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Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self‐sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery‐farmed) or naturalized/wild oysters to move onto a farm (naturalized‐farmed). It is therefore important to understand genetic variation among populations and farm types. Here, we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double‐digest RAD‐sequencing in 182 naturalized, 112 hatchery‐farmed, and 72 naturalized‐farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean FST = 0.0019) and low differentiation between countries in the Japan–Canada–France historical translocation lineage (France–Canada FST = 0.0024; Japan–Canada FST = 0.0060). Chinese populations were more differentiated (China–Japan FST = 0.0241). Hatchery‐propagated populations had higher interindividual relatedness suggesting family structure. Within‐population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate were lower in one farm population. Moving oysters from nature onto farms did not result in strong within‐generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting nonlocal origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery‐farmed oysters depend on whether naturalized populations are valued as a locally adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question. [ABSTRACT FROM AUTHOR]

Summary: Prasinophytes are widespread marine algae for which responses to nutrient limitation and viral infection are not well understood. We studied the picoprasinophyte, Micromonas pusilla, grown under phosphate‐replete (0.65 ± 0.07 d−1) and 10‐fold lower (low)‐phosphate (0.11 ± 0.04 d−1) conditions, and infected by the phycodnavirus MpV‐SP1. Expression of 17% of Micromonas genes in uninfected cells differed by >1.5‐fold (q < 0.01) between nutrient conditions, with genes for P‐metabolism and the uniquely‐enriched Sel1‐like repeat (SLR) family having higher relative transcript abundances, while phospholipid‐synthesis genes were lower in low‐P than P‐replete. Approximately 70% (P‐replete) and 30% (low‐P) of cells were lysed 24 h post‐infection, and expression of ≤5.8% of host genes changed relative to uninfected treatments. Host genes for CAZymes and glycolysis were activated by infection, supporting importance in viral production, which was significantly lower in slower growing (low‐P) hosts. All MpV‐SP1 genes were expressed, and our analyses suggest responses to differing host‐phosphate backgrounds involve few viral genes, while the temporal program of infection involves many more, and is largely independent of host‐phosphate background. Our study (i) identifies genes previously unassociated with nutrient acclimation or viral infection, (ii) provides insights into the temporal program of prasinovirus gene expression by hosts and (iii) establishes cell biological aspects of an ecologically important host‐prasinovirus system that differ from other marine algal‐virus systems. [ABSTRACT FROM AUTHOR]

The article discusses the policy issues surrounding the conservation and sustainable use of marine genetic resources. Topics covered include ocean diversity, the rules on the right of a developing country to share in the benefits gained from the commercial application of marine organisms under the Convention on Biological Diversity and its Nagoya Protocol, and the important role of scientists and scientific research in the realization of these benefits.

Reef-building corals form close associations with organisms from all three domains of life and therefore have many potential viral hosts. Yet knowledge of viral communities associated with corals is barely explored. This complexity presents a number of challenges in terms of the metagenomic assessments of coral viral communities and requires specialized methods for purification and amplification of viral nucleic acids, as well as virome annotation. In this minireview, we conduct a meta-analysis of the limited number of existing coral virome studies, as well as available coral transcriptome and metagenome data, to identify trends and potential complications inherent in different methods. The analysis shows that the method used for viral nucleic acid isolation drastically affects the observed viral assemblage and interpretation of the results. Further, the small number of viral reference genomes available, coupled with short sequence read lengths might cause errors in virus identification. Despite these limitations and potential biases, the data show that viral communities associated with corals are diverse, with double- and single-stranded DNA and RNA viruses. The identified viruses are dominated by double-stranded DNA-tailed bacteriophages, but there are also viruses that infect eukaryote hosts, likely the endosymbiotic dinoflagellates, Symbiodinium spp., host coral and other eukaryotes in close association. [ABSTRACT FROM AUTHOR]

Experiments were conducted to investigate spatiotemporal patterns in lytic and lysogenic viral infection using water samples collected on the Canadian Arctic Shelf, southern Beaufort Sea. Viral production (VP) and viral-induced mortality of bacteria (VMB) were determined using a viral reduction approach during a full seasonal cycle, while the percentage of lysogenic bacteria (PLB) in spring and summer was determined in virus-reduced samples by induction with mitomycin C. Overall, VP (range: 0.3 x 108-77 x 108 viruses L-1 d-1), VMB (range: 0.2 x 107-43 x 107 bacteria L-1 d-1), and PLB (range: 4-38%) displayed marked spatiotemporal variations concomitant with changes in chlorophyll a, bacterial abundance, and production. Highest VP and VMB occurred in summer when the water was warmest, stratified, and most productive, and when viruses removed up to 29% of bacterial standing stock d-1 and released up to 4.3 µg of organic carbon L-1 d-1. In contrast, the highest PLB occurred in spring when the water was colder, well mixed, and oligotrophic. Correlative and regression analyses indicated viral lytic and lysogenic variables were significantly coupled with chlorophyll a and the abundance, production, and growth rate of bacteria, implying that viral lytic and lysogenic lifestyles were dependent on system productivity. Furthermore, lytic VP and the proportion of lysogenized bacteria were inversely related, suggesting a dynamic interplay between viral infection pathways. Lytic infection was more pronounced when system productivity was high, while lysogeny prevailed when system productivity was low. These data demonstrate the important role of viruses in bacterial mortality and carbon cycling in the Arctic Ocean, and show how their effect is influenced by trophic status. [ABSTRACT FROM AUTHOR]

1. Samples from 16 lakes in central ( n = 145) and western ( n = 12) North America, the coastal northeast Pacific ( n = 302) and the western Canadian Arctic Oceans ( n = 142) were collected and analysed for viral, bacterial and cyanobacterial abundances and chlorophyll- a concentration. 2. Viral abundance was significantly different among the environments. It was highest in the coastal Pacific Ocean and lowest in the coastal Arctic Ocean. The abundances of bacteria and cyanobacteria as well as chlorophyll- a concentrations also differed significantly among the environments, with both bacterial abundance and chlorophyll- a concentration highest in lakes. As a consequence, the association of these variables with viral abundance varied among the environments. 3. Discriminant analyses with the abundance data indicated that the marine and freshwater environments were predictably different from each other. Multiple-regression analysis included bacterial and cyanobacterial abundances, and chlorophyll- a concentration as significant variables in explaining viral abundance in lakes. In regression models for the coastal Pacific Ocean, bacterial and cyanobacterial abundances were significant variables, and for the coastal Arctic Ocean viral abundance was predicted by bacterial abundance and chlorophyll- a concentration. 4. The relationship of viral and bacterial abundance differed between the investigated freshwater and marine environments, probably because of differences in viral production and loss rates. However, freshwaters had fewer viruses compared to bacteria, despite previously documented higher burst sizes and frequencies of infected cells, suggesting that loss rates may be more important in lakes. 5. Together, these findings suggest that there are different drivers of viral abundance in different aquatic environments, including lakes and oceans. [ABSTRACT FROM AUTHOR]

This study examined the distribution, susceptibility to viral infection and genetic diversity of Vibrio spp. in the coastal waters and sediments of British Columbia during summer (July and August). Abundances of presumptive Vibrio spp. ranged from 1.5 to 346 ml−1 within the water column (1–291 m); whereas, abundances at the water–sediment interface were much higher (up to ∼3 × 104 Vibrio spp. cc−1), and decreased with sediment depth (down to 30 cm). The genetic diversity of Vibrio spp. isolates was not tied to the location from which they originated and was only influenced in a minor way by the type of environment. However, the environment had a greater effect on phage-typing patterns. Vibrio parahaemolyticus isolates from environments with high abundances of cells (sediments and oysters) were generally more susceptible to viral infection than those from the water column which were highly resistant. Therefore, although Vibrio spp. were widespread in the areas investigated, the results show that there is segregation of bacterial host strains in different environments, under differing selection pressures, which ultimately will affect in situ phage production. [ABSTRACT FROM AUTHOR]

The purpose of this study was to characterize Vibrio parahaemolyticus viruses (VpVs) isolated from different environments within and adjacent to the Strait of Georgia, and to examine the relative influences of distance and environment on host-range and genetic richness. Nearly all seawater enrichment cultures (29/31) generated isolates, implying that VpVs were widespread in the virioplankton, yet at low abundances (< 1 l−1). Viruses were not detected in sediments ( n = 99). Fourteen of the 16 viruses characterized were siphoviruses, with genome sizes ranging from ∼45–106 kb, and half were capable of infecting other Vibrio species. The VpVs infected bacteria isolated from oysters and sediments fairly well (55% and 46% of the host-virus combinations, respectively), but were unable to infect many of the bacteria isolated from the water column (< 13% of 112 combinations). When compared with VpVs from oysters, it was clear that the major determinant of phenotypic (host-range) and genetic richness (by the DP-RAPD assay) was not geography, but the source environment from which the VpVs originated. Therefore, the VpV population within the Strait of Georgia is a highly diverse mixture of phenotypes and genotypes. [ABSTRACT FROM AUTHOR]

HaRNAV, a novel virus that infects the toxic bloom-forming alga Heterosigma akashiwo (Hada) Hada ex Hada et Chihara, was characterized based on morphology, pathology, nucleic acid type, structural proteins, and the range of host strains that it infects. HaRNAV is a 25-nm single-stranded RNA (ssRNA) virus with a genome size of approximately 9100 nucleotides. This is the first report of an ssRNA virus that causes lysis of a phytoplankton species. The virus particle is sensitive to chloroform and contains at least five structural proteins ranging in apparent size from 24 to 34 kDa. HaRNAV infection causes swelling of the endoplasmic reticulum and progeny virus particles assemble in the cytoplasm of the host, frequently in crystalline arrays. The infectivity of HaRNAV was tested against 15 strains of H. akashiwo isolated from Japanese waters, the Northeast Pacific, and the Northwest Atlantic. HaRNAV caused lysis of three strains from the Northeast Pacific and two strains from Japan but none from the Northwest Atlantic. The characterization of HaRNAV demonstrates that HaRNAV is a novel type of phytoplankton virus but has some similarities with plant viruses belonging to the Sequiviridae and to other known ssRNA viruses. Further genomic analysis, however, is necessary to determine any phylogenetic relationships. The discovery of HaRNAV emphasizes the diversity of H. akashiwo viral pathogens and, more importantly, algal–virus pathogens and the complexity of virus–host interactions in the environment. [ABSTRACT FROM AUTHOR]

We describe a previously unknown virus that causes lysis of the toxic bloom-forming alga Heterosigma akashiwo (Hada) Hara et Chihara (Raphidophyceae). Heterosigma akashiwo nuclear inclusion virus (HaNIV) does not resemble other algal viruses described to date. HaNIV is small (ca. 30 nm diameter), is assembled in the nucleus, and forms crystalline arrays. We estimate that approximately 105 HaNIV particles are released during lysis of a cell. During a time-course experiment, TEM revealed the first signs of HaNIV infection 24 h after viral addition, and by 74 h 98% of observed cells were visibly infected. The onset of cell lysis, as indicated by a decrease in the relative fluorescence of the cultures, was apparent by 42 h postinfection. The heterochromatin of infected cells is frequently found at the margin of the nucleoplasm, which is consistent with virus-mediated programmed cell death, or apoptosis. HaNIV is clearly different from other described viruses that infect algae, including other viral pathogens of H. akashiwo. These results indicate that viruses other than Phycodnaviridae are pathogens and cause mortality of microalgae in marine systems. It is likely that HaNIV plays an integral role in the population dynamics of H. akashiwo. [ABSTRACT FROM AUTHOR]

A planktonic alga similar in general morphology and pigments to Aureococcus anophagefferens Hargraves and Sieburth has caused persistent and ecologically damaging blooms along the south Texas coast. Experiments using 100 μM NO[SUB3][SUP-], NO[SUB2][SUP-], and NH[SUB4][SUP+] demonstrated that the alga could not use NO[SUB3][SUP-] for growth but could use NO[SUB2][SUP-] and NH[SUB4][SUP+]. Doubling iron or trace metal concentrations did not permit growth on NO[SUB3][SUP-]. Chemical composition data for cultures grown in excess NO[SUB3][SUP-] or NH[SUB4][SUP+], respectively, were as follows: N·cell[SUP-1](0.88 vs. 1.3 pg), C:N ratio (25:1 vs. 6.4:1), C:chlorophyll a (chl a) (560:1 vs. 44:1), and chl a·cell[SUP-1] (0.033 vs. 0.16 pg). These data imply that cells supplied with NO[SUB3][SUP-] were N-starved. Culture addition of 10 mM final concentration chlorate (a nitrate analog) did not affect the Texas isolate while NO[SUB3][SUP-]- utilizing A. anophagefferens was lysed, suggesting that the NO[SUB3][SUP-] reductase of the Texas isolate is nonfunctional. Rates of primary productivity determined during a dense bloom indicated that light-saturated growth rates were ca. 0.45 d[SUP-1], which is similar to maximum rates determined in laboratory experiments (0.58 d[SUP-1] ± 0.16). However, chemical composition data were consistent with the growth rate of these cells being limited by N availability (C:N 28, C:chl a 176, chl a·cell[SUP-1] 0.019). Calculations based on a mass balance for nitrogen suggest that the bloom was triggered by an input of ca. 69 μM NH[SUB4][SUP+] that resulted from an extensive die-off of benthos and fish. [ABSTRACT FROM AUTHOR]

A natural assemblage of freshwater phytoplankton was removed from an oligotrophic lake and grown at N:P supply ratios of 5:1, 15:1 and 45:1 (by atoms) in semi-continuous cultural. After a minimum of 31 days at an average daily growth rate 0.5 d[SUP-1], experiments were conducted examining the time-course of saturated ammonium uptake rates. Cultures grown under the two lowest N:P supply ratios demonstrated greatly elevated initial, specific uptake rates for ammonium and were able to sequester between 7 and 21% of their daily N requirement in less than 5 min. The initial rates declined rapidly but were followed by a subsequent increase and decrease over a 120 min period. [ABSTRACT FROM AUTHOR]

Concentrated stock solutions of sodium metasilicate (Na[sub2]SiO[sub3]·9H[sub2]O). prepared in distilled-distilled water and acidified to pH 2 as suggested by McLachlan (1973), were found to be polymerized; stocks kept at their alkaline pH of dissolution were not polymerized. Depolymerization studies using the acidified stock added to deionized-dis. tilled water, 3% NaCl or artificial saltwater medium showed that complete depolymerization took longer than 2 days. Studies of Si uptake, using the marine diatom Tha-lassiosira pseudonana (Hust.) Hasle and Heimdal. showed that use of an acidified Si stock for experiments can lead to anomolous results. It is recommended that concentrated Si stocks be stored at their pH of dissolution and not be acidified prior to addition to media. In instances where the pH must be adjusted prior to addition (e.g. in some Si-uptake experiments), it may be necessary to take into account polymerization/depolymeriztion effects. [ABSTRACT FROM AUTHOR]

The Texas brown tide alga (strain TBA-2) is described as Aureoumbra lagunensis Stockwell, DeYoe, Hargraves, et Johnson, gen. Et sp. Nov. Pigment composition, chloroplast structure, and I8S ribosomal RNA gene sequence data indicate that A. lagunensis and the east coast brown tide alga Aureococcus anophagefferens (originally placed in the Chrysophyceae) belong in the class Pelogophyceae. The new genus Aureoumbra with A. lagunensis as the type species differs from Aureococcus in 18S ribosomal RNA gene sequence, pyrenoid form, nitrogen, physiology, and possession of basal bodies. The genus Aureococcus is placed in the order pelagomonadales and family Pelagomonadaceae while ordinal placement of Aureoumbra is deferred. [ABSTRACT FROM AUTHOR]

Bacteria-free culture of the prasinophyte Micromonas pusilla (Butcher) Manton and Parke, UTEX LB 991, were produced by initially determining the effects of several antibiotics on the growth of this alga and then using a combination of these antibiotics to eliminate associated bacteria. Micromonas pusilla was resistant to penicillin G, neomycin, gentamicin, and streptomycin at bactericidal concentrations but sensitive to chloramphenicol and polymixin B, Passage of M. pusilla through the sequence of antibiotics penicillin G → neomycin → gentamicin → kanamycin resulted in an suitable for producing axenic cultures of other strains of M. pusilla. [ABSTRACT FROM AUTHOR]

Comments on the incorporation of viruses into the global ecosystem and its processes. Relationship between viruses and other organisms; Turnover of viral particles; Impact of viral-mediated cell lysis on nutrient release and recycling; Need to document the genetic richness in natural virus communities.

HaRNAV, a novel virus that infects the toxic bloom-forming alga Heterosigma akashiwo (Hada) Hada ex Hada et Chihara, was characterized based on morphology, pathology, nucleic acid type, structural proteins, and the range of host strains that it infects. HaRNAV is a 25-nm single-stranded RNA (ssRNA) virus with a genome size of approximately 9100 nucleotides. This is the first report of an ssRNA virus that causes lysis of a phytoplankton species. The virus particle is sensitive to chloroform and contains at least five structural proteins ranging in apparent size from 24 to 34 kDa. HaRNAV infection causes swelling of the endoplasmic reticulum and progeny virus particles assemble in the cytoplasm of the host, frequently in crystalline arrays. The infectivity of HaRNAV was tested against 15 strains of H. akashiwo isolated from Japanese waters, the Northeast Pacific, and the Northwest Atlantic. HaRNAV caused lysis of three strains from the Northeast Pacific and two strains from Japan but none from the Northwest Atlantic. The characterization of HaRNAV demonstrates that HaRNAV is a novel type of phytoplankton virus but has some similarities with plant viruses belonging to the Sequiviridae and to other known ssRNA viruses. Further genomic analysis, however, is necessary to determine any phylogenetic relationships. The discovery of HaRNAV emphasizes the diversity of H. akashiwo viral pathogens and, more importantly, algal–virus pathogens and the complexity of virus–host interactions in the environment. [ABSTRACT FROM AUTHOR]