the cytosol and different membranes. The Rab family appears to be essential for the regulation of intracellular membrane traffic in mammalian cells. Rab proteins are anchored to the cytoplasmic surface of specific intracellular membrane compartments via the geranyl-geranyl group that is post-translationally added to the C-terminal cysteines and is important for their function [95]. Each Rab protein regulates one (or more) specific step of intracellular membrane traffic in eukaryotic cells, probably by assembling the general tethering/docking/fusion machinery [96]. Moreover, several lines of evidence suggest an involvement of Rab proteins in actin- and microtubule- based processes [97]. Rab7, a member of the Rab family small G proteins, has been shown to regulate intracellular vesicle traffic to late endosome/lysosome and lysosome biogenesis, but the exact roles of Rab7 are still undetermined [98,99]. Accumulating evidence suggests that each Rab protein has multiple target proteins that function in the exocytic/endocytic pathway. Because no studies showing how temperature could affect Rab 7 expression, its down regulation observed in P. pandorae by temperature remains difficult to explain but could be associated with results observed for nidogen protein.

Specimens of both the hydrothermal vent mussel Bathymodiolus thermophilus (67.8 ± 30 mm in length) and the annelid worm Paralvinella pandorae irlandei (≤ 10 mm in length) were collected together from the Oasis site (17°25.42S, 113°12.28W) on the East Pacific Rise during the BIOSPEEDO cruise [100] by using the telemanipulated arm of the submersible Nautile. The individuals were collected in a cold zone associated with weak diffuse flow (< 10°C). Once on board the ship, animals were immediately transferred from the insulated collection basket to the pressurized aquaria IPOCAMP™ (Incubateur Pressurisé pour l'Observation et la Culture d'Animaux Marins Profonds [101]) under an in situ pressure of 260 bars. Indeed, several studies showed that experiments conducted on mussels at atmospheric pressure lead to a global increase of stress parameters (lipid peroxidation, anti-oxidant enzymes activity, DNA damage) and to a limitation of stress response capacity [14,23,102]. One group of 5 mussels and 20 worms was placed at 10°C, and another group at 20°C, inside two different pressure vessels for 43 hours. The pressure vessels were operated in a flow-through mode (20 L/hour) for the first 3 hours, and then isolated. Every 15 hours, seawater was re-circulated for 3 hours, until the end of the incubation. When in flow-through configuration, the pressure aquaria were fed with sea-water aerated with a low-oxygen (8%) air mixture. Therefore, oxygen levels during the experiments were at a maximum value of about 120 μM during circulation periods, and obviously decreased when the vessels were isolated, due to oxygen consumption by experimented animals. No mortality was observed at the end of the experiments, and samples of mussels (pool of gills, foot, mantle, adductor muscle) and worms (whole organisms) were collected and immediately frozen in liquid nitrogen until use.

Total RNA was extracted from the gill, adductor muscle, mantle and foot of 5 thermally-challenged mussels, and 6 whole worms with the Trizol Reagent according to the manufacturer's instructions. Total RNAs extracted from the different tissues were pooled and poly(A+) mRNA was isolated using the PolyATtract^®mRNA Isolation System (Promega, Madison, WI, USA) according to the manufacturer's instructions.

Both forward (individuals incubated at 10°C versus individuals incubated at 20°C) and reverse (individuals incubated at 20°C versus individuals incubated at 10°C) subtracted libraries were produced from 2 μg of mRNA extracted from experimented mussels and worms. First and second strand cDNA synthesis, RsaI endonuclease enzyme digestion, adapter ligation, hybridization, and PCR amplification were performed as described in the PCR-select cDNA subtraction kit manual (Clontech, Palo Alto, CA, USA).

The differentially expressed PCR products were ligated into a pGEM-T vector (Promega, Madison, WI, USA) and 200 white colonies per library were cultured in LB medium supplemented with 100 mg/L ampicillin. Plasmids were then extracted using an alkaline lysis plasmid minipreparation, and sequenced using the Big Dye Terminator V3.1 Kit (Perkins-Elmer) and run on an AB3100 sequencer (Applied Biosystems Perkins-Elmer).

Chromatograms obtained after sequencing were treated with the Seqclean software (TGIR, the Institute for Genomic Research, Rockville, MD, USA) to remove vector and adaptors sequences. Cluster and contigs were then formed on each library sequence set. BLAST analyses of the sequences were performed on the NCBI server. The sequences were analyzed for homology with known sequences in databases using the BlastX and BlastN programs .

A validation step of the differentially expressed genes identified in B. thermophilus and P. pandorae SSH libraries was carried out using real-time PCR and total RNA samples used for the SSH construction. For each sample, 5 μg of total RNA were submitted to reverse transcription using oligo-dT anchor primer (5'-GAC CAC GCG TAT CGA TGT CGA CT₍₁₆₎V-3') and M-MLV reverse transcriptase (Promega, Madison, WI, USA). Amplification of 20 genes isolated in the SSH libraries was carried out on the cDNA from both 10 and 20°C exposed mussel samples and 14 genes were amplified on pool of cDNA from samples of annelid exposed to both 10 and 20°C. The real-time PCR assay was performed in triplicate with 4 μL cDNA (1/20 dilution) in a final volume of 10 μL using the Chromo 4™ System (BioRad). The concentrations of the reaction components were as follows: 1× ABsolute™ QPCR SYBR^® Green mix (ABgene, UK) and 70 nM of each primer (Tables 5 and 6). The 18S ribosomal DNA was amplified as an endogenous PCR control, under the same amplification conditions using sense (5'-AAG GGC AGG AAA AGA AAC TAA C-3') and antisense (5'-GTT TCC CTC TAA GTG GTT TCA C-3') primers. The amplification was carried out as follows: initial enzyme activation at 94°C for 15 min, then 45 cycles of 94°C for 15 sec and 60°C for 1 min. A dissociation curve was generated and PCR efficiency (E) was estimated for each primer pair by using a serial dilution of reverse transcription products. Standard curves were generated for each primer pair and E was calculated using the formula E = 10^(-1/slope)-1. All primer pairs tested generated a single peak in the dissociation curve with a PCR efficiency estimated between 95 and 100%. Relative quantification (RQ) of each gene expression was calculated according to comparative CT method using the formula: RQ = exponential (2^-ΔΔCT) with ΔΔCT = ΔCT(10°C) - ΔCT(20°C) and ΔCT(10°C) = CT(gene X in the 10°C sample) – CT(18S) and ΔCT(20°C) = CT(gene X in the 20°C sample) – CT(18S); 18S ribosomal DNA being used as the endogenous control.