Human mucosal surfaces contain a wide range of microorganisms. The biological effects of these organisms are largely unknown. Large-scale metagenomic sequencing is emerging as a method to identify novel microbes. Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. The presence of ATCV-1 was associated with a modest but measurable decrease in cognitive functioning. A relationship between ATCV-1 and cognitive functioning was confirmed in a mouse model, which also indicated that exposure to ATCV-1 resulted in changes in gene expression within the brain. Our study indicates that viruses in the environment not thought to infect humans can have biological effects.
Marine microorganisms constitute the largest percentage of living biomass and serve as the major driving force behind nutrient and energy cycles. While viruses only comprise a small percentage of this biomass (i.e., 5%), they dominate in numerical abundance and genetic diversity. Through host infection and mortality, viruses affect microbial population dynamics, community composition, genetic evolution, and biogeochemical cycling. However, the field of marine viral ecology is currently limited by a lack of data regarding how different environmental factors regulate virus dynamics and host–virus interactions. The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production. Considering the ecological importance of viruses in the marine ecosystem and the increasing pressure from anthropogenic activity and global climate change on marine systems, a synthesis of existing information provides a timely framework for future research initiatives in viral ecology.
Marine mutants wash up on shore: two-headed dolphin a sign of chemical poisoning tipping point (Marine mutants wash up on shore: two-headed dolphin a sign of chemical poisoning tipping point http://t.co/4c0zQooEOH)...
Liquid water has been known to occur beneath the Antarctic ice sheet for more than 40 years, but only recently have these subglacial aqueous environments been recognized as microbial ecosystems that may influence biogeochemical transformations on a global scale. Here we present the first geomicrobiological description of water and surficial sediments obtained from direct sampling of a subglacial Antarctic lake. Subglacial Lake Whillans (SLW) lies beneath approximately 800 m of ice on the lower portion of the Whillans Ice Stream (WIS) in West Antarctica and is part of an extensive and evolving subglacial drainage network. The water column of SLW contained metabolically active microorganisms and was derived primarily from glacial ice melt with solute sources from lithogenic weathering and a minor seawater component. Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. Our results confirm that aquatic environments beneath the Antarctic ice sheet support viable microbial ecosystems, corroborating previous reports suggesting that they contain globally relevant pools of carbon and microbes that can mobilize elements from the lithosphere and influence Southern Ocean geochemical and biological systems.
Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established ‘core’ (180 PCs; one-third new to science) and ‘flexible’ (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron–sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.
Mya Breitbart's insight:
Very nice comparison of auxiliary metabolic genes throughout the water column - and interesting that they found photosynthetic AMGs in the deep ocean showing vertical flux of viral particles!
Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ~97 kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome.
Mya Breitbart's insight:
Not quite about Aquatic Viruses, but too cool not to share. PS - love the name!
Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 107 Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations. These population-based, host-linked viral ecological data suggest that, for this single host and seawater sample alone, there are at least 26 double-stranded DNA viral populations with estimated relative abundances ranging from 0.06 to 18.2%. These populations include previously cultivated cyanophage and new viral types missed by decades of isolate-based studies. Nucleotide identities of homologous genes mostly varied by less than 1% within populations, even in hypervariable genome regions, and by 42-71% between populations, which provides benchmarks for viral metagenomics and genome-based viral species definitions. Together these findings showcase a new approach to viral ecology that quantitatively links objectively defined environmental viral populations, and their genomes, to their hosts.
Mya Breitbart's insight:
Very cool method for linking marine phage with their hosts...
Marine photosynthesis is one of the major contributors to the global carbon cycle and the world’s oxygen supply. This process is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding photosystem-II (PSII) reaction center proteins are found in many cyanophage genomes, and are expressed during the infection of their hosts. On the basis of metagenomics, cyanophage photosystem-I (PSI) gene cassettes were recently discovered with two gene arrangements psaJFCABKED and psaDCAB. It was suggested that the horizontal transfer of PSII and PSI genes is increasing phage fitness. To better understand their diversity, we designed degenerate primers to cover a wide diversity of organisms, and using PCR we targeted the psaCA arrangement, which is unique to cyanophages cassettes. We examined viral concentrates from four islands in the Pacific Ocean and found samples containing the psaCA arrangement. Analyses of the amplified viral psaA gene revealed six subgroups varying in their level of similarity and %G+C content, suggesting that the diversity of cyanophage PSI genes is greater than originally thought.
Knowledge of ancient viruses is limited due to their low concentration and poor preservation in ancient specimens. Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. Using reverse genetics, we reconstituted the DNA virus, which replicated and systemically spread in a model plant species. Under constant freezing conditions, encapsidated viral nucleic acids may therefore be preserved for centuries. Our finding indicates that cryogenically preserved materials can be repositories of ancient viral nucleic acids, which in turn allow molecular genetics to regenerate viruses to study their biology
By some estimates, almost half of the world's organic carbon is fixed by marine organisms called phytoplankton -- single-celled photosynthetic organisms that account for less than one percent of the total photosynthetic biomass on Earth. When giant algal blooms get viral infections, global carbon cycles are affected, scientists have now discovered.
Seals Can Spread Avian Flu to People Environment News Service WASHINGTON, DC, September 3, 2014 (ENS) – The avian flu virus that caused widespread harbor seal deaths in 2011 can spread to and infect other mammals and potentially humans, new...
Ed Rybicki's insight:
Right up there with "Ebola is airborne!" if you ask me, but still....
Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks specific virus-host interaction dynamics remain cryptic. Here we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNACaudoviralesand ssDNAMicroviridae. Infection frequencies suggest that ~1/3 of SUP05 bacteria are viral-infected, with higher infection frequency where oxygen-deficiency was most severe. ObservedMicroviridaeclonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together these results demonstrate closely coupled SUP05 virus-host co-evolutionary dynamics with potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
The MMETSP is a significant step in recognizing that purpose-built reference databases from ecologically key biomes are essential for all domains of life. Nevertheless, it is only the beginning, and important biases remain that should be addressed. The MMETSP relies primarily on cultured organisms, and this introduces a different set of biases, most obviously, favoring organisms that are photosynthetic. Eukaryotic heterotrophs have critical ecological roles but are under-represented. Indeed, the natural diversity of eukaryotic heterotrophs is huge in general (Figure 1A), and the four most commonly recovered sequences retrieved in environmental surveys of marine samples worldwide correspond to lineages for which most members are uncultivated (e.g.,Marine Stramenopiles (MAST) and Marine Alveolates (MALV) –). These are probably heterotrophs, but we lack a solid biological definition for most of these cells and have become adroit at ignoring heterotrophs in general. Similarly, organisms from the open ocean are underrepresented. Culture-independent methods for generating transcriptomes and genomes and, in some cases, transcriptomes and genomes from single cells will be essential to moving beyond this problem. Methodologies for population – and single-cell genomics and transcriptomics are advancing rapidly ,–, transitioning from technological feats to something we should expect to work routinely. This transition holds great promise for filling the rather substantial gap in our knowledge imposed by uncultivated protists, as well as allowing us to carry out condition-specific analyses of expressed genes in difficult-to-work-with systems. The MMETSP program foreshadows this development by sequencing a small set of culture-independent samples.
Cyanobacteria coexist in the oceans with a wealth of phages that infect them. While numerous studies have investigated Synechococcus phages, much less data is available for Prochlorococcus phages. Furthermore, little is known about cyanophage composition. Here we examined the abundance and relative composition of cyanophages on six cyanobacterial hosts in samples collected during spring and summer from the Red Sea. Maximal abundances found on Synechococcus of 35,000 phages/ml are within ranges found previously whereas the 24,000 phages/ml found on Prochlorococcus are approximately 10-fold higher than previous findings. T7-like, T4-like and “unknown” phages were isolated on all hosts, including many T4-like phages on HL Prochlorococcus strains, whereas TIM5-like phages were found only on Synechococcus. Large differences in cyanophage abundance and composition were found for different hosts on the same sampling date as well as for the same host on different dates with few predictable patterns discerned. Host-range analyses showed that T7-like and TIM5-like phages were quite host-specific, whereas the breadth of hosts for T4-like phages was related to host type: those isolated on HL Prochlorococcus were considerably more host-specific than those on LL Prochlorococcus or Synechococcus. These host-related differences likely contribute to the complexity of host-phage interactions in the oceans.
Multiple studies have explored microbial shifts in diseased or stressed corals, however little is known about bacteriophage interactions with microbes in this context. This study characterized microbial 16S rRNA amplicons and phage metagenomes associated with Montastraea annularis corals during a concurrent white plague disease outbreak and bleaching event. Phage consortia differed between bleached and diseased tissues. Phages in the family Inoviridae were elevated in diseased or healthy tissues compared to bleached portions of diseased tissues. Microbial communities also differed between diseased and bleached corals. Bacteria in the orders Rhodobacterales and Campylobacterales were increased while Kiloniellales was decreased in diseased compared to other tissues. A network of phage-bacteria interactions was constructed of all phage strains and 11 bacterial genera that differed across health states. Phage-bacteria interactions varied in specificity: phages interacted with 1-8 bacterial hosts while bacteria interacted with up to 59 phages. Six phages were identified that interacted exclusively with Rhodobacterales and Camplyobacterales. These results suggest that phages have a role in controlling stress-associated bacteria, and that networks can be utilized to select potential phages for mitigating detrimental bacterial growth in phage therapy applications.
Mya Breitbart's insight:
Very interesting --- links between coral health, bacterial communities, and phages! Also one of the first studies to find Inoviruses in the oceans that I'm aware of.