Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges

Phosphate (PO(4)) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO(4) using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO(4) transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO(4) uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO(4) -availability may not serve as a simple bottom-up control of marine phytoplankton.     

Regional effects as important determinants of local diversity in both marine and terrestrial systems

Community ecologists have struggled to create unified theories across diverse ecosystems, but it has been difficult to acertain whether marine and terrestrial communities differ in the mechanisms responsible for structure and dynamics. One apparent difference between marine and terrestrial ecology is that the influence of regional processes on local populations and communities is better established in the marine literature. We examine three potential explanations: 1) influential early studies emphasized local interactions in terrestrial communities and regional dispersal in marine communities. 2) regional‐scale processes are actually more important in marine than in terrestrial communities. 3) recruitment from a regional species pool is easier to study in marine than terrestrial communities. We conclude that these are interrelated, but that the second and especially the third explanations are more important than the first. We also conclude that in both marine and terrestrial systems, there are ways to improve our understanding of regional influences on local community diversity. In particular, we advocate examining local vs regional diversity relationships at localities within environmentally similar regions that differ in their diversity either because of their sizes or their varying degrees of isolation from a species source.     

Current problems in marine biodiversity studies

This paper deals with a discussion of terminology and six proposed levels of biodiversity. Recent data and estimates were used to compare species and taxonomic diversity of terrestrial, freshwater, and marine organisms. About 1.5 million terrestrial species and 320000 aquatic species are hitherto known. In spite of a long history of research, only about 280000 marine species have been discovered, of which 180000 species are invertebrates. Of 33 metazoan phyla, 31 are found in the sea, 13 of these being exclusively marine. Seventeen metazoan phyla contain freshwater species, and only 11 phyla comprise terrestrial animals. Two phyla (freshwater Micrognathozoa and terrestrial Onychophora) possess no marine species. In this paper, we review the assessment reports on marine biological diversity in coral reefs, coastal ecosystems, macrobenthos, and meiofauna. Recent data on the number of known species are listed for each metazoan phylum; the number of anticipated new species to be discovered is estimated. Deep-sea macrobenthos are believed to comprise about 25 million species; meiofauna seems to be composed of 20 to 30 million species, ten million of whom are marine nematodes. Hypotheses are discussed that can account for the high species diversity of deep-sea macrobenthos and meiofauna.     

Pushing the limits in marine species distribution modelling: lessons from the land present challenges and opportunities

Aim Species distribution models (SDMs) have been used to address a wide range of theoretical and applied questions in the terrestrial realm, but marine‐based applications remain relatively scarce. In this review, we consider how conceptual and practical issues associated with terrestrial SDMs apply to a range of marine organisms and highlight the challenges relevant to improving marine SDMs. Location We include studies from both marine and terrestrial systems that encompass many geographic locations around the globe. Methods We first performed a literature search and analysis of marine and terrestrial SDMs in ISI Web of Science to assess trends and applications. Using knowledge from terrestrial applications, we critically evaluate the application of SDMs in marine systems in the context of ecological factors (dispersal, species interactions, aggregation and ontogenetic shifts) and practical considerations (data quality, alternative modelling approaches and model validation) that facilitate or create difficulties for model application. Results The relative importance of ecological factors to be considered when applying SDMs varies among terrestrial and marine organisms. Correctly incorporating dispersal is frequently considered an important issue for terrestrial models, but because there is greater potential for dispersal in the ocean, it is often less of a concern in marine SDMs. By contrast, ontogenetic shifts and feeding have received little attention in terrestrial SDM applications, but these factors are important to many marine SDMs. Opportunities also exist for applying more advanced SDM approaches in the marine realm, including mechanistic ecophysiological models, where water balance and heat transfer equations are simpler for some marine organisms relative to their terrestrial counterparts. Main conclusions SDMs have generally been under‐utilized in the marine realm relative to terrestrial applications. Correlative SDM methods should be tested on a range of marine organisms, and we suggest further development of methods that address ontogenetic shifts and feeding interactions. We anticipate developments in, and cross‐fertilization between, coupled correlative and process‐based SDMs, mechanistic eco‐physiological SDMs, and spatial population dynamic models for climate change and species invasion applications in particular. Comparisons of the outputs of different model types will provide insight that is useful for improved spatial management of marine species.     

Terrestrial or marine species distribution model: Why not both? A case study with seabirds

Species reliant on both the terrestrial and marine realms present a challenge for conventional species distribution models (SDMs). For such species, standard single‐realm SDMs may omit key information that could result in decreased model accuracy and performance. Existing approaches to habitat suitability modeling typically do not effectively combine information from multiple realms; this methodological gap can ultimately hamper management efforts for groups such as seabirds, seals, and turtles. This study, for the first time, jointly incorporates both terrestrial information and marine information into a single species distribution model framework. We do this by sampling nearby marine conditions for a given terrestrial point and vice versa using parameters set by each species’ mean maximum foraging distance and then use standard SDM methods to generate habitat suitability predictions; therefore, our method does not rely on post hoc combination of several different models. Using three seabird species with very different ecologies, we investigate whether this new multi‐realm approach can improve our ability to identify suitable habitats for these species. Results show that incorporating terrestrial information into marine SDMs, or vice versa, generally improves model performance, sometimes drastically. However, there is considerable variability between species in the level of improvement as well as in the particular method that produces the most improvement. Our approach provides a repeatable and transparent method to combine information from multiple ecological realms in a single SDM framework. Important advantages over existing solutions include the opportunity to, firstly, easily combine terrestrial and marine information for species that forage large distances inland or out to sea and, secondly, consider interactions between terrestrial and marine variables.     

Expanding diversity and ecological roles of RNA viruses

While the diversity of global environmental RNA viruses has remained largely unexplored, recent advances have reported on the discovery of over 10⁶ RNA viral contigs from both terrestrial and marine ecosystems that will help us to better understand the diversity, evolution, ecological roles, and transmission of RNA viruses.     

Nucleopolyhedrovirus Detection and Distribution in Terrestrial,Freshwater, and Marine Habitats of Appledore Island,Gulf of Maine

Viruses in aquatic ecosystems comprise those produced by both autochthonous and allochthonous host taxa. However, there is little information on the diversity and abundance of viruses of allochthonous origin, particularly from non-anthropogenic sources, in freshwater and marine ecosystems. We investigated the presence of nucleopolyhedroviruses (NPV) (Baculovirus), which commonly infect terrestrial lepidopteran taxa, across the landscape of Appledore Island, Gulf of Maine. PCR and qPCR primers were developed around a 294-bp fragment of the polyhedrin (polH) gene, which is the major constituent protein of NPV multivirion polyhedral occlusion bodies. polH was successfully amplified from several aquatic habitats, and recovered polH sequences were most similar to known lepidopteran NPV. Using quantitative PCR designed around a cluster of detected sequences, we detected polH in Appledore Island soils, supratidal freshwater ponds, nearshore sediments, near- and offshore plankton, and in floatsam. This diverse set of locations suggests that NPVs are widely dispersed along the terrestrial—marine continuum and that free polyhedra may be washed into ponds and eventually to sea. The putative hosts of detected NPVs were webworms (Hyphantria sp.) which form dense nests in late summer on the dominant Appledore Island vegetation (Prunus virginiana). Our data indicate that viruses of terrestrial origin (i.e., allochthonous viruses) may be dispersed widely in coastal marine habitats. The dispersal of NPV polH and detection within offshore net plankton (>64 μm) demonstrates that terrestrial viruses may interact with larger particles and plankton of coastal marine ecosystem, which further suggests that viral genomic information may be transported between biomes.     

Antibodies to marine caliciviruses in the Pacific walrus (Odobenus rosmarus divergens Illiger)

Sera from 155 Pacific walruses (Odobenus rosmarus divergens Illiger), sampled in the Chukchi Sea during the summer of 1983, were tested for serum neutralizing (SN) antibodies to six marine calicivirus serotypes. Serotypes tested included San Miguel sea lion virus (SMSV) types 1, 5, 8, and 10, previously isolated from northern fur seals (Callorhinus ursinus Linné) in the Bering Sea; walrus calicivirus (WCV), previously isolated from walrus feces collected off sea ice in the Chukchi Sea; and Tillamook calicivirus (TCV), a bovine isolate from Oregon of suspected marine origin. No antibodies were found to SMSV-1, SMSV-10, or TCV. Antibodies to SMSV-5 were found in two animals (titers 1:20 and 1:160); antibodies to SMSV-8 were found in four animals (all 1:20); and antibodies to WCV were found in one animal (titer 1:40). Antibodies to WCV have been found in the Pacific walrus previously; however, this represents the first report of antibodies to any of the SMSV serotypes in this marine mammal.     

Endemism and evolution in Hawaiian marine invertebrates

Endemism in Hawaiian marine invertebrates is strikingly lower than that in Hawaiian terrestrial organisms. Although marine speciation has been widespread, there have been no major radiations or species swarms comparable with those commonly reported for terrestrial animals and plants; the marine fauna of the Hawaiian islands is differentiated from its Indo-west Pacific roots but has not diversified. The marked differences between marine and terrestrial endemism provide broad support for several models in which speciation depends on dispersal, colonization rate, or effective population size. Distinguishing among these models will require detailed information on the genetic structure and phylogenies of marine species both in the Hawaiian archipelago and throughout the Pacific.     

Crystallization and preliminary crystallographic analysis of San Miguel sea lion virus: an animal calicivirus

The Caliciviridae is a family of nonenveloped, icosahedral, positive-sense single-stranded RNA viruses. This family of viruses consists of both animal and human pathogens. Adapting human caliciviruses to cell culture has not been successful, whereas some animal caliciviruses, including San Miguel sea lion virus, have been successfully propagated in vitro. Here we report the crystallization of San Miguel sea lion virus serotype 4 (SMSV4) and the preliminary X-ray crystallographic analysis of the crystals. SMSV4 have been crystallized using the hanging-drop method. These crystals diffracted to approximately 3A resolution using a synchrotron radiation source. A single crystal under cryo-conditions yielded a complete set of diffraction data. Data processing of the diffraction patterns showed that SMSV crystals belong to I23 space group with cell dimensions a=b=c=457 A. The crystallographic asymmetric unit includes five icosahedral asymmetric units, each consisting of three capsid protein subunits. In the space group I23, given the icosahedral symmetry and the size of the virus particle, the location of the particle is constrained to be at the point where the crystallographic 2- and 3-fold axes intersect. The orientation of the virus particle in the unit cell was ascertained by self-rotation function calculations.     

Conservation and restoration of New Zealand Island ecosystems

An ecological collapse has precipitated pioneering conservation initiatives in New Zealand. Many terrestrial communities in t he New Zealand archipelago have been devastated by over-exploitation, introduced mammals and habitat destruction. More recently, marine ecosystems have been depleted by over-harvesting. To mitigate against these losses, conservation in terrestrial environments has focused on protection of species and habitats. A similar approach is now under way in marine environments with the establishment of ‘no-take’ marine reserves. On land, conservation is now reaching beyond protection t o the eradication of pests from islands and restoration of their terrestrial ecosystems. Restoration on islands not only reduces threats to rare species; it also raises opportunities to investigate how species interact. In the sea, marine reserves not only enhance the diversity of depleted marine communities; they may also augment stocks of commercially harvested species. These initiatives provide many lessons that could be applied to degraded habitats elsewhere.     

Phylogeny and cladistic classification of terrestrial nemerteans: the genera Pantinonemertes Moore & Gibson and Geonemertes Semper

Evolutionary relationships among seven species from two genera ( Pantinonemertes and Geonemertes ) of terrestrial nemerteans (phylum Nemertea) were estimated by a Wagner analysis of 27 morphological, ecological and life history characters. Pantinonemertes was found to be a paraphyletic taxon, and it is suggested that this genus should be combined with Geonemertes to form a monophyletic group. A previous hypothesis for how terrestrial nemerteans evolved is discussed and compared to the results of the cladistic analysis. This suggests that terrestrial and semi-terrestrial species evolved from a marine ancestor; the upper littoral and marine environments have been recolonized by descendants from a terrestrial ancestor.     

Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage

Metagenomic analyses of viruses have revealed widespread diversity in the viriosphere, but it remains a challenge to identify specific hosts for a viral assemblage. To address this problem, we analyze the viral metagenome of a northeast Pacific hydrothermal vent with a comprehensive database of spacers derived from the clustered regularly interspaced short palindromic repeat (CRISPR) putative immune system. CRISPR spacer matches to the marine vent virome suggest that viruses infecting hosts from diverse taxonomic groups are present in this vent environment. Comparative virome analyses show that CRISPR spacers from vent isolates and from thermophiles in general have a higher percentage of matches to the vent virome than to other marine or terrestrial hot spring viromes. However, a high percentage of hits to spacers from mesophilic hosts, combined with a moderately high modeled alpha diversity, suggest that the marine vent virome is comprised of viruses that have the potential to infect diverse taxonomic groups of multiple thermal regimes in both the bacterial and the archaeal domains.     

Phylogeny and Cladistic Classification of the Paramonostiliferous Family Plectonemertidae (Phylum Nemertea)

Abstract— Numerical phylogenetic analysis of nemertean species from the genera Plectonemertes, Katechonemertes and Acteonementes (marine), Argonemertes, Antiponemertes and Leptonemertes (terrestrial), Potamonemertes and Campbellonemertes (freshwater) in the family Plectonemertidae was carried out with the following aims. (1) To estimate the evolutionary relationships between and among these species. (2) To lest the hypothesis of Moore and Gibson that the analysed freshwater species originated from a terrestrial ancestor. (3) To classify the species in monophyletic genera. The analysis did not confirm the hypothesis that the freshwater habitat has been colonised via land. Instead, it suggests that both terrestrial and freshwater species within this family have evolved from a marine ancestor. The cladogram suggests that Antiponemetes is paraphyletic, and it is combined with Argonemertes to form a monophyletic genus.     

Diversification in the tropical pacific: comparisons between marine and terrestrial systems and the importance of founder speciation

Patterns of distribution and processes of differentiation haveoften been contrasted between terrestrial and marine biotas.The islands of Oceania offer an excellent setting to explorethis contrast, because the geographic setting for terrestrialand shallow-water, benthic, marine organisms are the same: themyriad islands strewn across the vast Pacific. The size of speciesranges and the geographic distribution of endemism are two biogeographicattributes that are thought to differ markedly between terrestrialand marine biotas in the Pacific. While terrestrial speciesare frequently confined to single islands or archipelagoes throughoutOceania, marine species tend to have wide to very wide distributions,and are rarely restricted to single island groups except forthe most isolated archipelagoes. We explore the conditions underwhich species can reach an island by dispersal and differentiate.Genetic differentiation can occur either through founder speciationor vicariance; these processes are requisite ends of a continuum.We show that founder speciation is most likely when few propagulesenter the dispersal medium and survive well while they travelfar. We argue that conditions favorable to founder speciationare common in marine as well as terrestrial systems, and thatterrestrial-type, archipelagic-level endemism is likely commonin marine taxa. We give examples of marine groups that showarchipelagic level endemism on most Pacific island groups aswell as of terrestrial species that are widespread. Thus boththe patterns and processes of insular diversification are variable,and overlap more between land and sea than previously considered.     

Population genetic structure of the striped silverside, Atherinomorus endrachtensis (Atherinidae, Atheriniformes, Teleostei), inhabiting marine lakes and adjacent lagoons in Palau: marine lakes are "Islands" for marine species

Although evidence for the evolution of terrestrial species on islands continues to rapidly accumulate, little is known about the evolution of marine species in geographically isolated environments such as islands as ocean currents often facilitate gene flow among populations. In this study, we focused on marine lakes of the Palau Islands, which are considered to be true analogues of terrestrial islands for marine species. To examine evolutionary processes in marine lakes, we conducted population genetic analyses on marine lake and lagoon populations of the striped silverside, Atherinomorus endrachtensis, using two mitochondrial DNA markers differing in evolutionary rate, the cytochrome b gene and the control region. The analyses revealed that the amount of genetic diversity of marine lake populations is much lower than that of lagoon populations and high levels of genetic differentiation occur among marine lake and lagoon populations. The present study has shown that marine lake populations have been completely isolated and have differentiated from lagoon populations, and each marine lake population is experiencing different evolutionary processes. These findings clearly demonstrate that marine lakes are excellent environments for the evolutionary study of marine species.     

Scent of death: Evolution from sea to land of an extreme collective attraction to conspecific death

All living organisms must eventually die, though in some cases their death can bring life‐giving opportunities. Few studies, however, have experimentally tested how animals capitalize on conspecific death and why this specialization would evolve. Here, we conducted experiments on the phylogenetically most closely‐related marine and terrestrial hermit crabs to investigate the evolution of responses to death during the sea‐to‐land transition. In the sea, death of both conspecifics and heterospecifics generates unremodeled shells needed by marine hermit crabs. In contrast, on land, terrestrial hermit crabs are specialized to live in architecturally remodeled shells, and the sole opportunity to acquire these essential resources is conspecific death. We experimentally tested these different species’ responsiveness to the scent of conspecific versus heterospecific death, predicting that conspecific death would have special attractive value for the terrestrial species. We found the terrestrial species was overwhelmingly attracted to conspecific death, rapidly approaching and forming social groupings around conspecific death sites that dwarfed those around heterospecific death sites. This differential responsiveness to conspecific versus heterospecific death was absent in marine species. Our results thus reveal that on land a reliance on resources associated exclusively with conspecifics has favored the evolution of an extreme collective attraction to conspecific death.     

Marine isolates of Aspergillus flavus: denizens of the deep or lost at sea?

Most fungal species from marine environments also live on land. It is not clear whether these fungi reach the sea from terrestrial sources as spores or other propagules, or if there are separate ecotypes that live and reproduce in the sea. The emergence of marine diseases has created an urgency to understand the distribution of these fungi. Aspergillus flavus is ubiquitous in both terrestrial and marine environments. This species is an opportunistic pathogen in many hosts, making it a good model to study the relationship between genetic diversity and specificity of marine fungi. In this study, an intraspecific phylogeny of A. flavus isolates based on Amplified Fragment Length Polymorphisms (AFLPs) was used to determine if terrestrial and marine isolates form discrete populations, and to determine if phylogeny predicts substratum specificity. Results suggest lack of population structure in A. flavus. All isolates may compose a single population, with no clade particular to marine environments.     

The Distribution and Evolution of Terrestrial Nemertines

The occurrence of terrestrial nemertines on widely separatedoceanic islands is described: there are three groups of species(in Australia, New Zealand and the Indopacific islands) andthree separate species on Atlantic islands. Parallel evolutionfrom separate marine ancestors is indicated. The evolutionaryrelationship between different species is established on securemorphological grounds, with particular reference to the genusPantinonemertes which comprises marine, semi-terrestrial andfully terrestrial species. The distribution of terrestrial nemertinesis discussed. Most species are extremely localised but a fewhave become widely dispersed, notably Argonemertes dendyi butalso Geonemertes pelaensis and to a lesser extent Leptonemerteschalicophora. At least two of these widespread species are hermaphrodite.