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Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria)
PeerJ
Abstract
Background
Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality.
Methods
We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana , using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2.
Results
D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.
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Flaviviruses cause some of the most detrimental vertebrate diseases, yet little is known of their impacts on invertebrates. Microbial activities at the animal-water interface are hypothesized to influence viral replication and possibly contribute to pathology of echinoderm wasting diseases due to hypoxic stress. We assessed the impacts of enhanced microbial production and suboxic stress on Apostichopus californicus associated flavivirus (PcaFV) load in a mesocosm experiment. Organic matter amendment and suboxic stress resulted in lower PcaFV load, which also correlated negatively with animal mass loss and microbial activity at the animal-water interface. These data suggest that PcaFV replication and persistence was best supported in healthier specimens. Our results do not support the hypothesis that suboxic stress or microbial activity promote PcaFV replication, but rather that PcaFV appears to be a neutral or beneficial symbiont of Apostichopus californicus.
Diadema antillarum scuticociliatosis (DaSc), caused by a scuticociliate closely related to Philaster apodigitiformis , has affected Caribbean long-spined urchins since at least January 2022. Quantitative PCR (qPCR) is currently the standard method for detection of this ciliate in tissue and coelomic fluid samples, yet this method requires specialized equipment and is more expensive than standard PCR methods. The DaSc scuticociliate occurs against a backdrop of endo- and ecto-symbiotic ciliates which complicate detection using universal or pan-phylum PCR primer sets. To overcome these limitations, we designed and validated a sensitive and specific PCR primer (scutico-634F) and nested two-step PCR protocol to detect this taxon, which excludes other ciliates associated with D. antillarum and has poor affinity for other related ciliates. This primer and protocol for the DaSc-associated Philaster clade (DaScPc) allow for widely-accessible investigation of this pathogen in new regions and within environmental reservoirs.
Echinoderm mass mortality events shape marine ecosystems by altering the dynamics among major benthic groups. The sea urchin Diadema antillarum, virtually extirpated in the Caribbean in the early 1980s by an unknown cause, recently experienced another mass mortality beginning in January 2022. We investigated the cause of this mass mortality event through combined molecular biological and veterinary pathologic approaches comparing grossly normal and abnormal animals collected from 23 sites, representing locations that were either affected or unaffected at the time of sampling. Here, we report that a scuticociliate most similar to Philaster apodigitiformis was consistently associated with abnormal urchins at affected sites but was absent from unaffected sites. Experimentally challenging naïve urchins with a Philaster culture isolated from an abnormal, field-collected specimen resulted in gross signs consistent with those of the mortality event. The same ciliate was recovered from treated specimens postmortem, thus fulfilling Koch's postulates for this microorganism. We term this condition D. antillarum scuticociliatosis.
Some tropical sea cucumbers of the family Holothuriidae can efficiently repel or even fatally ensnare predators by sacrificially ejecting a bioadhesive matrix termed the Cuvierian organ (CO), so named by the French zoologist Georges Cuvier who first described it in 1831. Still, the precise mechanisms for how adhesiveness genetically arose in CO and how sea cucumbers perceive and transduce danger signals for CO expulsion during defense have remained unclear. Here, we report the first high-quality, chromosome-level genome assembly of Holothuria leucospilota, an ecologically significant sea cucumber with prototypical CO. The H. leucospilota genome reveals characteristic long-repeat signatures in CO-specific outer-layer proteins, analogous to fibrous proteins of disparate species origins, including spider spidroin and silkworm fibroin. Intriguingly, several CO-specific proteins occur with amyloid-like patterns featuring extensive intramolecular cross-β structures readily stainable by amyloid indicator dyes. Distinct proteins within the CO connective tissue and outer surface cooperate to give the expelled matrix its apparent tenacity and adhesiveness, respectively. Genomic evidence offers further hints that H. leucospilota directly transduces predator-induced mechanical pressure onto the CO surface through mediation by transient receptor potential channels, which culminates in acetylcholine-triggered CO expulsion in part or in entirety. Evolutionarily, innovative events in two distinct regions of the H. leucospilota genome have apparently spurred CO's differentiation from the respiratory tree to a lethal defensive organ against predators.
In highly diverse systems such as coral reefs, many species appear to fulfil similar ecological roles, suggesting that they might be ecologically equivalent. However, even if species provide similar functions, the magnitude of those roles could modulate their impact within ecosystems. Here, we compare the functional contributions of two common, co-occurring Caribbean sea cucumber species, Holothuria mexicana and Actynopyga agassizii , in terms of ammonium provisioning and sediment processing on Bahamian patch reefs. We quantified these functions through empirical measures of ammonium excretion, and in situ observations of sediment processing coupled with fecal pellet collections. On a per-individual level, H. mexicana excreted approximately 23% more ammonium and processed approximately 53% more sediment per hour than A. agassizii . However, when we combined these species-specific functional rates to species abundances to produce reef-wide estimates, we found that A. agassizii contributed more than H. mexicana to sediment processing at 57% of reefs (1.9 times more per unit area across all surveyed reefs), and more to ammonium excretion at 83% of reefs (5.6 times more ammonium per unit area across all surveyed reefs), owing to its higher abundance. We conclude that sea cucumber species can differ in the rates at which they deliver per capita ecosystem functions but their ecological impacts at the population level depend on their abundance at a given location.
The 1983-1984 die-off of the long-spined sea urchin Diadema antillarum stands out as a catastrophic marine event because of its detrimental effects on Caribbean coral reefs. Without the grazing activities of this key herbivore, turf and macroalgae became the dominant benthic group, inhibiting coral recruitment and compromising coral reef recovery from other disturbances. In the decades that followed, recovery of D. antillarum populations was slow to non-existent. In late January 2022, a new mass mortality of D. antillarum was first observed in the U.S. Virgin Islands. We documented the spread and extent of this new die-off using an online survey. Infected individuals were closely monitored in the lab to record signs of illness, while a large population on Saba, Dutch Caribbean, was surveyed weekly before and during mortality to determine the lethality of this event. Within four months the die-off was distributed over 1,300 km from north to south and 2,500 km east to west. Whereas the 1983-1984 die-off advanced mostly with the currents, the 2022 event has appeared far more quickly in geographically distant areas. First die-off observations in each jurisdiction were often close to harbor areas, which, together with their rapid appearance, suggests that anthropogenic factors may have contributed to the spread of the causative agent. The signs of illness in sick D. antillarum were very similar to those recorded during the 1983-1984 die-off: lack of tube feet control, slow spine reaction followed by their loss, and necrosis of the epidermis were observed in both lab and wild urchins. Affected populations succumbed fast; within a month of the first signs of illness, a closely monitored population at Saba, Dutch Caribbean, had decreased from 4.05 individuals per m² to 0.05 individuals per m². Lethality can therefore be as high as 99%. The full extent of the 2022 D. antillarum die-off event is not currently known. The slower spread in the summer of 2022 might indicate that the die-off is coming to a (temporary) standstill. If this is the case, some populations will remain unaffected and potentially supply larvae to downstream areas and augment natural recovery processes. In addition, several D. antillarum rehabilitation approaches have been developed in the past decade and some are ready for large scale implementation. However, active conservation and restoration should not distract from the primary goal of identifying a cause and, if possible, implementing actions to decrease the likelihood of future D. antillarum die-off events.
The mitochondrial genome of the long-spined black sea urchin, Diadema antillarum, was sequenced using Illumina next-generation sequencing technology. The complete mitogenome is 15,708 bp in length, containing two rRNA, 22 tRNA and 13 protein-coding genes, plus a noncoding control region of 133 bp. The nucleotide composition is 18.37% G, 23.79% C, 26.84% A and 30.99% T. The A + T bias is 57.84%. Phylogenetic analysis based on 12 complete mitochondrial genomes of sea urchins, including four species of the family Diadematidae, supported familial monophyly; however, the two Diadema species, D. antillarum and D. setosum were not recovered as sister taxa.
Echinoderms are a phylum of marine invertebrates that include model organisms, keystone species, and animals commercially harvested for seafood. Despite their scientific, ecological, and economic importance, there is little known about the diversity of RNA viruses that infect echinoderms compared to other invertebrates. We screened over 900 transcriptomes and viral metagenomes to characterize the RNA virome of 38 echinoderm species from all five classes (Crinoidea, Holothuroidea, Asteroidea, Ophiuroidea and Echinoidea). We identified 347 viral genome fragments that were classified to genera and families within nine viral orders - Picornavirales, Durnavirales, Martellivirales, Nodamuvirales, Reovirales, Amarillovirales, Ghabrivirales, Mononegavirales, and Hepelivirales. We compared the relative viral representation across three life stages (embryo, larvae, adult) and characterized the gene content of contigs which encoded complete or near-complete genomes. The proportion of viral reads in a given transcriptome was not found to significantly differ between life stages though the majority of viral contigs were discovered from transcriptomes of adult tissue. This study illuminates the biodiversity of RNA viruses from echinoderms, revealing the occurrence of viral groups in natural populations.
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.
The Anacostia River is a highly impacted watershed in the Northeastern United States which experiences combined sewage outfall in downstream waters. We examined the composition of RNA viruses at three sites in the river using viral metagenomics. Viromes had well represented Picornaviruses, Tombusviruses, Wolframviruses, Nodaviruses, with fewer Tobamoviruses, Sobemoviruses, and Densoviruses (ssDNA). Phylogenetic ana-lyses of detected viruses provide evidence for putatively autochthonous and allochthonous invertebrate, plant, and vertebrate host origin. The number of viral genomes matching Ribovaria increased downstream, and assemblages were most disparate between distant sites, suggesting impacts of the combined sewage overflows at these sites. Additionally, we recovered a densovirus genome fragment which was highly similar to the Clinch ambidensovirus 1, which has been attributed to mass mortality of freshwater mussels in Northeastern America. Taken together, these data suggest that RNA viromes of the Anacostia River reflect autochthonous production of virus particles by benthic metazoan and plants, and inputs from terrestrial habitats including sewage.
Asteroid wasting events and mass mortality have occurred for over a century. We currently lack a fundamental understanding of the microbial ecology of asteroid disease, with disease investigations hindered by sparse information about the microorganisms associated with grossly normal specimens. We surveilled viruses and protists associated with grossly normal specimens of three asteroid species (Patiriella regularis, Stichaster australis, Coscinasterias muricata) on the North Island / Te Ika-a-Māui, Aotearoa New Zealand, using metagenomes prepared from virus and ribosome-sized material. We discovered several densovirus-like genome fragments in our RNA and DNA metagenomic libraries. Subsequent survey of their prevalence within populations by quantitative PCR (qPCR) demonstrated their occurrence in only a few (13%) specimens (n = 36). Survey of large and small subunit rRNAs in metagenomes revealed the presence of a mesomycete (most closely matching Ichthyosporea sp.). Survey of large subunit prevalence and load by qPCR revealed that it is widely detectable (80%) and present predominately in body wall tissues across all 3 species of asteroid. Our results raise interesting questions about the roles of these microbiome constituents in host ecology and pathogenesis under changing ocean conditions.
Cross-species transmission of emerging viruses happens occasionally due to epidemiological, biological, and ecological factors, and it has caused more concern recently. Covert mortality nodavirus (CMNV) was revealed to be a unique shrimp virus that could cross species barrier to infect vertebrate fish. In the present study, CMNV reverse transcription-nested PCR (RT-nPCR)-positive samples were identified from farmed sea cucumber (Apostichopus japonicas) in the CMNV host range investigation. The amplicons of RT-nPCR from sea cucumber were sequenced, and its sequences showed 100% identity with the RNA-dependent RNA polymerase gene of the original CMNV isolate. Histopathological analysis revealed pathologic changes, including karyopyknosis and vacuolation of the epithelial cells, in the sea cucumber intestinal tissue. The extensive positive hybridization signals with CMNV probe were shown in the damaged epithelial cells in the in situ hybridization assay. Meanwhile, transmission electron microscopy analysis revealed CMNV-like virus particles in the intestine epithelium. All the results indicated that the sea cucumber, an Echinodermata, is a new host of CMNV. This study supplied further evidence of the wide host range of CMNV and also reminded us to pay close attention to its potential risk to threaten different aquaculture animal species.
Bioturbation of reef sediments aerates the upper sediment layers and releases organic material to benthic communities. Despite being the larger and more conspicuous bioturbators on coral reefs, the value of holothurians (sea cucumbers) to reef ecosystems is less often attributed to their ecosystem services than their value for fisheries. This may be because they are considered to have an insignificant effect on reef health relative to other animals. Here, we ground-truthed remote sensing data obtained from drone and satellite imagery to estimate the bioturbation rates of holothurians across the 19 km² Heron Island Reef in Queensland, Australia. Ex situ bioturbation rates of the most abundant holothurian, Holothuria atra, were assessed during 24-h feeding experiments. Using density measurements of holothurians across reef flat zones in a 27,000 m² map produced from drone imagery, we extrapolated bioturbation across the reef using satellite remote sensing data. Individual H. atra were estimated to produce approximately 14 kg of bioturbated sediment per year. On a reef scale (excluding the reef lagoon) and accounting for varying densities of holothurians across different reef zones, total bioturbation from holothurians at Heron Reef was estimated at over 64,000 metric tonnes per year, slightly more than the mass of five Eiffel Towers. These results highlight the scale of structural and biochemical impacts that holothurians have on reef flats and their importance to ecosystem functioning and services. Management of these animals on reefs is imperative as overharvesting would likely cause substantial negative effects on sedimentary ecosystems and their biogeochemistry in corals reefs.
Graphical abstract
Aquacultivated sea cucumbers often suffer from SKin Ulceration Diseases (SKUDs). SKUDs have
been observed in six holothuroid species from nine countries. All SKUDs present a similar symptom—
the skin ulceration—and can be induced by bacteria, viruses, or abiotic factors. We here provide
an update on SKUDs in holothuroids and analyse the case of the SKUD observed in Holothuria
scabra in Madagascar. Field observations revealed a seasonality of the disease (i.e. wintertime
maximum peak). Morphological analyses of integument ulcers showed that sea cucumbers react by
forming a collagen fibre plug. Metagenomic analyses revealed a higher proportion of Vibrionaceae
(Gammaproteobacteria) in ulcers in comparison to the healthy integument of the same individuals.
Experimental infection assays were performed with ulcer crude extracts and bacteria isolated from
these extracts (e.g. Vibrio parahaemolyticus) but did not significantly induce skin ulceration. Our
results suggest that the disease is not induced by a pathogen or, at the very least, that the pathogen is
not found within the ulcers as the disease is not transmissible by contact. An initial cause of the SKUD
in Madagascar might be the repeated and prolonged exposures to cold temperatures. Opportunistic
bacteria could settle in the dermis of ulcerated individuals and promote the ulcer extension. We
propose a general nomenclature for SKUDs based on the acronym of the disease, the affected sea
cucumber species (e.g. Hs for Holothuria scabra), the concerned region using an ISO code 3166-2 (e.g.
MG for Madagascar), the description date (e.g. 20 for the year 2020), and, when known, the inducing
agent (first letter of the general taxon, b for bacteria, v for virus in currently known cases; a a if it is
an abiotic inducing parameter; nothing if the inducing cause has not been precisely identified). The
disease described in this work will be designated under the name SKUD Hs-MG-20.
Sea star wasting disease (SSWD) is a condition that has affected asteroids for over 120 years, yet mechanistic understanding of this wasting etiology remains elusive. We investigated temporal virome variation in two Pisaster ochraceus specimens that wasted in the absence of external stimuli and two specimens that did not experience SSWD for the duration of our study, and compared viromes of wasting lesion margin tissues to both artificial scar margins and grossly normal tissues over time. Global assembly of all SSWD-affected tissue libraries resulted in 24 viral genome fragments represented in >1 library. Genome fragments mostly matched densoviruses and picornaviruses with fewer matching nodaviruses, and a sobemovirus. Picornavirus-like and densovirus-like genome fragments were most similar to viral genomes recovered in metagenomic study of other marine invertebrates. Read recruitment revealed only two picornavirus-like genome fragments that recruited from only SSWD-affected specimens, but neither was unique to wasting lesions. Wasting lesion margin reads recruited to a greater number of viral genotypes (i.e., richness) than did either scar tissue and grossly normal tissue reads. Taken together, these data suggest that no single viral genome fragment was associated with SSWD. Rather, wasting lesion margins may generally support viral proliferation.
Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.
The primary interest in sea star densoviruses, specifically SSaDV, has been their association with sea star wasting syndrome (SSWS), a disease that has decimated sea star populations across the West Coast of the United States since 2013. The association of SSaDV with SSWS was originally drawn from metagenomic analysis, which was further studied through field surveys using quantitative PCR (qPCR), with the conclusion that it was the most likely viral candidate in the metagenomic data based on its representation in symptomatic sea stars compared to asymptomatic sea stars. We reexamined the original metagenomic data with additional genomic data sets and found that SSaDV was 1 of 10 densoviruses present in the original data set and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations.
Background:
For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus relative abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems.
Methods:
For a comprehensive assessment of each tool, we compare the computational resources and speed of QIIME 2's q2-feature-classifier, Kraken 2, and Bracken in generating the three main 16S rRNA databases: Greengenes, SILVA, and RDP. For an evaluation of accuracy, we evaluated each tool using the same simulated 16S rRNA reads from human gut, ocean, and soil metagenomes that were previously used to compare QIIME, MAPseq, mothur, and QIIME 2. We evaluated accuracy based on the accuracy of the final genera read counts assigned by each tool. Finally, as Kraken 2 is the only tool providing per-read taxonomic assignments, we evaluate the sensitivity and precision of Kraken 2's per-read classifications.
Results:
For both the Greengenes and SILVA database, Kraken 2 and Bracken are up to 100 times faster at database generation. For classification, using the same data as previous studies, Kraken 2 and Bracken are up to 300 times faster, use 100x less RAM, and generate results that more accurate at 16S rRNA profiling than QIIME 2's q2-feature-classifier.
Conclusion:
Kraken 2 and Bracken provide a very fast, efficient, and accurate solution for 16S rRNA metataxonomic data analysis. Video Abstract.
The molecular evolutionary genetics analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5–0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries. Of these, only 13 were found in >2 libraries and recruited >100 reads (of 9.13 x 10⁷ total reads), representing several picornaviruses, two tobamoviruses and a reovirus. We quantified the abundance of four picornaviruses and the reovirus monthly from August 2014 to May 2015. Patterns of viral abundance in the >5 μm size fraction and representation in microbial-sized community RNA libraries over time suggest that one picornavirus genotype (TS24835) and the reovirus (TS148892) may infect small (<5 μm) eukaryotic microorganisms, while two other picornaviruses (TS24641 and TS4340) may infect larger (>5 μm) eukaryotic microorganisms or metazoa. Our data also suggest that picornavirus TS152062 may originate from an allochthonous host. All five viral genotypes were present in at least one size fraction across all 3 lakes during the year, suggesting that RNA viruses may easily disperse between adjacent aquatic habitats. Our data therefore demonstrate that RNA viruses are widespread in temperate lacustrine ecosystems, and may provide evidence of viral infection in larger eukaryotes (including metazoa) inhabiting the lakes.
Sea Star Wasting Disease (SSWD) describes a suite of disease signs that affected >20 species of asteroid since 2013 along a broad geographic range from the Alaska Peninsula to Baja California. Previous work identified the Sea Star associated Densovirus (SSaDV) as the best candidate pathogen for SSWD in three species of common asteroid (Pycnopodia helianthoides, Pisaster ochraceus, and Evasterias troscheli), and virus-sized material (<0.22 μm) elicited SSWD signs in P. helianthoides. However, the ability of virus-sized material to elicit SSWD in other species of asteroids was not known. Discordance between detection of SSaDV by qPCR and by viral metagenomics inspired the redesign of qPCR primers to encompass SSaDV and two densoviral genotypes detected in wasting asteroids. Analysis of asteroid samples collected during SSWD emergence in 2013–2014 showed an association between wasting asteroid-associated densoviruses (WAaDs) and SSWD in only one species (P. helianthoides). WAaDs were found in association with asymptomatic asteroids in contemporary (2016 and later) populations, suggesting that they may form subclinical infections at the times they were sampled. WAaDs were found in SSWD-affected P. helianthoides after being absent in asymptomatic individuals a year earlier at one location (Kodiak). Direct challenge of P. ochraceus, Pisaster brevispinus, and E. troscheli with virus-sized material from SSWD-affected individuals did not elicit SSWD in any trial. RNA viral genomes discovered in viral metagenomes and host transcriptomes had viral loads and metagenome fragment recruitment patterns that were inconsistent with SSWD. Analysis of water temperature and precipitation patterns on a regional scale suggests that SSWD occurred following dry conditions at several locations, but mostly was inconsistently associated with either parameter. Semi-continuous monitoring of SSWD subtidally at two sites in the Salish Sea from 2013 to 2017 indicated that SSWD in E. troscheli and P. ochraceus was associated with elevated water temperatures, but wasting in P. helianthoides occurred irrespective of environmental conditions. Our data therefore do not support that widespread SSWD is associated with potential viral pathogens in species other than P. helianthoides. Rather, we speculate that SSWD may represent a syndrome of heterogeneous etiologies between geographic locations, between species, or even within a species between locations.
Establishing virus–host relationships has historically relied on culture-dependent approaches.
Here we report on the use of marine metatranscriptomics to probe virus–host relationships.
Statistical co-occurrence analyses of dsDNA, ssRNA and dsRNA viral markers of
polyadenylation-selected RNA sequences from microbial communities dominated by
Aureococcus anophagefferens (Quantuck Bay, NY), and diatoms (Narragansett Bay, RI) show
active infections by diverse giant viruses (NCLDVs) associated with algal and nonalgal hosts.
Ongoing infections of A. anophagefferens by a known Mimiviridae (AaV) occur during bloom
peak and decline. Bloom decline is also accompanied by increased activity of viruses other
than AaV, including ( þ ) ssRNA viruses. In Narragansett Bay, increased temporal resolution
reveals active NCLDVs with both ‘boom-and-bust’ and ‘steady-state infection’-like ecologies
that include known as well as novel virus–host interactions. Our approach offers a method for
screening active viral infections and develops links between viruses and their potential
hosts in situ. Our observations further demonstrate that previously unknown virus–host
relationships in marine systems are abundant.
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, as-sembly of metagenomic data remains challenging thus stifling biological discoveries. Moreover, re-cent studies revealed that complex bacterial populations may be composed from dozens of related strains thus further amplifying the challenge metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse datasets.
Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence. The invertebrate virome also reveals remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements. Together, these data present a view of the RNA virosphere that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution.
Echinoderms are prone to large population fluctuations that can be mediated by pervasive disease events. For the majority of echinoderm disease events the causative pathogen is unknown. Viruses have only recently been explored as potential pathogens using culture-independent techniques though little information currently exists on echinoderm viruses. In this study, ten circular ssDNA viruses were discovered in tissues among an asteroid (Aste-rias forbesi), an echinoid (Strongylocentrotus droebachiensis) and a holothurian (Parasti-chopus californicus) using viral metagenomics. Genome architecture and sequence similarity place these viruses among the rapidly expanding circular rep-encoding single stranded (CRESS) DNA viral group. Multiple genomes from the same tissue were no more similar in sequence identity to each other than when compared to other known CRESS DNA viruses. The results from this study are the first to describe a virus from a holothurian and continue to show the ubiquity of these viruses among aquatic invertebrates.
Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden–Meyerhof–Parnas pathway on coral-dominated reefs to the less efficient Entner–Doudoroff and pentose phosphate pathways on algal-dominated reefs. This ‘yield-to-power’ switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.
Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.
Background
Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform¿s sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects.ResultsHere we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the required memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics.Conclusion
FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.
Significance
Sea stars inhabiting the Northeast Pacific Coast have recently experienced an extensive outbreak of wasting disease, leading to their degradation and disappearance from many coastal areas. In this paper, we present evidence that the cause of the disease is transmissible from disease-affected animals to apparently healthy individuals, that the disease-causing agent is a virus-sized microorganism, and that the best candidate viral taxon, the sea star-associated densovirus (SSaDV), is in greater abundance in diseased than in healthy sea stars.
The black sea urchin Diadema antillarum was until 1983 an important
component of Caribbean coral reef communities, affecting the
distribution and abundance of all major guilds of sedentary organisms.
Between 1983 and 1984 this species suffered the most extensive and
severe mass mortality ever recorded for a marine animal. Continuous
monitoring in Panama shows that in the subsequent 10 years D. antillarum
densities remained at < 3.5% of their pre-mortality levels. Despite
pre-1983 evidence that D. antillarum competed with other echinoids,
there has been no competitive release by other sea urchin species.
Reef-wide inclusions and exclusions of echinoids indicate that: (i) the
low rate of Diadema recruitment does not result from absence of
settlement cues for the larvae or from lack of protection by conspecific
adults but from paucity of larvae in the water column; and (ii)
Echinometra viridis-an echinoid previously shown to compete with adult
Diadema-actually facilitates the latter's recruitment. The lack of
recovery of D. antillarum despite its high fecundity, planktonic larvae
and the assistance of E. viridis, demonstrates that unique disturbance
events in the history of a species can have long-lasting effects on its
abundance, independently of community-level processes.
Diadema antillarum is a large, mobile sea urchin which until 1983 was ubiquitous on Caribbean coral reefs, seagrass beds, mangrove roots and sand habitats. In January 1983, specimens at Punta Galeta, Panama, began to show symptoms of ill health; over the next 13 months similar symptoms and massive deaths were found in many other parts of the species' range. The mortality front advanced E to Tobago, taking c1 yr to cover 2000 km. At the same time, mass mortality was spreading at a faster rate W to Costa Rica and N to the Cayman Islands, Belize, Mexico and Jamaica. Mortality advanced into the Gulf of Mexico, reaching the Flower Garden Banks off Texas before August 1984. It moved to Florida, and thence to Bermuda. A minimum of 93% (mean 98%) of Diadema at each location perished. Although a waterborne, host-specific pathogen is implication, its nature remains unknown. Subsequent recruitment and population recovery is traced, and effects on genetic structure and community structure are examined. -P.J.Jarvis
As dominant members of marine mesozooplankton communities, copepods play critical roles in oceanic food webs and biogeochemical cycling. Despite the ecological significance of copepods, little is known regarding the causes of copepod mortality, and up to 35% of total copepod mortality cannot be accounted for by predation alone. Viruses have been established as ecologically important infectious agents in the oceans; however, viral infection has not been investigated in mesozooplankton communities. Here we used molecular and microscopic techniques to document viral infection in natural populations of the calanoid copepods Acartia tonsa (Dana) and Labidocera aestiva (Wheeler) in Tampa Bay, FL. Viral metagenomics revealed previously undocumented viruses in each species, named Acartia tonsa copepod circo-like virus (AtCopCV) and Labidocera aestiva copepod circo-like virus (LaCopCV). LaCopCV was found to be extremely prevalent and abundant in L. aestiva populations, with up to 100% prevalence in some samples and average viral loads of 1.13 × 10(5) copies per individual. LaCopCV transcription was also detected in the majority of L. aestiva individuals, indicating viral activity. AtCopCV was sporadically detected in A. tonsa populations year-round, suggesting temporal variability in viral infection dynamics. Finally, virus-like particles of unknown identity were observed in the connective tissues of A. tonsa and L. aestiva by transmission electron microscopy, demonstrating that viruses were actively proliferating in copepod connective tissue as opposed to infecting gut contents, parasites, or symbionts. Taken together, these results provide strong independent lines of evidence for active viral infection in dominant copepod species, indicating that viruses may significantly influence mesozooplankton ecology.
Worldwide, most sea cucumber fisheries are ineffectively managed, leading to declining stocks and potentially eroding the resilience of fisheries. We analyse trends in catches, fishery status, fishing participation and regulatory measures among 77 sea cucumber fisheries through data from recent fishery reports and fishery managers. Critical gaps in fisheries biology knowledge of even commonly targeted species undermine the expected success of management strategies. Most tropical fisheries are small-scale, older and typified by numerous (>8) species, whereas temperate fisheries are often emerging, mono-specific and industrialized. Fisher participation data indicated about 3 million sea cucumber fishers worldwide. Fisher participation rates were significantly related to the average annual yield. permanova analysis showed that over-exploited and depleted fisheries employed different sets of measures than fisheries with healthier stocks, and a non-metric multidimensional scaling ordination illustrated that a broad set of regulatory measures typified sustainable fisheries. SIMPER and regression tree analyses identified that the dissimilarity was most related to enforcement capacity, number of species harvested, fleet (vessel) controls, limited entry controls and rotational closures. The national Human Development Index was significantly lower in countries with over-exploited and depleted fisheries. Where possible, managers should limit the number of fishers and vessel size and establish short lists of permissible commercial species in multispecies fisheries. Our findings emphasize an imperative to support the enforcement capacity in low-income countries, in which risk of biodiversity loss is exceptionally high. Solutions for greater resilience of sea cucumber stocks must be embedded within those for poverty reduction and alternative livelihood options.
The close coupling between producers and consumers of inorganic nutrients is generally assumed to be important to maintaining high productivity on coral reefs. I examined whether a tight cycling of nutrients exists between benthic microalgae and sediment-feeding holothurians (Stichopus chloronotus and Holothuria atra). Benthic microalgae had an increased production (measured as O-2 evolution) after exposure for more than 3 h to effluent water from tanks containing holothurians. Direct addition of phosphate and ammonium suggested that this increase was mainly caused by the excretion of ammonium. In experiments in which a part of the sediment area was inaccessible to the holothurians, microalgae production significantly increased in aquaria containing holothurians, irrespective of whether microalgae were grazed or protected from grazing. Thus, it could be inferred that production enhancement is solely a nutrient effect and not due to other effects described for other grazers (e.g. removal of senescent cells or reduction of self-shading). The effects on the microalgal biomass (measured as chlorophyll a and phaeophytin) depended on the actual grazing intensity. When a high grazing pressure was simulated (e.g. 2 H. atra on 0.116 m(2)), microalgal biomass was reduced significantly after 7 d compared to control aquaria. At lower grazing intensities (e.g. 1 S. chloronotus on 0.232 m(2)), the microalgal biomass increased significantly. A significant negative correlation was found between the amount of sediment consumed in each single aquarium (measured as the weight of the faeces produced) and the increase in chlorophyll a and phaeophytin concentrations in the sediment. A comparison with in situ sediment-consumption rates suggested that holothurians in natural densities have an overall beneficial effect on the benthic microalgal community. I propose that holothurians and other sediment-feeders are important components of a benthic recycling system that may have some similarity to the planktonic microbial loop.
Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found in great number among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes highlights the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the microviruses. In addition, a peptidase gene was found in 10 Microviridae and its analysis indicates a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in Microviridae. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
Despite their small size and limited protein-coding capacity, the rapid evolution rates of single-stranded DNA (ssDNA) viruses have led to their emergence as serious plant and animal pathogens. Recently, metagenomics has revealed an unprecedented diversity of ssDNA viruses, expanding their known environmental distributions and host ranges. This review summarizes and contrasts the basic characteristics of known circular ssDNA viral groups, providing a resource for analyzing the wealth of ssDNA viral sequences identified through metagenomics. Since ssDNA viruses are largely identified based on conserved rolling circle replication proteins, this review highlights distinguishing motifs and catalytic residues important for replication. Genomes identified through metagenomics have demonstrated unique ssDNA viral genome architectures and revealed characteristics that blur the boundaries between previously well-defined groups. Metagenomic discovery of ssDNA viruses has created both a challenge to current taxonomic classification schemes and an opportunity to revisit hypotheses regarding the evolutionary history of these viruses.
The ecologically important sea urchin Diadema antillarum suffered mass mortalities in 1983, first noted in Panama and then reported from the rest of the Caribbean. We documented the effects of this mortality at two localities on the Atlantic coast of Panama, Punta Galeta and the San Blas Archipelago. At Punta Galeta, affected by the mortality in January 1983, the numbers of D. antillarum changed from an estimated 14,000 per ha in June 1982 to 0.5 per ha in May 1983; by February 1984 they had increased to 38 per ha. In the San Blas, where mass mortality started in April 1983, the number of D. antillarum in permanent quadrats on 8 reefs was reduced by an average of 94.2%. The average reduction in population density measured in transects on nine reefs was 98.9%. Data taken in permanent quadrats on four reefs in 1978, 1979 and 1980 indicate that population fluctuations of D. antillarum are normally much smaller, justifying the labeling of the 1983 event as mass mortality. Size structure of the San Blas populations was also affected; mean test diameter of D. antillarum on four reefs was reduced from 48.6 mm to 25.0 mm. Other echinoids (Echinometra viridis, E. lucunter, Lytechinus variegatus, L. williamsi, Eucidaris tribuloides, Tripneustes ventricosus, Clypeaster rosaceus and Echinoneus cyclostomus) suffered no ill effects at either Galeta or the San Blas; their population densities remained stable or increased. Density determinations of Diadema mexicanum at the island of Taboguilla on the Pacific side of Panama indicate that Diadema mass mortality did not extend to the eastern Pacific. Sea surface temperatures, tidal levels, rainfall and salinity showed no abnormal fluctuations during the time of D. antillarum mass mortality at Galeta, suggesting that mortality was not due to physical stress. The wide geographical spread and species-specificity of the mortality suggest a water-borne pathogen as the most likely causative agent. Recovery of D. antillarum populations is likely to be slow because there are few, if any, unaffected populations in the Caribbean to contribute larvae for the recolonization of depleted areas. The absence of D. antillarum will probably be reflected by changes in the algal, coral and echinoid communities, and by altered patterns of bioerosion.
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
Introduction:
Viruses are the most abundant and diverse life forms on the earth. Both DNA viruses and RNA viruses play important roles in marine ecosystems via regulating biogeochemical cycles.
Objectives:
However, the virome of marine RNA viruses has been rarely explored so far. In this study, therefore, the environmental viromes of deep-sea sediment RNA viruses were characterized on a global scale to reveal the global virosphere of deep-sea RNA viruses.
Methods:
The viral particles were purified from each of 133 deep-sea sediment samples and then characterized based on metagenomes of RNA viruses.
Results:
In this study, we established the global virome dataset of deep-sea RNA viruses purified from 133 sediment samples that were collected from typical deep-sea ecosystems of three oceans. A total of 85,059 viral operational taxonomic units (vOTUs) were identified, of which only 1.72% were hitherto known, indicating that the deep-sea sediment is a repository of novel RNA viruses. These vOTUs were classified into 20 viral families, including prokaryotic (7.09%) and eukaryotic (65.81%) RNA viruses. Furthermore, 1,463 deep-sea RNA viruses with complete genomes were obtained. The differentiation of RNA viral communities was driven by the deep-sea ecosystems as opposed to geographical region. Specifically, the virus-encoded metabolic genes took great effects on the differentiation of RNA viral communities by mediating the energy metabolism in the deep-sea ecosystems.
Conclusions:
Therefore, our findings indicate that the deep sea is a vast reservoir of novel RNA viruses for the first time, and the differentiation of RNA viral communities is driven by the deep-sea ecosystems through energy metabolism.
To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible central currency in reef production, nutrient cycling, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient recycling efficiency, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophic transfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe–DOM interactions, creating feedbacks that reduce reef resilience to global change.
Expected final online publication date for the Annual Review of Marine Science, Volume 15 is January 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Tropical sea cucumbers are in peril due to overharvest. Sixteen species are endangered or vulnerable (IUCN) with high-value teatfish recently listed on CITES Appendix II. In light of these listings, we review the Queensland Sea Cucumber Fishery, which harvests CITES-listed black teatfish (Holothuria whitmaei) and white teatfish (H. fuscogilva), and other IUCN-species, from the Great Barrier Reef (GBR), Australia. Teatfish harvest on the GBR has experienced serial catch reductions and fishery closure due to local depletion, a trend observed globally for sea cucumbers and of concern for the at-risk GBR World Heritage Area. We provide the first case study for teatfish while their trade continues, and highlight other species of concern. The major target species of the fishery, Actinopyga spinea (~ 50% of total catch), is not a traditional species in the global trade. With over one million individuals harvested annually, its fishery and its ecological consequences require attention. We synthesise knowledge on teatfish population parameters, identify knowledge gaps and suggest measures to reduce fishery impacts. Continued global exploitation of at-risk marine invertebrate species, coupled with scientific uncertainties, emphasise the urgent need for targeted research and to apply the precautionary principle to avoid detrimental outcomes in their conservation status.
Covert mortality nodavirus (CMNV), a unique aquatic pathogen first isolated from shrimp, has a broad host range that includes crustaceans and teleosts. The sea cucumber Apostichopus japonicus, an Echinoderm, was recently shown to be a host for CMNV. To investigate the histopathology of CMNV infection in sea cucumber, four out of 61 A. japonicus individuals that tested positive in reverse transcription nested PCR (RT-nPCR) assays were furtherly analyzed through in situ hybridization (ISH), histology, and transmission electron microscopy (TEM). Extensive bluish-purple positive hybridization signals of CMNV probe were found in tissues of the respiratory trees, intestine, and gonad in conjunction with a variety of pathological lesions, including vacuolation, karyopyknosis, and muscle necrosis. Also, masses of CMNV-like particles were observed through TEM in these tissues, as well as in the body wall and longitudinal muscle. Sea cucumber is important in Chinese aquaculture, and CMNV infection of gonad tissue indicates a potential for vertical transmission that could negatively impact larval rearing.
In 1983-1984, the sea urchin Diadema antillarum suffered mass mortality throughout the Caribbean, Florida, and Bermuda. The demise of this herbivore contributed to a phase shift of Caribbean reefs from coral-dominated to alga-dominated communities. A compilation of published data of D. antillarum population densities shows that there has been moderate recovery since 1983, with the highest rates on islands of the eastern Caribbean. On the average the current population densities are approximately 12% of those before the die-off, apparently because of recruitment limitation, but the exact factors that are constraining the recovery are unclear. Scattered D. antillarum cohorts in some localities and aggregation of settled individuals in shallow water have created zones of higher herbivory in which juvenile coral recruitment, survivorship, and growth are higher than they are in alga-dominated areas. Unlike other stressors on Caribbean coral reefs, recent changes in D. antillarumd populations progress toward aiding the recovery of coral cover. Expected final online publication date for the Annual Review of Marine Science Volume 8 is January 03, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
We used a metagenomic approach to identify viruses that may be involved in the ecology of Daphnia spp. in Oneida and Cayuga lakes (upstate New York). We identified several highly represented, putative eukaryotic, circular, single-stranded deoxyribonucleic acid (DNA) viral genomes. Among these, we discovered a genotype similar in both sequence and genomic architecture to a virus previously reported from a hyperthermal lake that shares characteristics of both single-stranded ribonucleic acid (RNA) and single-stranded DNA viruses. We used quantitative polymerase chain reactions to study the prevalence and viral load of both positive-sense and negative-sense strands of the Daphnia mendotae-associated (Cladocera) hybrid virus (DMClaHV) over a summer season in Oneida and Cayuga lakes. DMClaHV had high prevalence within Daphnia populations, where viral load and the proportion of virus-positive individuals were higher preceding host population decline. DMClaHV viral load was different between two species of Daphnia (D. mendotae and D. retrocurva), and the dynamics between viruses and their hosts varied between the two lakes. We detected DMClaHV in eggs (ephippia) retrieved from Oneida Lake sediments with an estimated age of 30 yr. Using transmission electron microscopy, we observed small (20 nm diameter) virus-like particles in Daphnia that were well away from gut tissues and not associated with intracellular parasites. Because Daphnia plays a critical role in many lake ecosystems, DMClaHV may have important effects on herbivory and thus carbon flow through the lake ecosystem.
Echinoderms are important constituents of marine ecosystems, where they may influence the recruitment success of benthic flora and fauna, and are important consumers of detritus and plant materials. There are currently no described viruses of echinoderms. We used a viral metagenomic approach to examine viral consortia within three urchins - Colobocentrotus atratus, Tripneustes gratilla, and Echinometra mathaei - which are common constituents of reef communities in the Hawaiian archipelago. Metagenomic libraries revealed the presence of bacteriophage and densoviruses (Parvoviridae) in tissues of all three urchins. Densoviruses are typically known to infect terrestrial and aquatic arthropods. Urchin-associated densoviruses were detected by qPCR in all tissues tested, and were also detected in filtered suspended matter (> 0.2µm) from plankton and in sediments at several locations near to where urchins were collected for metagenomic analysis. This is the first report of echinoderm-associated viruses, which extends the known host range of parvoviruses.
A outbreak of disease with symptoms of evisceration and skin ulteration led to mass mortality in sea cucumber Apostichopus japonicus cultivated in indoor ponds near the Dalian coast from December 2004 to April 2005. Spherical virus particles with a diameter
of 75–200 nm were found in the cytoplasm of cells in the water-system, the alimentary canal and in the respiratory trees of
the diseased and dying sea cucumber individuals by electron microscopic observation of ultrathin sections. Examination by
negative stained samples revealed that all the diseased sea cucumbers were infected by the virus, while the healthly ones
cultivated outside the contagious area were not. Two bacterial strains were also isolated from the diseased animals. When
exposed to a medium containing the virus particles, regardless of whether the bacterial suspension was added, healthy sea
cucumbers exhibited identical disease symptoms as the ones in the indoor ponds, and had a mortality of 90%–100%. However,
when exposed to a medium in which there was only one of the two bacterial strains, 30%–80% of the sea cucumbers were infected
and nearly 20% died. Negative staining showed that the viral particles were detected only in the bodies of the tested animals
that were exposed to the viral medium. Histopathologically, the diseased sea cucumbers are characterized by karyopycnosis,
and disintegration of the endoplasmic reticula and mitochondria in the epithelial cells in the water-system, the respiratory
tree and the alimentary canal.
Overfishing due to high demand in Asian markets, have encouraged illegal fisheries of sea cucumbers in non-traditional areas of the tropical Caribbean. This work assesses the population structure, distribution, and abundance of three commercially important Caribbean species (Isostichopus badionotus, Holothuria mexicana, and Astichopus multifidus) in 47 158 hectares of shallow habitats in Bocas del Toro (Panama), from May to October 2000. Mean size class distribution was unimodal; 26.5 cm in I. badionotus and 16 cm in H. mexicana, and dominated by adult individuals of 25-30 cm for both species. Body wall wet weight (gutted) showed a similar distribution, with a higher number of individuals between 200-300 g, but with a lower mean in I. badionotus (214 g) than in H. mexicana (258g). A total of 6017 individuals of H. mexicana, 4431 I. badionotus and 208 A. multifidus were quantified, with mean densities of 161.8 ind./ha, 117.4 ind./ha., and 4.9 ind./ha, respectively. Based on these results and the total area of the archipelago, we estimated a stock of 7 630 164 individuals for H. mexicana, 5 536 349 for I. badionotus, and 231 074 for A. multifidus. This assessment is discouraging because during the 1997 30-day legal fishing period, a catch of ca. 750 000 holothuroids was estimated for the archipelago.
The holothurians Isostichopus badionotus, Holothuria mexicana, H. thomasi, Actinopyga agassizi and Euapta lappa, and the clypeastroid echinoid Clypeaster rosaceus had distinctly nocturnal patterns of activity and feeding. The spatangoid echinoid Meoma ventricosa was more active at night than by day. Except in E. lappa, which was strictly nocturnal, activity increased during the afternoon, peaked before midnight, then declined to a minimum before midday. All species exhibited some form of diurnal concealment except I. badionotus and H. mexicana, which remained fully exposed at all times. These and other data suggest nocturnal activity, which may have evolved as a predation avoidance mechanism, as the paradigm of ancestral holothurian behavior. The two spatangoid species and H. arenicola were major agents of bioturbation where they occurred at maximum densities. In the short-term (<1 day), movements of I. badionotus, H. mexicana, M. ventricosa and P. grandis were random. Over a 10-day period, I. badionotus and H. mexicana moved less than predicted by the random walk theorem, attributed to boundary effects in an heterogeneous environment; this may explain how the patchy dispersion of each species is maintained. Density of the cryptic H. thomasi in a patch of coral heads may have been limited by the number of available, suitable crevices. The stability of burrows of H. arenicola over long periods of time can be related to their association with buried rubble, which provides a physical refuge from disturbance by bioturbation.-from Author