Energy Bioengineering Group Publications

Publications

Energy Bioengineering Group 

2019

  1. Novotnik, B., Nandy, A., Venkatesan, S.V., Radovic, J., De La Fuente, J., Nejadi, S., Silva, R. C., Kouris, A., Thangadurai, V., Bryant, S., Karan, K., Shor, R., Strous, M., Larter, S. Can fossil fuel energy be recovered and used without any CO2 emissions to the atmosphere?. OSF Preprints, (2019) doi:10.31219/osf.io/tb59f
  2. Yu, J., Zhang, T., Xu, H., Dong, X., Cai, Y., Pan, Y., Cao, C. Thermostable iron oxide nanoparticle synthesis within recombinant ferritins from the hyperthermophile Pyrococcus yayanosii CH1. RSC Adv 9, 39381-39393 (2019) doi:10.1039/C9RA07397C
  3. Dong, X., Strous, M. An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front Genet 10, 999 (2019) doi:10.3389/fgene.2019.00999
  4. Zorz, J., Sharp, C., Kleiner, M., Gordon, P., Pon, R., Dong, X., Strous, M. A shared core microbiome in soda lakes separated by large distances. Nat Commun 10, 4230 (2019) 10.1038/s41467-019-12195-5.
  5. Novotnik, B., Zorz, J., Bryant, S., Strous, M. The effect of dissimilatory manganese reduction on lactate fermentation and microbial community assembly. Front Microbiol 10, 1007 (2019) doi:10.3389/fmicb.2019.01007
  6. Ataeian, M., Liu, Y., Canon-Rubio, K.A., Nightingale, M., Strous, M., Vadlamani, A. Direct capture and conversion of CO2 from air by growing a cyanobacterial consortium at pH up to 11.2. Biotechnol Bioeng 116, 1604-1611 (2019) doi:10.1002/bit.26974.

  7. Raffa, C., Rizzo, C., Strous, M., Domenico, E.D., Sanfilippo, M., Michaud, L., Giudice, A.L. Prokaryotic Dynamics in the Meromictic Coastal Lake Faro (Sicily, Italy). Diversity 11, 37 (2019) doi:10.3390/d11030037

  8. Borgonie, G., Maganabosco, C., Garcia-Moyano A., Linage-Alvarez, Ojo, A.O., B., Freese, B., Van Jaarsveld, C., Van Rooyen, C., Kuloyo, O., et al. New ecosystems in the deep subsurface follow the flow of water driven by geological activity. Sci Rep 9, 3310 (2019) doi:10.1038/s41598-019-39699-w

  9. Hinzke, T., Kouris, A., Hughes, R-A., Strous, M., Kleiner, M. More is not always better: evaluation of 1D and 2D-LC-MS/MS methods for metaproteomics. Front Microbiol 10, 238 (2019) doi:10.3389/fmicb.2019.00238

  10. McIntosh, J.C., Hendry, M.J., Ballentine, C., Haszeldine, R.S., Mayer, B., Elsner, M., Darrah, T.H., Prinzhofer, A., Osborn, S., Stalker, L., Kuloyo, O., et al. A critical review of state-of-the-art and emerging approaches to identify fracking-derived gases and associated contaminants in aquifers. Environ Sci Technol 53, 1063-1077 (2019) doi:10.1021/acs.est.8b05807

2018

  1. Marchant, H.K., Tegetmeyer, H.E., Ahmerkamp, S., Holtappels, M., Lavik, G., Graf, J., Schreiber, F., Mussmann, M., Strous, M., Kuypers, M. (2018). Metabolic specialization of denitrifiers in permeable sediments controls N2O emissions. Environmental Microbiology 20, 4486-4502 (2018) doi:10.1111/1462-2920.14385

  2. Luvizotto, D.M., Araujo, J.E., Silva, M.P., Dias, A.C.F., Kraft, B., Tegetmeye, H., Strous, M., Andreote, F.D. The rates and players of denitrification, dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonia oxidation (anammox) in mangrove soils. Anais da Academia Brasileira de Ciências 91, (2018) doi:10.1590/0001-3765201820180373

  3. Li, T., Sharp, C.E., Ataeian, M., Strous, M., de Beer, D. Role of Extracellular Carbonic Anhydrase in Dissolved Inorganic Carbon Uptake in Alkaliphilic Phototrophic Biofilm. Front Microbiol 9, 2490 (2018) doi:10.3389/fmicb.2018.02490

  4. Kleiner, M., Dong, X., Hinzke, T., Wippler, J., Thorson, E., Mayer, B., Strous, M. Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. PNAS 115, E5576-E5584 (2018) doi:10.1073/pnas.1722325115i

  5. Strous, M., Sharp, C. Designer microbiomes for environmental, energy and health biotechnology. Current Opinion in Microbiology 43, 117-123 (2018) doi:10.1016/j.mib.2017.12.007

  6. Fida, T.T., Voordouw, J., Ataeian, M., Kleiner, M., Okpala, G., Mand, J., Voordouw, G. Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors. Front Microbiol 9, 981 (2018) doi:10.3389/fmicb.2018.00981

  7. Zorz, J.K., Kozlowski, J.A., Stein, L.Y., Strous, M., Kleiner, M. Comparative proteomics of three species of ammonia-oxidizing bacteria. Front Microbiol 9, 938 (2018) doi:10.3389/fmicb.2018.00938

  8. Magbabosco, C., Timmers, P., Lau, M., Borgonie, G., Linage, B., Kuloyo, O., Alleva, R., Kieft, T., et al. Fluctuations in the population of subsurface methane oxidizers in coordination with changes in electron acceptor availability. FEMS Microbiol Ecol 94, (2018) doi:10.1093/femsec/fiy089

2017

  1. Kleiner, M., Thorson, E., Sharp, C.E., Dong, X., Liu, D., Li, C., Strous, M. Assessing species biomass contributions in microbial communities via metaproteomics. Nat Commun 8, 1558 (2017) doi:10.1038/s41467-017-01544-x.

  2. Li, T., Strous, M., Melkonian, M. Biofilm-based photobioreactors: their design and improving productivity through efficient supply of dissolved inorganic carbon. FEMS Microbiology Letters 364, (2017) doi:10.1093/femsle/fnx218

  3. Sczyrba, A., Hofmann, P., Belmann, P. et al. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nat Methods 14, 1063–1071 (2017) doi:10.1038/nmeth.4458

  4. Rochman, F.F., Sheremet, A., Tamas, I., Saidi-Mehrabad, A., Kim, J-J., Dong, X., Sensen, C.W., Gieg, L.M., Dunfield, P.F. Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond. Front Microbiol 8, 1845 (2017) doi:10.3389/fmicb.2017.01845

  5. Saad, S., Bhatnagar, S., Tegetmeyer, H.E., Geelhoed, J.S., Strous, M., Ruff, S.E. Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate‐reducing benthic microbial populations. Environ Microbiol 19, 4866–4881 (2017) doi:10.1111/1462-2920.13895

  6. Dong, X., Kleiner, M., Sharp, C.E., Thorson, E., Li, C., Liu, D., Strous, M. Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp. Front Microbiol 8, 1461 (2017) doi:10.3389/fmicb.2017.01461

  7. Sharp, C.E., Urschel, S., Dong, X., Brady, A.L., Strous, M. Robust, high-productivity phototrophic carbon capture at high pH and alkalinity using natural microbial communities. Biotechnol Biofuels 10, 84 (2017) doi:10.1186/s13068-017-0769-1

  8. Cahill, A., Steelman, C., Forde, O., Kuloyo, O., Ruff, S.E., Mayer, B., Mayer, K.U., Strous, M., Ryan, C., Cherry, J. Methane Mobility and Fate in Groundwater Determined from a Controlled Release Field Experiment. Nature Geosci 10, 289–294 (2017) doi:10.1038/ngeo2919

  9. Hamann, E., Tegetmeyer, H.E., Riedel, D., Littmann, S., Ahmerkamp, S., Chen, J., Hach, P.F., Strous, M. Syntrophic linkage between predatory Carpediemonas and specific prokaryotic populations. ISME J 11, 1205-1217 (2017) doi:10.1038/ismej.2016.197

  10. Chen, J., Hanke, A., Tegetmeyer, H.E., Kattelmann, I., Sharma, R., Hamann, E., Hargesheimer, T., Kraft, B., Lenk, D., Geelhoed, J.S., Hettich, R.L., Strous, M. Impacts of chemical gradients on microbial community structure. ISME J 11, 920–931 (2017) doi:10.1038/ismej.2016.175

2016

  1. Daelman, M.R., Sorokin, D., Kruse, O., Van, Loosdrecht. M.C.M., Strous, M. Haloalkaline Bioconversions for Methane Production from Microalgae Grown on Sunlight. Trends in Biotechnology 34, 450-457 (2016) doi:10.1016/j.tibtech.2016.02.008

  2. Hamann, E., Gruber-Vodicka, H., Kleiner, M., Tegetmeyer, H.E., Riedel, D., Littmann, S., Chen, J., Milucka, J., Viehweger, B., Becker, K.W., Dong, X., Stairs, C.W., Hinrichs, K.U., Brown, M.W., Roger, A.J., Strous, M. Environmental Breviatea harbour mutualistic Arcobacter epibionts. Nature 534, 254–258 (2016) doi:10.1038/nature18297

  3. Ruff, S.E., Kuhfuss, H., Wegener, G., Lott, C., Ramette, A., Wiedling, J., Knittel, K., Weber, M. Microbial communities of shallow water methane cold seeps off Elba, Mediterranean Sea. Front Microbiol 7, 374 (2016) doi:10.3389/fmicb.2016.00374

  4. Canon-Rubio, K.A., Sharp, C.E., Bergerson, J., Strous, M., De la Hoz-Siegler, H. Use of highly alkaline conditions to improve cost-effectiveness of algal biotechnology. Applied Microbiology and Biotechnology 100, 1611-1622 (2016) doi:10.1007/s00253-015-7208-7

  5. Wegener, G., Krukenberg, V., Ruff, S.E., Kellermann, M.Y., Knittel, K. Metabolic capabilities of microorganisms involved in and associated with the anaerobic oxidation of methane. Front Microbiol 7, 46 (2016) doi:10.3389/fmicb.2016.00046

  6. Zimmermann, J., Wentrup, C., Sadowski, M., Blazejak, A., Gruber-Vodicka, H., Kleiner, M., et al. Closely coupled evolutionary history of ecto- and endosymbionts from two distantly-related animal phyla. Molecular Ecology 25, 3203-3223 (2016) doi:10.1111/mec.13554

  7. Dowell, F., Cardman, Z., Dasarathy, S., Kellermann, M.Y., Lipp, J., Ruff, S.E., Biddle, J.F., McKay, L., MacGregor, B., Lloyd, K.G., Albert, D., Mendlovitz, H., Hinrichs, K.U., Teske, A. Microbial communities in methane- and short chain alkane-rich hydrothermal sediments of Guaymas Basin. Front Microbiol 7, 17 (2016) doi:10.3389/fmicb.2016.00017

  8. An, D., Dong, X., An, A., Park, H.S., Strous, M., Voordouw, G. Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite. Front Microbiol 7,28 (2016) doi:10.3389/fmicb.2016.00028.

  9. Stagars, M.H., Ruff, S.E., Amann, R., Knittel, K. High diversity of anaerobic alkane-degrading microbial communities in marine seep sediments based on (1-methylalkyl)-succinate synthase genes. Front Microbiol 6, 1511 (2016) doi:10.3389/fmicb.2015.01511

  10. Schimak, M., M. Kleiner, S. Wetzel, M. Liebeke, N. Dubilier and B. Fuchs. MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells. Applied and Environmental Microbiology 82, 62-70 (2016) doi:10.1128/AEM.02776-15

2015

  1. Nolla-Ardèvol, V., Peces, M., Strous, M., Tegetmeyer, H.E. Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads. BMC Microbiology 15, 277 (2015) doi:10.1186/s12866-015-0615-1.

  2. Sayavedra, L., Kleiner, M., Ponnudurai, R., Wetzel, S., Pelletier, E., et al. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. eLife 4, (2015) doi:10.7554/eLife.07966

  3. Brady, A.L., Sharp, C.E., Grasby, S.E., Dunfield, P.F. Anaerobic carboxydotrophic bacteria in Canadian geothermal springs identified using stable isotope probing. Front Microbiol 6, 897 (2015) doi:10.3389/fmicb.2015.00897

  4. Borgonie, G., Linage-Alvarez, B., Ojo, A., Shivambu, S., Kuloyo, O., et al. Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas. Front Microbiol 6, 833 (2015) doi:10.3389/fmicb.2015.00833

  5. Wong, M., An, D., Caffrey, S., Soh, J., Dong, X., Sensen, C., Oldenburg, T., Larter, S., Voordouw, G. Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops. Applied and Environmental Microbiology 81, 6825-6838 (2015) doi:10.1128/AEM.02221-15

  6. Nolla-Ardèvol, V., Strous, M., Tegetmeyer, H.E. Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome. Front Microbiol 6, 597 (2015) doi:10.3389/fmicb.2015.00597

  7. Sharp, C.E., Smirnova, A.V., Kalyuzhnaya, M.G., Bringel, F., Hirayama, H., Jetten, M.S.M., Khmelenima, V.N., Klotz, M.G., Knief, C., Kyrpides, N., Op den Camp, H.J.M., Reshetnikov, A.S., Sakai, Y., Shapiro, N., Trotsenko, Y.A., Vuilleumier, S., Woyke, T., Dunfield, P.F. Draft genome sequence of the moderately halophilic methanotroph, Methylohalobius crimeensis strain 10Ki. Genome Announc 3, e00644-15 (2015) doi:10.1128/genomeA.00644-15.

  8. Kleiner, M., Wentrup, C., Holler, T., Lavik, G., Harder, J., Lott, C., Littmann, S., Kuypers, M.M.M., Dubilier, N. Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments. Environmental Microbiology 17, 5023-5035 (2015) doi:10.1111/1462-2920.12912

  9. Wang, X., Sharp, C.E., Jones, G.M., Grasby, S.E., Brady, A.L., Dunfield, P.F. Stable-isotope-probing identifies uncultured Planctomycetes as primary degraders of a complex heteropolysaccharide in soil. Applied and Environmental Microbiology 81, 4607-4615 (2015) doi:10.1128/AEM.00055-15.

  10. Kleiner, M., Hooper, L.V., Duerkop, B.A. Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 16, 7 (2015) doi:10.1186/s12864-014-1207-4

  11. Hanke, A., Berg, J., Hargesheimer, T., Tegetmeyer, H.E., Sharp, C.E., Strous, M. Selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities. Front Microbiol 6, 1461 (2015) doi:10.3389/fmicb.2015.01461

2014

  1. Magnabosco, C., Tekere, M., Lau, M.C.Y., Linage, B., Kuloyo, O., Erasmus, M., Cason, E., van Heerden, E., Borgonie, G., Kieft, T.L., Olivier, J., Onstott, T.C. Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water. Front Microbiol 5, 679 (2014) doi:10.3389/fmicb.2014.00679

  2. Abed, R.M.M., Polerecky, L., Al-Habsi, A., Oetjen, J., Strous, M., et al. Rapid Recovery of Cyanobacterial Pigments in Desiccated Biological Soil Crusts following Addition of Water. PLoS ONE 9, e112372 (2014) doi:10.1371/journal.pone.0112372

  3. Sharp, C.E., Martínez-Lorenzo, A., Brady, A.L., Grasby, S.E., Dunfield, P.F. Methanotrophic bacteria in warm geothermal spring sediments identified using stable-isotope probing. FEMS Microbiology Ecology 90, 92-102 (2014) doi:10.1111/1574-6941.12375

  4. Kuloyo, O.O., du Preez, J.C., García-Aparicio, M. del P., Kilian, S.G., Steyn, L., Görgens, J. Opuntia ficus-indica cladodes as feedstock for ethanol production by Kluyveromyces marxianus and Saccharomyces cerevisiae. World J Microbiol Biotechnol 30, 3173-3183 (2014) doi:10.1007/s11274-014-1745-6.

  5. Kraft, B., Tegetmeyer, H.E., Sharma, R., Klotz, M.G., Ferdelman, T.G., Hettich, R.L., Geelhoed, J.S., Strous, M. The environmental controls that govern the end product of bacterial nitrate respiration. Science 345, 676-679 (2014) doi:10.1126/science.1254070

  6. Kraft, B., Tegetmeyer, H.E., Meier, D., Geelhoed, J.S., Strous, M. Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture. Environmental Microbiology 16, 3275–3286 (2014) doi:10.1111/1462-2920.12552

  7. Hanke, A., Hamann, E., Sharma, R., Geelhoed, J.S., Hargesheimer, T., Kraft, B., Meyer, V., Lenk, S., Osmers, H., Wu, R., Makinwa, K., Hettich, R.L., Banfield, J.F., Tegetmeyer, H.E., Strous M. Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Front Microbiol 5, 231 (2014) doi:10.3389/fmicb.2014.00231

  8. Hahnke, S.M., Moosmann, P., Erb, T.J., Strous, M. An improved medium for the anaerobic growth of Paracoccus denitrificans Pd1222. Front Microbiol 5, 18 (2014) doi:10.3389/fmicb.2014.00018

  9. Sheik, A., Brussaard, C., Lavik, G., Lam, P., Musat, N., Krupke, A., Littmann, S., Strous, M., Kuypers, M.M.M. Responses of the coastal bacterial community to viral infection of the algae Phaeocystis globosa. ISME J 8, 212–225 (2014) doi:10.1038/ismej.2013.135