The EF-P aminoacylation pathway may be a potential new target for antimicrobial drugs

Antibiotic resistance is a growing problem in both the developing world and industrialized nations. Bacterial infections are no longer cleared with a single round of antibiotics. The problem could be combated by discovering new pathways to target with drug treatment. One such possible pathway involves elongation factor P (EF-P), a bacterial protein involved in the regulation of antibiotic resistance and survival in other cellular stress. The modification of EF-P with (R)-β-Lysine by the lysyl-tRNA synthetase paralog PoxA affects protein synthesis in the ribosome by relieving stalling during translation of polyproline stretches (7). In PoxA deletion strains, EF-P is not modified decreasing cell replication rate, cell survival to stressful conditions and virulence of Salmonella enterica. By analyzing the contact surface between EF-P and PoxA and comparing it to the complex of a tRNA and an aminoacyl-tRNA synthetase, we were able to identify the novel interactions that could be a potential drug target. Most of the conserved interactions in the EF-P and PoxA complex correspond to the acceptor arm of the tRNA, but many of the contacts are unique. Through mutating amino acids involved in polar contacts between PoxA and EF-P and replacing them with alanine through site directed mutagenesis, it was determined which contacts (both novel and conserved) are important for EF-P recognition. This was measured by analyzing the aminoacylation kinetics using either EF-P or PoxA mutants. Our results suggest that recognition of EF-P by PoxA is mainly accomplished through binding of conserved amino acids that resemble the acceptor stem of a tRNA, but the arginine 235 contact may provide a target for antibiotic development.Howard Hughes Medical InstituteNo embargoAcademic Major: Microbiolog

Host-linked soil viral ecology along a permafrost thaw gradient

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1,2,3,4,5,6,7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8,9,10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling

The KnotLink Game

Recently, several new games have been introduced that can be played on knot and link diagrams. One of the first such games, played on knot diagrams, is called the Knotting-Unknotting Game. In this game, one player aims to create an unknot while their opponent tries to produce a nontrivial knot. The Linking-Unlinking Game is similar, but is played on link diagrams. In this game, one player's goal is to produce an unlink while the other player aims to create any nontrivial link. In our paper, we introduce a hybrid of these two games, called the KnotLink game, that can be played on either a knot or a link diagram. Moves and players' goals are similar to those of the previous two games, with one key difference that allows the game board to be transformed from a knot to a link or vice versa during game play. We describe this new game, provide a sample game, and prove several results regarding winning strategies for infinite families of rational knots and links

Molecular Evolution of Protein-RNA Mimicry as a Mechanism for Translational Control

Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by the lysyl-tRNA synthetase paralog PoxA. To investigate how recognition of EF-P by PoxA evolved from tRNA recognition by aminoacyl-tRNA synthetases, we compared the roles of EF-P/PoxA polar contacts with analogous interactions in a closely related tRNA/synthetase complex. PoxA was found to recognize EF-P solely via identity elements in the acceptor loop, the domain of the protein that interacts with the ribosome peptidyl transferase center and mimics the 3\u27-acceptor stem of tRNA. Although the EF-P acceptor loop residues required for PoxA recognition are highly conserved, their conservation was found to be independent of the phylogenetic distribution of PoxA. This suggests EF-P first evolved tRNA mimicry to optimize interactions with the ribosome, with PoxA-catalyzed aminoacylation evolving later as a secondary mechanism to further improve ribosome binding and translation control

The impact of insecticide treated curtains on dengue virus transmission: A cluster randomized trial in Iquitos, Peru

Dengue is one of the most important vector-borne diseases, resulting in an estimated hundreds of millions of infections annually throughout the tropics. Control of dengue is heavily dependent upon control of its primary mosquito vector, Aedes aegypti. Innovative interventions that are effective at targeting the adult stage of the mosquito are needed to increase the options for effective control. The use of insecticide-treated curtains (ITCs) has previously been shown to significantly reduce the abundance of Ae. aegypti in and around homes, but the impact of ITCs on dengue virus (DENV) transmission has not been rigorously quantified. A parallel arm cluster-randomized controlled trial was conducted in Iquitos, Peru to quantify the impact of ITCs on DENV seroconversion as measured through plaque-reduction neutralization tests. Seroconversion data showed that individuals living in the clusters that received ITCs were at greater risk to seroconverting to DENV, with an average seroconversion rate of 50.6 per 100 person-years (PY) (CI: 29.9–71.9), while those in the control arm had an average seroconversion rate of 37.4 per 100 PY (CI: 15.2–51.7). ITCs lost their insecticidal efficacy within 6 months of deployment, necessitating re-treatment with insecticide. Entomological indicators did not show statistically significant differences between ITC and non-ITC clusters. It’s unclear how the lack of protective efficacy reported here is attributable to simple failure of the intervention to protect against Ae. aegypti bites, or the presence of a faulty intervention during much of the follow-up period. The higher risk of dengue seroconversion that was detected in the ITC clusters may have arisen due to a false sense of security that inadvertently led to less routine protective behaviors on the part of households that received the ITCs. Our study provides important lessons learned for conducting Randomized Cluster Trials for vector control interventions against Aedes-transmitted virus infections

Unveiling microbial structures during raw microalgae digestion and co-digestion with primary sludge to produce biogas using semi-continuous AnMBR systems

[EN] Methane production from microalgae can be enhanced through anaerobic co-digestion with carbon-rich substrates and thus mitigate the inhibition risk associated with its low C:N ratio. Acclimated microbial communities for microalgae disruption can be used as a source of natural enzymes in bioenergy production. However, co-substrates with a certain microbial diversity such as primary sludge might shift the microbial structure. Substrates were generated in a Water Resource Recovery Facility (WRRF) and combined as follows: Scenedesmus or Chlorella digestion and microalgae co-digestion with primary sludge. The study was performed using two lab-scale Anaerobic Membrane Bioreactors (AnMBR). During three years, different feedstocks scenarios for methane production were evaluated with a special focus on the microbial diversity of the AnMBR. 57% of the population was shared between the different feedstock scenarios, revealing the importance of Anaerolineaceae members besides Smithella and Methanosaeta genera. The addition of primary sludge enhanced the microbial diversity of the system during both Chlorella and Scenedesmus co-digestion and promoted different microbial structures. Aceticlastic methanogen Methanosaeta was dominant in all the feedstock scenarios. A more remarkable role of syntrophic fatty acid degraders (Smithella, Syntrophobacteraceae) was observed during co-digestion when only microalgae were digested. However, no significant changes were observed in the microbial composition during anaerobic microalgae digestion when feeding only Chlorella or Scenedesmus. This is the first work revealing the composition of complex communities for semi-continuous bioenergy production from WRRF streams. The stability and maintenance of a microbial core over-time in semi-continuous AnMBRs is here shown supporting their future application in full-scale systems for raw microalgae digestion or codigestion.The Ministry of Economy and Competitiveness (MINECO) and the European Regional Development Fund (ERDF) are gratefully acknowledged for their support to this research work through CTM2011-28595-C02-02 and CTM2014-54980-C2-1-R projects. The authors are thankful to Ph.D. Silvia Greses and Ph.D. candidate Rebecca Serna-Garcia (Universitat de Valencia, Spain) for allowing the collection of digestate samples from their bioreactors and providing a brief data characterization of their performance. As well, authors thank the support of Maria Paches (IIAMA, Valencia, Spain) during phytoplankton monitoring in the photobioreactor plant. Finally, the sequencing service from FISABIO (Valencia, Spain) is also gratefully acknowledged for their technical support during the design stage of this work.Zamorano-López, N.; Borrás, L.; Seco, A.; Aguado García, D. (2020). Unveiling microbial structures during raw microalgae digestion and co-digestion with primary sludge to produce biogas using semi-continuous AnMBR systems. The Science of The Total Environment. 699:1-12. https://doi.org/10.1016/j.scitotenv.2019.134365S112699APHA, APHA/AWWA/WEF, 2012. In: Standard Methods for the Examination of Water and Wastewater. Stand. Methods, pp. 541 doi.org/ISBN 9780875532356.Astals, S., Musenze, R. S., Bai, X., Tannock, S., Tait, S., Pratt, S., & Jensen, P. D. (2015). Anaerobic co-digestion of pig manure and algae: Impact of intracellular algal products recovery on co-digestion performance. Bioresource Technology, 181, 97-104. doi:10.1016/j.biortech.2015.01.039Baudelet, P.-H., Ricochon, G., Linder, M., & Muniglia, L. (2017). 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Microbiome, 6(1). doi:10.1186/s40168-018-0449-9Dodsworth, J. A., Blainey, P. C., Murugapiran, S. K., Swingley, W. D., Ross, C. A., Tringe, S. G., … Hedlund, B. P. (2013). Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature Communications, 4(1). doi:10.1038/ncomms2884Dojka, M. A., Harris, J. K., & Pace, N. R. (2000). Expanding the Known Diversity and Environmental Distribution of an Uncultured Phylogenetic Division of Bacteria. Applied and Environmental Microbiology, 66(4), 1617-1621. doi:10.1128/aem.66.4.1617-1621.2000Farag, I. F., Davis, J. P., Youssef, N. H., & Elshahed, M. S. (2014). Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8). PLoS ONE, 9(3), e92139. doi:10.1371/journal.pone.0092139Fontana, A., Kougias, P. G., Treu, L., Kovalovszki, A., Valle, G., Cappa, F., … Campanaro, S. (2018). Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics. Microbiome, 6(1). doi:10.1186/s40168-018-0583-4Garrido-Cardenas, J. A., Manzano-Agugliaro, F., Acien-Fernandez, F. G., & Molina-Grima, E. (2018). Microalgae research worldwide. Algal Research, 35, 50-60. doi:10.1016/j.algal.2018.08.005González-Camejo, J., Jiménez-Benítez, A., Ruano, M. V., Robles, A., Barat, R., & Ferrer, J. (2019). Optimising an outdoor membrane photobioreactor for tertiary sewage treatment. Journal of Environmental Management, 245, 76-85. doi:10.1016/j.jenvman.2019.05.010Gonzalez-Fernandez, C., Sialve, B., & Molinuevo-Salces, B. (2015). Anaerobic digestion of microalgal biomass: Challenges, opportunities and research needs. Bioresource Technology, 198, 896-906. doi:10.1016/j.biortech.2015.09.095Gonzalez-Fernandez, C., Barreiro-Vescovo, S., de Godos, I., Fernandez, M., Zouhayr, A., & Ballesteros, M. (2018). Biochemical methane potential of microalgae biomass using different microbial inocula. Biotechnology for Biofuels, 11(1). doi:10.1186/s13068-018-1188-7González-González, L. M., Correa, D. F., Ryan, S., Jensen, P. D., Pratt, S., & Schenk, P. M. (2018). Integrated biodiesel and biogas production from microalgae: Towards a sustainable closed loop through nutrient recycling. Renewable and Sustainable Energy Reviews, 82, 1137-1148. doi:10.1016/j.rser.2017.09.091Greses, S., Gaby, J. C., Aguado, D., Ferrer, J., Seco, A., & Horn, S. J. (2017). Microbial community characterization during anaerobic digestion of Scenedesmus spp. under mesophilic and thermophilic conditions. Algal Research, 27, 121-130. doi:10.1016/j.algal.2017.09.002Greses, S., Zamorano-López, N., Borrás, L., Ferrer, J., Seco, A., & Aguado, D. (2018). Effect of long residence time and high temperature over anaerobic biodegradation of Scenedesmus microalgae grown in wastewater. Journal of Environmental Management, 218, 425-434. doi:10.1016/j.jenvman.2018.04.086Herrmann, C., Kalita, N., Wall, D., Xia, A., & Murphy, J. D. (2016). Optimised biogas production from microalgae through co-digestion with carbon-rich co-substrates. Bioresource Technology, 214, 328-337. doi:10.1016/j.biortech.2016.04.119Ju, F., Lau, F., & Zhang, T. (2017). Linking Microbial Community, Environmental Variables, and Methanogenesis in Anaerobic Biogas Digesters of Chemically Enhanced Primary Treatment Sludge. Environmental Science & Technology, 51(7), 3982-3992. doi:10.1021/acs.est.6b06344Kadnikov, V. V., Mardanov, A. V., Beletsky, A. V., Karnachuk, O. V., & Ravin, N. V. (2019). Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle. Extremophiles, 23(2), 189-200. doi:10.1007/s00792-018-01073-5Klassen, V., Blifernez-Klassen, O., Wobbe, L., Schlüter, A., Kruse, O., & Mussgnug, J. H. (2016). Efficiency and biotechnological aspects of biogas production from microalgal substrates. Journal of Biotechnology, 234, 7-26. doi:10.1016/j.jbiotec.2016.07.015Klassen, V., Blifernez-Klassen, O., Wibberg, D., Winkler, A., Kalinowski, J., Posten, C., & Kruse, O. (2017). Highly efficient methane generation from untreated microalgae biomass. Biotechnology for Biofuels, 10(1). doi:10.1186/s13068-017-0871-4Leng, L., Yang, P., Singh, S., Zhuang, H., Xu, L., Chen, W.-H., … Lee, P.-H. (2018). A review on the bioenergetics of anaerobic microbial metabolism close to the thermodynamic limits and its implications for digestion applications. Bioresource Technology, 247, 1095-1106. doi:10.1016/j.biortech.2017.09.103Li, R., Duan, N., Zhang, Y., Liu, Z., Li, B., Zhang, D., & Dong, T. (2017). Anaerobic co-digestion of chicken manure and microalgae Chlorella sp.: Methane potential, microbial diversity and synergistic impact evaluation. Waste Management, 68, 120-127. doi:10.1016/j.wasman.2017.06.028Li, R., Duan, N., Zhang, Y., Liu, Z., Li, B., Zhang, D., … Dong, T. (2017). Co-digestion of chicken manure and microalgae Chlorella 1067 grown in the recycled digestate: Nutrients reuse and biogas enhancement. Waste Management, 70, 247-254. doi:10.1016/j.wasman.2017.09.016Mahdy, A., Mendez, L., Ballesteros, M., & González-Fernández, C. (2015). Algaculture integration in conventional wastewater treatment plants: Anaerobic digestion comparison of primary and secondary sludge with microalgae biomass. Bioresource Technology, 184, 236-244. doi:10.1016/j.biortech.2014.09.145Mansfeldt, C., Achermann, S., Men, Y., Walser, J.-C., Villez, K., Joss, A., … Fenner, K. (2019). Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities. The ISME Journal, 13(6), 1589-1601. doi:10.1038/s41396-019-0371-6McIlroy, S. J., Kirkegaard, R. H., Dueholm, M. 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Effects of various feedstocks on isotope fractionation of biogas and microbial community structure during anaerobic digestion. Waste Management, 84, 211-219. doi:10.1016/j.wasman.2018.11.04

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

The Rowett Institute and SRUC are core funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The Roslin Institute forms part of the Royal (Dick) School of Veterinary Studies, University of Edinburgh. This project was supported by the Biotechnology and Biological Sciences Research Council (BBSRC; BB/N016742/1, BB/N01720X/1), including institute strategic programme and national capability awards to The Roslin Institute (BBSRC: BB/P013759/1, BB/P013732/1, BB/J004235/1, BB/J004243/1); and by the Scottish Government as part of the 2016–2021 commission.Peer reviewedPublisher PD

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.</p