Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

Background  

Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets.     

Molecular diversity and evolution of myticin-C antimicrobial peptide variants in the Mediterranean mussel, Mytilus galloprovincialis

Mussels have diverse groups of cysteine rich, cationic antimicrobial peptides (AMPs) (defensins, mytilins, myticins, and mytimycin) that constitute an important component of their innate immune defence. Despite the identification and characterization of these AMPs in mussels, the underlying genetic mechanisms that maintain high diversity among multiple variants of the myticin-C isoform are poorly understood. Using phylogeny-based models of sequence evolution and several site-by-site frequency spectrum statistical tests for neutrality, herein we report that positive selection has been the major driving force in maintaining high diversity among the allelic-variants of the myticin-C AMP of Mytilus galloprovincialis. The statistical tests rejected the hypothesis that all polymorphism within myticin-C loci is neutral. Although a majority of the codons constrained to purifying selection (rate of amino acid replacement to the silent substitution, omega < 1), approximately 8% of the codons with omega approximately equal to 5.5 are under positive selection (omega > 1), thus indicating adaptive evolution of certain amino acids. Direct interaction of these peptides with the surrounding pathogens and/or altered/new pathogens in the changing environment is the likely cause of molecular adaptation of certain amino acid sites in myticin-C variants.     

Cloning and sequencing of a novel metallothionein gene in Mytilus galloprovincialis Lam

Metallothionein (MT) is a ubiquitous, metal-inducible protein with an important role in the homeostasis and in the detoxification of heavy metals. This work reports the cloning and sequencing of a MT gene encoding a MT isoform (MT20-IIIa) in the mussel Mytilus galloprovincialis Lam, a lamellibranch mollusc known to accumulate and to detoxify large amounts of metal. The MT gene, lacking the 5' promoter region, is 1865 bp long and has a tripartite structure consisting of three exons and two introns. The putative open reading frame (ORF) encodes a polypeptide of 72 amino acids, which corresponds to the MT-I class, type 2 family (http://www.unizh.ch/~mtpage/classif.html). The structure of the gene and the putative MT20-III protein have been compared with those of other species. The putative biological significance of the differences at the amino acid level among the different MTs is discussed.     

Genomic organization, molecular diversification, and evolution of antimicrobial peptide myticin-C genes in the mussel (Mytilus galloprovincialis)

Myticin-C is a highly variable antimicrobial peptide associated to immune response in Mediterranean mussel (Mytilus galloprovincialis). In this study, we tried to ascertain the genetic organization and the mechanisms underlying myticin-C variation and evolution of this gene family. We took advantage of the large intron size variation to find out the number of myticin-C genes. Using fragment analysis a maximum of four alleles was detected per individual at both introns in a large mussel sample suggesting a minimum of two myticin-C genes. The transmission pattern of size variants in two full-sib families was also used to ascertain the number of myticin-C genes underlying the variability observed. Results in both families were in accordance with two myticin-C genes organized in tandem. A more detailed analysis of myticin-C variation was carried out by sequencing a large sample of complementary (cDNA) and genomic DNA (gDNA) in 10 individuals. Two basic sequences were detected at most individuals and several sequences were constituted by combination of two different basic sequences, strongly suggesting somatic recombination or gene conversion. Slight within-basic sequence variation detected in all individuals was attributed to somatic mutation. Such mutations were more frequently at the C-terminal domain and mostly determined non-synonymous substitutions. The mature peptide domain showed the highest variation both in the whole cDNA and in the basic-sequence samples, which is in accordance with the pathogen recognition function associated to this domain. Although most tests suggested neutrality for myticin-C variation, evidence indicated positive selection in the mature peptide and C-terminal region. Three main highly supported clusters were observed when reconstructing phylogeny on basic sequences, meiotic recombination playing a relevant role on myticin-C evolution. This study demonstrates that mechanisms to generate molecular variation similar to that observed in vertebrates are also operating in molluscs.     

Genetic variability of the marine mussel Mytilus galloprovincialis assessed using two-dimensional electrophoresis

Two-dimensional electrophoresis (2-DE) has been used to measure the degree of genetic variability of the marine mussel Mytilus galloprovincialis. Genetic polymorphisms were detected in 33 of a total of 86 polypeptides scored among the most abundant proteins from foot samples in 38 individuals. Estimates of average heterozygosity were 0.101+/-0.018 and 0.114+/-0.021 in a natural and a cultured population, respectively, from the NW of the Iberian Peninsula. These are the highest estimates of average heterozygosity reported by 2-DE in an animal species to date. We consider that these data throw open the question of the level of genetic variability detectable by two-dimensional electrophoresis. Multilocus genotype data were used to infer haplotypic frequencies by means of the EM algorithm in order to detect linkage disequilibrium between loci coding abundant proteins. Significant associations were found in 22.7% of the 406 two-locus pairs analysed. Also, clusters of loci in which all pairwise combinations exhibit statistically significant associations were detected and physical linkage between some of these loci is postulated from the linkage disequilibrium data.     

Free amino acid composition in juveniles of Mytilus galloprovincialis: spatial variability after Prestige oil spill

Composition of free amino acids (FAA) in juveniles of Mytilus galloprovincialis was analysed along a large geographical coastline area in Galicia (NW Spain). Individuals were sampled in February 2003, three months after the Prestige oil spill. Pollution values at sampling time were reported as polycyclic aromatic hydrocarbons (PAHs) concentrations in soft tissues of individuals and varied between the highest amount observed in Carrumeiro mussels (502 ng/g dw) and the lowest in Pindo mussels (196 ng/g dw), both locations being close to each other in the centre of the geographical area under study. Pollution values in the other populations varied within the range of 241-347 ng/g dw. Total free amino acids (TFAA) were highest in Agui?o-Pindo-Carrumeiro juveniles at the centre of the Coastline area studied (420-462 micromol/g dw) as compared to the other populations at North and South of Galicia (312-347 micromol/g dw). TFAA results were based on the variability observed in protein free amino acids (PFAA micromol/g dw) among populations (214-249 micromol/g dw for Agui?o-Pindo-Carrumeiro mussels and 98-149 micromol/g dw for the other populations) whereas non-protein free amino acids (NPFAA) taurine and ornithine did not show any significant spatial pattern of variation. Glycine and alanine represented the most abundant PFAA (16-29% and 2.7-11.9% of TPFAA, respectively) and significant correlations between PFAA and both the protein content of soft tissues (r=-0.82) and the condition index of juveniles (r=0.86) were observed. No significant relationships were detected, however, between pollution values in soft tissues as PAHs and FAA profiles with the exception of alanine concentrations as percentage of TFAA (r=0.88; P<0.01). The latter seemed to be an "all or nothing" effect likely due to the influence of other abiotic factors at one of the sampling sites. Such relationship was found not significant when the outlier represented by Carrumeiro mussels was removed from the analysis. The most abundant free amino acid taurine (43.2-68.5%TFAA) followed an inverse variability of that of glycine and by extension of the group PFAA most likely as a compensatory decrease in mussel populations with low protein content (and high condition index). Accordingly, taurine:glycine (t:g) ratio varied between 1 and 2 in most mussel populations but increased up to 3.2-4.2 in Miranda and Bueu mussels at both ends of the geographical interval studied with a corresponding PAHs concentrations of 261 and 304 ng/g dw, respectively. These mussel populations with the highest t:g ratios were characterised by the lowest PFAA contents (below 40%) and condition index values (below 10%). Results of the present study established a significant link between energetic status of growing juveniles and FAA concentrations in environments with different pollution degrees. Variability of the free amino acids profiles in soft tissues were related to endogenous factors of juveniles (protein content, condition index) whereas no relationship with contamination values could be observed. The utility of t:g ratio as general condition factor for M. galloprovincialis is also corroborated for in situ growing juveniles.     

Cadmium induction of metallothionein synthesis in Mytilus galloprovincialis

1. The accumulation and subcellular distribution of cadmium and resulting induction of metallothionein has been studied in mussels, Mytilus galloprovincialis, exposed to 400 μg Cd 1⁻¹.2. Cadmium accumulated by mussels was primarily associated with metallothionein: a maximum four-fold increase in concentrations of the metal-binding protein (3 mg g⁻¹ to 12 mg g⁻¹) was observed after 30 days.3. Results for M. galloprovincialis confirm the importance of metallothionein in the detoxification of intracellular cadmium and indicate that induction rates are identical to those observed in the closely-related M. edulis.4. Intercomposition of data between these species may therefore be valid when employing metallothionein assays to determine sub-lethal response to cadmium contamination.     

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.     

Antioxidant responses of the Mediterranean mussel, Mytilus galloprovincialis, to environmental variability of dissolved oxygen

Physiological responses of Mytilus galloprovincialis against environmental dissolved oxygen partial pressure (pO(2)) variation were studied in terms of the modulated induction of the main antioxidant enzymes: superoxide dismutase (SOD), catalase (CAT) and selenium-dependent glutathione peroxidase (GPX). Field in vivo studies were performed at two sites of the Lagoon of Venice, characterized by different aquatic environmental conditions implying different pO(2). SOD and GPX are more active in gills, and their complementary role is discussed. CAT is more active in the digestive gland, where the enzyme dismutates H(2)O(2) derived from divalent reduction of O(2) performed by various oxidases in peroxisomes. Antioxidant enzyme activities are correlated with water dissolved oxygen (DO), especially in the gills. This tissue, because of its anatomical localization and its physiological role, responds to DO variations modulating the induction of the antioxidant enzymes as a protection mechanism against potential toxicity due to increases in ROS formation.     

Cadmium accumulation in tissues of the mussel Mytilus galloprovincialis

Studies have been made on cadmium accumulation in tissues of mussels kept within 20-60 days in water artificially enriched by Cd up to 20-100 micrograms/l. Irrespectively of cadmium concentration in the medium, its accumulation in tissues decreases in the following order: mid-gut gland, gills, gonads, mantle, adductor. Maximum concentration of Cd was found in the digestive tubuli of the mid-gut gland by X-ray microanalysis. The increase in S and, to a lower extent, P concentrations in these tubuli was also observed. It is suggested that the latter is due to immobilization of Cd by metal-binding proteins as well as to lyzosomal vesicles involved into detoxication of Cd. The increase in the external cadmium up to 100 micrograms/l did not affect the level of K, Ca and Mg in tissues of the mussel.     

Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels

Since the completion of the bovine sequencing projects, a substantial number of genetic variations such as single nucleotide polymorphisms have become available across the cattle genome. Recently, cataloguing such genetic variations has been accelerated using massively parallel sequencing technology. However, most of the recent studies have been concentrated on European Bos taurus cattle breeds, resulting in a severe lack of knowledge for valuable native cattle genetic resources worldwide. Here, we present the first whole-genome sequencing results for an endangered Korean native cattle breed, Chikso, using the Illumina HiSeq 2,000 sequencing platform. The genome of a Chikso bull was sequenced to approximately 25.3-fold coverage with 98.8% of the bovine reference genome sequence (UMD 3.1) covered. In total, 5,874,026 single nucleotide polymorphisms and 551,363 insertion/deletions were identified across all 29 autosomes and the X-chromosome, of which 45% and 75% were previously unknown, respectively. Most of the variations (92.7% of single nucleotide polymorphisms and 92.9% of insertion/deletions) were located in intergenic and intron regions. A total of 16,273 single nucleotide polymorphisms causing missense mutations were detected in 7,111 genes throughout the genome, which could potentially contribute to variation in economically important traits in Chikso. This study provides a valuable resource for further investigations of the genetic mechanisms underlying traits of interest in cattle, and for the development of improved genomics-based breeding tools.     

Molecular characterisation and antimicrobial resistance of Vibrio vulnificus and Vibrio alginolyticus isolated from mussels (Mytilus galloprovincialis)

Twelve Vibrio vulnificus biotype 1 and 11 Vibrio alginolyticus isolated from mussels in Italy were analysed by antimicrobial resistance, plasmid profiles, random amplification of polymorphic DNA (RAPD), and single enzyme amplified fragment length polymorphism (sAFLP). Plasmid DNA was detected in three V. vulnificus and four V. alginolyticus cultures. All isolates were resistant to at least two antimicrobial agents: all isolates were resistant to ampicillin, carbenicillin and streptomycin, except one V. alginolyticus which was sensitive to carbenicillin and two V. alginolyticus which were sensitive to streptomycin. No association was detected between the presence of plasmid DNA and antimicrobial resistance. Seven of the twelve V. vulnificus and two of the eleven V. alginolyticus cultures were susceptible to the 10 microg of the vibriostatic compound O/129; all cultures were susceptible to the 150 microg of O/129. Both RAPD and sAFLP was found to be reproducible. Ten sAFLP and seven RAPD profiles were detected amongst the 12 V. vulnificus cultures: three cultures were identified as indistinguishable by both methods. RAPD and sAFLP analysis of V. alginolyticus generated nine and seven profiles respectively, and these two methods were independent. These results demonstrate extreme variability of V. vulnificus and V. alginolyticus isolated from mussels, and both RAPD and sAFLP provided information on intraspecific differences which will be useful for molecular epidemiological or ecological studies. A combination of methods gave optimal discrimination, although a single method could provide sufficient information to characterise V. vulnificus isolates.     

Within-host competition between Borrelia afzelii ospC strains in wild hosts as revealed by massively parallel amplicon sequencing

Infections frequently consist of more than one strain of a given pathogen. Experiments have shown that co-infecting strains often compete, so that the infection intensity of each strain in mixed infections is lower than in single strain infections. Such within-host competition can have important epidemiological and evolutionary consequences. However, the extent of competition has rarely been investigated in wild, naturally infected hosts, where there is noise in the form of varying inoculation doses, asynchronous infections and host heterogeneity, which can potentially alleviate or eliminate competition. Here, we investigated the extent of competition between Borrelia afzelii strains (as determined by ospC genotype) in three host species sampled in the wild. For this purpose, we developed a protocol for 454 amplicon sequencing of ospC, which allows both detection and quantification of each individual strain in an infection. Each host individual was infected with one to six ospC strains. The infection intensity of each strain was lower in mixed infections than in single ones, showing that there was competition. Rank-abundance plots revealed that there was typically one dominant strain, but that the evenness of the relative infection intensity of the different strains in an infection increased with the multiplicity of infection. We conclude that within-host competition can play an important role under natural conditions despite many potential sources of noise, and that quantification by next-generation amplicon sequencing offers new possibilities to dissect within-host interactions in naturally infected hosts.     

Membrane-active antimicrobial peptide identified in Rana arvalis by targeted DNA sequencing

Antimicrobial peptides (AMPs) are naturally produced, gene encoded molecules with a direct antimicrobial activity against pathogens, often also showing other immune-related properties. Anuran skin secretions are rich in bioactive peptides, including AMPs, and we have reported a novel targeted sequencing approach to identify novel AMPs simultaneously in different frog species, from small quantities of skin tissue. Over a hundred full-length peptides were identified from specimens belonging to five different Ranidae frog species, out of which 29 were novel sequences. Six of these were selected for synthesis and testing against a panel of Gram-negative and Gram-positive bacteria. One peptide, identified in Rana arvalis, proved to be a potent and broad-spectrum antimicrobial, active against ATCC bacterial strains and a multi-drug resistant clinical isolate. CD spectroscopy suggests it has a helical conformation, while surface plasmon resonance (SPR) that it may self-aggregate/oligomerize at the membrane surface. It was found to disrupt the bacterial membrane at sub-MIC, MIC and above-MIC concentrations, as observed by flow cytometry and/or visualized by atomic force microscopy (AFM). Only a limited toxicity was observed towards peripheral blood mononuclear cells (PBMC) with a more pronounced effect observed against the MEC-1 cell line.