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  • 1.
    Buck, Moritz
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Nilsson, Louise K. J.
    Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden..
    Brunius, Carl
    Swedish Univ Agr Sci SLU, Dept Food Sci, S-75007 Uppsala, Sweden..
    Dabire, Roch K.
    Inst Rech Sci Sante, Ctr Muraz, O1 BP 390, Bobo Dioulasso 01, Burkina Faso..
    Hopkins, Richard
    Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden.;Univ Greenwich, Nat Resources Inst, Cent Ave, Chatham ME4 4TB, Kent, England..
    Terenius, Olle
    Swedish Univ Agr Sci SLU, Dept Ecol, S-75007 Uppsala, Sweden..
    Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 22806Article in journal (Refereed)
    Abstract [en]

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world.

  • 2.
    Garcia, Sarahi L.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    McMahon, Katherine D.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.;Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA..
    Grossart, Hans-Peter
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, D-16775 Ot Neuglobsow, Stechlin, Germany.;Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany..
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Warnecke, Falk
    Univ Jena, Jena Sch Microbial Commun, D-07743 Jena, Germany..
    Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 17, 4449-4459 p.Article in journal (Refereed)
    Abstract [en]

    Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.

  • 3.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tan, BoonFei
    University of Alberta, Edmonton, Canada; Singapore-MIT Alliance for Research and Technology, Leipzig, Germany.
    Foght, Julia
    University of Alberta, Edmonton, Canada.
    Wendeberg, Annelie
    Centre for Environmental Research, Leipzig, Germany.
    Berry, David
    University of Vienna, Vienna, Austria.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. eDNA Solutions AB, Mölndal, Sweden.
    Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions2017In: mSystems, E-ISSN 2379-5077, Vol. 2, no 5, e00038-17Article in journal (Refereed)
    Abstract [en]

    Syntrophy among Archaea and Bacteria facilitates the anaerobic degra- dation of organic compounds to CH4 and CO2 . Particularly during aliphatic and aro- matic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutu- alistic microbial partners are of central importance. Using micromanipulation com- bined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methano- genic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermenta- tion of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and inter- mediate fermentation products derived from detrital biomass was a common fea- ture. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2 -producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocar- bon transformation. IMPORTANCE

  • 4.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wu, Xiaofen
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Heim, Christine
    Univ Gottingen, GZG Geobiol, Gottingen, Germany.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ionescu, Danny
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Neuglobsow, Germany.
    Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 10, 2447-2458 p.Article in journal (Refereed)
    Abstract [en]

    Little research has been conducted on microbial diversity deep under the Earth/'s surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

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