Suchergebnisse

10 páginas, 5 figuras ; Sponges are important components of marine benthic communities. High microbial abundance sponges host a large diversity of associated microbial assemblages. However, the dynamics of such assemblages are still poorly known. In this study, we investigated whether bacterial assemblages present in Spongia lamella remained constant or changed as a function of the environment and life cycle. Sponges were collected in multiple locations and at different times of the year in the western Mediterranean Sea and in nearby Atlantic Ocean to cover heterogeneous environmental variability. Cooccurring adult sponges and offsprings were compared at two of the sites. To explore the composition and abundance of the main bacteria present in the sponge mesohyl, embryos, and larvae, we applied both 16S rRNA gene-denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands and quantitative polymerase chain reactions (qPCR). On average, the overall core bacterial assemblage showed over 60 % similarity. The associated bacterial assemblage fingerprints varied both within and between sponge populations, and the abundance of specific bacterial taxa assessed by qPCR significantly differed among sponge populations and between adult sponge and offsprings (higher proportions of Actinobacteria in the latter). Sequences showed between 92 and 100%identity to sequences previously reported in GenBank, and allwere affiliatedwith uncultured invertebrate bacterial symbionts (mainly sponges). Sequences were mainly related to Chloroflexi and Acidobacteria and a fewto Actinobacteria and Bacteroidetes. Additional populations may have been present under detection limits. Overall, these results support that both ecological and biological sponge features may shape the composition of endobiont bacterial communities in S. lamella. ; Financial support was provided by the European Union project BIOCAPITAL (MRTN-CT-2004-512301) and the French Agence Nationale de la Recherche on Biodiversity (ECIMAR program ANR- 06-BDIV-001). EOC contribution was supported by grant DARKNESS CGL2012-32747 from the Spanish Office for Science (MINECO). ; Peer reviewed

10 pages, 6 figures, 1 table. ; The planktonic archaeal assemblages of several anaerobic, sulfide-rich, aquatic environments were analyzed in space and time by PCR-denaturing gradient gel electrophoresis and sequencing of 16S rRNA gene fragments. The systems were sampled in different years between 1992 and 1998. PCR products were obtained directly from the original DNA without previous nested amplification and yielded successful fingerprints with mostly sharp bands in the gel. Nineteen samples from the anaerobic hypolimnia of 8 lakes and 1 coastal lagoon in NE Spain, Mallorca and Switzerland were compared and a temporal survey was carried out in one of the lakes (Lake Vilar). Between 4 and 14 well-defined bands appeared. All the sequenced bands belonged to Archaea. Although most of the water bodies shared the same climatic conditions and presence of sulfide, the limnological parameters were different among them and different fingerprints were observed in different lakes. Euryarchaeota, i.e., methanogen- and thermoplasma-related sequences, appeared in all the samples but crenarchaeota were recovered only from Lake Vilar. A temporal shift in the predominant members of the archaeal assemblage from crenarchaeota to members of the cluster of thermoplasmales and relatives took place in Lake Vilar between February and June. Sequences related to thermoplasmales and crenarchaeota were distantly related to cultured strains (81% similarity in 16S rDNA) and clustered with branches represented only by environmental clones, whereas sequences related to methanogens grouped with a sequence from an endosymbiont of 1 anaerobic ciliate. A new branch of freshwater euryarchaeota appeared within the cluster of thermoplasmales and relatives. Our study indicates the presence of dynamic archaeal populations in the water column of nonthermophilic, sulfide-rich environments, further extending the diversity and distribution of Archaea in nature. The temporal shift in community composition in Lake Vilar suggests that Archaea grow under in situ conditions. If this is the case, Archaea would be active players in the anaerobic biogeochemical cycles of these environments ; This work was financed by the Max Planck Society in Germany, by DGICyT grant number PB95-0222 from the Spanish Ministerio de Educación y Cultura and by project MIDAS (Microbial Diversity in Aquatic Systems, MAS3-CT97-0154) from the European Union. ; Peer reviewed

Este artículo contiene 6 páginas, 4 figuras ; Airborne microbes (bacteria, archaea, protists, and fungi) were surveyed over a 7-y period via high-throughput massive sequencing of 16S and 18S rRNA genes in rain and snow samples collected fortnightly at a high-elevation mountain Long-Term Ecological Research (LTER) Network site (LTER-Aigüestortes, Central Pyrenees, Spain). This survey constitutes the most comprehensive mountain-top aerobiology study reported to date. The air mass origins were tracked through modeled back-trajectories and analysis of rain water chemical composition. Consistent microbial seasonal patterns were observed with highly divergent summer and winter communities recurrent in time. Indicative microbial taxa were unveiled as a forensic signature, and ubiquitous taxa were observed as common atmosphere inhabitants, highlighting aerosols as a potentially successful mechanism for global microbial dispersal. Source-tracking analyses identified freshwater, cropland, and urban biomes as the most important sources for airborne bacteria in summer, while marine and forest biomes prevailed in winter, in agreement with air mass retrotrajectories and the prevailing general and regional atmospheric circulation. ; This research is included within the global surveillance activities of the Long-Term Ecological Research node Aigüestortes (LTERAT) and was supported by Grant ECOSENSOR-BIOCON 04/009 from BBVA Foundation; Grants AERBAC 079/2007, AERBAC-2 178/2010, and DISPERSAL 829/2013 from the Spanish Office for the Environment's National Parks Research Network (OAPN; to E.O.C.); and the Catalan Government's Support Program for Consolidated Research Groups Grant GECA 2017 SGR 910. ; Peer reviewed

13 pages, 8 figures, 3 tables ; The microbial assemblages of Petit Saut reservoir and Sinnamary river (French Guiana, South America) were analyzed by biochemical analyses (pigments and specific fatty acids), and by polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) and sequence analysis of 16S rRNA gene fragments. Samples from a vertical profile in the reservoir and from a longitudinal profile downstream of the dam were analyzed and compared to a reference sample taken in the river, upstream of the reservoir. The distribution of bacterial populations could be explained by the physico-chemical conditions of the water and the hydrodynamics induced by the hydroelectric plant. Two bacterial Œbio-filters¹ were detected by biochemical analyses: methanotrophs at the oxycline level and phototrophic green sulfur bacteria below the oxycline. A statistical analysis of the DGGE fingerprints obtained for each sample showed that the different stations could be related in a dendrogram in good agreement with their geographic location. We detected 53 bands in the bacterial DGGE fingerprints and 3 bands in the archaeal DGGE. The phylogenetic affiliation of the predominant DGGE bands was inferred by a comparative 16S rDNA partial sequence analysis (450 to 500 base pairs). Sequences obtained from the reservoir and the river were related to Proteobacteria (α, β, and γ), Cyanobacteria, green sulfur bacteria, Cytophaga, Methanomicrobiaceae and Thermoplasmales. Thus, methanotrophs and green sulfur bacteria were detected, and bacteria involved in the iron biogeochemical cycle were also shown to be dominant. The 16S rDNA-based analysis indicated that new bacterial and archaeal lineages, not detected upstream of the dam, were present in the reservoir and that the microbial diversity of these assemblages was greater than previously described by biochemical analyses. Our data provide evidence that the former bacterial assemblage was completely modified by the impounding of the reservoir, in agreement with the different biogeochemical cycles established. Minor groups of bacteria became dominant in the reservoir while others disappeared, in adaptation to the new conditions induced by flooding of rain forest ; We thank sincerely all the staff of Petit Saut Laboratory for help, and technical and human support. We are also grateful to EDF/CNEH for financial support, and particularly to Chantal Sissakian. Parts of this work were also funded by project MIDAS (Microbial Diversity in Aquatic Systems, MAS3-CT97-0154) from the European Union. We also thank Professor Louis Labroue for starting this project and Mrs Yvette Durand for managing the administrative part of the project with virtuosity ; Peer reviewed

8 pages, 2 figures, 4 tables ; The present study assesses the contribution of dark carbon fixation to the primary production in the oxic/anoxic interface of a shallow estuarine environment that develops a salt-water wedge with the presence of sulfide. Primary production was partitioned into oxygenic photosynthesis, anoxygenic photosynthesis and dark fixation. The results show the importance of dark fixation in the oxic/anoxic interface with values higher than 5 mg carbon fixed per cubic meter and per hour in some cases. The average rate of primary production in the dark during the anoxic season for the Ebro River salt wedge resulted in 42 mg C m-2 d-1 in the interface. This represents at least twice the contribution of oxygenic photosynthesis to the primary production in such interface. Because this process is probably important in other salt-wedge or highly stratified estuaries with oxic/anoxic interfaces containing sulfide, the estimates of carbon fixation made so far for these systems may have been underestimated, and should therefore be revised taking into account the contribution of dark processes ; This work was financed by DGICyT grant PB87-0183 from the Spanish Ministerio de Educación y Ciencia. J.G.-C. was supported by a FPI scholarship from the Spanish Ministerio de Educación y Ciencia. During the writing of this work, E.O.C. was supported by MIDAS (MIcrobial Diversity in Aquatic Systems, MAS3-CT97-0154) from the European Union ; Peer reviewed

Este artículo contiene 10 páginas, 5 figuras, 1 tabla ; We studied the core bacterial communities of 19 sponge species from Nha Trang Bay (Central Vietnam), with particular emphasis on the contribution of planktonic seawater bacteria to the sponge core microbiomes. To ensure consistent sponge-microbe associations and accurate identification of planktonic bacteria transmitted from seawater, we were very restrictive with the definition of the sponge core microbiomes (present in all the replicates), and with the identification of valid biological 16S rRNA gene sequences (100% sequence identity) that belonged to potentially different bacterial taxa. We found a high overlap (>50% relative abundance) between the sponge species core microbiome and the seawater bacterial core in ca. a half of the studied species, including representatives of both, HMA and LMA sponges. From our restrictive analysis, we point to horizontal transmission as a relevant way of symbiont acquisition in sponges. Some species-specific recognition mechanisms may act in sponges to enrich specific seawater bacteria in their tissues. These mechanisms would allow the maintenance of bacterial communities in a species across geographical ranges. Moreover, besides contrasting preferences in bacteria selection from seawater, divergent physiological traits may also account for the different microbiomes in species of HMA and LMA sponges. ; This research was partially funded by projects MarSymbiOmics (CTM2013-43287-P) and PopCOmics (CTM2017-88080, MINECO/AEI/FEDER/UE) from the Spanish Government. JC and EOC were supported by the project BRIDGES (CGL2015-69043-P). ; Peer reviewed

7 páginas, 7 figuras ; To date different electrode materials have been used to improve the performance and reduce the costs of microbial fuel cells (MFCs). Particularly, there is a need to avoid the use of expensive Pt-based cathode materials. Here, we explored the use of vertically aligned carbon nanotubes (CNTs) deposited by plasma-enhanced chemical vapor deposition as cathode material in single chamber MFCs. In order to improve cell performance and lower the oxygen reduction reaction resistance at the cathode side, MnO2 catalyst was electrochemically deposited on the CNTs. Results show an increase in the output voltage and power density by two orders of magnitude when compared to plain stainless-steel electrodes, with a maximum power density of 24 mW m-2. Furthermore, the influence of medium solution in the electrolyte was also examined. Results demonstrate that microbial communities developed as biofilm in the anode were limited by substrate metabolic liability. The presence of a labile organic source (acetate) promoted an increase of one order of magnitude in cell performance. Overall, this study shows the potential of aligned CNTs to increase yield of MFCs. ; This work was supported by projects 2009SGR00185 of AGAUR of Generalitat de Catalunya and CTQ2009-14674-CO2-01 and MAT2010-20468 from MICINN of Spanish Government. The authors thank Centres Cientı´fics i Tecnolo` gics de la Universitat de Barcelona (CCiTUB) for measurement facilities and EDAR Sant Feliu de Llobregat for providing wastewater samples. ; Peer reviewed

Este artículo contiene 8 páginas, 5 figuras. ; Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal. ; This research is included within the global surveillance activities of the Long-Term Ecological Research node Aigüestortes (LTER-AT) and was supported by Grant ECOSENSOR-BIOCON 04/009 from BBVA Foundation; Grants AERBAC 079/2007, AERBAC-2 178/2010, and DISPERSAL 829/2013 from the Spanish Office for the Environment's- National Parks Research Programme (OAPN); and INTERACTOMA RTI2018-101205-B-I00 from the Spanish Agency of Research (AEIMICINN) and European funding (ERDF) to EOC. JC was supported by PTA2018-016527-I (AEI-MICINN) and XTM by grant INTERACTOMA. CB wish to thank the support from the Economy and Knowledge Department of the Catalan Government through Consolidated Research Group (ICRA-ENV 2017 SGR 1124). ; Peer reviewed

11 páginas, 3 tablas, 5 figuras ; Root functional diversity of submerged vegetation exerts a major effect on nitrogen (N) cycling in lake sediments. This fact, however, is neglected in current N-balance models because the links between the engineering role of plants and in situ microbial N cycling are poorly understood. We hypothesized that macrophyte species with high root oxygen loss (ROL) capacity promote the highest denitrification because of a higher abundance of ammonia oxidizers and tighter coupling between nitrifiers and denitrifier communities. We sampled five small ultraoligotrophic shallow lakes with abundant macrophyte cover including sediments dominated either by Isoetes spp. (high ROL), mixed communities of natopotamids (low ROL), and unvegetated sandy sediments. At each site, we quantified denitrification (DNT) rates and proxies for the abundance of denitrifiers (nirS and nirK genes), and both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) and the diversity of nirS-harboring bacteria. Vegetated sediments showed significantly higher abundances of N-cycling genes than bare sediments. Plant communities dominated by Isoetes generated sediments with higher redox and NO2 3 concentrations and significantly higher DNT rates than natopotamidsdominated landscapes. Accordingly, increasing DNT rates were observed along the gradient from low ROL plants-bare sediments-high ROL plants. Significantly higher abundance of the archaeal amoA gene was recorded in sediments colonized by high ROL plants unveiling a key biogeochemical role for AOA in coupling macrophyte landscape and ecosystem denitrification. ; MVC was supported by a Juan de la Cierva fellowship from the Spanish Office for Research (MINECO) and a Beatriu de Pin os from the Catalan Government. This research was granted by projects DARKNESS CGL2012-32747 (MINECO) to EOC and AQUAREST (OAPN 212/2010) to EG. EC, EOC and EG are members of the Environmental Changes Ecology Group (GECA), an Excellence Research Group (SGRDGR), of the Generalitat de Catalunya (Ref. 2014 SGR 1249. 2014–2017). ; Peer reviewed

9 páginas, 5 figuras. ; We report a long-term (i.e., 4.5 consecutive yr) monitoring of surface marine archaeal assemblages of the coastal Mediterranean Sea using quantitative polymerase chain reaction against specific phylogenetic and functional genes, and, for some specific samples, clone libraries of the 16S ribosomal ribonucleic acid gene. Archaea had a marked seasonal periodicity, with recurrent peaks of abundance in December and January and very low occurrence during summer, parallel to temporal changes in community composition. Group II.b Euryarchaeota sequences were mostly present during winter when water was nutrient-enriched, and phytoplankton were abundant. Group II.a sequences were, in turn, more abundant during summer when the water column is stratified, and nutrient concentrations and phytoplankton stocks were lower. Group I Crenarchaeota abundance was highest during winter and significantly correlated with that of archaeal ammonia monooxygenase (amoA) gene copies and nitrite concentrations, suggesting that Group I Crenarchaeota were ammonia oxidizers. The periodicity of archaeal assemblages matched the strong and predictable seasonality of the surface-water conditions in the northwestern Mediterranean Sea, and suggests a low degree of functional redundancy between archaeal groups. The distinct seasonal dynamics for Group II.a and II.b Euryarchaeota, and their close association with major ecosystem processes, indicate that they may play an important but as yet largely unknown role in the ocean. ; PEG was supported by a European Marie Curie grant (CRENARC MEIFCT- 2007-040247), and CGP by CONSOLIDER-INGENIO 2010 project GRACCIE CSD2007-00067 from the Spanish Ministerio de Ciencia e Innovación (MICINN). Sampling was funded by various projects: European Union project BASICS (EVK3-CT- 2002-00078), and Spanish grants ESTRAMAR (CTM2004-12631/ MAR, MEC), MODIVUS (CTM2005-04795/MAR), and SUMMER (CTM2008-03309/MAR). Lab research was founded by grants CRENARC and MICINN grant CRENYC CGL2006- 12058-BOS to EOC. ; Peer reviewed

Este artículo contiene 15 páginas, 7 figuras. 2 tablas. ; Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N2O release. Loss as N2 was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N2O emissions from productive lakes. ; The Spanish Government provided funds through the Ministerio de Educación as a predoctoral fellowship to CP-L (FPU12–00644) and research grants of the Ministerio de Economia y Competitividad: NitroPir (CGL2010–19737), DARKNESS (CGL2012-32747), LACUS (CGL2013–45348-P), TRANSFER (CGL2016–80124-C2-1-P). The REPLIM grant (INRE - INTERREG Programme. EUUN – European Union. EFA056/15) and the ALTER-NET Mobility Scheme supported the final writing. ; Peer reviewed

Four stratified basins in Lake Kivu (Rwanda-DR Congo) were sampled in March 2007 to investigate the abundance, distribution and potential biogeochemical role of planktonic archaea. We used Fluorescence In Situ Hybridization with Catalyzed-Reported Deposition microscopic counts (CARD-FISH), Denaturing Gradient Gel Electrophoreses (DGGE) fingerprinting and qPCR of signature genes for ammonia-oxidizing archaea (16S rRNA for Marine Crenarchaeota Group 1.1a [MCG1] and amoA, ammonia monooxygenase subunit A). Abundance of archaea ranged from 1 to 4.5% of total DAPI counts with maximal concentrations at the oxic-anoxic transition zone ( approximately 50 m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher richness of Crenarchaeal 16S rRNA gene sequences (21 of the 28 Operational Taxonomic Units (OTUs) identified, 75%) over Euryarchaeotal ones (7 OTUs). Sequences affiliated with this latter kingdom were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0 to 100 m depth) with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal, OTUs were mainly assigned to Miscellaneous Crenarchaeotic Group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota Group 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.

Four stratified basins in Lake Kivu (Rwanda-DR Congo) were sampled in March 2007 to investigate the abundance, distribution and potential biogeochemical role of planktonic archaea. We used Fluorescence In Situ Hybridization with Catalyzed-Reported Deposition microscopic counts (CARD-FISH), Denaturing Gradient Gel Electrophoreses (DGGE) fingerprinting and qPCR of signature genes for ammonia-oxidizing archaea (16S rRNA for Marine Crenarchaeota Group 1.1a [MCG1] and amoA, ammonia monooxygenase subunit A). Abundance of archaea ranged from 1 to 4.5% of total DAPI counts with maximal concentrations at the oxic-anoxic transition zone ( approximately 50 m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher richness of Crenarchaeal 16S rRNA gene sequences (21 of the 28 Operational Taxonomic Units (OTUs) identified, 75%) over Euryarchaeotal ones (7 OTUs). Sequences affiliated with this latter kingdom were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0 to 100 m depth) with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal, OTUs were mainly assigned to Miscellaneous Crenarchaeotic Group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota Group 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.

12 páginas, 1 tabla, 5 figuras ; Subway systems worldwide transport more than 100 million people daily; therefore, air quality on station platforms and inside trains is an important urban air pollution issue. We examined the microbiological composition and abundance in space and time of bioaerosols collected in the Barcelona subway system during a cold period. Quantitative PCR was used to quantify total bacteria, Aspergillus fumigatus, influenza A and B, and rhinoviruses. Multitag 454 pyrosequencing of the 16S rRNA gene was used to assess bacterial community composition and biodiversity. The results showed low bioaerosol concentrations regarding the targeted microorganisms, although the bacterial bioburden was rather high (104 bacteria/m3). Airborne bacterial communities presented a high degree of overlap among the different subway environments sampled (inside trains, platforms, and lobbies) and were dominated by a few widespread taxa, with Methylobacterium being the most abundant genus. Human-related microbiota in sequence dataset and ascribed to potentially pathogenic bacteria were found in low proportion (maximum values below 2% of sequence readings) and evenly detected. Hence, no important biological exposure marker was detected in any of the sampled environments. Overall, we found that commuters are not the main source of bioaerosols in the Barcelona subway system. ; Spanish Ministry of Economy and Competitiveness (MINECO); FEDER, Grant/ Award Number: METRO CGL2012-33066 and BRIDGES CGL2015-69043-P; European Union Seventh Framework Programme, Grant/Award Number: FP7/2007-2013; Marie Curie ITN, Grant/Award Number: 315760 HEXACOMM; IMPROVE LIFE Project, Grant/Award Number: LIFE13 ENV/ ES/000263 ; Peer reviewed

AbstractOne of the biggest challenges in molecular biology is bridging the gap between the known and the unknown coding sequence space. This challenge is especially extreme in microbial systems, where between 40% and 60% of the predicted genes are of unknown function. Discarding this uncharacterized fraction should not be an option anymore. Here, we present a conceptual framework and a computational workflow that bridges this gap and provides a powerful strategy to contextualize the investigations of genes of unknown function. Our approach partitions the coding sequence space removing the known-unknown dichotomy, unifies genomic and metagenomic data and provides a framework to expand those investigations across environments and organisms. By analyzing 415,971,742 genes predicted from 1,749 metagenomes and 28,941 bacterial and archaeal genomes we showcase our approach and its application in ecological, evolutionary and biotechnological investigations. As a result, we put into perspective the extent of the unknown fraction, its diversity, and its relevance in genomic and environmental contexts. By identifying a target gene of unknown function for antibiotic resistance, we demonstrate how a contextualized unknown coding sequence space enables the generation of hypotheses that can be used to augment experimental data. ; The authors thankfully acknowledge the computer resources at MareNostrum and the technical support provided by Barcelona Supercomputing Center (RES-AECT-2014-2-0085), the BMBF795 funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B), the University of Oxford Advanced Research Computing (http://dx.doi.org/10.5281/zenodo.22558) and the MARBITS bioinformatics core at ICM-CSIC. CV was supported by the Max Planck Society. AFG received funding from the European Union's Horizon 2020 research and innovation program Blue Growth: Unlocking the potential of Seas and Oceans under grant agreement no. 634486 (project acronym INMARE). AM was supported by the Biotechnology and Biological Sciences Research Council [BB/M011755/1, BB/R015228/1] and RDF by the European Molecular Biology Laboratory core funds. EOC was supported by project INTERACTOMA RTI2018-101205-B-I00 from the Spanish Agency of Science MICIU/AEI. SGA and PS received additional funding by the project MAGGY (CTM2017-87736-R) from the Spanish Ministry of Economy and Competitiveness. The Malaspina 2010 Expedition was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (ref. CSD2008-00077). The authors thank Johannes Söding and Alex Bateman for helpful discussions.