The Effects of Salinity on Dimethylsulfoniopropionate Production in the Green Alga Ulva fenestrata Postels et Ruprecht (Chlorophyta)

Dimethylsulfoniopropionate (DMSP) in marine algae has been hypothesized to serve as a compatible solute which functions in osmotic acclimation or cryoprotection. However, many macroalgae that produce large quantities of DMSP live in habitats where they are unlikely to experience large fluctuations in salinities or freezing temperatures.We hypothesized that DMSP has other functions in these algae and that they should not show large changes in DMSP concentrations in response to salinity changes.We tested this hypothesis by placing 1.5 cm2 diameter disks of the chlorophyte Ulva fenestrata in artificial seawater (ASW) at salinities from 10% ASW to 300% ASW. Over the next 24 h, DMSP concentrations tended to be lower in the algae in the higher salinity media. After 4 weeks, the final DMSP concentrations tended to be highest in the algae grown at the highest salinities, but the mean DMSP concentrations were only 23% higher or 12% lower in algae grown in the high and low salinity media, respectively, relative to algae in 100% ASW. This suggests that osmotic acclimation is not a primary function of DMSP in U. fenestrata. Disks acclimated in 25% ASW, 100% ASW, or 200% ASW then transferred to a higher or lower salinity did not generate measurable amounts of dimethylsulfide (DMS), demonstrating that U. fenestrata is not using DMSP cleavage as a short-term mechanism for reducing internal DMSP stores, as occurs in some phytoplankton. Survival, as measured by the absence of bleaching, was highest in intermediate to high salinities. Growth was highest in low to intermediate salinities and reproduction only occurred in intermediate salinities.These results suggest that U. fenestrata can tolerate salinity changes, but uses metabolites other than DMSP for osmotic acclimation. Based on the results of this and previous studies, we propose that DMSP has other functions in U. fenestrata such as acting as an herbivore deterrent or antioxidant

Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida)

How from high-magnitude springs fed by the Floridan aquifer system contributes hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state's major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first-magnitude springs support unique communities.IMPORTANCE Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes

Active and covert infections of cricket Iridovirus and Acheta domesticus Densovirus in reared Gryllodes sigillatus crickets

Interest in developing food, feed, and other useful products from farmed insects has gained remarkable momentum in the past decade. Crickets are an especially popular group of farmed insects due to their nutritional quality, ease of rearing, and utility. However, production of crickets as an emerging commodity has been severely impacted by entomopathogenic infections, about which we know little. Here, we identified and characterized an unknown entomopathogen causing mass mortality in a lab-reared population of Gryllodes sigillatus crickets, a species used as an alternative to the popular Acheta domesticus due to its claimed tolerance to prevalent entomopathogenic viruses. Microdissection of sick and healthy crickets coupled with metagenomics-based identification and real-time qPCR viral quantification indicated high levels of cricket iridovirus (CrIV) in a symptomatic population, and evidence of covert CrIV infections in a healthy population. Our study also identified covert infections of Acheta domesticus densovirus (AdDNV) in both populations of G. sigillatus. These results add to the foundational research needed to better understand the pathology of mass-reared insects and ultimately develop the prevention, mitigation, and intervention strategies needed for economical production of insects as a commodity

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions.

Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions. Data from the Parasite Microbiome Project will help identify the mechanisms driving microbiome variation in parasites and infected hosts and how that variation is associated with the ecology and evolution of parasites and their disease outcomes. This is a call to arms to prevent fragmented research endeavors, encourage best practices in experimental approaches, and allow reliable comparative analyses across model systems. It is also an invitation to foundations and national funding agencies to propel the field of parasitology into the microbiome/metagenomic era

MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms

Funder: Marsden Fund (Royal Society of New Zealand).Funder: US NIH (grant reference number: RO1CA164719)Funder: FEDER (Grant reference number: InFoBioS n°EX011185)Funder: US NIH (Grant reference number: R01AI144016-01)Funder: EU horizon 2020 (Grant reference number: 773830)Abstract: The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established by the Parasite Microbiome Project (PMP) consortium, in collaboration with the Genomics Standard Consortium. The SA was built upon the host-associated MIxS standard, but reflects the nestedness of symbiont-associated microbiota within and across host-symbiont-microbe interactions. This package is designed to facilitate the collection and reporting of a broad range of metadata information that apply to symbionts such as life history traits, association with one or multiple host organisms, or the nature of host-symbiont interactions along the mutualism-parasitism continuum. To better reflect the inherent nestedness of all biological systems, we present a novel feature that allows users to co-localize samples, to nest a package within another package, and to identify replicates. Adoption of the MIxS-SA and of the new terms will facilitate reports of complex sampling design from a myriad of environments

ARIA 2016: Care pathways implementing emerging technologies for predictive medicine in rhinitis and asthma across the life cycle

The Allergic Rhinitis and its Impact on Asthma (ARIA) initiative commenced during a World Health Organization workshop in 1999. The initial goals were (1) to propose a new allergic rhinitis classification, (2) to promote the concept of multi-morbidity in asthma a

Enhancing Virus Surveillance through Metagenomics: Water Quality and Public Health Applications

Monitoring viruses circulating in the human population and the environment is critical for protecting public and ecosystem health. The goal of this dissertation was to incorporate a viral metagenomic approach into virus surveillance efforts (both clinical and water quality control programs) to enhance traditional virus detection methods. Clinical surveillance programs are designed to identify and monitor etiological agents that cause disease. However, the ability to identify viruses may be compromised when novel or unsuspected viruses are causing infection since traditional virus detection methods target specific known pathogens. Here we describe the successful application of viral metagenomics in a clinical setting using samples from symptomatic patients collected through the Enterovirus Surveillance (EVS) program in the Netherlands (Appendix A). Despite extensive PCR-based testing, the viruses in a small percentage of these samples (n = 7) remained unidentified for more than 10 years after collection. Viral metagenomics allowed the identification of viruses in all seven samples within a week using minimal sequencing, thus rapidly filling the diagnostic gap. The unexplained samples contained BK polyomavirus, Herpes simplex virus, Newcastle disease virus and the recently discovered Saffold viruses (SAFV) which dominated the unexplained samples (n = 4). This study demonstrated that metagenomic analyses can be added as a routine tool to investigate unidentified viruses in clinical samples in a public-health setting. In addition, metagenomic data gathered for SAFV was used to complete four genotype 3 SAFV (SAFV-3) genomes through primer walking, doubling the number of SAFV-3 full genomic sequences in public databases. In addition to monitoring viruses in symptomatic patients, it is also important to monitor viruses in wastewater (raw and treated) to protect the environment from biological contamination and prevent further spread of pathogens. To gain a comprehensive understanding of viruses that endure wastewater treatment, viral metagenomics was used to survey the total DNA and RNA viral community in reclaimed water (the reusable end-product of wastewater treatment) (Appendix B). Phages (viruses that infect bacteria) dominated the DNA viral community while eukaryotic viruses similar to known plant and insect viruses dominated RNA metagenomic libraries suggesting that highly stable viruses may be disseminated through this alternative water supply. A plant virus, the Pepper mild mottle virus (PMMoV), was identified as a potential indicator of wastewater contamination based on metagenomic data and quantitative PCR assays (Appendix C). The metagenomic analysis also revealed a wealth of novel single-stranded DNA (ssDNA) viruses in reclaimed water. Further investigation of sequences with low-level similarities to known ssDNA viruses led to the completion of ten novel ssDNA genomes from reclaimed water and marine environments (Appendix D). Unique genome architectures and phylogenetic analysis suggest that these ssDNA viruses belong to new viral genera and/or families. To further explore the ecology of the novel ssDNA viruses, a strategy was developed to take metagenomic analysis to the next level by combining expression analysis and immunotechnology (Appendix E). This dissertation made a significant contribution to current microbiological data regarding wastewater by uncovering viruses that endure the wastewater treatment and identifying a new viral bioindicator

A Field Guide to Eukaryotic Circular Single-stranded DNA Viruses: Insights Gained from Metagenomics

Despite their small size and limited protein-coding capacity, the rapid evolution rates of single-stranded DNA (ssDNA) viruses have led to their emergence as serious plant and animal pathogens. Recently, metagenomics has revealed an unprecedented diversity of ssDNA viruses, expanding their known environmental distributions and host ranges. This review summarizes and contrasts the basic characteristics of known circular ssDNA viral groups, providing a resource for analyzing the wealth of ssDNA viral sequences identified through metagenomics. Since ssDNA viruses are largely identified based on conserved rolling circle replication proteins, this review highlights distinguishing motifs and catalytic residues important for replication. Genomes identified through metagenomics have demonstrated unique ssDNA viral genome architectures and revealed characteristics that blur the boundaries between previously well-defined groups. Metagenomic discovery of ssDNA viruses has created both a challenge to current taxonomic classification schemes and an opportunity to revisit hypotheses regarding the evolutionary history of these viruses

Near-Complete Genome Sequence of a Novel Single-Stranded RNA Virus Discovered in Indoor Air

Viral metagenomic analysis of heating, ventilation, and air conditioning (HVAC) filters recovered the near-complete genome sequence of a novel virus, named HVAC-associated RNA virus 1 (HVAC-RV1). The HVAC-RV1 genome is most similar to those of picorna-like viruses identified in arthropods but encodes a small domain observed only in negative-sense single-stranded RNA viruses

Molecular Surveillance of Plant Viruses: Identification of New and Emerging Viruses of Tomato Before They Cause Epidemics

Tomato (Solanum lycopersicum) is a crop with a large number of viral pathogens (estimated at 136 in 2010). Therefore it is not surprising that viruses of tomato continue to emerge, either as new pathogens or as known pathogens that have appeared in new areas or have increased in incidence. Emerging viruses of tomato are found in a diverse array of genera: Annulavirus, Begomovirus, Crinivirus, Potexvirus, Tospovirus, Torradovirus. Three of these 6 genera contain viruses transmitted by the species complex Bemisia tabaci. In addition, viruses in the Carlavirus and Ipomovirus genera, some of which are transmitted by B. tabaci and infect other vegetable crops, are also potential sources of new viruses for tomato. Rapid detection and recognition of these new viruses can improve our management stratagies and mitigate losses. But how can we improve our response to these new threats? One approach is to survey an area and look for sequences of new viruses in a plant feeding insect; such molecular surveillance has been accomplished at two sites in Florida. Adults of B. tabaci, which are highly polyphagous and mobile, were collected and viruses were purified from them. Using deep sequencing, partial sequences of the nucleic acids from the purified viruses were obtained. A wide range of viruses, both RNA and DNA, were found. We identified partial sequences of known viruses, viruses known in other locations but new to Florida and completely new and uncharacterized viruses. Some but not all the viruses detected are transmitted by B. tabaci. For selected sequences, we used the partial sequences and primer walking to obtain complete viral genomes. Viral specific primers were then developed and used for detection and for further biological studies. These results demonstrate that molecular surveillance using metagenomic techniques is a powerful approach to identifying viruses before they emerge in epidemics