Host-hijacking and planktonic piracy: how phages command the microbial high seas

Microbial communities living in the oceans are major drivers of global biogeochemical cycles. With nutrients limited across vast swathes of the ocean, marine microbes eke out a living under constant assault from predatory viruses. Viral concentrations exceed those of their bacterial prey by an order of magnitude in surface water, making these obligate parasites the most abundant biological entities in the ocean. Like the pirates of the 17th and 18th centuries that hounded ships plying major trade and exploration routes, viruses have evolved mechanisms to hijack microbial cells and repurpose their cargo and indeed the vessels themselves to maximise viral propagation. Phenotypic reconfiguration of the host is often achieved through Auxiliary Metabolic Genes – genes originally derived from host genomes but maintained and adapted in viral genomes to redirect energy and substrates towards viral synthesis. In this review, we critically evaluate the literature describing the mechanisms used by bacteriophages to reconfigure host metabolism and to plunder intracellular resources to optimise viral production. We also highlight the mechanisms used when, in challenging environments, a ‘batten down the hatches’ strategy supersedes that of ‘plunder and pillage’. Here, the infecting virus increases host fitness through phenotypic augmentation in order to ride out the metaphorical storm, with a concomitant impact on host substrate uptake and metabolism, and ultimately, their interactions with their wider microbial community. Thus, the traditional view of the virus-host relationship as predator and prey does not fully characterise the variety or significance of the interactions observed. Recent advances in viral metagenomics have provided a tantalising glimpse of novel mechanisms of viral metabolic reprogramming in global oceans. Incorporation of these new findings into global biogeochemical models requires experimental evidence from model systems and major improvements in our ability to accurately predict protein function from sequence data

Estimates of tropical bromoform emissions using an inversion method

Abstract. Bromine plays an important role in ozone chemistry in both the troposphere and stratosphere. When measured by mass, bromoform (CHBr3) is thought to be the largest organic source of bromine to the atmosphere. While seaweed and phytoplankton are known to be dominant sources, the size and the geographical distribution of CHBr3 emissions remains uncertain. Particularly little is known about emissions from the Maritime Continent, which have usually been assumed to be large, and which appear to be especially likely to reach the stratosphere. In this study we aim to reduce this uncertainty by combining the first multi-annual set of CHBr3 measurements from this region, and an inversion process, to investigate systematically the distribution and magnitude of CHBr3 emissions. The novelty of our approach lies in the application of the inversion method to CHBr3. We find that local measurements of a short-lived gas like CHBr3 can be used to constrain emissions from only a relatively small, sub-regional domain. We then obtain detailed estimates of CHBr3 emissions within this area, which appear to be relatively insensitive to the assumptions inherent in the inversion process. We extrapolate this information to produce estimated emissions for the entire tropics (defined as 20° S–20° N) of 225 Gg CHBr3 yr−1. The ocean in the area we base our extrapolations upon is typically somewhat shallower, and more biologically productive, than the tropical average. Despite this, our tropical estimate is lower than most other recent studies, and suggests that CHBr3 emissions in the coastline-rich Maritime Continent may not be stronger than emissions in other parts of the tropics. M. Ashfold thanks the Natural Environment Research Council (NERC) for a research studentship, and is grateful for support through the ERC ACCI project (project number 267760). N. Harris is supported by a NERC Advanced Research Fellowship. This work was supported through the EU SHIVA project, through the NERC OP3 project, and NERC grants NE/F020341/1 and NE/J006246/1. We also acknowledge the Department of Energy and Climate Change for their support in the development of InTEM (contract GA0201). For field site support we thank S.-M. Phang, A. A. Samah and M. S. M. Nadzir of Universiti Malaya, S. Ong and H. E. Ung of Global Satria, Maznorizan Mohamad, L. K. Peng and S. E. Yong of the Malaysian Meteorological Department, the Sabah Foundation, the Danum Valley Field Centre and the Royal Society. This paper constitutes publication no. 613 of the Royal Society South East Asia Rainforest Research Programme.This is the final published version. It first appeared at http://www.atmos-chem-phys.net/14/979/2014/acp-14-979-2014.html

Introduction: In appreciation of K. Robert Clarke

BIOGRAPHY IN BRIEF Early years Professor Kenneth Robert Clarke (‘Bob’) was born on the 19th of June 1948. He was brought up largely in rural North Dorset in southern England, though his indefatigable love of travel can perhaps be traced to three years of childhood in Malta in the late 1950s, during which he was educated often as the sole English boy in the local schools, his father having taken the family there to head the English department of a newly opened secondary school for the island. Back in England in the 1960s, wise words from his older brother and an inspirational maths teacher at Blandford Grammar School determined Bob’s subject choice for life – and the specialised focus of English state education at that time ensured he was taught nothing except mathematics from the age of 16. This led to a first class degree in Mathematics at the University of Leicester in 1969 (which contained no statistics at all, as was the case at the time for both school and university mathematics)and, more importantly that year, marriage (a long and happy one) to Cathy, a Leicester classics graduate. An M.Sc. at the University of Newcastle upon Tyne, under a revered statistician, Robin Plackett, brought Bob into the world of statistical theory (and writing computer code, in the days when ‘cut and paste’ literally meant taking a pair of scissors and tape to hole-punched paper!). This was followed by a Newcastle Ph.D. in Stereology, a branch of geometric probability and integral equations which infers 3-d properties from 2-d sections and projections, with application in life sciences, metallurgy and other fields. Bob became known on the university seminar circuit for provisioning the audience at the tea break by slicing up a cherry cake to derive the cherry density and diameter distribution from the resulting plane sections. A 6-year stint (1973–1979) as a Lecturer in the Department of Statistics at the University of Glasgow, Scotland – under the tutelage and encouragement of two further giants of statistics, David Silvey and John Aitchison – turned Bob into a lecturer and taught him the trick of keeping just one step ahead of his students. It also showed him how rewarding it could be to work with academics from other departments to bring statistical theory to bear on their problems. He also, arguably, missed his vocation in life when in the mid-1970s a computerised golf game he programmed in machine code for a stand-alone pen plotter – with the correct differential equations for a ball in flight in the wind and on a sloping green with friction – stole the show of the Stats Department’s University Open Day offerin

Biodegradation of the Alkaline Cellulose Degradation Products Generated during Radioactive Waste Disposal.

The anoxic, alkaline hydrolysis of cellulosic materials generates a range of cellulose degradation products (CDP) including α and β forms of isosaccharinic acid (ISA) and is expected to occur in radioactive waste disposal sites receiving intermediate level radioactive wastes. The generation of ISA's is of particular relevance to the disposal of these wastes since they are able to form complexes with radioelements such as Pu enhancing their migration. This study demonstrates that microbial communities present in near-surface anoxic sediments are able to degrade CDP including both forms of ISA via iron reduction, sulphate reduction and methanogenesis, without any prior exposure to these substrates. No significant difference (n = 6, p = 0.118) in α and β ISA degradation rates were seen under either iron reducing, sulphate reducing or methanogenic conditions, giving an overall mean degradation rate of 4.7×10−2 hr−1 (SE±2.9×10−3). These results suggest that a radioactive waste disposal site is likely to be colonised by organisms able to degrade CDP and associated ISA's during the construction and operational phase of the facility

Towards the Industrial Production of Omega-3 Long Chain Polyunsaturated Fatty Acids from a Genetically Modified Diatom Phaeodactylum tricornutum.

The marine diatom Phaeodactylum tricornutum can accumulate up to 30% of the omega-3 long chain polyunsaturated fatty acid (LC-PUFA) eicosapentaenoic acid (EPA) and, as such, is considered a good source for the industrial production of EPA. However, P. tricornutum does not naturally accumulate significant levels of the more valuable omega-3 LC-PUFA docosahexaenoic acid (DHA). Previously, we have engineered P. tricornutum to accumulate elevated levels of DHA and docosapentaenoic acid (DPA) by overexpressing heterologous genes encoding enzyme activities of the LC-PUFA biosynthetic pathway. Here, the transgenic strain Pt_Elo5 has been investigated for the scalable production of EPA and DHA. Studies have been performed at the laboratory scale on the cultures growing in up to 1 L flasks a 3.5 L bubble column, a 550 L closed photobioreactor and a 1250 L raceway pond with artificial illumination. Detailed studies were carried out on the effect of different media, carbon sources and illumination on omega-3 LC-PUFAs production by transgenic strain Pt_Elo5 and wild type P. tricornutum grown in 3.5 L bubble columns. The highest content of DHA (7.5% of total fatty acids, TFA) in transgenic strain was achieved in cultures grown in seawater salts, Instant Ocean (IO), supplemented with F/2 nutrients (F2N) under continuous light. After identifying the optimal conditions for omega-3 LC-PUFA accumulation in the small-scale experiments we compared EPA and DHA levels of the transgenic strain grown in a larger fence-style tubular photobioreactor and a raceway pond. We observed a significant production of DHA over EPA, generating an EPA/DPA/DHA profile of 8.7%/4.5%/12.3% of TFA in cells grown in a photobioreactor, equivalent to 6.4 μg/mg dry weight DHA in a mid-exponentially growing algal culture. Omega-3 LC-PUFAs production in a raceway pond at ambient temperature but supplemented with artificial illumination (110 μmol photons m-2s-1) on a 16:8h light:dark cycle, in natural seawater and F/2 nutrients was 24.8% EPA and 10.3% DHA. Transgenic strain grown in RP produced the highest levels of EPA (12.8%) incorporated in neutral lipids. However, the highest partitioning of DHA in neutral lipids was observed in cultures grown in PBR (7.1%). Our results clearly demonstrate the potential for the development of the transgenic Pt_Elo5 as a platform for the commercial production of EPA and DHA

Long-term halocarbon observations from a coastal and an inland site in Sabah, Malaysian Borneo

Abstract. Short-lived halocarbons are believed to have important sources in the tropics, where rapid vertical transport could provide a significant source to the stratosphere. In this study, quasi-continuous measurements of short-lived halocarbons are reported for two tropical sites in Sabah (Malaysian Borneo), one coastal and one inland (rainforest). We present the observations for C2Cl4, CHBr3, CH2Br2* (actually ~80% CH2Br2 and ~20% CHBrCl2) and CH3I from November 2008 to January 2010 made using our μDirac gas chromatographs with electron capture detection (GC-ECD). We focus on the first 15 months of observations, showing over one annual cycle for each compound and therefore adding significantly to the few limited-duration observational studies that have been conducted thus far in southeast Asia. The main feature in the C2Cl4 behaviour at both sites is its annual cycle, with the winter months being influenced by northerly flow with higher concentrations, typical of the Northern Hemisphere, and with the summer months influenced by southerly flow and lower concentrations representative of the Southern Hemisphere. No such clear annual cycle is seen for CHBr3, CH2Br2* or CH3I. The baseline values for CHBr3 and CH2Br2* are similar at the coastal (overall median: CHBr3 1.7 ppt, CH2Br2* 1.4 ppt) and inland sites (CHBr3 1.6 ppt, CH2Br2* 1.1 ppt), but periods with elevated values are seen at the coast (overall 95th percentile: CHBr3 4.4 ppt, CH2Br2ast 1.9 ppt), presumably resulting from the stronger influence of coastal emissions. Overall median bromine values from [CHBr3 × 3] + [CH2Br2* × 2] are 8.0 ppt at the coast and 6.8 ppt inland. The median values reported here are largely consistent with other limited tropical data and imply that southeast Asia generally is not, as has been suggested, a hot spot for emissions of these compounds. These baseline values are consistent with the most recent emissions found for southeast Asia using the p-TOMCAT (Toulouse Off-line Model of Chemistry And Transport) model. CH3I, which is only observed at the coastal site, is the shortest-lived compound measured in this study, and the observed atmospheric variations reflect this, with high variability throughout the study period. This work was supported by a NERC consortium grant to the OP3 team, by NCAS, by the European Commission through the SCOUT-O3 project (505390-GOCE-CF2004) and by NERC western Pacific grant number NE/F020341/1 and NERC CAST grant number NE/J006246/1. L. M. O’Brien and M. J. Ashfold thank NERC for research studentships. A. D. Robinson acknowledges NERC for their support through small grant project NE/D008085/1. N. R. P. Harris is supported by a NERC Advanced Research Fellowship. We thank the Sabah Foundation, Danum Valley Field Centre and the Royal Society (Glen Reynolds) for field site support. The research leading to these results has received funding from the European Union’s Seventh Framework Programme FP7/2007–2013 under grant agreement no. 226224 – SHIVA. We thank David Oram and Stephen Humphrey at UEA for their assistance in checking the calibration of our Aculife cylinder in May 2009. This is paper number 626 of the Royal Society’s South East Asian Rainforest Research Programme.This is the final published version. It first appeared at http://www.atmos-chem-phys.net/14/8369/2014/acp-14-8369-2014.html

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and ‘universal’ gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The ‘VirION’ (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature

Environmental risk assessment of GE plants under low-exposure conditions

The requirement for environmental risk assessment (ERA) of genetically engineered (GE) plants prior to large scale or commercial introduction into the environment is well established in national laws and regulations, as well as in international agreements. Since the first introductions of GE plants in commercial agriculture in the 1990s, a nearly universal paradigm has emerged for conducting these assessments based on a few guiding principles. These include the concept of case-by-case assessment, the use of comparative assessments, and a focus of the ERA on characteristics of the plant, the introduced trait, and the receiving environment as well as the intended use. In practice, however, ERAs for GE plants have frequently focused on achieving highly detailed characterizations of potential hazards at the expense of consideration of the relevant levels of exposure. This emphasis on exhaustive hazard characterization can lead to great difficulties when applied to ERA for GE plants under low-exposure conditions. This paper presents some relevant considerations for conducting an ERA for a GE plant in a low-exposure scenario in the context of the generalized ERA paradigm, building on discussions and case studies presented during a session at ISBGMO 12

Renal cancer associated with recurrent spontaneous pneumothorax in Birt-Hogg-Dubé syndrome: a case report and review of the literature

<p>Abstract</p> <p>Introduction</p> <p>Birt-Hogg-Dubé syndrome is a rare genodermatosis characterized by hair follicle hamartomas, renal tumors and spontaneous pneumothorax. We present the case of a patient with pulmonary cysts and recurrent spontaneous pneumothorax. She had typical skin lesions, and was found to have a hybrid oncocytoma which was surgically excised.</p> <p>Case presentation</p> <p>A 60-year-old Caucasian woman had a 10-year history of cystic lung disease and recurrent spontaneous pneumothoraces. She was noted to have papular lesions over her face and forehead. The result of a biopsy showed these lesions to be fibrofolliculomas. A diagnosis of Birt-Hogg-Dubé syndrome was made and she was screened for renal tumors since these are a recognized association. A hybrid oncocytoma was detected which was surgically excised by partial nephrectomy.</p> <p>Conclusion</p> <p>It is important to consider a possible diagnosis of Birt-Hogg-Dubé syndrome in cases of recurrent pneumothorax. Affected individuals must be screened for renal tumors, a potentially lethal consequence of this syndrome.</p