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Macroecological relationships provide insights into rules that govern ecological systems. Bergmann's rule posits that members of the same clade are larger at colder temperatures. Whether temperature drives this relationship is debated because several other potential drivers covary with temperature. We conducted a near-global comparative analysis on marine copepods (97 830 samples, 388 taxa) to test Bergmann's rule, considering other potential drivers. Supporting Bergmann's rule, we found temperature better predicted size than did latitude or oxygen, with body size decreasing by 43.9% across the temperature range (-1.7 to 30ºC). Body size also decreased by 26.9% across the range in food availability. Our results provide strong support for Bergman's rule in copepods, but emphasises the importance of other drivers in modifying this pattern. As the world warms, smaller copepod species are likely to emerge as ‘winners', potentially reducing rates of fisheries production and carbon sequestration.

Kaute and its derivatives koute, ʻoute and ʻaute are Polynesian names for a red-flowered Hibiscus. Since its first botanical collection on Tahiti by Banks and Solander (1769), this hibiscus has been referred to as H. rosa-sinensis L. and assumed to have been introduced by the bearers of the archaeological culture known as Lapita. Lapita people settled West Polynesia around 2800 BP and spoke a language derived from Proto-Oceanic, the common ancestor of almost all the Austronesian languages of Island Melanesia and Micronesia as well as Polynesia. However, whereas Proto-Oceanic names can be reconstructed for many plants found in East Polynesia, the term kaute cannot be attributed to Proto-Oceanic, the name likely being locally derived in East Polynesia from that of paper mulberry (Broussonetia papyrifera (L.) L’Hér. ex Vent.). On the basis of linguistic evidence, we contend that kaute was domesticated in a high island area of Central Eastern Polynesia and then dispersed in relatively recent pre-European times (ca. 500–700 BP) westwards through West Polynesia, to nearby islands such as the Fiji archipelago and Rotuma and to Polynesian Outliers in Papua New Guinea and the Solomon Islands. Dissemination occurred before the -au- sequence changed to -ou- and k sporadically changed to ʻ, so that kaute rather than contemporary Marquesan koute and ʻoute was the term that was carried westward from the Marquesas. Kaute is here suggested to be an endemic East Polynesian species, different from H. rosa-sinensis L. Further field and genetic research is needed to definitively determine the phylogenetic relationships of kaute and a taxonomic description is required for formal recognition.

Viruses are recognised as the most abundant biological entities on the planet. In addition to their role in disease, they are crucial components of co-evolutionary processes, are instrumental in gl...

Rapid virus proliferation can exert a powerful control on phytoplankton host populations, playing a significant role in marine biogeochemistry and ecology. We explore how marine lytic viruses impact phytoplankton succession, affecting host and nonhost populations.\ud Using an in silico food web we conducted simulation experiments under a range of different abiotic and biotic conditions, exploring virus–host–grazer interactions and manipulating competition, allometry, motility and cyst cycles.\ud Virus-host and predator–prey interactions, and interactions with competitors, generate bloom dynamics with a pronounced ‘boom-and-busted’ dynamic (BBeD) which leads to the suppression of otherwise potentially successful phytoplankton species. The BBeD is less pronounced at low nutrient loading through distancing of phytoplankton hosts, while high sediment loading and high nonhost biomass decrease the abundance of viruses through adsorption. Larger hosts are inherently more distanced, but motility increases virus attack, while cyst cycles promote spatial and temporal distancing.\ud Virus control of phytoplankton bloom development appears more important than virus-induced termination of those blooms. This affects plankton succession – not only the growth of species infected by the virus, but also those that compete for the same resources and are collectively subjected to common grazer control. The role of viruses in structuring plankton communities via BBeDs can thus provide an explanation for the paradox of the plankton.

Megaphages, bacteriophages harbouring extremely large genomes, have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of megaphages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other megaphages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including a NADP-dependent isocitrate dehydrogenase [Idh] and nicotinamide-nucleotide amidohydrolase [PncC], which have not previously been identified in megaphages. Mar_Mega_1 was abundant in a marine virome sample and related phages are widely prevalent in the oceans.

Megaphages – bacteriophages harbouring extremely large genomes – have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of bacteriophages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other mega-phages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including isocitrate dehydrogenase [NADP] and nicotinamide-nucleotide amidohydrolase [PncC] which have not previously been identified in megaphages. The results of this study indicate that phages containing extremely large genomes can be found in abundance in the marine environment and augment host metabolism by mechanisms not previously described.

The significance of large tropical lakes as environmental reservoirs of Vibrio cholerae in cholera endemic countries has yet to be established. By combining large scale plankton sampling, microbial culture and ultrasensitive molecular methods, namely Droplet Digital PCR (ddPCR) and targeted genomics, the presence of Vibrio cholerae was investigated in a 96,600 L volume of surface water collected on a 322 nautical mile (596 km) transect in Lake Tanganyika. V. cholerae was detected and identified in a large area of the lake. In contrast, toxigenic strains of V. cholerae O1 or O139 were not detected in plankton samples possibly in relation to environmental conditions of the lake ecosystem, namely very low salinity compared to marine brackish and coastal environments. This represents to our knowledge, the largest environmental study to determine the role of tropical lakes as a reservoir of V. cholerae.

Autosomal-dominant, missense mutations in the leucine-rich repeat protein kinase 2 (LRRK2) gene are the most common genetic predisposition to develop Parkinson's disease (PD). LRRK2 kinase activity is increased in several pathogenic mutations (N1437H, R1441C/G/H, Y1699C, G2019S), implicating hyperphosphorylation of a substrate in the pathogenesis of the disease. Identification of the downstream targets of LRRK2 is a crucial endeavor in the field to understand LRRK2 pathway dysfunction in the disease. We have identified the signaling adapter protein p62/SQSTM1 as a novel endogenous interacting partner and a substrate of LRRK2. Using mass spectrometry and phospho-specific antibodies, we found that LRRK2 phosphorylates p62 on Thr138 in vitro and in cells. We found that the pathogenic LRRK2 PD-associated mutations (N1437H, R1441C/G/H, Y1699C, G2019S) increase phosphorylation of p62 similar to previously reported substrate Rab proteins. Notably, we found that the pathogenic I2020T mutation and the risk factor mutation G2385R displayed decreased phosphorylation of p62. p62 phosphorylation by LRRK2 is blocked by treatment with selective LRRK2 inhibitors in cells. We also found that the amino-terminus of LRRK2 is crucial for optimal phosphorylation of Rab7L1 and p62 in cells. LRRK2 phosphorylation of Thr138 is dependent on a p62 functional ubiquitin-binding domain at its carboxy-terminus. Co-expression of p62 with LRRK2 G2019S increases the neurotoxicity of this mutation in a manner dependent on Thr138. p62 is an additional novel substrate of LRRK2 that regulates its toxic biology, reveals novel signaling nodes and can be used as a pharmacodynamic marker for LRRK2 kinase activity.

Summary Coral reefs are in decline worldwide. Much of this decline is attributable to mass coral bleaching events and disease outbreaks, both of which are linked to anthropogenic climate change. Despite increased research effort, much remains unknown about these phenomena, especially the causative agents of many coral diseases. In particular, coral-associated viruses have received little attention, and their potential roles in coral diseases are largely unknown. Previous microscopy studies have produced evidence of viral infections in Symbiodinium, the endosymbiotic algae critical for coral survival, and more recently molecular evidence of Symbiodinium-infecting viruses has emerged from metagenomic studies of corals. Here, we took an exploratory whole-transcriptome approach to virus gene discovery in three different Symbiodinium cultures. An array of virus-like genes was found in each of the transcriptomes, with the majority apparently belonging to the nucleocytoplasmic large DNA viruses. Upregulation of virus-like gene expression following stress experiments indicated that Symbiodinium cells may host latent or persistent viral infections that are induced via stress. This was supported by analysis of host gene expression, which showed changes consistent with viral infection after exposure to stress. If these results can be replicated in Symbiodinium cells in hospite, they could help to explain the breakdown of the coral-Symbiodinium symbiosis, and possibly some of the numerous coral diseases that have yet to be assigned a causative agent.

As guest editors of this sustainability issue of Biopreservation and Biobanking focused on business planning, utilization, and marketing, we invited a number of experts from different sectors of the biobanking arena to provide their views on business planning issues. Each expert was asked to provide a brief background statement on their biobanks, to build a context to understand their answers to the sustainability questions. We hope that these insights and experiences can provide valuable considerations and ideas for other biobanks who wish to develop or refine their own business plans, measure their utilization rates, and work toward financial sustainability. In addition, after the expert input was gathered, the guest editors invited an additional expert to provide summary comments and observations on cost and operational optimization strategies. The broad experiences from all of the experts included and scope of the biobanks they represent should provide a level of relevant representation for all interested parties.

Coral-associated viruses are a component of the coral holobiont that have received attention only relatively recently. Given the global increase in the prevalence of coral disease, and the lack of positively identified etiological agents for many diseases, these virus consortia require increased investigation. Little is known about the viruses that are naturally associated with coral reefs and how they are affected by the local environment. In the present study, a short-term analysis of viral consortia associated with the coral Montipora capitata in Kaneohe Bay, Hawaii, USA, was carried out to determine the environmental factors influencing their composition. Coral surface microlayer (CSM) and seawater samples collected at 4 sites with a range of environmental characteristics were analyzed using transmission electron microscopy (TEM), and relative abundances of virus-like particle (VLP) morphotypes were correlated with environmental measurements. Relative proportions of several CSM-associated VLP types, including phages and filamentous VLPs, were correlated with water temperature, turbidity and chlorophyll a levels. In seawater samples, turbidity and temperature showed the strongest correlation, altering the proportion of Podoviridae-like, Geminiviridae-like and putative Archaeal viruses, among others. Overall VLP consortium composition differed significantly between the CSM and seawater only at the more degraded sites, suggesting that human activity may be affecting coral reef-associated virus consortia.

Radioargon isotopes, particularly (37)Ar, are currently being considered for use as an On-Site Inspection (OSI) relevant radionuclide within the context of the Comprehensive Nuclear-Test-Ban Treaty (CTBT). In order to understand any soil air measurements taken during an OSI, the radioargon background due to cosmic ray induced activation along with other sources must be understood. An MCNP6 model was developed using the cosmic ray source feature within the code to examine the neutron flux at ground level as a function of various conditions: date during the solar magnetic activity cycle, latitude of sampling location, geology of the sampling location, and sampling depth. Once the cosmic neutron flux was obtained, calculations were performed to determine the rate of radioargon production for the main interactions. Radioargon production was shown to be highly dependent on the soil composition, and a range of (37)Ar production values at 1 m depth was found with a maximum production rate of 4.012 atoms/sec/m(3) in carbonate geologies and a minimum production rate of 0.070 atoms/sec/m(3) in low calcium granite. The sampling location latitude was also shown to have a measurable effect on the radioargon production rate, where the production of (37)Ar in an average continental crust is shown to vary by a factor of two between the equator and the poles. The sampling date's position within the solar magnetic activity cycle was also shown to cause a smaller change, less than a factor of 1.2, in activation between solar maxima and solar minima.

The original publication of this Article included analysis of virus and microbial cell abundances and virus-to-microbial cell ratios. Data in the Article came from 25 studies intended to be exclusively from marine sites. However, 3 of the studies included in the original unified dataset were erroneously classified as marine sites during compilation. The records with mis-recorded longitude and latitude values were, in fact, taken from inland, freshwater sources. The three inland, freshwater datasets are ELA, TROUT and SWAT. The data from these three studies represent 163 of the 5,671 records in the original publication. In the updated version of the Article, all analyses have been recalculated using the same statistical analysis pipeline released via GitHub as part of the original publication. Removal of the three studies reduces the unified dataset to 5,508 records. Analyses involving all grouped datasets have been updated with changes noted in each figure. All key results remain qualitatively unchanged. All data and scripts used in this correction have been made available as a new, updated GitHub release to reflect the updated dataset and figures.

Viruses are major pathogens in all biological systems. Virus propagation and downstream analysis remains a challenge, particularly in the ocean where the majority of their microbial hosts remain recalcitrant to current culturing techniques. We used a cultivation-independent approach to isolate and sequence individual viruses. The protocol uses high-speed fluorescence-activated virus sorting flow cytometry, multiple displacement amplification (MDA), and downstream genomic sequencing. We focused on ‘giant viruses’ that are readily distinguishable by flow cytometry. From a single-milliliter sample of seawater collected from off the dock at Boothbay Harbor, ME, USA, we sorted almost 700 single virus particles, and subsequently focused on a detailed genome analysis of 12. A wide diversity of viruses was identified that included Iridoviridae, extended Mimiviridae and even a taxonomically novel (unresolved) giant virus. We discovered a viral metacaspase homolog in one of our sorted virus particles and discussed its implications in rewiring host metabolism to enhance infection. In addition, we demonstrated that viral metacaspases are widespread in the ocean. We also discovered a virus that contains both a reverse transcriptase and a transposase; although highly speculative, we suggest such a genetic complement would potentially allow this virus to exploit a latency propagation mechanism. Application of single virus genomics provides a powerful opportunity to circumvent cultivation of viruses, moving directly to genomic investigation of naturally occurring viruses, with the assurance that the sequence data is virus-specific, non-chimeric and contains no cellular contamination.

An eight year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically-sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton. However, variations in the composition of the phytoplankton community and particularly the prominence of Diatoms inferred from silicate drawdown, drive inter-annual differences in the magnitude of the virioplankton bloom; likely again mediated through changes in the bacterioplankton. Our findings suggest that future warming within the WAP will cause changes in sea ice that will influence viruses and their microbial hosts through changes in the timing, magnitude and composition of the phytoplankton bloom. Thus the flow of matter and energy through the viral shunt may be decreased with consequences for the Antarctic food web and element cycling.

Viruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism–virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host–virus system for examination of cellular and molecular processes in the marine environment.

Aureococcus anophagefferens causes economically and ecologically destructive “brown tides” in the United States, China and South Africa. Here we report the 370,920bp genomic sequence of AaV, a virus capable of infecting and lysing A. anophagefferens. AaV is a member of the nucleocytoplasmic large DNA virus (NCLDV) group, harboring 377 putative coding sequences and 8 tRNAs. Despite being an algal virus, AaV shows no phylogenetic affinity to the Phycodnaviridae family, to which most algae-infecting viruses belong. Core gene phylogenies, shared gene content and genome-wide similarities suggest AaV is the smallest member of the emerging clade “Megaviridae”. The genomic architecture of AaV demonstrates that the ancestral virus had an even smaller genome, which expanded through gene duplication and assimilation of genes from diverse sources including the host itself – some of which probably modulate important host processes. AaV also harbors a number of genes exclusive to phycodnaviruses – reinforcing the hypothesis that Phycodna- and Mimiviridae share a common ancestor.

A high speed framing camera and a particle image velocimetry instrument were used to determine the properties of explosively driven particle fields in early microsecond and later millisecond times. Test items were configured in a two inch long cylindrical shape with a half inch diameter core of organic explosive. The core was surrounded by a particle bed of aluminum or tungsten powder of a specific particle size distribution. Position data from the leading edge of the particle fronts for each charge was recorded with a high speed framing camera at early time and with a particle image velocimetry (PIV) instrument at later time to determine particle velocity. Using a PIV image, a velocity gradient along the length of the particle field was established by using the mean particle velocity value determined from three separate horizontal bands that transverse the particle field. The results showed slower particles at the beginning of the particle field closest to the source and faster ones at the end. Differences in particle dispersal, luminescence, and agglomeration were seen when changes in the initial particle size and material type were made. The aluminum powders showed extensive luminescence with agglomeration forming large particle structures while the tungsten powder showed little luminescence, agglomeration and no particle structures. Combining velocity data from the high speed framing camera and PIV, the average drag coefficient for each powder type was determined. The particle field velocities and drag coefficients at one meter showed good agreement with the numerical data produced from a computational fluid dynamics code that takes advantage of both Eulerian and Lagrangian solvers to track individual particles after a set post detonation time interval.

Why does the capacity to think certain thoughts imply the capacity to think certain other, structurally related, thoughts? Despite decades of intensive debate, cognitive scientists have yet to reach a consensus on an explanation for this property of cognitive architecture---the basic processes and modes of composition that together afford cognitive capacity---called systematicity. Systematicity is generally considered to involve a capacity to represent/process common structural relations among the equivalently cognizable entities. However, the predominant theoretical approaches to the systematicity problem, i.e. classical (symbolic) and connectionist (subsymbolic), require arbitrary (ad hoc) assumptions to derive systematicity. That is, their core principles and assumptions do not provide the necessary and sufficient conditions from which systematicity follows, as required of a causal theory. Hence, these approaches fail to fully explain why systematicity is a (near) universal property of human cognition, albeit in restricted contexts. We review an alternative, category theory approach to the systematicity problem. As a mathematical theory of structure, category theory provides necessary and sufficient conditions for systematicity in the form of universal construction: each systematically related cognitive capacity is composed of a common component and a unique component. Moreover, every universal construction can be viewed as the optimal construction in the given context (category). From this view, universal constructions are derived from learning, as an optimization. The ultimate challenge, then, is to explain the determination of context. If context is a category, then a natural extension towards addressing this question is higher-order category theory, where categories themselves are the objects of construction.

Marine viruses are critical drivers of ocean biogeochemistry, and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 108 per ml. Over many years, a consensus has emerged that virus abundances are typically tenfold higher than microbial cell abundances. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5,508 microbial cell and virus abundance estimates from 22 distinct marine surveys and find substantial variation in the virus-to-microbial cell ratio, in which a 10:1 model has either limited or no explanatory power. Instead, virus abundances are better described as nonlinear, power-law functions of microbial cell abundances. The fitted scaling exponents are typically less than 1, implying that the virus-to-microbial cell ratio decreases with microbial cell density, rather than remaining fixed. The observed scaling also implies that viral effect sizes derived from ‘representative’ abundances require substantial refinement to be extrapolated to regional or global scales. Analysis of microbial cell and virus abundance estimates from 25 distinct marine surveys reveals that virus-to-microbial cell ratio decreases with microbial cell density, questioning the idea that viral abundance is always 10-fold higher.

Anthropologists and linguists have long assumed that East Polynesia was first settled from Central Western Polynesia, most likely from Samoa. Presented here is a very different history, one involving a northern settlement pathway from atolls off the east coast of the Solomon Islands some 2,000 miles (3,200 km) northwest of Samoa. Evidence includes 73 lexical and grammatical innovations reconstructible in the development of several nested Northern Outlier subgroups. East Polynesian is shown to share all of those innovations and thus subgroup with the Northern Outliers. The 73 reconstructions also provide evidence against an "Ellicean" subgroup and associated theories that East Polynesia was settled from Tuvalu, Tokelau, and/or Pukapuka.

Carroll BJ, Iranmanesh A, Keenan DM, Cassidy F, Wilson WH, Veldhuis JD. Pathophysiology of hypercortisolism in depression: pituitary and adrenal responses to low glucocorticoid feedback. Objective: To test three theories of hypercortisolemia in depression–hypothalamic overdrive, impaired glucocorticoid feedback, or autonomous cortisol production. Method: We applied an overnight low-cortisol feedback strategy by administering metyrapone to hypercortisolemic depressed in-patients and control subjects. Results: Under metyrapone, the increases of plasma adrenocorticotropic hormone (ACTH) concentrations and of basal and pulsatile ACTH secretion were not exaggerated in hypercortisolemic depressed patients compared with control subjects. ACTH approximate entropy (ApEn) did not differ at baseline or under metyrapone. Thus, neither hypothalamic overdrive nor irregular ACTH secretion was seen. We did not detect impaired cortisol feedback: the ACTH response was not reduced, and ApEn measures that are sensitive to feedback changes were comparable in both groups. Metyrapone disrupted cortisol secretory regularity in depressed and control subjects. On the baseline day, basal cortisol secretion was significantly increased and was highly irregular (high ApEn), and ACTH-cortisol cross-ApEn was markedly elevated in high-cortisol patients. Conclusion: Classical feed-forward overdrive and impaired feedback theories of hypercortisolemia in depression were not supported. Depressive hypercortisolemia may result from alternative pathophysiological mechanisms involving irregular basal hypersecretion of cortisol, associated with adrenal enlargement, possibly through splanchnic sympathetic activation of the adrenal cortex.

Studies of the Phycodnaviridae have traditionally relied on the DNA polymerase (pol) gene as a biomarker. However, recent investigations have suggested that the major capsid protein (MCP) gene may be a reliable phylogenetic biomarker. We used MCP gene amplicons gathered across the North Atlantic to assess the diversity of Emiliania huxleyi-infecting Phycodnaviridae. Nucleotide sequences were examined across >6000 km of open ocean, with comparisons between concentrates of the virus-size fraction of seawater and of lysates generated by exposing host strains to these same virus concentrates. Analyses revealed that many sequences were only sampled once, while several were over-represented. Analyses also revealed nucleotide sequences distinct from previous coastal isolates. Examination of lysed cultures revealed a new richness in phylogeny, as MCP sequences previously unrepresented within the existing collection of E. huxleyi viruses (EhV) were associated with viruses lysing cultures. Sequences were compared with previously described EhV MCP sequences from the North Sea and a Norwegian Fjord, as well as from the Gulf of Maine. Principal component analysis indicates that location-specific distinctions exist despite the presence of sequences common across these environments. Overall, this investigation provides new sequence data and an assessment on the use of the MCP gene.

As major consumers of heterotrophic bacteria and phytoplankton, microzooplankton are a critical link in aquatic foodwebs. Here, we show that a major marine microflagellate grazer is infected by a giant virus, Cafeteria roenbergensis virus (CroV), which has the largest genome of any described marine virus (≈730 kb of double-stranded DNA). The central 618-kb coding part of this AT-rich genome contains 544 predicted protein-coding genes; putative early and late promoter motifs have been detected and assigned to 191 and 72 of them, respectively, and at least 274 genes were expressed during infection. The diverse coding potential of CroV includes predicted translation factors, DNA repair enzymes such as DNA mismatch repair protein MutS and two photolyases, multiple ubiquitin pathway components, four intein elements, and 22 tRNAs. Many genes including isoleucyl-tRNA synthetase, eIF-2γ, and an Elp3-like histone acetyltransferase are usually not found in viruses. We also discovered a 38-kb genomic region of putative bacterial origin, which encodes several predicted carbohydrate metabolizing enzymes, including an entire pathway for the biosynthesis of 3-deoxy- d - manno -octulosonate, a key component of the outer membrane in Gram-negative bacteria. Phylogenetic analysis indicates that CroV is a nucleocytoplasmic large DNA virus, with Acanthamoeba polyphaga mimivirus as its closest relative, although less than one-third of the genes of CroV have homologs in Mimivirus. CroV is a highly complex marine virus and the only virus studied in genetic detail that infects one of the major groups of predators in the oceans.

Emiliania huxleyi virus 86 (EhV-86) belongs to the family Phycodnaviridae, a group of viruses that infect a wide range of freshwater and marine eukaryotic algae. Phycodnaviridae is one of the five families that belong to a large and phylogenetically diverse group of viruses known as nucleocytoplasmic large dsDNA viruses (NCLDVs). To date, our understanding of algal NCLDV entry is based on the entry mechanisms of members of the genera Chlorovirus and Phaeovirus, both of which consist of non-enveloped viruses that 'inject' their genome into their host via a viral inner-membrane host plasma membrane fusion mechanism, leaving an extracellular viral capsid. Using a combination of confocal and electron microscopy, this study demonstrated for the first time that EhV-86 differs from its algal virus counterparts in two fundamental areas. Firstly, its capsid is enveloped by a lipid membrane, and secondly, EhV-86 enters its host via either an endocytotic or an envelope fusion mechanism in which an intact nucleoprotein core still encapsulated by its capsid is seen in the host cytoplasm. Real-time fluorescence microscopy showed that viral internalization and virion breakdown took place within the host on a timescale of seconds. At around 4.5 h post-infection, virus progeny were released via a budding mechanism during which EhV-86 virions became enveloped with host plasma membrane. EhV-86 therefore appears to have an infection mechanism different from that employed by other algal NCLDVs, with entry and exit strategies showing a greater analogy to animal-like NCLDVs.

Fatty acids profiles of Emiliania huxleyi strain CCMP1516 were determined in a virus- induced culture crash with E. huxleyi virus 86 (EhV-86). As cell numbers declined in the infected cul- tures due to virus lysis, a concomitant decrease in fatty acids was observed in the particulate fraction. The composition of fatty acids within infected E. huxleyi cells was restructured, with a shift from polyunsaturated to monounsaturated and saturated fatty acids (respective distributions changing from 70:10:20% at the start of the experiment to 44:24:32% at the final time point). In particular, decreases were seen in the major fatty acid 22:6(n-3) and in 18:5(n-3), whereas greatest increases were seen in 18:1(n-9) and 22:0. The increase in the amount and restructuring of the fatty acid pool in E. huxleyi was indicative of a combination of specific and non-specific effects of virus infection. Specific effects primarily included induction of metabolic pathways such as the synthesis of compo- nents involved in virus replication, the production of virions and signal transduction via sphingolipid biosynthesis. Non-specific effects due to stress were likely mediated by reactive oxygen species. Changes in the composition of virus-infected E. huxleyi are of significance to the food web since graz- ing on virus-infected blooms will decrease the amount of essential polyunsaturated fatty acids passed on to higher trophic levels. Consequently, this could decrease the overall productivity of marine ecosystems.

We examined whether virus infection of Emiliania huxleyi with the lytic E. huxleyi-specific virus, EhV-86, influenced it's palatability to the heterotrophic dinoflagellate Oxyrrhis marina. E. huxleyi mortality was assessed by comparing changes in the algae's concentration between four different incubations: (1) Grazer O. marina plus an equal concentration of infected and healthy E. huxleyi prey (grazed-infected); (2) the same equal concentration of healthy and infected E. huxleyi prey without grazer O. marina (infected); (3) healthy E. huxleyi prey (no infected cells) with grazer O. marina (grazed); and (4) healthy E. huxleyi prey alone (no grazer or infected cells; control). Grazing rates of O. marina increased in the presence of virus-infected E. huxleyi prey. An adapted plaque assay protocol revealed that the amount of infected cells in grazed-infected cultures was approximately one-quarter (0.28) of that observed in infected (minus grazer) controls. Given that these assays were normalized to cell number, they demonstrate that O. marina was preferentially feeding on virus-infected E. huxleyi over their healthy counterparts. The effects of marine viruses may have been misinterpreted since the likelihood of them being grazed during infection has not been previously considered. Preferential grazing of infected cells in the ocean would sequester more carbon in particulate form, making it available to higher trophic levels. Consequently, these results should be taken into consideration when modeling the ocean carbon budget.

This study tested the validity of the modified dilution method approach to partition nat- ural phytoplankton mortality into grazer versus virus-induced fractions. A series of experiments was conducted weekly between August and October 2005 from an offshore site in the western English Channel. The phytoplankton community during this period was dominated numerically by Syne- chococcus spp. and picoeukaryotes. Despite highly significant regression results, no discernible viral lysis of Synechococcus spp. or picoeukaryote populations was apparent during the 3 mo period. Microzooplankton grazing was the major source of mortality for Synechococcus spp. and picoeukary- otes during this time. Statistical analysis indicates that, using our experimental design, the modified dilution approach was not sensitive enough to be able to measure significant viral lysis during the experimental period. Sensitivity analysis indicated that viral mortality occurred at rates of

Dimethylsulfoniopropionate (DMSP) cleavage was investigated during culture studies of grazing by the microzooplankter Oxyrrhis marina and viral lysis by Emiliania huxleyi virus 86 (EhV-86) on two axenic strains of E. huxleyi. The cleavage products of DMSP, dimethyl sulfide (DMS) and acrylic acid (AA), accumulated during viral infection of both strains, confirming that viral lysis of algae can lead directly to DMSP cleavage. AA and DMS accumulated in parallel with compromised E. huxleyi cells, indicating that DMSP cleavage occurred during the physical disruption of the infected cells. This is in agreement with the hypothesis that DMSP and DMSP lyase ([DL] the enzyme responsible for cleaving DMSP) are segregated in healthy or undamaged cells. During grazing, the concentrations of DMS and AA produced per eaten cell were an order of magnitude higher than the concentrations resulting from cell death caused by viral infection, suggesting that grazing is the quantitatively more significant pathway of DMS production in E. huxleyi. Levels of DL activity decreased in infected cultures to a minimum of 0.00065 fmol cell−1 min−1 as compared with an average of 0.09 fmol cell−1 min−1 in the control cultures, indicating that reduced DL activity in virally infected cells was responsible for the lower levels of DMSP cleavage observed during viral lysis.

A latent virus-like agent, which we designated zooxanthella filamentous virus 1 (ZFV1), was isolated from Symbiodinium sp. strain CCMP 2465 and characterized. Transmission electron microscopy and analytical flow cytometry revealed the presence of a new group of distinctive filamentous virus-like particles after exposure of the zooxanthellae to UV light. Examination of thin sections of the zooxanthellae revealed the formation and proliferation of filamentous virus-like particles in the UV-induced cells. Assessment of Symbiodinium sp. cultures was used here as a model to show the effects of UV irradiance and induction of potential latent viruses. The unique host-virus system described here provides insight into the role of latent infections in zooxanthellae through environmentally regulated viral induction mechanisms.

Generation of DNA fragments by DNase digestion involves digesting DNA for a range of times, then picking the time that gives optimal-sized DNA fragments (typically 1000–4000 bp).

Marine viruses are critical drivers of ocean biogeochemistry and their abundances vary spatiotem- porally in the global oceans, with upper estimates exceeding 10 8 per ml. Over many years, a con- sensus has emerged that virus abundances are typically 10-fold higher than prokaryote abundances. The use of a fixed-ratio suggests that the relationship between virus and prokaryote abundances is both predictable and linear. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5671 prokaryote and virus abundance estimates from 25 distinct marine surveys to characterize the relationship between virus and prokaryote abundances. We find that the median virus-to-prokaryote ratio (VPR) is 10:1 and 16:1 in the near- and sub-surface oceans, respectively. Nonetheless, we observe substantial variation in the VPR and find either no or limited explanatory power using fixed-ratio models. Instead, virus abundances are better described as nonlinear, power-law functions of prokaryote abundances - par- ticularly when considering relationships within distinct marine surveys. Estimated power-laws have scaling exponents that are typically less than 1, signifying that the VPR decreases with prokaryote density, rather than remaining fixed. The emergence of power-law scaling presents a challenge for mechanistic models seeking to understand the ecological causes and consequences of marine virus- microbe interactions. Such power-law scaling also implies that efforts to average viral effects on microbial mortality and biogeochemical cycles using “representative” abundances or abundance- ratios need to be refined if they are to be utilized to make quantitative predictions at regional or global ocean scales.

Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.

Synechococcus-specific polymerase chain reaction (PCR) primers were developed and used to amplify fragments of the RNA polymerase core subunit gene rpoC1 of a set of 23 marine isolates from different oceanographic locations. Restriction fragment length polymorphism (RFLP) analysis of the PCR products differentiated between most strains and all phylogenetic clades, thus allowing the screening of large sample sets at high genetic resolution. The method was used to analyse changes in the genetic diversity of marine Synechococcus strains through an annual cycle at 100 m depth in the Gulf of Aqaba, Red Sea, and along the depth profile of a sample from June 1999. RFLP analysis of 36 clones of each of the 8 rpoC1 clone libraries screened showed that the Synechococcus population during summer and autumn was dominated by 1 to 3 genetically different clones, while maximum genetic richness was found during spring and winter. Analysis of the depth profile during the period of stratification revealed differences in relative abundance of particular RFLP types among depths (10, 30, 100 m), although the same genotypes dominated the assemblage throughout. Multivariate analysis of environmental variables and Synechococcus assemblage composition showed that Synechococcus genetic diversity was most closely, and significantly, correlated to a combination of temperature and NO3- (P = 0.645, p = 0.038). Phylogenetic analysis of the marine rpoC1 nucleotide sequences of the 40 different RFLP types identified in this study, and all Synechococcus rpoC1 sequences in the databases, demonstrates that the new PCR primers amplify rpoC1 gene fragments from all MC-A and some Cyanobium lineages of marine Synechococcus strains and are also useful for the identification of potentially novel lineages.

The genus Coccolithovirus is a recently discovered group of viruses that infect the globally important marine calcifying microalga Emiliania huxleyi. Surprisingly, the viral genome contains a cluster of putative sphingolipid biosynthetic genes not found in other viral genus. To address the role of these genes in viral pathogenesis, the ehv050 gene predicted to encode a serine palmitoyltransferase (SPT), the first and rate-limiting enzyme of sphingolipid biosynthesis, was expressed and characterized in Saccharomyces cerevisiae. We show that the encoded protein is indeed a fully functional, endoplasmic reticulum-localized, single-chain SPT. In eukaryotes SPT is a heterodimer comprised of long chain base 1 (LCB1) and LCB2 subunits. Sequence alignment and mutational analysis showed that the N-terminal domain of the viral protein most closely resembled the LCB2 subunit and the C-terminal domain most closely resembled the LCB1 subunit. Regardless of whether the viral protein was expressed as a single polypeptide or as two independent domains, it exhibited an unusual preference for myristoyl-CoA rather than palmitoyl-CoA. This preference was reflected by the increased presence of C16-sphingoid bases in yeast cells expressing the viral protein. The occurrence of a single-chain SPT suggested to us that it might be possible to create other fusion SPTs with unique properties. Remarkably, when the two subunits of the yeast SPT were thus expressed, the single-chain chimera was functional and displayed a novel substrate preference. This suggests that expression of other multisubunit membrane proteins as single-chain chimera could provide a powerful approach to the characterization of integral membrane proteins.

We examined the ability of dimethylsulfoniopropionate (DMSP), its cleavage products dimethyl sulfide (DMS) and acrylic acid (AA), and the oxidized form of DMS dimethylsulfoxide (DMSO), to inhibit infection of Emiliania huxleyi virus 86 (EhV-86). Infectivity was assessed by plaque assay of viral stock that had been exposed to these compounds. The initial concentrations of the compounds tested were 250 mmol L-1 for DMSP, DMS, and AA, and 14 mmol L-1 for DMSO. These are the maximum concentrations thought to occur in E. huxleyi and therefore the highest EhV-86 might encounter. DMSP and DMSO had no effect on EhV-86; however, both DMS and AA diminished viral titers. Further experiments established that both DMS and AA significantly reduced titers from a concentration of 100 mmol L-1 and that they had a greater antiviral effect when applied in combination. The DMSP system in algae could function as a chemical defense against viral infection that would benefit the surviving cells in the population by reducing infective titers of progeny viruses and therefore decreasing the probability of infection of further cells.

Mesocosm experiments are important for studies of the pelagic ecosystem, and reproducibility of population dynamics and the effect of enclosing the water mass are essential aspects of such experiments. Nine mesocosms manipulated with daily nutrient additions were divided into three treatment groups, each of three units. All units were filled on the same day, but the three treatment groups differed in the timing of the start of nutrient additions. Abundance of phytoplankton, viruses and bacteria was followed for 12 days after filling, and 80% of the variance was ascribed to the population dynamics initiated by the nutrient perturbation, only 3% to the difference in the starting time of the perturbation and 1% to the placement of individual mesocosms at the raft. Although within-group variance of nutrient perturbation was small, there was a continuous increase over time, demonstrating a tendency for mesocosms to slowly diverge. We conclude that the transient response induced by the experimental perturbation strongly dominates the observed abundance variations and that, although present, the effects of delaying the onset of nutrient perturbation and of differences in along-raft position of the mesocosms were comparatively much smaller. Consequences for design of numerical models of microbial population dynamics are discussed.

Researchers working on environmentally relevant organisms, populations, and communities are increasingly turning to the application of OMICS technologies to answer fundamental questions about the natural world, how it changes over time, and how it is influenced by anthropogenic factors. In doing so, the need to capture meta-data that accurately describes the biological "source" material used in such experiments is growing in importance. Here, we provide an overview of the formation of the "Env" community of environmental OMICS researchers and its efforts at considering the meta-data capture needs of those working in environmental OMICS. Specifically, we discuss the development to date of the Env specification, an informal specification including descriptors related to geographic location, environment, organism relationship, and phenotype. We then describe its application to the description of environmental transcriptomic experiments and how we have used it to extend the Minimum Information About a Microarray Experiment (MIAME) data standard to create a domain-specific extension that we have termed MIAME/Env. Finally, we make an open call to the community for participation in the Env Community and its future activities.

Bacteriophage S-PM2 infects several strains of the abundant and ecologically important marine cyanobacterium Synechococcus . A large lytic phage with an isometric icosahedral head, S-PM2 has a contractile tail and by this criterion is classified as a myovirus (1). The linear, circularly permuted, 196,280-bp double-stranded DNA genome of S-PM2 contains 37.8% G+C residues. It encodes 239 open reading frames (ORFs) and 25 tRNAs. Of these ORFs, 19 appear to encode proteins associated with the cell envelope, including a putative S-layer-associated protein. Twenty additional S-PM2 ORFs have homologues in the genomes of their cyanobacterial hosts. There is a group I self-splicing intron within the gene encoding the D1 protein. A total of 40 ORFs, organized into discrete clusters, encode homologues of T4 proteins involved in virion morphogenesis, nucleotide metabolism, gene regulation, and DNA replication and repair. The S-PM2 genome encodes a few surprisingly large (e.g., 3,779 amino acids) ORFs of unknown function. Our analysis of the S-PM2 genome suggests that many of the unknown S-PM2 functions may be involved in the adaptation of the metabolism of the host cell to the requirements of phage infection. This hypothesis originates from the identification of multiple phage-mediated modifications of the host's photosynthetic apparatus that appear to be essential for maintaining energy production during the lytic cycle.

Analytical flow cytometry (AFC) and denaturing gradient gel electrophoresis (DGGE) were used to investigate the diversity and dynamics of viruses, bacteria and phytoplankton commu- nities in a hypereutrophic freshwater lake. Samples were taken from different depths throughout the water column over an annual cycle. Priest Pot is a small lake in the Lake District in NW England (UK), and has been well characterised in previous studies; however, little is known of the diversity and dynamics of the virus community. Virus abundance was shown to change over both spatial and tem- poral scales, and appeared to be closely linked to other biotic and abiotic parameters. The highest virus concentrations occurred in the deepest part of the lake at a depth of 3.2 m, in the anoxic layer, at the same time as a peak of abundance of green sulphur bacteria. Sequence analysis of a DGGE band that occurred at the same time suggested a bacterium similar to Chlorobium spp., a green sulphur bacterium, comprised part of this bacterial bloom.

In early 2002 coral mortality occurred along 600 km of coastline from Tanzania to Kenya. Astreopora, Echinopora, and Montipora species were severely affected, with Montipora being nearly eliminated from Kenyan reefs. Acropora, Platygyra, Goniopora, and massive Porites were also affected; however, Porites and Goniopora rarely died and often recovered, whereas death for most other species occurred within 2 weeks. In Echinopora and Montipora, a dull ashy tissue color and brittle skeletons characterized the early stages of this event with a mucus layer on the tissue surface in intermediate stages. Mucus and embedded debris then disappeared and surfaces were left covered in a white calcareous dust that sometimes capped a black layer. Astreopora tissues became dull and pale, and seldom produced mucus; eventually the skeleton became bare and white. Either a colorless translucent or brownish thin margin of tissue was visible between living tissue and bare skeleton, depending on species. Scanning electron micrographs of affected corals revealed the presence of fungi. Histology and staining showed that the fungi were mostly in the three genera that died from the syndrome and it may be that fungi invaded and killed corals weakened by another unidentified pathogen.