Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga-which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.

Mono- and Dimeric Naphthalenones from the Marine-Derived Fungus Leptosphaerulina chartarum 3608

Five new naphthalenones, two enantiomers (−)-1 and (+)-1 leptothalenone A, (−)-4,8-dihydroxy-7-(2-hydroxy-ethyl)-6-methoxy-3,4-dihydro-2H-naphthalen-1-one ((−)-2), (4S, 10R, 4’S)-leptotha-lenone B (5), (4R, 10S, 4’S)-leptothalenone B (6), and a new isocoumarine, 6-hydroxy-5,8-dimethoxy-3-methyl-1H-isochromen-1-one (4), along with two known compounds (+)-4,8-dihydroxy-7-(2-hydroxy-ethyl)-6-methoxy-3,4-dihydro-2H-naphthalen-1-one ((+)-2) and (+)-10-norparvulenone (3) were isolated from the marine-derived fungus Leptosphaerulina chartarum 3608. The structures of new compounds were elucidated by HR-ESIMS, NMR, and ECD analysis. All compounds were evaluated for cytotoxicity and anti-inflammatory activity. Compound 6 showed moderate anti-inflammatory activity by inhibiting the production of nitric oxide (NO) in lipopolysaccharide-stimulated RAW264.7 cells, with an IC₅₀ value of 44.5 μM.

Antimicrobial peptides in echinoderm host defense

Antimicrobial peptides (AMPs) are important effector molecules in innate immunity. Here we briefly summarize characteristic traits of AMPs and their mechanisms of antimicrobial activity. Echinoderms live in a microbe-rich marine environment and are known to express a wide range of AMPs. We address two novel AMP families from coelomocytes of sea urchins: cysteine-rich AMPs (strongylocins) and heterodimeric AMPs (centrocins). These peptide families have conserved preprosequences, are present in both adults and pluteus stage larvae, have potent antimicrobial properties, and therefore appear to be important innate immune effectors. Strongylocins have a unique cysteine pattern compared to other cysteine-rich peptides, which suggests a novel AMP folding pattern. Centrocins and SdStrongylocin 2 contain brominated tryptophan residues in their native form. This review also includes AMPs isolated from other echinoderms, such as holothuroidins, fragments of beta-thymosin, and fragments of lectin (CEL-III). Echinoderm AMPs are crucial molecules for the understanding of echinoderm immunity, and their potent antimicrobial activity makes them potential precursors of novel drug leads.

Echinoderms from Azores islands: an unexpected source of antibiotic resistant Enterococcus spp. and Escherichia coli isolates

The prevalence of antibiotic resistance and the implicated mechanisms of resistance were evaluated in Enterococcus spp. and Escherichia coli, isolated from a total of 250 faecal samples of echinoderms collected from Azorean waters (Portugal). A total of 144 enterococci (120 Enterococcus faecium, 14 E. hirae, 8 E. faecalis, 2 E. gallinarum) and 10 E. coli were recovered. High percentages of resistance in enterococci were found for erythromycin, ampicillin, tetracyclin and ciprofloxacin. The erm(A) or erm(B), tet(M) and/or tet(L), vat(D), aac(6')-aph(2″) and aph(3')-IIIa genes were found in isolates resistant to erythromycin, tetracycline, quinupristin/dalfopristin, high-level gentamicin and high-level kanamycin, respectively. Resistance in E. coli isolates was detected for streptomycin, amikacin, tetracycline and tobramycin. The aadA gene was found in streptomycin-resistant isolates and tet(A)+tet(B) genes in tetracycline-resistant isolates. The data recovered are essential to improve knowledge about the dissemination of resistant strains through marine ecosystems and the possible implications involved in transferring these resistances either to other animals or to humans.

Sewage-exposed marine invertebrates: survival rates and microbiological accumulation

A large number of bacteria, including agents responsible for diseases, characterise sewage-polluted seawaters. Apart from standards for bathing waters and bivalve aquaculture waters, there are no general microbiological standards applicable to seawaters to help decide if bacterial pollution is within acceptable ranges. This study represents an attempt towards the issue of comparing the susceptibility of different marine invertebrates subjected to polluted seawater with a high microbial contamination. We explored the survival rates and the microbiological accumulation of mollusc bivalves, echinoderms and crustaceans species exposed to sewage-polluted seawaters. Microbiological analyses were performed on the polluted seawater and on the homogenates of exposed and unexposed specimens. Culturable bacteria (22 °C and 37 °C) and microbial pollution indicators (total coliforms, Escherichia coli and intestinal enterococci) were measured. When exposed to the sewage-polluted seawater, the examined invertebrates showed different survival rates. In the filter feeders, bacterial densities at 22 °C and 37 °C rose after 96 h of exposure to sewage. The highest concentrations of total coliforms and intestinal enterococci were found in exposed bivalve Mytilus galloprovincialis. The concentrations of bacteria growing at 37 °C were lower in the exposed deposit feeders compared to the polluted seawater. Some yeasts were absent in several exposed species although these yeasts were present in the polluted seawater. Our data suggest that the examined filter feeders, given their capability to survive and accumulate bacteria, may counteract the effects of sewage and restore seawater quality.

The effects of chronic inorganic and organic phosphate exposure on bactericidal activity of the coelomic fluid of the sea urchin Lytechinus variegatus (Lamarck) (Echinodermata: Echinoidea)

The sea urchin Lytechinus variegatus can survive chronic exposure to sodium phosphate (inorganic phosphate) concentrations as high as 3.2 mg L-1, and triethyl phosphate (organic phosphate) concentrations of 1000 mg L-1. However, chronic exposure to low (0.8 mg L-1 inorganic and 10 mg L-1 organic phosphate), medium (1.6 mg L-1 inorganic and 100 mg L-1 organic phosphate) or high (3.2 mg L-1 inorganic and 1000 mg L-1 organic phosphate) sublethal concentrations of these phosphates inhibit bactericidal clearance of the marine bacterium Vibrio sp. Bacteria were exposed to coelomic fluid collected from individuals maintained in either artificial seawater, or three concentrations of either inorganic phosphate or organic phosphate. Sterile marine broth, natural seawater and cell free coelomic fluid (cfCF) were employed as controls. Bacterial survival indices were measured at 0, 24 and 48 h periods once a week for four weeks. Bacteria were readily eliminated from the whole coelomic fluid (wCF) of individuals maintained in artificial seawater. Individuals maintained in inorganic phosphates were able to clear bacteria following a two week exposure period, while individuals maintained at even low concentrations of organic phosphates failed to clear all bacteria from their coelomic fluid. Exposure to phosphates represses antimicrobial defenses and may ultimately compromise survival of L. variegatus in the nearshore environment.

Marixanthomonas ophiurae gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a deep-sea brittle star

An aerobic, Gram-negative, non-motile, yellow-pigmented bacterium, strain KMM 3046T, was isolated from a deep-sea brittle star from the Fiji Sea and was subjected to a polyphasic taxonomic analysis. Strain KMM 3046T grew at 5–32 °C and in the presence of 1–12 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and 3-OH i16 : 0, 3-OH i17 : 0 and 3-OH a17 : 0 as the major fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 3046T forms a distinct evolutionary lineage within the family Flavobacteriaceae (phylum Bacteroidetes), displaying 92.3–91.9 % sequence similarity with respect to Salegentibacter species. On the basis of the phenotypic and phylogenetic data, strain KMM 3046T represents a novel genus and species of the family Flavobacteriaceae, for which the name Marixanthomonas ophiurae gen. nov., sp. nov. is proposed. The type strain of Marixanthomonas ophiurae is KMM 3046T (=NRIC 0684T=JCM 14121T).

Subcuticular bacteria from the brittle star Ophiactis balli (Echinodermata: Ophiuroidea) represent a new lineage of extracellular marine symbionts in the alpha subdivision of the class Proteobacteria

Many species of echinoderms, in all five extant classes, contain subcuticular bacterial symbionts (SCB). The role of these extracellular symbionts and the nature of the relationship remain unclear. We have sequenced 16S rRNA genes from symbionts to determine their phylogenetic affinities. Symbionts of an ophiuroid, Ophiactis balli, appear closely related to bacteria within the alpha group of the class Proteobacteria, including intracellular endosymbionts and pathogens. SCB are clearly of separate origin from other documented major groups of marine symbiotic bacteria.

[Yersinia pseudotuberculosis in a model marine ecosystem (experimental research)]

Materials on the behavior of Y. pseudotuberculosis in the model of marine ecosystem are presented. Y. pseudotuberculosis, both carrying and having lost the virulence plasmid of 45 MD, die in nonsterile sea water, but are capable of prolonged survival in sterile sea water and in the bodies of echinoderms. The death of these bacteria is accelerated in the presence of larvae of echinoderms. In sea water at low temperature Y. pseudotuberculosis maintained their high pathogenicity potential which they use on contact with eukaryotes. Under these conditions Y. pseudotuberculosis preserve their virulence plasmid, thus causing the disease and death of animals.

Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples

Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments.