The link between the ecology of the prokaryotic rare biosphere and its biotechnological potential

Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.info:eu-repo/semantics/publishedVersio

SWINE WASTE PHYTOREMEDIATION USING DUCKWEED (Landoltia punctata, Les & Crawford) IN A FULL SCALE PLANT

Banner Apresentado em Congresso: 11th International Conference, Heraklion, Crete, Greece PhytotechnologiesThe large amount of nitrogen and phosphorous compounds found in pig manure has caused ecological imbalances, with eutrophication of major river basins in the producing regions. Therefore, the aquatic macrophytes group named duckweeds (Araceae; Lemnoideae) have been successfully used for phytoextraction and rhizodegradation of nutrient and heavy metals from swine waste, generating further a biomass with high protein content. The present study evaluated the phytoremediation of nitrogen and phosphorus from swine waste using the duckweed Landoltia punctata and also their protein biomass production as by-product

Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria

Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness - were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.PTDC/MAR-BIO/1547/2014; full PhD scholarship from the Erasmus Mundus Programme/SALAM EMA2 lot7/SALA1206422info:eu-repo/semantics/publishedVersio

Cultivating the macroalgal holobiont: effects of integrated multi-trophic aquaculture on the microbiome of Ulva rigida (chlorophyta)

Ulva is a ubiquitous macroalgal genus of commercial interest. Integrated Multi-Trophic Aquaculture (IMTA) systems promise large-scale production of macroalgae due to their high productivity and environmental sustainability. Complex host-microbiome interactions play a decisive role in macroalgal development, especially in Ulva spp. due to algal growth- and morphogenesis-promoting factors released by associated bacteria. However, our current understanding of the microbial community assembly and structure in cultivated macroalgae is scant. We aimed to determine (i) to what extent IMTA settings influence the microbiome associated with U. rigida and its rearing water, (ii) to explore the dynamics of beneficial microbes to algal growth and development under IMTA settings, and (iii) to improve current knowledge of host-microbiome interactions. We examined the diversity and taxonomic composition of the prokaryotic communities associated with wild versus IMTA-grown Ulva rigida and surrounding seawater by using 16S rRNA gene amplicon sequencing. With 3141 Amplicon Sequence Variants (ASVs), the prokaryotic richness was, overall, higher in water than in association with U. rigida. Bacterial ASVs were more abundant in aquaculture water samples than water collected from the lagoon. The beta diversity analysis revealed distinct prokaryotic communities associated with Ulva collected in both aquacultures and coastal waters. Aquaculture samples (water and algae) shared 22% of ASVs, whereas natural, coastal lagoon samples only 9%. While cultivated Ulva selected 239 (8%) host-specific ASVs, wild specimens possessed more than twice host-specific ASVs (17%). Cultivated U. rigida specimens enriched the phyla Cyanobacteria, Planctomycetes, Verrucomicrobia, and Proteobacteria. Within the Gammaproteobacteria, while Glaciecola mostly dominated the microbiome in cultivated algae, the genus Granulosicoccus characterized both Ulva microbiomes. In both wild and IMTA settings, the phylum Bacteroidetes was more abundant in the bacterioplankton than in direct association with U. rigida. However, we observed that the Saprospiraceae family within this phylum was barely present in lagoon water but very abundant in aquaculture water. Aquaculture promoted the presence of known morphogenesis-inducing bacteria in water samples. Our study suggests that IMTA significantly shaped the structure and composition of the microbial community of the rearing water and cultivated U. rigida. Detailed analysis revealed the presence of previously undetected taxa associated with Ulva, possessing potentially unknown functional traits.European Union (EU)642575; German Research Foundation (DFG) CRC 1127 ChemBioSys;COST Action "Phycomorph" FA1406info:eu-repo/semantics/publishedVersio

Server Placement with Shared Backups for Disaster-Resilient Clouds

A key strategy to build disaster-resilient clouds is to employ backups of virtual machines in a geo-distributed infrastructure. Today, the continuous and acknowledged replication of virtual machines in different servers is a service provided by different hypervisors. This strategy guarantees that the virtual machines will have no loss of disk and memory content if a disaster occurs, at a cost of strict bandwidth and latency requirements. Considering this kind of service, in this work, we propose an optimization problem to place servers in a wide area network. The goal is to guarantee that backup machines do not fail at the same time as their primary counterparts. In addition, by using virtualization, we also aim to reduce the amount of backup servers required. The optimal results, achieved in real topologies, reduce the number of backup servers by at least 40%. Moreover, this work highlights several characteristics of the backup service according to the employed network, such as the fulfillment of latency requirements.Comment: Computer Networks 201

Genomic insights into aquimarina sp. strain EL33, a bacterial symbiont of the gorgonian coral eunicella labiata.

To address the metabolic potential of symbiotic Aquimarina spp., we report here the genome sequence of Aquimarina sp. strain EL33, a bacterium isolated from the gorgonian coral Eunicella labiata This first-described (to our knowledge) animal-associated Aquimarina genome possesses a sophisticated repertoire of genes involved in drug/antibiotic resistance and biosynthesis

A Hidden Complication of Pigtail Catheter Insertion

Pigtail catheters have emerged as an effective and less morbid alternative to traditional chest tubes for evacuation of pleural air. Rare complications in the literature have been reported. We report a case of a 92-year-old male who presented with dyspnea and shock, noted to have a pneumothorax requiring tube thoracostomy. Computed tomography demonstrated pigtail within the lung parenchyma. We discuss the implications of this occurrence