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Pseudomonas stutzeri AN10 has two ISL3-like insertion sequences (ISs). One of them has been recently described as ISPst9. In this study we show that the second IS, situated 4.5 kb upstream of ISPst9, is an isoform of ISPpu12 from Pseudomonas putida mt-2. Although both ISL3-like ISs are flanked by nearly identical (21/24 conserved residues) inverted repeats (IRs) and harbor similar transposases (93% amino acid identity), they differ in their accompanying genes. As described for ISPst9, the isoform of ISPpu12 also transposes by a conservative mechanism, forms circular double-stranded DNA (dsDNA) transposition intermediates, and is induced by interaction with the conjugative strain Escherichia coli S17-1[[lambda].sub.pir] (conjugative interaction) but not with the nonconjugative E. coli DH5[alpha]. In fact, we demonstrate that ISPst9 transposition after conjugative interaction occurs only when ISPpu12 is present, indicating that ISPpu12 is upregulating transposition of both ISs under such conditions. We also demonstrate that this conjugative interaction-mediated induction of ISPpu12 is not exclusive to the P. stutzeri AN10 strain but is a more general phenomenon, at least in Pseudomonas. Mutation of TnpR, a MerR-like transcriptional regulator present in ISPpu12 but not in ISPst9, reduced the transcription of tnpA (ISPpu12 transposase-encoding gene) and decreased formation of circular dsDNA transposition intermediates after conjugative interaction. Complementation of the TnpR mutant restored the phenotype. In addition, the presence of TnpR in an ISPpu12.free genetic background did not induce ISPst9 after conjugative interaction. Thus, our results suggest that TnpR, after conjugative interaction, activates transcription of tnpA of ISPpu12. Then, TnpA of ISPpu12 would bind to IRs of both ISs, ISPpu12 and ISPst9, causing their transposition. doi: 10.1128/JB.01336-09

ISPst9 is an ISL3-like insertion sequence (IS) that was recently described in the naphthalene-degrading organism Pseudomonas stutzeri strain AN10. In this paper we describe a novel strong IS regulation stimulus; transposition of ISPst9 is induced in all P. stutzeri AN10 cells after conjugative interaction with Escherichia coli. Thus, we observed that in all P. stutzeri AN10 cells that received genetic material by conjugation the ISPst9 genomic dose and/or distribution was changed. Furthermore, ISPst9 transposition was also observed when P. stutzeri AN10 cells were put in contact with the plasmidless conjugative strain E. coli S17-1[[lambda].sub.pir], but not when they were put in contact with E. coli DH5[alpha] (a nonconjugative strain). The mechanism of ISPst9 transposition was analyzed, and transposition was shown to proceed by excision from the donor DNA using a conservative mechanism, which generated 3- to 10-bp deletions of the flanking DNA. Our results indicate that ISPst9 transposes, forming double-stranded DNA circular intermediates consisting of the IS and a 5-bp intervening DNA sequence probably derived from the ISPst9 flanking regions. The kinetics of IS circle formation are also described.

Plastics are versatile materials that have the potential to propel humanity towards circularity and ultimate societal sustainability. However, the escalating concern surrounding plastic pollution has garnered significant attention, leading to widespread negative perceptions of these materials. Here, we question the role microbes may play in plastic pollution bioremediation by (i) defining polymer biodegradability (i.e., recalcitrant, hydrolysable and biodegradable polymers) and (ii) reviewing best practices for evaluating microbial biodegradation of plastics. We establish recommendations to facilitate the implementation of rigorous methodologies in future studies on plastic biodegradation, aiming to push this field towards the use of isotopic labelling to confirm plastic biodegradation and further determine the molecular mechanisms involved., (© 2024 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd.)

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.

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.

Network Function Virtualization (NFV) has been regarded as one of the key enablers for the 5 th Generation of mobile networks, or 5G. This paradigm allows to reduce the dependence on specialized hardware to deploy telecommunications and vertical services. To this purpose, it relies on virtualization techniques to softwarize network functions, simplifying their development and reducing deployment time and costs. In this context, Universidad Carlos III de Madrid, Telefónica, and IMDEA Networks Institute have developed an NFV ecosystem inside 5TONIC, an open network innovation center focused on 5G technologies, enabling the creation of complex, close to reality experimentation scenarios across a distributed set of NFV infrastructures, which can be made available by stakeholders at different geographic locations. This article presents the protocol that has been defined to incorporate new remote NFV sites into the multi-site NFV ecosystem based on 5TONIC, describing the requirements for both the existing and the newly incorporated infrastructures, their connectivity through an overlay network architecture, and the steps necessary for the inclusion of new sites. The protocol is exemplified through the incorporation of an external site to the 5TONIC NFV ecosystem. Afterwards, the protocol details the verification steps required to validate a successful site integration. These include the deployment of a multi-site vertical service using a remote NFV infrastructure with Small Unmanned Aerial Vehicles (SUAVs). This serves to showcase the potential of the protocol to enable distributed experimentation scenarios.

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.

The Network Function Virtualization (NFV) paradigm is one of the key enabling technologies in the development of the 5 th generation of mobile networks. This technology aims to lessen the dependence on hardware in the provision of network functions and services by using virtualization techniques that allow the softwarization of those functionalities over an abstraction layer. In this context, there is increasing interest in exploring the potential of unmanned aerial vehicles (UAVs) to offer a flexible platform capable of enabling cost-effective NFV operations over delimited geographic areas. To demonstrate the practical feasibility of utilizing NFV technologies in UAV platforms, a protocol is presented to set up a functional NFV environment based on open source technologies, in which a set of small UAVs supply the computational resources that support the deployment of moderately complex network services. Then, the protocol details the different steps needed to support the automated deployment of an internet protocol (IP) telephony service over a network of interconnected UAVs, leveraging the capacities of the configured NFV environment. Experimentation results demonstrate the proper operation of the service after its deployment. Although the protocol focuses on a specific type of network service (i.e., IP telephony), the described steps may serve as a general guide to deploy other type of network services. On the other hand, the protocol description considers concrete equipment and software to set up the NFV environment (e.g., specific single board computers and open source software). The utilization of other hardware and software platforms may be feasible, although the specific configuration aspect of the NFV environment and the service deployment may present variations with respect to those described in the protocol.

In this paper, we present a practical solution to support the adaptable and automated deployment of applications of Small Unmanned Aerial Vehicles (SUAVs). Our solution is based on virtualization technologies, and considers SUAVs as programmable network platforms capable of executing virtual functions and services, which may be dynamically selected according to the requirements specified by the operator of the aerial vehicles. This way, SUAVs can be flexibly and rapidly adapted to different missions with heterogeneous objectives. The design of our solution is based on Network Function Virtualization (NFV) technologies, developed under the umbrella of the fifth generation of mobile networks (5G), as well as on existing Internet protocol standards, including flying ad hoc network routing protocols. We implemented a functional prototype of our solution using well-known open source technologies, and we demonstrated its practical feasibility with the execution of an IP telephony service. This service was implemented as a set of virtualized network functions, which were automatically deployed and interconnected over an infrastructure of SUAVs, being the telephony service tested with real voice-over-IP terminals.

We claim the strong potential of data-centric communications in Unmanned Aircraft Systems (UAS), as a suitable paradigm to enhance collaborative operations via efficient information sharing, as well as to build systems supporting flexible mission objectives. In particular, this paper analyzes the primary contributions to data dissemination in UAS that can be given by the Data Distribution Service (DDS) open standard, as a solid and industry-mature data-centric technology. Our study is not restricted to traditional UAS where a set of Unmanned Aerial Vehicles (UAVs) transmit data to the ground station that controls them. Instead, we contemplate flexible UAS deployments with multiple UAV units of different sizes and capacities, which are interconnected to form an aerial communication network, enabling the provision of value-added services over a delimited geographical area. In addition, the paper outlines an approach to address the issues inherent to the utilization of network-level multicast, a baseline technology in DDS, in the considered UAS deployments. We complete our analysis with a practical experience aiming at validating the feasibility and the advantages of using DDS in a multi-UAV deployment scenario. For this purpose, we use a UAS testbed built up by heterogeneous hardware equipment, including a number of interconnected micro aerial vehicles, carrying single board computers as payload, as well as real equipment from a tactical UAS from the Spanish Ministry of Defense.

Strains V113 T , V92 and V120 have been isolated from sand samples taken at the Atlantic intertidal shore in Galicia, Spain, after the Prestige oil spill. A preliminary analysis of the 16S rRNA and the partial rpoD gene sequences indicated that these strains belonged to the Pseudomonas genus, but they were distinct from any known Pseudomonas species. They were extensively characterized by a polyphasic taxonomic approach and phylogenetic data that confirmed that these strains belonged to the Pseudomonas pertucinogena group. Phylogenetic analysis of 16S rRNA, gyrB and rpoD gene sequences showed that the three strains were 99% similar and were closely related to members of the P. pertucinogena group, with less than 94% similarity to strains of established species; Pseudomonas pachastrellae was the closest relative. The Average Nucleotide Index based on blast values was 89.0% between V113 T and the P. pachastrellae type strain, below the accepted species level (95%). The predominant cellular fatty acid contents and whole cell protein profiles determined by MALDI-TOF mass spectrometry also differentiated the studied strains from known Pseudomonas species. We therefore conclude that strains V113 T , V92 and V120 represent a novel species of Pseudomonas, for which the name Pseudomonas gallaeciensis is proposed; the type strain is V113 T (=CCUG 67583 T =LMG 29038 T )., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

We report the draft genome sequence of two new members of the Roseobacter lineage, Thalassobacter strains 1CONIMAR09 and 16PALIMAR09, which were isolated from the seawater coast of Mallorca Island. Each genome harbored putative genes for obtaining energy by chemolithotrophy and making aerobic anoxygenic photosynthesis., (Copyright © 2015 Mas-Lladó et al.)

Blue biotechnology, in which aquatic environments provide the inspiration for various products such as food additives, aquaculture, biosensors, green chemistry, bioenergy, and pharmaceuticals, holds enormous promise. Large-scale efforts to sequence aquatic genomes and metagenomes, as well as campaigns to isolate new organisms and culture-based screenings, are helping to push the boundaries of known organisms. Mass spectrometry-based proteomics can complement 16S gene sequencing in the effort to discover new organisms of potential relevance to blue biotechnology by facilitating the rapid screening of microbial isolates and by providing in depth profiles of the proteomes and metaproteomes of marine organisms, both model cultivable isolates and, more recently, exotic non-cultivable species and communities. Proteomics has already contributed to blue biotechnology by identifying aquatic proteins with potential applications to food fermentation, the textile industry, and biomedical drug development. In this review, we discuss historical developments in blue biotechnology, the current limitations to the known marine biosphere, and the ways in which mass spectrometry can expand that knowledge. We further speculate about directions that research in blue biotechnology will take given current and near-future technological advancements in mass spectrometry., (Copyright © 2014 Elsevier B.V. All rights reserved.)

The protocatechuate branch of the β-ketoadipate pathway is the most common pathway for degradation of monoaromatic compounds in the Roseobacter lineage. We analyzed 43 Roseobacter genomes in order to determine if they possessed all genetic elements for this pathway and if there were common patterns in gene organization. The eight genes of the pathway (pcaG, -H, -B, -C, -D, -I, -J, and -F), possible regulators, and genes encoding for proteins with related function (i.e. catabolism of 4-hydroxybenzoate, catechol, and meta-cleavage of protocatechuate) were predicted by sequence homology analysis. Most of the Roseobacters studied had putatively a complete protocatechuate branch of the β-ketoadipate pathway while 11 of them would probably have an incomplete pathway. Thirty-one Roseobacters would be potentially able of transforming 4-hydroxybenzoate to protocatechuate, and 13 of them might transform catechol via ortho-cleavage, the starting reaction of the catechol branch of the β-ketoadipate pathway. We observed variability in gene organization, with no clear relationship between gene order and Roseobacter taxonomy. Genes were usually organized in several gene clusters. One of the clusters (pcaRIJF) was not reported previously in Roseobacters. The presence of the putative regulator pcaR in these bacteria was also a novel finding. The conserved ORF (chp), encoding for a protein of family DUF849 whose functional role has been proven recently, was detected in 34 genomes. Sequence homology confirmed that proteins encoded by chp corresponded to putative BKACE G4 proteins, which are able to transform β-ketoadipate. Therefore, most Roseobacters seemed to possess two different enzymes for transforming β-ketoadipate. We also report two possible regulation mechanisms of gene pobA (encoding for the enzyme transforming 4-hydroxybenzoate to protocatechuate): via PcaQ, the regulator commonly found with pca genes, and via an independent regulator (PobR). The results of this study evidence the relevance of 4-hydroxybenzoate, protocatechuate and β-ketoadipate degradation pathways in Roseobacters and provide a more complex view of possible regulation mechanisms., (Copyright © 2014 Elsevier B.V. All rights reserved.)

We present the draft genome sequences of two isolates of the Roseobacter lineage, 3SOLIMAR09 and 1FIGIMAR09, which were obtained from harbors of Mallorca Island, Spain, and are affiliated with the Sulfitobacter genus. Both isolates harbor the complete gene set for protocatechuate catabolism and incomplete pathways for several additional monoaromatic compounds., (Copyright © 2014 Mas-Lladó et al.)

Countries of Southern Europe are currently suffering from severe socio-economic pain resulting from high debt levels and austerity measures which constrain investment in innovation-based recovery strategies that are essential for entry into a long-term sustainable period of increasing employment and wealth creation. Young university-educated people are particularly innovative, and hence vital to the development of such strategies, but employment opportunities are poor and many are forced to seek employment that neither profits from their training nor satisfies their justified career expectations, or to emigrate. They are the 'lost generation'. A strategy is proposed here for the creation of Pipelines for New Chemicals, national centre-network partnerships for the discovery-synthesis of new chemicals obtained though harvesting new biological diversity, and their exploitation to develop new medicines, agrochemicals, materials, and other products and applications. The goal is to create new regional motors of economic growth and development, by harnessing the knowledge, motivation and innovation potential of the excellently educated young people of Europe to catalyse the development of new small, medium and large enterprises centred around novel chemicals, and the value chains that will evolve with them, and thereby develop a powerful sector of sustainable growth in employment and social and economic prosperity in Southern Europe., (© 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Pseudomonas stutzeri strain B1SMN1 is a naphthalene-degrading and simultaneously nitrogen-fixing strain isolated from a wastewater sample taken at a lagooning treatment plant in Menorca (Balearic Islands, Spain). Here we report the draft genome sequence of P. stutzeri B1SMN1. It is composed of a chromosome of an estimated size of 5.2 Mb and two plasmids of 44,324 bp and 56,118 bp.

Pseudomonas stutzeri strain NF13 was isolated from a water sample taken at a hydrothermal vent in the Galapagos rift. It was selected for its ability to metabolize sulfur compounds and to grow diazotrophically. Here, we report the first draft genome of a member of genomovar 19 of the species.