Single-amplified genomes reveal most streamlined free-living marine bacteria.

Evolutionary adaptations of prokaryotes to the environment sometimes result in genome reduction. Our knowledge of this phenomenon among free-living bacteria remains scarce. We address the dynamics and limits of genome reduction by examining one of the most abundant bacteria in the ocean, the SAR86 clade. Despite its abundance, comparative genomics has been limited by the absence of pure cultures and the poor representation in metagenome-assembled genomes. We co-assembled multiple previously available single-amplified genomes to obtain the first complete genomes from members of the four families. All families showed a convergent evolutionary trajectory with characteristic features of streamlined genomes, most pronounced in the TMED112 family. This family has a genome size of ca. 1 Mb and only 1 bp as median intergenic distance, exceeding values found in other abundant microbes such as SAR11, OM43 and Prochlorococcus. This genomic simplification led to a reduction in the biosynthesis of essential molecules, DNA repair-related genes, and the ability to sense and respond to environmental factors, which could suggest an evolutionary dependence on other co-occurring microbes for survival (Black Queen hypothesis). Therefore, these reconstructed genomes within the SAR86 clade provide new insights into the limits of genome reduction in free-living marine bacteria.

Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates.

BACKGROUND: Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. RESULTS: Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ggp/gpg/gmg clusters and glycerolipids glpK/glpA), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. CONCLUSIONS: The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system.

Microbe Profile: Alteromonas macleodii - a widespread, fast-responding, 'interactive' marine bacterium.

Alteromonas macleodii is a marine heterotrophic bacterium with widespread distribution - from temperate to tropical oceans, and from surface to deep waters. Strains of A. macleodii exhibit considerable genomic and metabolic variability, and can grow rapidly on diverse organic compounds. A. macleodii is a model organism for the study of population genomics, physiological adaptations and microbial interactions, with individual genomes encoding diverse phenotypic traits influenced by recombination and horizontal gene transfer.

Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea.

Ammonia-oxidizing archaea (AOA) from the phylum Thaumarchaeota are ubiquitous in marine ecosystems and play a prominent role in carbon and nitrogen cycling. Previous studies have suggested that, like all microbes, thaumarchaea are infected by viruses and that viral predation has a profound impact on thaumarchaeal functioning and mortality, thereby regulating global biogeochemical cycles. However, not a single virus capable of infecting thaumarchaea has been reported thus far. Here we describe the isolation and characterization of three Nitrosopumilus spindle-shaped viruses (NSVs) that infect AOA and are distinct from other known marine viruses. Although NSVs have a narrow host range, they efficiently infect autochthonous Nitrosopumilus strains and display high rates of adsorption to their host cells. The NSVs have linear double-stranded DNA genomes of ∼28 kb that do not display appreciable sequence similarity to genomes of other known archaeal or bacterial viruses and could be considered as representatives of a new virus family, the "Thaspiviridae." Upon infection, NSV replication leads to inhibition of AOA growth, accompanied by severe reduction in the rate of ammonia oxidation and nitrite reduction. Nevertheless, unlike in the case of lytic bacteriophages, NSV propagation is not associated with detectable degradation of the host chromosome or a decrease in cell counts. The broad distribution of NSVs in AOA-dominated marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities. Collectively, our results shed light on the diversity, evolution, and potential impact of the virosphere associated with ecologically important mesophilic archaea.

Genotype FBN1/phenotype relationship in a cohort of patients with Marfan syndrome.

Marfan syndrome (MFS) is a systemic connective tissue disorder caused by mutations in the fibrillin-1 (FBN1) gene, and cardiovascular involvement is the leading cause of mortality. We sought to examine the genotype/phenotype realtionship in 61 consecutive patients with a phenotype and genotype compatible with MFS. The FBN1 gene was analyzed by massive sequencing using a hybridization capture-based target enrichment custom panel. Forty-three different variants of FBN1 were identified, of which 17 have not been previously reported. The causal variants of MFS were grouped into mutations resulting in haploinsufficiency (HI group; 23 patients) and mutations producing a dominant-negative effect (DN group; 38 patients). Patient information was collected from electronic medical records and clinical evaluation. While no significant differences were found between the two groups, the HI group included more cases with aortic dissection and occurring at a younger age that the DN group (34.7% vs. 15.8%; p = 0.160). Irrespective of the mutation group, males presented with a higher probability of aortic involvement (4-fold higher risk than females) and aortic dissections events occurred at younger ages. Patients with DN variants carrying a cysteine substitution had a higher incidence of ectopia lentis.

Influence of colony traits on ectoparasite infestation in birds breeding in mixed-species colonies.

Coloniality in birds is often associated with an increase in parasite burden, but whether the co-occurrence of several host species influences the prevalence and abundance of ectoparasites and their relationship with colony size or density remains poorly known. Here, we studied mixed-species breeding colonies formed after the provision of artificial breeding structures for restoring the lesser kestrel (Falco naumanni) population in Portugal, to investigate the influence of colony traits on ectoparasite infestation. We sampled four groups of ectoparasites (carnid flies, haematophagous mites, louse flies and chewing lice) in four hosts: lesser kestrels, European rollers (Coracias garrulus), feral pigeons (Columba livia) and spotless starlings (Sturnus unicolor). Each host species had a distinct infracommunity of ectoparasites, regardless of colony traits such as size, density or host richness. The abundance of the most common ectoparasite, Carnus hemapterus, was influenced by colony composition ­ number of nests of each host species ­ rather than by colony size or density, with its abundance being diluted with increasing numbers of less suitable hosts such as starlings. The increased contact between multiple species of hosts in breeding colonies may complexify host­parasite interactions and challenge our current knowledge on the ecological relationships between host sociality and parasitism.

Using Aerial and Vehicular NFV Infrastructures to Agilely Create Vertical Services.

5G communications have become an enabler for the creation of new and more complex networking scenarios, bringing together different vertical ecosystems. Such behavior has been fostered by the network function virtualization (NFV) concept, where the orchestration and virtualization capabilities allow the possibility of dynamically supplying network resources according to its needs. Nevertheless, the integration and performance of heterogeneous network environments, each one supported by a different provider, and with specific characteristics and requirements, in a single NFV framework is not straightforward. In this work we propose an NFV-based framework capable of supporting the flexible, cost-effective deployment of vertical services, through the integration of two distinguished mobile environments and their networks: small sized unmanned aerial vehicles (SUAVs), supporting a flying ad hoc network (FANET) and vehicles, promoting a vehicular ad hoc network (VANET). In this context, a use case involving the public safety vertical will be used as an illustrative example to showcase the potential of this framework. This work also includes the technical implementation details of the framework proposed, allowing to analyse and discuss the delays on the network services deployment process. The results show that the deployment times can be significantly reduced through a distributed VNF configuration function based on the publish-subscribe model.

Cellular and Virtualization Technologies for UAVs: An Experimental Perspective.

The Unmanned Aircraft System (UAS) ecosystem is exponentially growing in both recreational and professional fields to provide novel services and applications to consumers from multiple engineering fields. However, this technology has only scraped the surface of its potential, especially in those cases that require fast reaction times. Accordingly, the UAS Traffic Management (UTM) project aims at efficiently managing the air traffic for Unmanned Aerial Vehicle (UAV) operations, including those cases where UAVs might be remotely managed from a completely different geographical location. With these considerations in mind, this article presents a cellular-assisted UAVs testbed used to complete a mission managed beyond the radio line-of-sight (BRLoS), as well as introducing a virtualization platform for deploying services using containerization technology. In addition, the article conducts a communication performance evaluation in order to determine if the testbed equipment meets the requirements to carry out this BRLoS management. Finally, indoor flight operations are carried out to demonstrate the feasibility and proper operation of the testbed.

Deploying an NFV-Based Experimentation Scenario for 5G Solutions in Underserved Areas.

Presently, a significant part of the world population does not have Internet access. The fifth-generation cellular network technology evolution (5G) is focused on reducing latency, increasing the available bandwidth, and enhancing network performance. However, researchers and companies have not invested enough effort into the deployment of the Internet in remote/rural/undeveloped areas for different techno-economic reasons. This article presents the result of a collaboration between Brazil and the European Union, introducing the steps designed to create a fully operational experimentation scenario with the main purpose of integrating the different achievements of the H2020 5G-RANGE project so that they can be trialed together into a 5G networking use case. The scenario encompasses (i) a novel radio access network that targets a bandwidth of 100 Mb/s in a cell radius of 50 km, and (ii) a network of Small Unmanned Aerial Vehicles (SUAV). This set of SUAVs is NFV-enabled, on top of which Virtual Network Functions (VNF) can be automatically deployed to support occasional network communications beyond the boundaries of the 5G-RANGE radio cells. The whole deployment implies the use of a virtual private overlay network enabling the preliminary validation of the scenario components from their respective remote locations, and simplifying their subsequent integration into a single local demonstrator, the configuration of the required GRE/IPSec tunnels, the integration of the new 5G-RANGE physical, MAC and network layer components and the overall validation with voice and data services.

Ecogenomics of the SAR11 clade.

Members of the SAR11 clade, despite their high abundance, are often poorly represented by metagenome-assembled genomes. This fact has hampered our knowledge about their ecology and genetic diversity. Here we examined 175 SAR11 genomes, including 47 new single-amplified genomes. The presence of the first genomes associated with subclade IV suggests that, in the same way as subclade V, they might be outside the proposed Pelagibacterales order. An expanded phylogenomic classification together with patterns of metagenomic recruitment at a global scale have allowed us to define new ecogenomic units of classification (genomospecies), appearing at different, and sometimes restricted, metagenomic data sets. We detected greater microdiversity across the water column at a single location than in samples collected from similar depth across the global ocean, suggesting little influence of biogeography. In addition, pangenome analysis revealed that the flexible genome was essential to shape genomospecies distribution. In one genomospecies preferentially found within the Mediterranean, a set of genes involved in phosphonate utilization was detected. While another, with a more cosmopolitan distribution, was unique in having an aerobic purine degradation pathway. Together, these results provide a glimpse of the enormous genomic diversity within this clade at a finer resolution than the currently defined clades.

Microorganisms of Lake Baikal-the deepest and most ancient lake on Earth.

Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments. KEY POINTS: • The chemical composition and limnic features of the deepest lake on Earth determine the vital activity of microorganisms. • The diversity, ecology, and role of individual taxa of microorganisms were studied using cultivation and molecular methods. • Data of large metagenomic datasets in the epipelagic and bathypelagic layers of the water column in southern Baikal were discussed.

Human Development Index of the maternal country of origin and its relationship with maternal near miss: A systematic review of the literature.

BACKGROUND: The reduction in maternal mortality worldwide has increased the interest in studying more frequent severe events such as maternal near miss. The Human Development Index is a sociodemographic country-specific variable that includes key human development indicators such as living a long and healthy life, acquiring knowledge, and enjoying a decent standard of living, allowing differentiation between countries. In a globalised environment, it is necessary to study whether the Human Development Index of each patient's country of origin can be associated with the maternal near-miss rate and thus classify the risk of maternal morbidity and mortality. METHODS: A systematic review of the literature published between 2008 and 2019 was conducted, including all articles that reported data about maternal near miss in their sample of pregnant women, in addition to describing the study countries of their sample population. The Human Development Index of the study country, the maternal near-miss rate, the maternal mortality rate, and other maternal-perinatal variables related to morbidity and mortality were used. RESULTS: After the systematic review, eighty two articles from over thirty countries were included, for a total of 3,699,697 live births, 37,191 near miss cases, and 4029 mortality cases. A statistically significant (p <0.05) inversely proportional relationship was observed between the Human Development Index of the study country and the maternal near-miss and mortality rates. The most common cause of maternal near miss was haemorrhage, with an overall rate of 38.5%, followed by hypertensive disorders of pregnancy (34.2%), sepsis (7.5%), and other undefined causes (20.9%). CONCLUSIONS: The Human Development Index of the maternal country of origin is a sociodemographic variable allowing differentiation and classification of the risk of maternal mortality and near miss in pregnant women. The most common cause of maternal near miss published in the literature was haemorrhage. TRIAL REGISTRATION: PROSPERO ID: CRD 42019133464.

Quantitative Transthoracic Echocardiography of the Response to Dobutamine in Cardiac Surgery Patients With Low Cardiac Output Syndrome.

OBJECTIVE: To quantify the acute effects of dobutamine in postoperative low cardiac output syndrome (LCOS) using transthoracic echocardiographic, hemodynamic, and blood biomarker monitoring and to assess its association with clinical outcomes. DESIGN: Observational prospective study. SETTING: Single university hospital. PARTICIPANTS: Patients undergoing elective cardiac surgery. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Echocardiographic parameters, hemodynamic data, and plasma biomarkers were obtained before and early after inotrope initiation. The diagnostic value of transthoracic echocardiographic parameters and their association with clinical outcome were evaluated. Thirty-eight LCOS patients and 12 control patients were included. The left ventricular outflow tract velocity time integral was significantly lower in LCOS patients (11.75 v 19.08 cm; p < 0.001) and showed a marked improvement after dobutamine administration (∼37% increase). Dobutamine improved left and right ventricular function, increased mean arterial pressure and urine output, and lowered lactate levels. The duration of dobutamine support, but not in-hospital mortality, was associated with echocardiographic estimates of cardiac performance early after dobutamine initiation. CONCLUSIONS: Early transthoracic echocardiographic assessment and the acute response to inotropic therapy may provide rapid and highly valuable information in the diagnostic workup and risk evaluation of patients with suspected LCOS after cardiac surgery.

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters.

Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (>0.2 µm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assembly.

Energy-Aware Management in Multi-UAV Deployments: Modelling and Strategies.

Nowadays, Unmanned Aerial Vehicles (UAV) are frequently present in the civilian environment. However, proper implementations of different solutions based on these aircraft still face important challenges. This article deals with multi-UAV systems, forming aerial networks, mainly employed to provide Internet connectivity and different network services to ground users. However, the mission duration (hours) is longer than the limited UAVs' battery life-time (minutes). This paper introduces the UAV replacement procedure as a way to guarantee ground users' connectivity over time. This article also formulates the practical UAV replacements problem in moderately large multi-UAV swarms and proves it to be an NP-hard problem in which an optimal solution has exponential complexity. In this regard, the main objective of this article is to evaluate the suitability of heuristic approaches for different scenarios. This paper proposes betweenness centrality heuristic algorithm (BETA), a graph theory-based heuristic algorithm. BETA not only generates solutions close to the optimal (even with 99% similarity to the exact result) but also improves two ground-truth solutions, especially in low-resource scenarios.

Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes.

Marine Group I (MGI) Thaumarchaeota are some of the most abundant microorganisms in the deep ocean and responsible for much of the ammonia oxidation occurring in this environment. In this work, we present 35 sequences assembled from metagenomic samples of the first uncultivated Caudovirales viruses associated with Thaumarchaeota, which we designated marthavirus. Most of the sequences were obtained from cellular metagenomes confirming that they represent an important tool to study environmental viral communities due to cells retrieved while undergoing viral lysis. Metagenomic recruitment showed that this viral population is formed by very divergent entities with high intrapopulation homogeneity. However, metatranscriptomic analyses revealed the same differential expression profile with the capsid as major transcript, indicative of viruses during the lytic cycle. The cobalamine biosynthesis gene cobS, an auxiliary metabolic gene, was also highly expressed during the infection. These analyses expand our understanding of the global diversity of archaeal viruses.

Off-host longevity of the winged dispersal stage of Carnus hemapterus (Insecta: Diptera) modulated by gender, body size and food provisioning.

Highlighting the dispersal ecology of parasites is important for understanding epidemiological, demographic and coevolutionary aspects of host-parasite interactions. Yet, critical aspects of the dispersal stage of parasites, such as longevity and the factors influencing it, are poorly known. Here we study the lifespan of the dispersal stage of an ectoparasitic dipteran, Carnus hemapterus, and the impact of gender, body size and food provisioning on longevity. We found that freshly emerged imagoes survive at most less than 4 days. Longevity increased with body size and, since this parasite exhibits sexual size dimorphism, the bigger females lived longer than males. However, controlling for body size suggests that males lived relatively longer than females. Furthermore, a humid environment and food provisioning (flowers) significantly increased individual life spans. We discuss the relative importance of spatial and temporal dispersal in relation to the infectious potential of this parasite.

Defining host range: host-parasite compatibility during the non-infective phase of the parasite also matters.

Host range and parasite specificity determine key epidemiological, ecological and evolutionary aspects of host-parasite interactions. Parasites are usually classified as generalists or specialists based on the number of hosts they feed on. Yet, the requirements of the various stages of a parasite may influence the suitability of a given host species. Here, we investigate the generalist nature of three common ectoparasites (the dipteran Carnus hemapterus and two species of louse flies, Pseudolynchia canariensis and Ornithophila metallica), exploiting two avian host species (the European roller Coracias garrulus and the Rock pigeon Columba livia), that frequently occupy the same breeding sites. We explore the prevalence and abundance of both the infective and the puparial stages of the ectoparasites in both host species. Strong preferences of Pseudolynchia canariensis for pigeons and of Carnus hemapterus for rollers were found. Moderate prevalence of Ornithophila metallica was found in rollers but this louse fly avoided pigeons. In some cases, the infestation patterns observed for imagoes and puparia were consistent whereas in other cases host preferences inferred from imagoes differed from the ones suggested by puparia. We propose that the adult stages of these ectoparasites are more specialist than reported and that the requirements of non-infective stages can restrict the effective host range of some parasites.

Enabling the Orchestration of IoT Slices through Edge and Cloud Microservice Platforms.

This article addresses one of the main challenges related to the practical deployment of Internet of Things (IoT) solutions: the coordinated operation of entities at different infrastructures to support the automated orchestration of end-to-end Internet of Things services. This idea is referred to as "Internet of Things slicing" and is based on the network slicing concept already defined for the Fifth Generation (5G) of mobile networks. In this context, we present the architectural design of a slice orchestrator addressing the aforementioned challenge, based on well-known standard technologies and protocols. The proposed solution is able to integrate existing technologies, like cloud computing, with other more recent technologies like edge computing and network slicing. In addition, a functional prototype of the proposed orchestrator has been implemented, using open-source software and microservice platforms. As a first step to prove the practical feasibility of our solution, the implementation of the orchestrator considers cloud and edge domains. The validation results obtained from the prototype prove the feasibility of the solution from a functional perspective, verifying its capacity to deploy Internet of Things related functions even on resource constrained platforms. This approach enables new application models where these Internet of Things related functions can be onboarded on small unmanned aerial vehicles, offering a flexible and cost-effective solution to deploy these functions at the network edge. In addition, this proposal can also be used on commercial cloud platforms, like the Google Compute Engine, showing that it can take advantage of the benefits of edge and cloud computing respectively.

Transport-Layer Limitations for NFV Orchestration in Resource-Constrained Aerial Networks.

In this paper, we identify the main challenges and problems related with the management and orchestration of Virtualized Network Functions (VNFs) over aerial networks built with Small Unmanned Aerial Vehicles (SUAVs). Our analysis starts from a reference scenario, where several SUAVs are deployed over a delimited geographic area, and provide a mobile cloud environment that supports the deployment of functions and services using Network Functions Virtualization (NFV) technologies. After analyzing the main challenges to NFV orchestration in this reference scenario from a theoretical perspective, we undertake the study of one specific but relevant aspect following a practical perspective, i.e., the limitations of existing transport-layer solutions to support the dissemination of NFV management and orchestration information in the considered scenario. While in traditional cloud computing environments this traffic is delivered using TCP, our simulation results suggest that using this protocol over an aerial network of SUAVs presents certain limitations. Finally, based on the lessons learned from our practical analysis, the paper outlines different alternatives that could be followed to address these challenges.