Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers.

Molecular gut content analysis is a popular tool to study food web interactions and has recently been suggested as an alternative source for DNA-based biomonitoring. However, the overabundant consumer's DNA often outcompetes that of its diet during PCR. Lineage-specific primers are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. Here, we designed an amplicon sequencing assay to monitor the eukaryotic diet of mussels and other metazoan filter feeders and explore the utility of mussels as natural eDNA samplers to monitor planktonic communities. We designed several lineage-specific rDNA primers with broad taxonomic suitability for eukaryotes. The primers were tested using DNA extracts of different limnic and marine mussel species and the results compared to eDNA water samples collected next to the mussel colonies. In addition, we analysed several 25-year time series samples of mussels from German rivers. Our primer sets efficiently prevent the amplification of mussels and other metazoans. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also show the utility of a reversed version of our primers, which prevents amplification of nonmetazoan taxa from complex eukaryote community samples, by enriching fauna associated with the marine brown algae Fucus vesiculosus. Our protocol will enable large-scale dietary analysis in metazoan filter feeders, facilitate aquatic food web analysis and allow surveying of aquacultures for pathogens. Moreover, we show that mussels and other aquatic filter feeders can serve as complementary DNA source for biomonitoring.

Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea.

The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read sequencing, this study, for the first time, estimated the genome size, unique genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon, in T. crocea. Furthermore, we tested if the mitochondrial genome can be assembled from RNA sequencing data. The haploid genome size estimated using a k-mer strategy was 1.31-1.39 Gbp, which is well within the range reported before for other members of the family Cardiidae. Unique genome content estimates using different k-mers indicated that nearly a third and probably at least 50% of the genome of T. crocea was composed of repetitive elements. A large portion of repetitive sequences could not be assigned to known repeat element families. Taking into consideration only annotated repetitive elements, the most common were classified as Satellite DNA which were more common than Class I-LINE and Class I-LTR Ty3-gypsy retrotransposon elements. The nuclear ribosomal operon in T. crocea was partially assembled into two contigs, one encoding the complete ssrDNA and 5.8S rDNA unit and a second comprising a partial lsrDNA. A nearly complete mitochondrial genome (92%) was assembled from RNA-seq. These newly developed genomic resources are highly relevant for improving our understanding of the biology of T. crocea and for the development of conservation plans and the fisheries management of this iconic reef-dwelling invertebrate.

Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment.

BACKGROUND: To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA. RESULTS: The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor. CONCLUSIONS: The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

Biodiversity Assessment, DNA Barcoding, and the Minority Majority.

The majority of species on Earth are in "under-studied" groups, and indeed probably the majority of species remain undiscovered and undescribed. Species are natural units of evolution, and they are formed from branching phylogenetic processes that have a mathematical structure. So it follows that we should be able to develop a set of general principles that describe global patterns of species groups, like genera. Understanding such patterns would lend considerable power to the approach of "taxonomic surrogacy." In environmental assessments, ecology, and paleontology, it is common to substitute genus-level or family-level identification where definitive species identification is impractical. Clarity and confidence in fundamental patterns, based on a robust null model for species and genus level diversity, can accelerate species discovery: there are more species in the tropics, species-poor genera are very common, large genera are rare. Much hope has been placed in DNA barcoding as an effective tool to increase the pace of species discovery, but it is abundantly clear that certain mitochondrial DNA (mtDNA) markers are more or less variable in different clades and universal threshold values are impractical to delimit species. This study further examines the patterns of divergence in one common mtDNA barcode fragment, cytochrome c oxidase subunit 1at the genus level. We compared pairwise divergence in this fragment between two animal clades that have similar species richness but different evolutionary histories: birds and bivalves. We analyzed quality controlled alignments of over 39,000 published sequences in 1223 genera. Median pairwise differences at the genus level are positively correlated with the species richness of a genus, and this is not dependent of the number of sequences sampled. Unsurprisingly, sequence divergence in vertebrates was far more constrained than in evolutionarily more ancient non-vertebrate clades. Differences among the groups examined highlight the need for DNA barcode approaches to be considered in the context of specific biological groups. Vertebrates are better studied, but not necessarily representative of the majority of biodiversity. A technique that provides powerful insights for vertebrate species may be ineffective for the majority of organisms.

The Backwater Clam (Meretrix casta) as a bioindicator species for monitoring the pollution of an estuarine environment by genotoxic agents.

The coast of Goa receives anthropogenic stress through its major rivers, which carry mining wastes, including iron and manganese ores from upstream mining sites, and petroleum hydrocarbons from shipping activities. These contaminants show seasonal variation in concentration and may be bioaccumulated by fauna inhabiting these waters. These fauna, including the bivalve molluscs, are particularly at risk due to these insults. In the present study, the use of the backwater clam, Meretrix casta (Chemnitz), as a bioindicator species was evaluated, comparing two sites (Vasco and Palolem) on the Goan coast. DNA damage was assessed in the gill cells using the micronucleus and comet assays; physiological condition was determined from the condition index. These values were tested for correlations with the concentrations of total petroleum hydrocarbons and trace metals in the whole soft tissues and with the physico-chemical parameters of water from these sites. Specimens collected from Vasco showed high incidence of micronuclei and % tail DNA and a low condition index ratio compared to those from Palolem, which correlates with the higher level of pollutants in the bivalves the former site. We believe that M. casta is a suitable species for biomonitoring studies of this type.

Biomarkers of oxidatively induced DNA damage in dreissenid mussels: A genotoxicity assessment tool for the Laurentian Great Lakes.

Activities of fast growing human population are altering freshwater ecosystems, endangering their inhabitants and public health. Organic and trace compounds have a high potential for adverse impacts on aquatic organisms in some Great Lakes tributaries. Toxic compounds in tissues of organisms living in contaminated environments change their metabolism and alter cellular components. We measured oxidatively induced DNA damage in the soft tissues of dreissenid mussels to check on the possible contaminant-induced impact on their DNA. The animals were obtained from archived samples of the National Oceanic and Atmospheric Administration (NOAA) Mussel Watch Program. Mussels were collected from the harbor of Ashtabula River in Ohio, and a reference area located at the Lake Erie shore. Using gas chromatography-tandem mass spectrometry with isotope dilution, we identified and quantified numerous oxidatively modified DNA bases and 8,5'-cyclopurine-2'-deoxynucleosides. We found significant differences in the concentrations of these potentially mutagenic and/or lethal lesions in the DNA of mussels from the harbor as compared to the animals collected at the reference site. These results align NOAA's data showing that elevated concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and heavy metals were found in mussels within the harbor as compared to mussels collected in the reference site. The measured DNA lesions can be used as biomarkers for identifying DNA damage in mussels from polluted and reference sites. Such biomarkers are needed to identify the bioeffects of contaminants in affected organisms, as well as whether remedial actions have proven successful in reducing observed toxic effects.

The discovery of novel LPMO families with a new Hidden Markov model.

BACKGROUND: Renewable biopolymers, such as cellulose, starch and chitin are highly resistance to enzymatic degradation. Therefore, there is a need to upgrade current degradation processes by including novel enzymes. Lytic polysaccharide mono-oxygenases (LPMOs) can disrupt recalcitrant biopolymers, thereby enhancing hydrolysis by conventional enzymes. However, novel LPMO families are difficult to identify using existing methods. Therefore, we developed a novel profile Hidden Markov model (HMM) and used it to mine genomes of ascomycetous fungi for novel LPMOs. RESULTS: We constructed a structural alignment and verified that the alignment was correct. In the alignment we identified several known conserved features, such as the histidine brace and the N/Q/E-X-F/Y motif and previously unidentified conserved proline and glycine residues. These residues are distal from the active site, suggesting a role in structure rather than activity. The multiple protein alignment was subsequently used to build a profile Hidden Markov model. This model was initially tested on manually curated datasets and proved to be both sensitive (no false negatives) and specific (no false positives). In some of the genomes analyzed we identified a yet unknown LPMO family. This new family is mostly confined to the phyla of Ascomycota and Basidiomycota and the class of Oomycota. Genomic clustering indicated that at least some members might be involved in the degradation of ß-glucans, while transcriptomic data suggested that others are possibly involved in the degradation of pectin. CONCLUSIONS: The newly developed profile hidden Markov Model was successfully used to mine fungal genomes for a novel family of LPMOs. However, the model is not limited to bacterial and fungal genomes. This is illustrated by the fact that the model was also able to identify another new LPMO family in Drosophila melanogaster. Furthermore, the Hidden Markov model was used to verify the more distant blast hits from the new fungal family of LPMOs, which belong to the Bivalves, Stony corals and Sea anemones. So this Hidden Markov model (Additional file 3) will help the broader scientific community in identifying other yet unknown LPMOs.

Is the step-wise tiered approach for ERA of pharmaceuticals useful for the assessment of cancer therapeutic drugs present in marine environment?

Methotrexate (MTX) and tamoxifen (TMX) cancer therapeutic drugs have been detected within the aquatic environment. Nevertheless, MTX and TMX research is essentially bio-medically orientated, with few studies addressing the question of its toxicity in fresh water organisms, and none to its' effect in the marine environment. To the authors' knowledge, Environmental Risk Assessments (ERA) for pharmaceuticals has mainly been designed for freshwater and terrestrial environments (European Medicines Agency-EMEA guideline, 2006). Therefore, the purpose of this research was (1) to assess effect of MTX and TMX in marine organism using the EMEA guideline, (2) to develop an ERA methodology for marine environment, and (3) to evaluate the suitability of including a biomarker approach in Phase III. To reach these aims, a risk assessment of MTX and TMX was performed following EMEA guideline, including a 2-tier approach during Phase III, applying lysosomal membrane stability (LMS) as a screening biomarker in tier-1 and a battery of biochemical biomarkers in tier-2. Results from Phase II indicated that MTX was not toxic for bacteria, microalgae and sea urchin at the concentrations tested, thus no further assessment was required, while TMX indicated a possible risk. Therefore, Phase III was performed for only TMX. Ruditapes philippinarum were exposed during 14 days to TMX (0.1, 1, 10, 50 µg L(-1)). At the end of the experiment, clams exposed to environmental concentration indicated significant changes in LMS compared to the control (p<0.01); thus a second tier was applied. A significant induction of biomarkers (activity of Ethoxyresorufin O-deethylase [EROD], glutathione S-transferase [GST], glutathione peroxidase [GPX], and lipid peroxidation [LPO] levels) was observed in digestive gland tissues of clams compared with control (p<0.01). Finally, this study indicated that MTX was not toxic at an environmental concentration, whilst TMX was potentially toxic for marine biota. This study has shown the necessity to create specific guidelines in order to evaluate effects of pharmaceuticals in marine environment which includes sensitive endpoints. The inadequacy of current EMEA guideline to predict chemotherapy agents toxicity in Phase II was displayed whilst the usefulness of other tests were demonstrated. The 2-tier approach, applied in Phase III, appears to be suitable for an ERA of cancer therapeutic drugs in the marine environment.

Transcriptomic resources for environmental risk assessment: a case study in the Venice lagoon.

The development of new resources to evaluate the environmental status is becoming increasingly important representing a key challenge for ocean and coastal management. Recently, the employment of transcriptomics in aquatic toxicology has led to increasing initiatives proposing to integrate eco-toxicogenomics in the evaluation of marine ecosystem health. However, several technical issues need to be addressed before introducing genomics as a reliable tool in regulatory ecotoxicology. The Venice lagoon constitutes an excellent case, in which the assessment of environmental risks derived from the nearby industrial activities represents a crucial task. In this context, the potential role of genomics to assist environmental monitoring was investigated through the definition of reliable gene expression markers associated to chemical contamination in Manila clams, and their subsequent employment for the classification of Venice lagoon areas. Overall, the present study addresses key issues to evaluate the future outlooks of genomics in the environmental monitoring and risk assessment.

Development of molecular resources for an intertidal clam, Sinonovacula constricta, using 454 transcriptome sequencing.

BACKGROUND: The razor clam Sinonovacula constricta is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait. RESULTS: Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated. CONCLUSION: De novo sequencing of the razor clam S. constricta transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of S. constricta.

Oxidative DNA damage may not mediate Ni-induced genotoxicity in marine mussels: assessment of genotoxic biomarkers and transcriptional responses of key stress genes.

Nickel (Ni) is a known carcinogenic and mutagenic compound and an important contaminant of aquatic environments. Ni toxicity and its potential impact on aquatic organisms are, however, not well understood. This study used an integrated approach to evaluate genotoxic effects, tissue-specific accumulation and transcriptional profiles of key genes in mussels, Mytilus galloprovincialis, exposed to a range of concentrations of Ni. The genotoxic effects assessed were total and oxidative DNA damage (DNA strand breaks measured using the enzyme modified comet assay), and induction of micronuclei (MN; clastogenic and/or aneugenic effects) using haemocytes as the target cells. Six genes (pgp, mt10, mt20, sod, hsp70 and gst) were selected for transcriptional analysis in the gills based on their key role in the stress response. Following exposure to sublethal concentrations of Ni (0-3600µgL(-1)) for 5 days, mussel haemocytes showed significant genotoxicity at >1800µgL(-1) (4-fold increase for DNA strand breaks and 3-fold increase for MN induction). There was no significant difference between buffer (control) and enzyme treatments which target oxidised DNA bases (formamidopyrimidine glycosylase or endonuclease IIII). This suggested that, in haemocytes, oxidative DNA damage is not a major mechanism for Ni-induced genotoxicity. The expression of mt20 and gst genes in gill was up-regulated at genotoxic concentrations, whilst pgp expression was markedly up-regulated, particularly at 18µgL(-1) Ni (19-fold increase). Pearson's correlation analysis revealed significant associations between % tail DNA and MN induction in haemocytes (r=0.88, p<0.05), and between Ni accumulation in foot (r=0.47, p<0.05) and digestive gland (r=0.41, p<0.05) and induction of MN in the haemocytes. Our results are the first to suggest that Ni-induced genotoxicity in mussel haemocytes may not be a result of oxidative DNA damage, and that multixenobiotic resistance (MXR) may play an important role in Ni detoxification in this species.

Integration of biochemical, histochemical and toxicogenomic indices for the assessment of health status of mussels from the Tamar Estuary, U.K.

The aim of this study was to examine whether a combination of biochemical, histopathological and toxicogenomic data could be used as a valuable tool for the assessment of biological risk associated with pollutants within the Tamar River and Estuary, S.W. England, U.K. Accordingly, biochemical and histopathological biomarkers (protein carbonyls, lipofuscin, neutral lipids, lysosomal stability [N-acetyl-ß-hexosaminidase and neutral red], lysosomal volume, ferric reducing antioxidant power [FRAP] and malonaldehyde [MDA]) and gene expression profiles were assessed in 5 sites from the Tamar River and Estuary (Neal Point, Town Quay, Wilcove, Cremyll Ferry and Whitsand; and a reference site, Trebarwith Strand, N. Cornwall). PAHs were measured in mussel tissue and sediment and metals were measured in mussel tissue only. Data from the biomarkers was integrated into a Mussel Expert System (MES) model to produce a simple assessment of mussel stress. Clear gradients of mussel toxicity were identified by the biomarkers (with the exception of neutral lipids) with the highest impacted animals found furthest up the Tamar, whilst the MES was unable to identify a gradient of effect. Gene expression profiles also indicated a gradient of stress with the greatest number of significantly up- or down- regulated genes found at the uppermost 2 sites. The MES did, however, determine that mussels from all sites, except the reference site, were highly stressed; a conclusion that could not be inferred from the biomarker data alone. It is concluded that the MES is a valuable tool that permits integration and interpretation of complex sets of biomarker data by identifying the biological meaning of biomarker changes.

Biomarker responsiveness in different tissues of caged Ruditapes philippinarum and its use within an integrated sediment quality assessment.

Biomarkers comprising activities of biotransformation enzymes (ethoxyresorufin-O-deethylase -EROD-, dibenzylfluorescein dealkylase -DBF-, glutathione S-transferase -GST), antioxidant enzymes (glutathione reductase -GR- and glutathione peroxidase -GPX), lipid peroxidation -LPO- and DNA strand breaks were analyzed in the clam Ruditapes philippinarum caged at Cádiz Bay, Santander Bay and Las Palmas de Gran Canaria (LPGC) Port (Spain). Sediments were characterized. Digestive gland was the most sensitive tissue to sediment contamination. In Cádiz Bay, changes in LPO regarding day 0 were related with metals. In LPGC Port, DBF, EROD, and GST activity responses suggested the presence of undetermined contaminants which might have led to DNA damage. In Santander Bay, PAHs were related with EROD activity, organic and metal contamination was found to be associated with GR and GST activities and DNA damage presented significant (p < 0.05) induction. R. philippinarum was sensitive to sediment contamination at biochemical level. Biomarkers allowed chemical exposure and sediment quality assessment.

Interactions of a pesticide/heavy metal mixture in marine bivalves: a transcriptomic assessment.

BACKGROUND: Mixtures of chemicals present in aquatic environments may elicit toxicity due to additive or synergistic effects among the constituents or, vice versa, the adverse outcome may be reduced by antagonistic interactions. Deviations from additivity should be explained either by the perturbations of toxicokinetic parameters and/or chemical toxicodynamics. We addressed this important question in marine mussels exposed subchronically to a binary mixture made of two wide-spread pollutants: the heavy metal nickel and the organic phosphorus pesticide Chlorpyrifos. To this aim, we carried out in tissues of Mytius galloprovincialis (Lam) a systems approach based on the evaluation and integration of different disciplines, i.e. high throughput gene expression profiling, functional genomics, stress biomakers and toxicokinetics. RESULTS: Cellular and tissue biomarkers, viz. digestive gland lysosomal membrane stability, lysosomal/cytosol volume ratio, neutral lipid content and gill acetylcholinesterase activity were, in general, altered by either the exposure to nickel and Chlorpyrifos. However, their joint action rendered (i) an overall decrease of the stress syndrome level, as evaluated through an expert system integrating biomarkers and (ii) statistically significant antagonistic deviations from the reference model systems to predict mixture toxicity. While toxicokinetic modeling did not explain mixture interactions, gene expression profiling and further Gene Ontology-based functional genomics analysis provided clues that the decrement of toxicity may arise from the development of specific toxicodynamics. Multivariate statistics of microarray data (238 genes in total, representing about 14% of the whole microarray catalogue) showed two separate patterns for the single chemicals: the one belonging to the heavy metal -135 differentially expressed genes (DEGs) was characterized by the modulation of transcript levels involved in nucleic acid metabolism, cell proliferation and lipid metabolic processes. Chlorpyrifos exposure (43 DEGs) yielded a molecular signature which was biased towards carbohydrate catabolism (indeed, chitin metabolism) and developmental processes. The exposure to the mixture (103 DEGs) elicited a composite complex profile which encompassed the core properties of the pesticide but also a relevant set of unique features. Finally, the relative mRNA abundance of twelve genes was followed by Q-PCR to either confirm or complement microarray data. These results, in general, were compatible with those from arrays and indeed confirmed the association of the relative abundance of two GM-2 ganglioside activator genes in the development of the hyperlipidosis syndrome observed in digestive gland lysosomes of single chemical exposed mussels. CONCLUSION: The transcriptomic assessment fitted with biological data to indicate the occurrence of different toxicodynamic events and, in general, a decrease of toxicity, driven by the mitigation or even abolition of lysosomal responses. Furthermore, our results emphasized the importance of the application of mechanistic approaches and the power of systems assessment to study toxicological responses in ecologically relevant organisms.

Comet and micronucleus assays in zebra mussel cells for genotoxicity assessment of surface drinking water treated with three different disinfectants.

The aim of this research was to study the influence of classic (sodium hypochlorite and chlorine dioxide) and alternative (peracetic acid [PAA]) disinfectants on the formation of mutagens in surface waters used for human consumption. For this proposal, in vivo genotoxicity tests (Comet and micronucleus assay) were performed in an experimental pilot plant set up near Lake Trasimeno (Central Italy). The effects were detected in different tissues (haemocytes for the Comet assay and gills for the micronucleus test [MN]) of Dreissena polymorpha exposed in experimental basins supplied with lake water with/without the different disinfectants. Specimen collection was performed before disinfectant input for both tests and after the start of disinfection (3 h and 20 days for the Comet assay and 10 and 20 days for micronucleus test, respectively) to assess short- and long- term exposure effects during three sampling campaigns (October 2000, February 2001, and June 2001). Seasonal differences in baseline levels of DNA migration and micronucleus frequency were observed. Raw water quality modulation on disinfection by-product formation was shown. The results of the micronucleus and Comet assays on zebra mussel cells after in situ exposure to water disinfected with the two chlorinated compounds clearly indicate DNA/by-product interaction. PAA did not induce either clastogenic/aneugenic effects or DNA damage on this bioindicator.

Cytonuclear disequilibrium in a hybrid zone involving deep-sea hydrothermal vent mussels of the genus Bathymodiolus.

A hybrid zone involving the deep-sea mussels, Bathymodiolus azoricus and B. puteoserpentis, was recently discovered at Broken Spur hydrothermal vent field (29 degrees 10' N, 43 degrees 10' W) along an intermediate segment of the Mid-Atlantic Ridge axis. Examination of nuclear (allozymes) and cytoplasmic (mitochondrial DNA) gene markers in a new sample from Broken Spur revealed significant cytonuclear disequilibrium caused by an excess of the parental types (coupling phase) and a deficiency of recombinants (repulsion phase). An assignment test of individual multilocus genotypes also revealed an excess of parental genotypes in the admixed population. These results support the hypothesis that the Broken Spur mussel population comprises a nonequilibrium mixture of parental immigrants and hybrid individuals.

Protein metabolism, the costs of growth, and genomic heterozygosity: experiments with the mussel Mytilus galloprovincialis Lmk.

A single cohort of small individuals (31 mm mean shell length, 112 mg mean dry flesh weight) of the marine bivalve mollusc Mytilus galloprovincialis Lmk. was held sequentially for 2 wk at each of four food levels equivalent to ingested rations of less than 0.1%, 2.6%, 3.1%, and 7.4% of dry body weight per day. Growth rate reached a maximum at the highest ration level and was strongly correlated, amongst individuals, with mean heterozygosity measured across nine enzyme loci. Rates of energy expenditure were analysed separately as maintenance metabolic rate and the energy costs of growth (J mg-1 dry tissue). The maintenance metabolic rate correlated with traits of protein metabolism (protein synthesis, deposition, and breakdown), and the separate energy costs of both maintenance and growth correlated with the efficiency of protein deposition (protein growth as a proportion of synthesis). The energy costs of growth also varied in negative relation to mean individual heterozygosity. In a multiple regression analysis, the energy allocation to the costs of growth, body size, mean heterozygosity, and the efficiency of protein deposition together explained 90% of the variance amongst individuals in observed rates of growth. The results support the hypothesis that individual variability in the energy costs of protein turnover and in the efficiency of protein deposition during rapid growth are significant factors providing a link between individual genotype and its phenotypic expression as growth.