Symbiont Community Composition in Rimicaris kairei Shrimps from Indian Ocean Vents with Notes on Mineralogy.

Hydrothermal vent ecosystems are home to a wide array of symbioses between animals and chemosynthetic microbes, among which shrimps in the genus Rimicaris is one of the most iconic. So far, studies of Rimicaris symbioses have been restricted to Atlantic species, including Rimicaris exoculata, which is totally reliant on the symbionts for nutrition, and the mixotrophic species Rimicaris chacei. Here, we expand this by investigating and characterizing the symbiosis of the Indian Ocean species Rimicaris kairei using specimens from two vent fields, Kairei and Edmond. We also aimed to evaluate the differences in mineralogy and microbial communities between two cephalothorax color morphs, black and brown, through a combination of 16S metabarcoding, scanning electron microscopy, fluorescent in situ hybridization, energy-dispersive X-ray spectroscopy, and synchrotron near-edge X-ray absorption structure analyses. Overall, our results highlight that R. kairei exhibits similar symbiont lineages to those of its Atlantic congeners, although with a few differences, such as the lack of Zetaproteobacteria. We found distinct mineralization processes behind the two color morphs that were linked to differences in the vent fluid composition, but the symbiotic community composition was surprisingly similar. In R. exoculata, such mineralogical differences have been shown to stem from disparity in the microbial communities, but our results indicate that in R. kairei this is instead due to the shift of dominant metabolisms by the same symbiotic partners. We suggest that a combination of local environmental factors and biogeographic barriers likely contribute to the differences between Atlantic and Indian Ocean Rimicaris symbioses. IMPORTANCE Hydrothermal vent shrimps in the genus Rimicaris are among the most charismatic deep-sea animals of Atlantic and Indian Oceans, often occurring on towering black smokers in dense aggregates of thousands of individuals. Although this dominance is only possible because of symbiosis, no study on the symbiosis of Indian Ocean Rimicaris species has been conducted. Here, we characterize the Rimicaris kairei symbiosis by combining molecular, microscopic, and elemental analyses, making comparisons with those of the Atlantic species possible for the first time. Although most symbiotic partners remained consistent across the two oceans, some differences were recognized in symbiont lineages, as well as in the mechanisms behind the formation of two color morphs with distinct mineralogies. Our results shed new light on relationships among mineralogy, environmental factors, and microbial communities that are useful for understanding other deep-sea symbioses in the future.

Transcriptome analysis of Neocaridina denticulate sinensis challenged by Vibrio parahemolyticus.

As a common aquatic pathogen, Vibrio parahaemolyticus can cause a variety of diseases of shrimp, especially acute hepatopancreatic necrosis disease (AHPND), which leads to great losses to the aquaculture industry around the world. However, the molecular mechanism of V. parahaemolyticus infection is still unclear. Neocaridina denticulate sinensis is a kind of small ornamental shrimp that is popular in aquarium trade, and due to its tenacious vitality, rapid growth, high reproductive capacity, it is very suitable to be developed as an animal model for basic research on decapod crustaceans. Thus, in this paper, transcriptomes of N. denticulate sinensis hepatopancreas with or without V. parahaemolyticus injection were explored. The results showed that a total of 23,624 genes with the N50 of 2705 bp were obtained. Comparative transcriptomic analysis revealed 21,464 differentially expressed genes between the V. parahaemolyticus infected and non-infected group, of which, 11,127 genes were up-regulated and 10,337 genes were down-regulated. Functional enrichment analysis suggested that many DEGs enriched in immune related pathways, including MAPK signaling pathway, Phosphatidylinositol signaling system, Chemokine signaling pathway, Phagosome and Jak-STAT signaling pathway and so on. Eight genes were selected randomly for qRT-PCR to verify the transcriptome sequencing results and the results showed the expression of these genes were consistent with the transcriptome results. Our work provides a unique and important dataset that contributes to the understanding of the molecular mechanisms of the immune response to V. parahaemolyticus infection and may further provide the basis for the prevention and resolution of bacterial diseases.

Optimization of metabolite extraction and analytical methods from shrimp intestine for metabolomics profile analysis using LC-HRMS/MS.

INTRODUCTION: Intestinal microbiota and metabolites play important roles for further improvement of animal production. Metabolomics of shrimp intestine to understand roles and their relationship to the host is hampered by the lack of metabolome profiling method. OBJECTIVES: This study aims to develop extraction and analytical methods to allow accurate metabolic analysis in shrimp intestine. METHODS: Conditions for extraction and LC-HRMS/MS analysis were optimized. RESULTS: Extraction with ethyl acetate:acetone (15:2 v/v) acidified with 0.5% acetic acid, elution with acetonitrile:water acidified with 0.01% acetic acid for 25 min, and mass fragmentation at 15% HCD were the optimal conditions, yielding the highest signal intensity and numbers of putative metabolites. CONCLUSION: Our method enabled in-depth study for shrimp-microbial interaction at metabolite level.

Vibrio and major commercially important vibriosis diseases in decapod crustaceans.

Bacteria fromthe Vibriogenus are autochthonous to aquatic environments and ubiquitous in aquaculture production systems. Many Vibrio species are non-pathogenic and can be commonly found in healthy farmed aquatic animals. However, some Vibrio species and strains are pathogenic leading to a variety of 'vibriosis' diseases. These diseases can have a significant negative impact on animal production, including farmed crustaceans such as shrimps, lobsters, and crabs. As such, vibriosis can pose a threat to meeting growing food demand and global food security. Preventive management is essential to avoid the onset of vibriosis. This includes a robust health management plan, the use of prophylaxis and treatment measures, and enhancing animal health through nutrition. Furthermore, the use of probiotics, prebiotics, synbiotics, quorum sensing disruption, green water, biofloc, bacteriophages, and immune priming could also play a role in preventing and controlling a vibriosis outbreak. This review aims to inform and update the reader about the current state of knowledge about Vibrio and associated vibriosis in farmed crustaceans (i.e. shrimp, lobster, and crabs). Furthermore, the review will identify potential knowledge gaps in the literature, which serves as a basis for future research priorities.

"Candidatus Desulfobulbus rimicarensis," an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata.

The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus, representing a potential novel species for which the name "Candidatus Desulfobulbus rimicarensis" is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of Deltaproteobacteria in deep-sea hydrothermal vent shrimps.IMPORTANCE The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe "Candidatus Desulfobulbus rimicarensis," an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host.

Carideicomes alvinocaridis gen. nov., sp. nov., a marine bacterium isolated from shrimp gill in a hydrothermal field of Okinawa Trough.

A Gram-stain-negative, strictly aerobic, oval-shaped, non-motile bacterium with no flagella, designated strain SCR17T, was isolated from a shrimp gill habitat in Tangyin hydrothermal field of Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SCR17T formed a lineage within the family 'Rhodobacteraceae', and shared 16S rRNA gene sequence similarity of 93.2-96.2 % to the related genera Aquicoccus and Roseivivax. Strain SCR17T was able to grow with 0-14 % (w/v) NaCl (optimum, 9-10 %). The sole respiratory quinone was ubiquinone-10. The major polar lipids of strain SCR17T comprised phosphatidylcholine (PC), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unidentified aminolipid (AL), an unidentified phospholipid (PL) and an unidentified lipid (L). The predominant fatty acids (more than 10 % of the total fatty acids) were C18 : 1ω7c or/and C18 : 1ω6c, anteiso-C15 : 0, C16 : 0 and C19 : 0 cyclo ω8c . The genomic DNA G+C content of strain SCR17T was 67.7 mol%. Based on polyphasic taxonomic analyses, strain SCR17T is considered to represent a novel species in a new genus of the family 'Rhodobacteraceae', for which the name Carideicomes alvinocaridis gen. nov., sp. nov. is proposed. The type strain of Carideicomes alvinocaridis is SCR17T (=JCM 33426T=MCCC 1K03732T). The discovery of a novel host-associated bacterium in hydrothermal fields provides an opportunity for the study of host-bacterial symbiosis in extreme environments.

Muricauda alvinocaridis sp. nov., isolated from shrimp gill from the Okinawa Trough.

A Gram-stain-negative, strictly aerobic, non-motile, long, straight-rod and non-flagellated marine bacterium strain, designated SCR12T, was isolated from the gill of a shrimp collected in the Tangyin hydrothermal field of the Okinawa Trough. The growth temperature was in the range of 16-40 °C and the optimum temperature was 37 °C. Optimal growth occurred at pH 6.5 and in the presence of 3 % (w/v) NaCl. The predominant isoprenoid quinone of strain SCR12T was menaquinone-6 (MK-6). The predominant fatty acids (>10 %) were iso-C15 : 0 (44.2 %), iso-C15 : 1 G (19.0 %) and iso-C17 : 0 3-OH (12.1 %). The major polar lipids comprised one phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminolipids and three unidentified lipids. Based on the results of 16S rRNA gene sequence analysis, strain SCR12T was found to be most closely related to Muricauda olearia CL-SS4T (98.09 %), followed by Muricauda beolgyonensis BB-My12T (97.65 %), Muricauda aquimarina SW-63T (97.58 %) and Muricauda ruestringensis DSM 13258T (97.31 %) and with lower sequence similarities (95.74-97.10 %) to other species of the genus Muricauda. Genome relatedness between strain SCR12T and M. olearia CL-SS4T was computed using both average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) and resulted in values of 85.6 % and 29.3±2.3 %, respectively. The genomic DNA G+C content of strain SCR12T was 42.3 mol%. On the basis of polyphasic analysis, the strain SCR12T was considered to represent a novel species of the genus Muricauda, for which the name Muricauda alvinocaridis sp. nov. is proposed. The type strain is SCR12T (=MCCC 1K03731T=JCM 33425T).

Biological ball filters regulate bacterial communities in marron (Cherax cainii) culture system.

This study aimed to characterize the bacterial communities in rearing water treated with commercial plastic biological ball filters named as Bio-ball in marron culture for 60 days. Inclusion of Bio-ball in the aquaculture tanks showed improvement in water quality parameters and enrichment of bacterial communities in terms of operational taxonomic units. The water treated with Bio-ball showed significantly less nitrate, nitrite, ammonia, phosphorus and high dissolved oxygen concentration than untreated control group. At phylum level, Proteobacteria was dominant in both control and treated water, whereas Firmicutes was found to be significantly (P < 0·05) enriched in Bio-ball treated water. Among the classified genus, Aquabacterium and Polunucleobacter were most dominant in control and Bio-ball treated water respectively. Linear Discriminant Analysis Effect Size exhibited 31 indicator bacterial genus, 10 in control and 21 in treated condition, suggesting the enrichment of microbial lineages with addition of Bio-ball. The bacteria Haliscomenobacter, Hypnocyclicus, Pajaroellobacter and Vibrio were found to be significantly (P < 0·001) correlated with higher pH, nitrate, nitrite, phosphorus and ammonia in control tanks, whereas Corynebacterium was linked to higher temperature in treated water. Overall results suggest that Bio-ball filter media significantly improved the water quality and microbial populations in aquaculture tanks. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study revealed the positive impacts of Bio-ball in enrichment of microbial flora associated with the degradation process of nitrogenous and organic compounds. Bio-ball also showed the capability to prevent the colonization of harmful bacteria, and favoured the growth of beneficial microbes in aquatic system. This study therefore could pave the ways of increasing the aquaculture production by improving the water quality.

New Polyketides from the Marine-Derived Fungus Letendraea sp. 5XNZ4-2.

Marine-derived fungi have been reported to have great potential to produce structurally unique metabolites. Our investigation on secondary metabolites from marine-derived fungi resulted in the isolation of seven new polyketides (phomopsiketones D-G (1-4) and letendronols A-C (5-7)) as well as one known xylarinol (8) in the cultural broth of Letendraea sp. Their structures and absolute configurations were elucidated using a set of spectroscopic and chemical methods, including HRESIMS, NMR, single-crystal X-ray diffraction, ECD calculation, and a modified version of Mosher's method. Compound 2 showed weak inhibition against nitric oxide production in lipopolysaccaride-activated macrophages with an IC50 value of 86 µM.

First comprehensive analysis of lysine acetylation in Alvinocaris longirostris from the deep-sea hydrothermal vents.

BACKGROUND: Deep-sea hydrothermal vents are unique chemoautotrophic ecosystems with harsh conditions. Alvinocaris longirostris is one of the dominant crustacean species inhabiting in these extreme environments. It is significant to clarify mechanisms in their adaptation to the vents. Lysine acetylation has been known to play critical roles in the regulation of many cellular processes. However, its function in A. longirostris and even marine invertebrates remains elusive. Our study is the first, to our knowledge, to comprehensively investigate lysine acetylome in A. longirostris. RESULTS: In total, 501 unique acetylation sites from 206 proteins were identified by combination of affinity enrichment and high-sensitive-massspectrometer. It was revealed that Arg, His and Lys occurred most frequently at the + 1 position downstream of the acetylation sites, which were all alkaline amino acids and positively charged. Functional analysis revealed that the protein acetylation was involved in diverse cellular processes, such as biosynthesis of amino acids, citrate cycle, fatty acid degradation and oxidative phosphorylation. Acetylated proteins were found enriched in mitochondrion and peroxisome, and many stress response related proteins were also discovered to be acetylated, like arginine kinases, heat shock protein 70, and hemocyanins. In the two hemocyanins, nine acetylation sites were identified, among which one acetylation site was unique in A. longirostris when compared with other shallow water shrimps. Further studies are warranted to verify its function. CONCLUSION: The lysine acetylome of A. longirostris is investigated for the first time and brings new insights into the regulation function of the lysine acetylation. The results supply abundant resources for exploring the functions of acetylation in A. longirostris and other shrimps.

Development of a colloidal gold immunochromatographic assay (GICA) for the rapid detection of Spiroplasma eriocheiris in commercially exploited crustaceans from China.

Spiroplasma eriocheiris is an emerging pathogen in freshwater crustaceans. In recent years, Eriocheir sinensis, Procambarus clarkii, Litopenaeus vannamei, Macrobrachium rosenbergii and Macrobrachium nipponense had been infected by this pathogen in China. An immunochromatographic strip test using gold nanoparticles was developed for rapidly detecting this pathogen. The strip test based on the principle of sandwich immunoassay by the specific combination between the pathogen and polyclonal antibody on a nitrocellulose membrane. Positive samples were displayed as red lines at the test and control zones of the nitrocellulose membrane, while negative samples resulted in a red line only at the control zone. The limit of detection was proved to be 106 Color Change Unit/ml. The test strip could be visually detected within 15 min and do not have cross-reaction with other aquatic bacteria. This test strip allows on-site rapid detection of S. eriocheiris in crustacean without the requirement of specialized equipment and professional personnel. The one-step test strips developed in our study had high sensitivity, specificity, reproducibility and stability. In conclusion, this method was proved to be convenient, feasible, rapid and effective for detecting S. eriocheiris.

MICROSPORIDIOSIS IN PEPPERMINT SHRIMP (DECAPODA: HIPPOLYTIDAE: LYSMATA SPP.).

Microsporidia are a diverse, parasitic phylum closely related to fungi. They infect a broad range of host species and tissues. This report describes microsporidiosis infection in a captive, wild-caught peppermint shrimp ( Lysmata spp.). The animal was found dead in its enclosure approximately 5 days after molting. Grossly, the skeletal musculature was diffusely swollen, opaque, and pale tan to white. Histologically, skeletal myofibers were replaced by large aggregates of sporophorous vesicles containing up to eight spores and earlier stages of sporogony. Tissue inflammation was minimal. Spores had positive staining with Luna's, Giemsa, Fites acid fast, and Brown and Brenn Gram stains. Ultrastructurally, spores were ovoid with an exo- and endospore, lamellar polaroplast, and polar tube arranged in 9 to 14 basilar, bilayered coils with a straight, apical manubrium. Spores and earlier stages of sporogony were contained within sporophorous vesicles. This is the first report of microsporidiosis in a shrimp from the family Hippolytidae.

Penicillium pedernalense sp. nov., isolated from whiteleg shrimp heads waste compost.

Novel Penicillium-like strains were isolated during the characterization of the mycobiota community dynamics associated with shrimp waste composting. Phylogenetic analysis of the partial ß-tubulin (BenA) gene and the ribosomal DNA internal transcribed spacer region (ITS1-5.8S-ITS2) sequences revealed that the novel strains were members of section Lanata-Divaricata and were closely related to Penicillium infrabuccalum DAOMC 250537T. On the basis of morphological and physiological characterization, and phylogenetic analysis, a novel Penicillium species, Penicillium pedernalense sp. nov., is proposed. The type strain is F01-11T (=CBS 140770T=CECT 20949T), which was isolated from whiteleg shrimp (Litopenaeus vannamei) heads waste compost in the Pedernales region (Manabí province, Ecuador).

Photobacterium sanguinicancri sp. nov. isolated from marine animals.

Six strains were isolated from the hemolymph of the spider crab Maja brachydactyla, captured in Spain, and one from a diseased blue mussel, Mytilus edulis. The 16S rRNA gene sequences showed close similarity to the recently described Photobacterium swingsii (98.1 %) and to a lesser degree to Photobacterium aquimaris (97.8 %). MLSA analyses showed a monophyletic group including P. swingsii that form a new subclade. All genomic analyses (Average Nucleotide Identity, Average Amino Acid Identity, and in silico DNA-DNA) clearly separate the strains analysed from P. swingsii with values below the thresholds to delimit a new species. The phenotypic, genotypic and genomic data presented here clearly place these strains as a coherent group within the genus Photobacterium, for which we propose the name Photobacterium sanguinicancri sp. nov. Strain CAIM 1827(T) (=CECT 7579(T), =DSM 24670(T)) is proposed as the type strain of the species.

Feasibility of Using Multiple-Locus Variable-Number Tandem-Repeat Analysis for Epidemiology Study of Vibrio parahaemolyticus Infections.

Vibrio parahaemolyticus causes foodborne gastroenteritis, which is often associated with the consumption of raw or undercooked shellfish. Molecular typing can provide critical information for detecting outbreaks and for source attribution. In this study, we describe the development and evaluation of an optimized multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) for the characterization of V. parahaemolyticus isolates. The discriminatory power of MLVA was compared to that of pulsed-field gel electrophoresis (PFGE) by typing 73 sporadic isolates. Epidemiologic concordance was evaluated by typing 23 isolates from five epidemiologically well-characterized outbreaks. The optimized MLVA was applied in early warning, epidemiological surveillance, and source tracking for V. parahaemolyticus infections. There was no significant difference in the discriminatory power of PFGE and MLVA with six or eight VNTR loci for the sporadic isolates. All isolates within an outbreak were indistinguishable by MLVA with six loci, except for one outbreak. Typically, the epidemiological survey could be initiated according to PFGE clusters. We applied MLVA with six loci on 22 isolates in two PFGE clusters. Isolates in one PFGE cluster were distinguished by MLVA. Although a follow-up investigation showed that both clusters had no epidemiological concordance, MLVA decreased the frequency of initiation of epidemiological surveys, thereby reducing labor costs. The ability of MLVA to trace the source of infection was evaluated by isolates from two outbreaks and shrimp samples. The isolates from one of outbreaks and a shrimp had the same MLVA type, suggesting that an epidemiological survey was initiated. Data from the epidemiological investigation subsequently indicated that contaminated shrimp from a nearby city (Dongguan) might be the source of the outbreak. In conclusion, these results indicate that the optimized MLVA may be a promising tool for early warning and epidemiological surveillance of V. parahaemolyticus infections.

Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792.

Vibrio harveyi CAIM 1792 is a marine bacterial strain that causes mortality in farmed shrimp in north-west Mexico, and the identification of virulence genes in this strain is important for understanding its pathogenicity. The aim of this work was to compare the V. harveyi CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions in silico that differentiate this strain from other V. harveyi strains. Twenty-one newly sequenced genomes were compared in silico against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to those of other V. harveyi strains (78%) than to those of the other closely related species Vibrio owensii (67%), Vibrio rotiferianus (63%) and Vibrio campbellii (59%). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DNA-DNA hybridization and multi-locus sequence analysis of 11 concatenated housekeeping genes. SNP analysis clustered 34/38 genomes within their accepted species. The pangenomic and SNP trees showed that V. harveyi is the most conserved of the four species studied and V. campbellii may be divided into at least three subspecies, supported by intergenomic distance analysis. blastp atlases were created to identify unique regions among the genomes most related to V. harveyi CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems and a transcriptional regulator, LysR, reported to be involved in virulence, metabolism, quorum sensing and motility.

Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics.

The shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (≤52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (≤356 U mg(-1)) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.

Characterization of the dominant bacterial communities during storage of Norway lobster and Norway lobster tails (Nephrops norvegicus) based on 16S rDNA analysis by PCR-DGGE.

The aim of this study was to investigate the microbial quality of whole Norway lobster (Nephrops norvegicus) and Norway lobster tails to optimize handling conditions. This was done by assessing the total viable count (TVC) and characterizing the dominant microbiota. The cultivable microorganisms were quantified via classical microbiological plating methods. To characterize as many bacterial species present as possible, we performed advanced molecular identification techniques (PCR-DGGE). The initial TVC of fresh Norway lobster meat was high (3.0 log cfu/g) as compared to fish. No significant difference between whole Norway lobster and Norway lobster tails could be found during the storage period. From day 6 of storage, a significant difference between Plate Count Agar (PCA) and Marine Agar (MA) was observed. The microbiota of Norway lobster was dominated by members of the Gram-negative genera such as Psychrobacter spp., Pseudoalteromonas spp., Pseudomonas spp., Luteimonas spp., and Aliivibrio spp. From these bacteria, mainly Psychrobacter spp. and Pseudomonas spp. remained present until the end of the storage period. These are known spoilage organisms in fishery products. Other known spoilage organisms of crustaceans such as Photobacterium spp. could not be identified.

Isolation and screening of probiotic candidates from marron, Cherax cainii (Austin, 2002) gastrointestinal tract (GIT) and commercial probiotic products for the use in marron culture.

Six strains of bacteria including Bacillus mycoides (A10) and Shewanella species (A12) isolated from healthy marron intestine, Bacillus species (PM1), Bacillus subtilis (PM3), Bacillus sp. (PM4) and Bacillus sp. (AQ) from commercial probiotic products were investigated for probiotic potential in marron culture. Antibiotic susceptibility tests indicated PM3 and PM4 were susceptible to all nine antibiotics evaluated. A10, A12 and AQ were resistant to class penicillins, whereas PM1 was resistant to class penicillin and macrolides. All strains were non-pathogenic for marron. Strong inhibition against Vibrio mimicus and Vibrio cholerae non-01 was exhibited by PM4 and PM3. A10 inhibited V. mimicus at 72 h of growth, but not V. cholerae non-01, whereas A12 inhibited V. cholerae non-01 but not V. mimicus, and AQ showed no inhibition activity. A wide range of enzymes were produced by A10 and AQ using the API ZYM test. Protease enzymes were produced by PM3, PM4, AQ and PM1. In order of effectiveness, the following bacteria have probiotic potential: B. subtilis (PM3), Bacillus sp. (PM4) and B. mycoides (A10). Further study is required to determine the bacterium or any combination that gives a multibeneficial effect on marron.

The gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata: an in-depth metagenomic investigation and discovery of Zetaproteobacteria.

The gill chamber of deep-sea hydrothermal vent shrimp Rimicaris exoculata hosts a dense community of epibiotic bacteria dominated by filamentous Epsilonproteobacteria and Gammaproteobacteria. Using metagenomics on shrimp from the Rainbow hydrothermal vent field, we showed that both epibiont groups have the potential to grow autotrophically and oxidize reduced sulfur compounds or hydrogen with oxygen or nitrate. For carbon fixation, the Epsilonproteobacteria use the reductive tricarboxylic acid cycle, whereas the Gammaproteobacteria use the Calvin-Benson-Bassham cycle. Only the epsilonproteobacterial epibionts had the genes necessary for producing ammonium. This ability likely minimizes direct competition between epibionts and also broadens the spectrum of environmental conditions that the shrimp may successfully inhabit. We identified genes likely to be involved in shrimp-epibiont interactions, as well as genes for nutritional and detoxification processes that might benefit the host. Shrimp epibionts at Rainbow are often coated with iron oxyhydroxides, whose origin is intensely debated. We identified 16S rRNA sequences and functional genes affiliated with iron-oxidizing Zetaproteobacteria, which indicates that biological iron oxidation might play a role in forming these deposits. Fluorescence in situ hybridizations confirmed the presence of active Zetaproteobacteria in the R. exoculata gill chamber, thus providing the first evidence for a Zetaproteobacteria-invertebrate association.