Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance.
Chloroviruses are large, icosahedral, dsDNA-containing viruses that replicate in certain unicellular, chlorella-like green algae [1,2]. They exist in freshwater throughout the world with titers as high as thousands of plaque-forming units (PFU) per ml of indigenous water although titers are typically 1–100 PFU/ml. Titers fluctuate during the year with the highest titers typically occurring in the spring and late fall. Known chlorovirus hosts, which are normally symbionts and are often referred to as zoochlorellae, are associated with either the protozoan Paramecium bursaria (Fig 1A), the coelenterate Hydra viridis, or the heliozoan Acanthocystis turfacea. Zoochlorellae are resistant to viruses in their symbiotic state. Fortunately, some zoochlorellae grow independently of their partners in the laboratory, permitting plaque assay of the viruses (Fig 1B) and synchronous infection of their hosts, which allows one to study the virus life cycle in detail.
South African universities are awarded annual subsidy from the Department of Higher Education and Training (DHET) based on their research publication output. Journal article subsidy is based on the number of research publications in DHET-approved journals as well as the proportional contribution of authors from the university. Co-authorship with other institutions reduces the subsidy received by a university, which may be a disincentive to collaboration. Inter-institutional collaboration may affect the scientific impact of resulting publications, as indicated by the number of citations received. We analysed 812 journal articles published in 2011 by authors from the University of Cape Town’s Faculty of Health Sciences to determine if there was a significant relationship between subsidy units received and (1) citation count and (2) field-weighted citation impact. We found that subsidy units had a significant inverse relationship with both citation count (r= -0.247; CI = -0.311 – -0.182; p<0.0001) and field-weighted citation impact (r= -0.192; CI= -0.258 – -0.125; p<0.0001). These findings suggest that the annual subsidy awarded to universities for research output may inadvertently penalise high-citation publication. Revision of the funding model to address this possibility would better align DHET funding allocation with the strategic plans of the South African Department of Science and Technology, the National Research Foundation and the South African Medical Research Council, and may better support publication of greater impact research.
Ed Rybicki's insight:
Well,of course: any scheme that awards more money to papers having more authors from your own institution will do that!
The foundation for any ecological study and the for effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.
Bacteriophage play an important role in host-driven biological processes by controlling bacterial population size, horizontally transferring genes between hosts, and expressing host-derived genes to alter host metabolism. Metagenomics provides the genetic basis for understanding the interplay between uncultured bacteria, their phage, and the environment. In particular, viral metagenomes (viromes) are providing new insight into phage-encoded host genes (i.e., auxiliary metabolic genes; AMGs) that reprogram host metabolism during infection. Yet, despite deep sequencing efforts of viral communities, the majority of sequences have no match to known proteins. Reference-independent computational techniques, such as protein clustering, contig spectra, and ecological profiling are overcoming these barriers to examine both the known and unknown components of viromes. As the field of viral metagenomics progresses, a critical assessment of tools is required as the majority of algorithms have been developed for analyzing bacteria. The aim of this paper is to offer an overview of current computational methodologies for virome analysis and to provide an example of reference-independent approaches using human skin viromes. Additionally, we present methods to carefully validate AMGs from host contamination. Despite computational challenges, these new methods offer novel insights into the diversity and functional roles of phage in diverse environments.
Lymphocystis disease is a geographically widespread disease affecting more than 150 different species of marine and freshwater fish. The disease, provoked by the iridovirus lymphocystis disease virus (LCDV), is characterized by the appearance of papilloma-like lesions on the skin of affected animals that usually self-resolve over time. Development of the disease is usually associated with several environmental factors and, more frequently, with stress conditions provoked by the intensive culture conditions present in fish farms. In gilthead seabream (Sparus aurata), an economically important cultured fish species in the Mediterranean area, a distinct LCDV has been identified but not completely characterized yet. We have used direct sequencing of the virome of lymphocystis lesions from affected S. aurata to obtain the complete genome of a new LCDV-Sa species that is the largest vertebrate iridovirus sequenced to date. Importantly, this approach allowed us to assemble the full-length circular genome sequence of two previously unknown viruses belonging to the papilloma- and polyomaviruses termed Sparus aurata papillomavirus 1 (SaPV1) and Sparus aurata polyomavirus 1 (SaPyV1), respectively. Epidemiological surveys showed that lymphocystis disease was frequently associated with the concurrent appearance of one or both of the new viruses. SaPV1 has unique characteristics such as an intron within the L1 gene and, as the first member of the Papillomaviridae family described in fish, provides evidence for a more ancient origin of this family than previously thought.
Abstract: Hepatitis A virus is a pathogen associated with water pollution. Contaminated drinking water can cause hepatitis A outbreaks, lead to economic losses, and even threaten human lives. It is difficult to detect low levels of hepatitis A virus in water, so the virus must be concentrated in order to quantify it accurately. Here, we present a simple, rapid, efficient technique for the concentration and detection of hepatitis A virus in water. Our data showed that adding phosphate-buffered saline to the water, pre-filtering the water, and adding Trizol reagent directly to the filtration membrane can significantly improve concentration efficiency. Of three types of filtration membranes studied (mixed cellulose ester membrane, polyvinylidene fluoride membrane, and nylon membrane), the concentration efficiency using mixed cellulose ester membrane with a 0.1-μm pore size was the highest, reaching 92.62 ± 5.17%. This method was used to concentrate hepatitis A virus in water samples from Donghu Lake. Using SYBR Green real-time reverse transcription polymerase chain reaction analysis, the detection sensitivity of this method reached 101 copies/μL and its concentration efficiency reached 79.45 ± 9.88%.
Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold. Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses. Using CRISPR spacers and transfer RNA matches to link viral groups to microbial host(s), we doubled the number of microbial phyla known to be infected by viruses, and identified viruses that can infect organisms from different phyla. Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups. Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host–virus interactions.
"Venus is too hot, Mars is too cold, and Earth is just right," says planetary scientist Dave Brain. But why? In this pleasantly humorous talk, Brain explores the fascinating science behind what it takes for a planet to host life -- and why humanity may just be in the right place at the right time when it comes to the timeline of life-sustaining planets.
Ed Rybicki's insight:
Oceans: it needs water oceans. And if Earth, Enceladus, Europa, Ganymede, and possibly Triton and Pluto all have them, AND Titan has hydrocarbon oceans...then maybe they all have life too. Which would mean the solar system is CRAWLING with it. And viruses, obviously B-)
Iron is an essential nutrient and the sub-nanomolar concentrations of iron in open ocean surface waters are often insufficient to support optimal biological activity. More than 99.9% of dissolved iron in these waters is bound to organic ligands, yet determining the identity of these ligands in seawater remains a major challenge. Among the potential dissolved organic ligands in the colloidal fraction captured between a 0.02 µm and a 0.2 µm filter persists an extremely abundant biological candidate: viruses, most of which are phages (viruses that infect bacteria). Recent work in non-marine model systems has revealed the presence of iron ions within the tails of diverse phages infecting Escherichia coli. Based on these findings and the presence of conserved protein motifs in marine phages, here we present several lines of evidence to support the hypothesis that phages are organic iron-binding ligands in the oceans. With average concentrations of 10^7 phages per milliliter surface seawater, we predict that phages could contain up to 0.7 pM iron, a value equivalent to as much as 70% of the colloidal fraction of organically complexed dissolved iron in the surface ocean. Additionally, the production and uptake of siderophores, a strategy that bacteria have developed for assimilating iron, renders cells vulnerable to phage infection due to the dual-function of these cell surface receptors. Iron ions present in phage tails enable phages to exploit their bacterial host’s iron-uptake mechanism via the “Ferrojan Horse Hypothesis” proposed herein, where the apparent gift of iron leads to cell lysis. Finally, if host iron stores are recycled during the assembly of progeny phages, as much as 14% of the cellular iron released into the water column upon lysis would already be incorporated into new phage tails. The potential role of phages as iron-binding ligands has significant implications for both oceanic trace metal biogeochemistry and marine phage-host interactions.
Ed Rybicki's insight:
Viruses as agents of biogeochemical engineering of our planet!
Prof Helen Rees (internationally renowned expert in HIV prevention, reproductive health and vaccines) was recently honoured with a national order.
“Wits congratulates all those honoured, and especially those Witsies who have made a mark in our society. We commend the countless contributions made by Prof Helen Rees to address today’s biggest global health challenges through her outstanding research and intellectual achievement at the highest level,” says Prof Adam Habib, Wits Vice-Chancellor and Principal.
ORDER OF THE BAOBAB
Recognising South Africans who have contributed to community service, business and economy, science, medicine and technological innovation, was awarded to:
Professor Helen Rees (OBE) – Order of the Baobab (Silver)
Executive Director of the Wits Reproductive Health and HIV Institute, Rees has a long and distinguished career as an internationally renowned expert in HIV prevention, reproductive health, vaccines and drug regulation. She serves in leadership roles in both national and international structures and chaired, and continues to chair, various councils and research bodies of the World Health Organization related to Ebola vaccines, polio and immunisation. She is currently chair of the Medicines Control Council and was appointed to this position by the Minister of Health.
In 2001 Professor Rees was made an Officer of the Most Excellent Order of the British Empire (OBE).
The Order of the Baobab (Silver) is awarded to Rees for her excellent contribution in the field of medical science and research. Her work gives hope to communities who have been affected by the scourge of HIV and AIDS.
Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterise holobiont viral communities across species, environments, or experiments.
In this study, which was carried out within the ChEsSO consortium project (Chemosynthetically driven ecosystems south of the Polar Front), we sampled two hydrothermal vent sites on the East Scotia Ridge, Scotia Sea, one in the Kemp Caldera, South Sandwich Arc and one in the Bransfield Strait, north-west of the Antarctic Peninsula, which exhibit strong differences in their chemical characteristics. We compared a subset of their bacteriophage population by Sanger- and 454-sequencing of g23, which codes for the major capsid protein of T4likeviruses. We found that the sites differ vastly in their bacteriophage diversity, which reflects the differences in the chemical conditions and therefore putatively the differences in microbial hosts living at these sites. Comparing phage diversity in the vent samples to other aquatic samples, the vent samples formed a distinct separate cluster, which also included the non-vent control samples that were taken several hundred meters above the vent chimneys. This indicates that the influence of the vents on the microbial population and therefore also the bacteriophage population extends much further than anticipated.
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