Summary
We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO‐2. This phage is lytic for related Vibrio species of great ecological interest including the ...broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V. harveyi ATTC BAA‐1116 and V. campbellii ATCC 25920). Vibrio phage SIO‐2 has a circularly permuted genome of 80 598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO‐2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO‐2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO‐2 emerges as a model of considerable interest in ecological and evolutionary studies.
Twelve lytic viruses (PgV) infecting the marine unicellular eukaryotic harmful algal bloom species
Phaeocystis globosa were isolated from the southern North Sea in 2000–2001 and partially ...characterized. All PgV isolates shared common phenotypic features with other algal viruses belonging to the family Phycodnaviridae and could be categorized in four different groups. Two main groups (PgV Group I and II) were discriminated based on particle size (150 and 100 nm respectively), genome size (466 and 177 kb) and structural protein composition. The lytic cycle showed a latent period of 10 h for PgV Group I and latent periods of 12 h and 16 h for PgV Group IIA and IIB. Host specificity and temperature sensitivity finally defined a fourth group (PgV Group IIC). Our results imply that viral infection plays an important role not only in
P. globosa dynamics but also in the diversity of both host and virus community.
The identification of the mechanisms by which marine dissolved organic matter (DOM) is produced and regenerated is critical to develop robust prediction of ocean carbon cycling. Polysaccharides ...represent one of the main constituents of marine DOM and their degradation is mainly attributed to polysaccharidases derived from bacteria. Here, we report that marine viruses can depolymerize the exopolysaccharides (EPS) excreted by their hosts using five bacteriophages that infect the notable EPS producer, Cobetia marina DSMZ 4741. Degradation monitorings as assessed by gel electrophoresis and size exclusion chromatography showed that four out of five phages carry structural enzymes that depolymerize purified solution of Cobetia marina EPS. The depolymerization patterns suggest that these putative polysaccharidases are constitutive, endo-acting and functionally diverse. Viral adsorption kinetics indicate that the presence of these enzymes provides a significant advantage for phages to adsorb onto their hosts upon intense EPS production conditions. The experimental demonstration that marine phages can display polysaccharidases active on bacterial EPS lead us to question whether viruses could also contribute to the degradation of marine DOM and modify its bioavailability. Considering the prominence of phages in the ocean, such studies may unveil an important microbial process that affects the marine carbon cycle.
The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by ...abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regard to the genetic diversity of this host. For 1 year, we monitored the abundance of three clades of Micromonas and their viruses in the Western English Channel, both in the environment using clade‐specific probes and flow cytometry, and in the laboratory using clonal strains of Micromonas clades to assay for their viruses by plaque‐forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundance of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies and genetic diversity. However, some viruses can also cross‐infect different host clades, suggesting a mechanism of horizontal gene transfer within the Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.
Summary
Viruses represent a driving force in the evolution of microorganisms including those thriving in extreme environments. However, our knowledge of the viral diversity associated to ...microorganisms inhabiting the deep‐sea hydrothermal vents remains limited. The phylum of Thermotogae, including thermophilic bacteria, is well represented in this environment. Only one virus was described in this phylum, MPV1 carried by Marinitoga piezophila. In this study, we report on the functional and genomic characterization of two new bacterioviruses that infect bacteria from the Marinitoga genus. Marinitoga camini virus 1 and 2 (MCV1 and MCV2) are temperate siphoviruses with a linear dsDNA genome of 53.4 kb and 50.5 kb respectively. Here, we present a comparative genomic analysis of the MCV1 and MCV2 viral genomes with that of MPV1. The results indicate that even if the host strains come from geographically distant sites, their genomes share numerous similarities. Interestingly, heavy metals did not induce viral production, instead the host of MCV1 produced membrane vesicles. This study highlights interaction of mobile genetic elements (MGE) with their hosts and the importance of including hosts‐MGEs' relationships in ecological studies.
Recent studies showed changes in phytoplankton lipid composition during viral infection and have indicated roles for specific lipids in the mechanisms of algal virus-host interaction. To investigate ...the generality of these findings and obtain a better understanding of the allocation of specific lipids to viruses, we studied the intact polar lipid (IPL) composition of virally infected and non-infected cultures of the prymnesiophyte Phaeocystis globosa G(A) and its lytic virus PgV-07T. The P. globosa IPL composition was relatively stable over a diel cycle and not strongly affected by viral infection. Glycolipids, phospholipids and betaine lipids were present in both the host and virus, although specific groups such as the diacylglyceryl-hydroxymethyltrimethyl-β-alanines and the sulfoquinovosyldiacylglycerols, were present in a lower proportion or were not detected in the virus. Viral glycosphingolipids (vGSLs), which have been shown to play a role in the infection strategy of the virus EhV-86, infecting the prymnesiophyte Emiliania huxleyi CCMP374, were not encountered. Our results show that the involvement of lipids in virus–algal host interactions can be very different amongst virus–algal host systems.
Summary
Background
Inflammatory bowel diseases (IBD) are chronic relapsing diseases in which pro‐inflammatory immune cells and cytokines induce intestinal tissue damage and disability. Mesenchymal ...stromal cells (MSCs) exert powerful immunomodulatory effects and stimulate tissue repair.
Aim
To review the current data on mesenchymal stromal cell therapy in IBD.
Method
We searched PubMed and ‘ClinicalTrials.gov’ databases using the terms ‘mesenchymal stromal cells’, ‘mesenchymal stem cell transplantation’, ‘inflammatory bowel diseases’, ‘Crohn disease’ and ‘colitis, ulcerative’. Additional publications were identified from individual article reference lists.
Results
MSCs include inhibition of Th1/Th17 lymphocytes and recruitment of regulatory T lymphocytes, induction of antigen‐presenting cells into a regulatory‐like profile, and stimulation of epithelial cell differentiation and proliferation. More than 200 patients with refractory fistulas have been treated with local injections of MSCs, resulting in complete response in more than half, and in overall response in approximately two thirds of patients. In refractory luminal Crohn's disease, 49 cases of systemic MSC infusions have been reported, while trials with autologous MSCs resulted in mitigated responses, studies using allogeneic MSCs were promising, with around 60% of patients experiencing a response and around 40% achieving clinical remission.
Conclusions
Mesenchymal stromal cells might represent a promising therapy for IBD, especially for Crohn's disease. There remain many unsolved questions concerning the optimal origin and source of mesenchymal stromal cells, dosage and modalities of administration. Moreover, mesenchymal stromal cells still need to prove their effectiveness compared with conventional treatments in randomised controlled trials.
N2 fixation rates were measured in the 0–1000 m layer at 13 stations located in the open western and central Mediterranean Sea (MS) during the PEACETIME cruise (late spring 2017). While the spatial ...variability in N2 fixation was not related to Fe, P nor N stocks, the surface composition of the diazotrophic community indicated a strong longitudinal gradient increasing eastward for the relative abundance of non-cyanobacterial diazotrophs (NCDs) (mainly γ-Proteobacteria) and conversely decreasing eastward for photo-heterotrophic group A (UCYN-A) (mainly UCYN-A1 and UCYN-A3), as didN2 fixation rates. UCYN-A4 and UCYN-A3 were identified for the first time in the MS. The westernmost station influenced by Atlantic waters and characterized by highest stocks of N and P displayed a patchy distribution of diazotrophic activity with an exceptionally high rate in the euphotic layer of 72.1 nmolNL-1d-1, which could support up to 19 % of primary production. At this station at 1 %PAR (photosynthetically available radiation) depth, UCYN-A4 represented up to 94 % of the diazotrophic community. These in situ observations of greater relative abundance of UCYN-A at stations with higher nutrient concentrations and dominance of NCDs at more oligotrophic stations suggest that nutrient conditions – even in the nanomolar range – may determine the composition of diazotrophic communities and in turn N2 fixation rates. The impact of Saharan dust deposition on N2 fixation and diazotrophic communities was also investigated, under present and future projected conditions of temperature and pH during short-term (3–4 d) experiments at three stations. New nutrients from simulated dust deposition triggered a significant stimulation of N2 fixation (from 41 % to 565 %). The strongest increase in N2 fixation was observed at the stations dominated by NCDs and did not lead on this short timescale to changes in the diazotrophic community composition. Under projected future conditions, N2 fixation was either increased or unchanged; in that later case this was probably due to a too-low nutrient bioavailability or an increased grazing pressure. The future warming and acidification likely benefited NCDs (Pseudomonas) and UCYN-A2, while disadvantaged UCYN-A3 without knowing which effect (alone or in combination) is the driver, especially since we do not know the temperature optima of these species not yet cultivated as well as the effect of acidification.
High-frequency pCO2 and ancillary data were recorded for seven years during the first deployment of a CARbon Interface OCean Atmosphere (CARIOCA) sensor in the surface waters of a temperate coastal ...ecosystem, the Bay of Brest, which is impacted by both coastal (via estuaries) and oceanic (North Atlantic via the Iroise Sea) water inputs. The CARIOCA sensor proved to be an excellent tool to constrain the high pCO2 variability in such dynamic coastal ecosystem. Biological processes (e.g. pelagic photosynthesis/respiration) were the main drivers of the seasonal and diurnal pCO2 dynamics throughout seven years of observations. Autotrophic processes were responsible for abrupt pCO2 drawdown of 100 to 200 mu atm in spring. During the spring bloom, diurnal variations were driven by diel biological cycle. The average daily drawdown due to autotrophy (observed during highest daily PAR) was equivalent to 10 to 60% of the total pCO2 drawdown observed every year during the spring season. From late summer to fall, heterotrophic processes increased pCO2 in the surface water of the Bay back to the pre-bloom level. The average daily increase due to heterotrophy (observed during lowest daily PAR) corresponded to 10 to 70% of the total pCO2 increase observed every year during the late summer to fall period. Air-sea CO2 fluxes estimates based on hourly, daily and monthly calculations showed that careful consideration of the diurnal variability was needed to accurately estimate air-sea CO2 fluxes in the Bay of Brest. Sampling only during daytime or night-time would induce 8 to 36% error on monthly air-sea CO2 fluxes. This would in turn reverse the direction of the fluxes at annual level for the Bay. The annual emissions of CO2 from the surface waters of the Bay to the atmosphere showed relatively low inter-annual variations with an average of +0.7+/-0.4molCm-2yr super(-1) computed for the study period. Further, air-sea CO2 fluxes computed for the adjacent inner-estuaries and Iroise Sea for an annual cycle were +17+/-3molCm-2yr super(-1) and -0.2+/-0.2molCm-2yr super(-1), respectively. The spatial gradient showed a clear pattern from strong source to sink of CO2, from the inner-estuaries to the open oceanic waters of the North Atlantic. We suggest that semi-enclosed Bays act as buffers for sea to air emissions of CO2 from inner estuaries to adjacent costal seas.
This review deals with recent advances in the investigation of ionic liquids (ILs) in the field of chirality, i.e. asymmetric synthesis and new chiral solvents.
This review deals with recent advances ...in the investigation of ionic liquids (ILs) in the field of chirality, i.e. asymmetric synthesis and new chiral solvents.
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