EBG publication list

Publications

Microbial Markets and Geomicrobiology Group

2023

  1. Jackie Zorz, Alexandre J Paquette, Timber Gillis, Angela Kouris, Varada Khot, Cigdem Demirkaya, Hector De La Hoz Siegler, Marc Strous, Agasteswar Vadlamani (2023) Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium. The ISME Journal. doi.org/10.1038/s41396-023-01545-3

  2. Shengjie Li, Damon Mosier, Xiaoli Dong, Angela Kouris, Guodong Ji, Marc Strous, Muhe Diao (2023) Frequency of change determines effectiveness of microbial response strategies. The ISME Journal. doi.org/10.1038/s41396-023-01515-9

  3. S Emil Ruff, Pauline Humez, Isabella Hrabe de Angelis, Muhe Diao, Michael Nightingale, Sara Cho, Liam Connors, Olukayode O. Kuloyo, Alan Seltzer, Samuel Bowman, Scott D. Wankel, Cynthia N. McClain, Bernhard Mayer & Marc Strous (2023) Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems. Nature Communications 14: 3194. nature.com/articles/s41467-023-38523-4

  4. Marianne Haines, Varada Khot, Marc Strous (2023) The vigor, futility, and application of microbial element cycles in alkaline soda lakes. Elements 19:1, 30-36. doi.org/10.2138/gselements.19.1.30

  5. Cigdem Demirkaya, Agasteswar Vadlamani, Taina Tervahauta, Marc Strous, Hector De la Hoz Siegler (2023) Autofermentation of alkaline cyanobacterial biomass to enable biorefinery approach. Biotechnology for Biofuels and Bioproducts 16:1, 1-14. doi 10.1186/s13068-023-02311-5

  6. Manuel Kleiner, Angela Kouris, Marlene Violette, Grace D’Angelo, Yihua Liu, Abigail Korenek, Nikola Tolić, Timo Sachsenberg, Janine McCalder, Mary S Lipton, Marc Strous (2023) Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome 11:1, 1-23. doi 10.1186/s40168-022-01454-1

  7. Zorz J, Li C, Chakraborty A, Gittins DA, Surcon T, Morrison N, Bennett R, MacDonald A, Hubert CRJ (2023) SituSeq: An offline protocol for rapid and remote Nanopore amplicon sequence analysis. ISME Communications 3: 33.

  8. Gittins DA, Bhatnagar S, Hubert CRJ (2023) Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs. mSystems 8: e00884-22.

  9. Rattray JE, Elizondo G, Sloan K, Morrison N, Fowler M, Gittins DA, Webb J, Campbell DC, MacDonald A, Hubert CRJ (2023) Elevated bacterial endospores associated with thermogenic hydrocarbon seeps in deep sea sediments. Organic Geochemistry 177: 104568.

  10. Acosta N, Bautista MA, Waddell BJ, Du K, McCalder J, Pradhan P, Sedaghat N, Papparis C, Buchner Beaudet A, Chen J, Van Doorn J, Xiang K, Chan L, Vivas L, Low K, Lu X, Lee J, Westlund P, Chekouo T, Dai X, Cabaj J, Bhatnagar S, Ruecker N, Achari G, Clark RG, Pearce D, Harrison JJ, Meddings J, Leal J, Ellison J, Missaghi B, Kanji JN, Larios O, Rennert-May E, Kim J, Hrudey S, Lee BE, Pang X, Frankowski K, Conly J, Hubert CRJ, Parkins MD (2023) Hospital wastewater monitoring for variants of SARS-CoV-2 reveals correlations with variant-specific cases and outbreaks. Journal of Medical Virology 95: e28442.

  11. Li C, Adebayo O, Ferguson DK, Wang S, Rattray JE, Fowler M, Webb J, Campbell C, Morrison N, MacDonald A, Hubert CRJ. (2023) Bacterial anomalies in seabed sediments associated with deep water hydrocarbon seepage. Deep Sea Research 193: 103955.

2022

  1. Chakraborty A, Suchy M, Hubert CRJ, Ryan MC (2022) Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer. Science of the Total Environment 820: 153092.

  2. Afenyo M, Hubert CRJ, Bhatnagar S, Jiang C (2022) Informing marine shipping insurance premiums in the Arctic using marine microbial genomics. Genomics and the Bioeconomy Elsevier, Eds Catalina Lopez-Correa and Adriana Suarez-Gonzalez.

  3. Rattray JE, Chakraborty A, Elizondo G, Ellefson E, Bernard BB, Brooks J, Hubert CRJ (2022) Endospores associated with deep seabed geofluid features in the Eastern Gulf of Mexico. Geobiology 20: 823-836.

  4. Gittins DA, Desiage PA, Morrison N, Rattray JE, Bhatnagar S, Chakraborty A, Zorz J, Li C, Horanszky O, Cramm MA, Webb J, MacDonald A, Fowler M, Campbell DC, Hubert CRJ (2022) Geological processes mediate a microbial dispersal loop in the deep biosphere. Science Advances 8: eabn3485.

  5. Hubert CRJ, Acosta N, Waddell BJ, Hasing ME, Qiu Y, Fuzzen M, Harper NBJ, Bautista MA, Gao T, Papparis C, Van Doorn J, Du K, Xiang K, Chan L, Vivas L, Pradhan P, McCalder J, Low K, England WE, Kuzma D, Conly J, Ryan MC, Achari G, Hu J, Cabaj JL, Sikora C, Svenson L, Zelyas N, Servos M, Meddings J, Hrudey SE, Frankowski K, Parkins MD, Pang X, Lee BE (2022) Tracking Emergence and Spread of SARS-CoV-2 Omicron Variant in Large and Small Communities by Wastewater Monitoring in Alberta, Canada. Emerging Infectious Diseases 28: 1770-1776.

  6. Acosta N, Bautista MA, Waddell BJ, McCalder J, Buchner Beaudet A, Man L, Pradhan P, Sedaghat N, Papparis C, Bacanu A, Hollman J, Krusina A, Southern D, Williamson T, Li C, Bhatnagar S, Murphy S, Chen J, Kuzma D, Meddings J, Hu J, Cabaj JL, Conly JM, Ruecker NJ, Achari G, Ryan CM, Frankowski K, Hubert CRJ, Parkins MD (2022) Longitudinal SARS-CoV-2 RNA Wastewater Monitoring Across a Range of Scales Correlates with Total and Regional COVID-19 Burden in a Well-Defined Urban Population. Water Research 220: 118611

  7. Hrudey SE, Bische, HN, Charrois J, Chik AHS, Conant B, Delatolla R, Dorner S, Graber T, Hubert CRJ, Isaac-Renton J, Pons W, Safford H, Servos M, Sikora C (2022) Wastewater Surveillance for SARS-CoV-2 RNA in Canada. Facets 7: 1493-1597.
  8. Chakraborty A, Rattray JE, Drake SS, Matthews S, Li C, Jørgensen BB, Hubert CRJ (2022) Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples. Frontiers in Microbiology 13: 958417. doi: 10.3389/fmicb.2022.958417
  9. Bell E, Rattray JE, Sloan K, Sherry A, Pilloni G, Hubert CRJ (2022) Hyperthermophilic endospores germinate and metabolize organic carbon in sediments heated to 80°C. Environmental Microbiology 24: 5534-5545.
  10. Voegtlin SP, Barnes RJ, Hubert CRJ, Larter SR, Bryant SL (2022) Formation of biologically influenced palladium microstructures by Desulfovibrio desulfuricans and Desulfovibrio ferrophilus IS5. New Biotechnology 72, 128-138. 10.1016/j.nbt.2022.11.001
  11. Paquette AJ, Vadlamani A, Strous M, De La Hoz Siegler H (2022) Nutrient management and medium reuse for cultivation of a cyanobacterial consortium at high pH and alkalinity. Frontiers in Bioengineering and Biotechnology 10:942771. doi.org/10.3389/fbioe.2022.942771
  12. Barnes RJ, Voegtlin SP, Hubert CRJ, Larter SR, Bryant SL (2022) The Critical Role of Environmental Synergies in the Creation of Bionanohybrid Microbes. Applied and Environmental Microbiology, 88 (7): e02321-21. 10.1128/aem.02321-21
  13. Khot V, Zorz J, Gittins DA, Chakraborty A, Bell E, Bautista MA, Paquette AJ, Hawley AK, Novotnik B, Hubert CRJ, Strous M, Bhatnagar S (2022) CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. Frontiers in Microbiology 12:764058. doi.org/10.3389/fmicb.2021.764058
  14. Li S, Liao Y, Pang Y, Dong X, Strous M, Ji G (2022) Denitrification and dissimilatory nitrate reduction to ammonia in long-term lake sediment microcosms with iron (II). Science of the Total Environment 807:150835. doi.org/10.1016/j.scitotenv.2021.150835
  15. Ataeian M, Liu Y, Kouris A, Hawley AK, Strous M (2022) Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration. Frontiers in Microbiology 13:780346. doi: 10.3389/fmicb.2022.780346
  16. Ruhl IA, Sheremet A, Smirnova AV, Sharp CE, Grasby SE, Strous M, Dunfield PF (2022) Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient. MSystems 7:1 doi.org/10.1128/msystems.00991-21
  17. Haines M, Vadlamani A, Richardson WDL, Strous M (2022) Pilot-scale outdoor trial of a cyanobacterial consortium at pH 11 in a photobioreactor at high latitude. Bioresource Technology 354 doi: 10.1016/j.biortech.2022.127173
  18. Barnes RJ, Voegtlin SP, Naik SR, Gomes R, Hubert CRJ, Larter SR, Bryant SL (2022) Inhibition of sulfate reduction and cell division by Desulfovibrio desulfuricans coated in palladium metal. Applied and Environmental Microbiology, 88 (12): e00580-22. doi: 10.1128/aem.00580-22
  19. Li S, Diao M, Wang S, Zhu X, Dong X, Strous M, Ji G (2022) Distinct oxygen isotope fractionations driven by different electron donors during microbial nitrate reduction in lake sediments. Environmental Microbiology Reports doi: 10.1111/1758-2229.13101

2021

  1. Scheffer G, Hubert CRJ, Enning DR, Lahme SA, Mand J, de Rezende JR (2021) Adaptation and Persistence of a Low Diversity Microbiome in a High Salinity Offshore Oil Reservoir. Microorganisms 9: 2266.

  2. Murphy SMC, Bautista MA, Cramm MA, Hubert CRJ (2021) Biodegradation of diesel and crude oil by Labrador Sea cold adapted microbial communities. Applied & Environmental Microbiology 87: e00800-21. https://doi.org/10.1128/AEM.00800-21.

  3. Ataeian M, Vadlamani A, Haines M, Mosier D, Dong X, Kleiner M, Strous M, Hawley AK (2021) Proteome and strain analysis of cyanobacterium Candidatus “Phormidium alkaliphilum” reveals traits for success in biotechnology. iScience 24:12, 103405. doi.org/10.1016/j.isci.2021.103405

  4. Shi LD, Lv PL, McIlroy SJ, Wang Z, Dong X, Kouris A, Lai CY, Tyson GW, Strous M, Zhao HP (2021) Methane-dependent selenate reduction by a bacterial consortium. The ISME Journal. doi.org/10.1038/s41396-021-01044-3

  5. Haines M, Strous M (2021) Operation of Laboratory Photobioreactors with Online Growth Measurements and Customizable Light Regimes. Journal of visualized experiments 176. doi.org/10.3791/62910

  6. Castro SP, Borton MA, Regan K, Hrabe de Angelis I, Wrighton KC, Teske AP, Strous M, Ruff SE (2021) Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments. The ISME Journal. doi.org/10.1038/s41396-021-01026-5

  7. Zorz J, Richardson WDL, Laventure A, Haines M, Cieplechowicz E, Aslani A, Vadlamani A, Bergerson J, Welch GC, Strous M (2021) Light manipulation using organic semiconducting materials for enhanced photosynthesis. Cell Reports Physical Science 2:4, 100390. doi:10.1016/j.xcrp.2021.100390

  8. Kleiner M, Kouris A, Jensen M, Liu Y, McCalder J, Strous M (2021) Ultra-sensitive Protein-SIP to quantify activity and substrate uptake in microbiomes with stable isotopes. BioRxiv doi:10.1101/2021.03.29.437612.

  9. Zhang C, Meckenstock RU, Weng S, Wei G, Hubert CRJ, Wang JH, Dong X (2021) Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition. FEMS Microbiology Ecology 97, fiab045. doi.org/10.1093/femsec/fiab045

  10. Desmond DS, Saltymakova D, Smith A, Wolfe T, Snyder N, Polcwiartek K, Bautista M, Lemes M, Hubert CRJ, Barber DG, Isleifson D, Stern GA (2021) Photooxidation and biodegradation potential of a light crude oil in first-year sea ice. Marine Pollution Bulletin 165, 112154. doi.org/10.1016/j.marpolbul.2021.112154

  11. Cramm MA, de Moura Neves B, Manning CCM, Oldenburg TBP, Archambault P, Chakraborty A, Cyr-Parent A, Edinger EN, Jaggi A, Mort A, Tortell P, Hubert CRJ (2021) Characterization of marine microbial communities around an Arctic seabed hydrocarbon seep at Scott Inlet, Baffin Bay. Science of the Total Environment 762, 143961. doi.org/10.1016/j.scitotenv.2020.143961

  12. Rattray JE, Chakraborty A, Li C, Elizondo G, John N, Wong M, Radović JR, Oldenburg TBP, Hubert CRJ (2021) Sensitive quantification of dipicolinic acid from bacterial endospores in soils and sediments. Environmental Microbiology 23, 1397-1406. doi.org/10.1111/1462-2920.15343

  13. Li Z, Pan D, Wei G, Pi W, Zhang C, Wang JH, Peng Y, Zhang L, Wang Y, Hubert CRJ, Dong X (2021) Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. The ISME Journal. doi.org/10.1038/s41396-021-00932-y

  14. Acosta N, Bautista M, Hollman J, McCalder J, Beaudet AB, Man L, Waddell BJ, Chen J, Li C, Kuzma D, Bhatnagar S, Leal J, Meddings J, Hu J, Cabaj J, Ruecker NJ, Naugler C, Pillai DR, Achari G, Ryan MC, Conly JM, Frankowski K, Hubert CRJ, Parkins MD (2021) Wastewater monitoring of SARS-CoV-2 from acute care hospitals identifies nosocomial transmission and outbreaks. medRxiv. doi.org/10.1101/2021.02.20.21251520

2020

  1. Bell E, Sherry A, Pilloni G, Suárez-Suárez A, Cramm MA, Cueto G, Head IM, Hubert CRJ (2020) Sediment cooling triggers germination and sulfate reduction by heat-resistant thermophilic spore-forming bacteria. Environmental Microbiology 22: 456-465.

  2. Lahme S, Callbeck CM, Eland LE, Wipat A, Enning D, Head IM, Hubert CRJ (2020) Comparison of sulfide-oxidizing Sulfurimonas strains reveals a new mode of thiosulfate formation in subsurface environments. Environmental Microbiology 22 (5): 1784-1800. 

  3. Sorokin DY, Mosier D, Zorz J, Dong X, Strous M (2020) Wenzhouxiangella strain AB-CW3, a proteolytic bacterium from hypersaline soda lakes that preys on cells of Gram-positive bacteria. Frontiers in Microbiology 11:597686. doi: 10.3389/fmicb.2020.597686.

  4. Khot V, Strous M, Hawley AK (2020) Computational approaches in viral ecology. Computational and Structural Biotechnology Journal 18, 1605-1612. doi:10.1016/j.csbj.2020.06.019

  5. Novotnik B, Nandy A, Venkatesan SV, Radović JR, De la Fuente J, Nejadi S, Silva RC, Kouris A, Thangadurai V, Bryant S, Karan K, Shor R, Strous M, Larter SR (2020) Can fossil fuel energy be recovered and used without any CO2 emissions to the atmosphere? Reviews in Environmental Science and Bio/Technology 19, 217–240. doi:10.1007/s11157-020-09527-z

  6. Kuloyo O, Ruff SE, Cahill A, Connors L, Zorz JK, Hrabe de Angelis I, Nightingale M, Mayer B, Strous M (2020) Methane oxidation and methylotroph population dynamics in groundwater mesocosms. Environmental Microbiology 22, 1222-1237. doi:10.1111/1462-2920.14929

  7. Schute A, Wang A, Jayme TS, Strous M, McKoy KD, Buret AG, McKay DM (2019) Worm expulsion is independent of alterations in composition of the colonic bacteria that occur during experimental Hymenolepis diminuta-infection in mice. Gut Microbes 11, 497-510. doi:10.1080/19490976.2019.1688065

  8. Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo, O, Matthews S, Li C, Fowler M, Morrison NM, MacDonald A, Groves RA, Lewis IA, Wang SH, Mayumi, D, Greening, C, Hubert CRJ (2020) Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nature Communications 11, 5825. doi.org/10.1038/s41467-020-19648-2

  9. de Rezende JR, Oldenburg TBP, Korin T, Richardson WDL, Fustic M, Aitken CM, Bowler BFJ, Sherry A, Grigoryan A, Voordouw G, Larter SR, Head IM, Hubert CRJ (2020) Anaerobic microbial communities and their potential for bioenergy production in heavily biodegraded petroleum reservoirs. Environmental Microbiology 22, 3049-3065. doi.org/10.1111/1462-2920.14995

  10. Ferguson, DK, Li C, Jiang C, Chakraborty A, Grasby SE, Hubert CRJ (2020) Natural attenuation of spilled crude oil by cold-adapted soil bacterial communities at a decommissioned High Arctic oil well site. Science of the Total Environment 722, 137258. doi.org/10.1016/j.scitotenv.2020.137258

  11. Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong W, Hettich RL, Frutschi M, Bernier-Latmani R (2020) Active sulfur cycling in the terrestrial deep subsurface. The ISME Journal 14, 1260-1272. doi.org/10.1038/s41396-020-0602-x

  12. Chakraborty A, Ruff SE, Dong X, Ellefson ED, Li C, Brooks JM, McBee J, Bernard BB, Hubert CRJ (2020) Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. PNAS 117, 11029-11037. doi.org/10.1073/pnas.2002289117

2019

  1. Hanson CA, Müller AL, Loy A, Dona C, Appel R, Jørgensen BB, Hubert CRJ (2019) Historical factors associated with past environments influence the biogeography of thermophilic endospores in Arctic marine sediments. Frontiers in Microbiology 10: 245.

  2. Lahme S, Enning DE, Callbeck CM, Menendez-Vega D, Curtis TP, Head IM, Hubert CRJ (2019) Metabolites of an oil field sulfide-oxidizing nitrate-reducing Sulfurimonas sp. cause severe corrosion. Applied & Environmental Microbiology 85: e01891-18

  3. Lahme, S., Callbeck, C.M., Eland, L.E., Wipat, A., Enning, D., Head, I.M., Hubert, C.R.J. Comparison of sulfide‐oxidizing Sulfurimonas strains reveals a new mode of thiosulfate formation in subsurface environments. Environmental Microbiology, (2019) doi:10.1111/1462-2920.14894

  4. 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

  5. Bell, E., Sherry, A., Pilloni, G., Suárez‐Suárez, A., Cramm, M.A., Cueto, G., Head, I.M., Hubert, C.R.J. Sediment cooling triggers germination and sulfate reduction by heat‐resistant thermophilic spore‐forming bacteria. Environmental Microbiology 22, 456-465 (2019) doi:10.1111/1462-2920.14866

  6. 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

  7. 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.

  8. 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

  9. Cramm, M.A., Chakraborty, A., Li, C., Ruff, E., Jørgensen, B.B., Hubert, C.R.J. Freezing tolerance of thermophilic bacterial endospores in marine sediments. Front Microbiol 10, 945 (2019) doi:10.3389/fmicb.2019.00945

  10. Dong, X., Greening, C., Rattray, J.E., Chakraborty, A., Chuvochina, M., Mayumi, D., Dolfing, J., Li., C, Brooks, J.M., Bernard, B.B., Groves, R.A., Lewis, I.A., Hubert, C.R.J. Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nat Commun 10, 1816 (2019) doi:10.1038/s41467-019-09747-0

  11. 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.

  12. 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

  13. 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

  14. Hanson, C.A., Mueller, A.L., Loy, A., Dona, C., Appel, R., Jørgensen, B.B., Hubert, C.R.J. Historical Factors Associated With Past Environments Influence the Biogeography of Thermophilic Endospores in Arctic Marine Sediments. Front Microbiol 10, 245 (2019) doi:10.3389/fmicb.2019.00245

  15. Carlson, H.K., Hubert, C.R.J. Mechanisms and Monitoring of Oil Reservoir Souring Control by Nitrate or Perchlorate Injection. McGenity T. (eds) Microbial Communities Utilizing Hydrocarbons and Lipids: Members, Metagenomics and Ecophysiology. Handbook of Hydrocarbon and Lipid Microbiology, (2019) doi:10.1007/978-3-319-60063-5_17-1

  16. 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

  17. 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

  18. Lahme, S., Enning, D., Callbeck, C.M., Menendez Vega, D., Curtis, T.P., Head, I.M., Hubert, C.R.J. Metabolites of an oil field sulfide-oxidizing, nitrate-reducing Sulfurimonas sp. cause severe corrosion. Appl Environ Microbiol 85, e01891-18 (2019) doi:10.1128/AEM.01891-18

  19. Wasmund, K., Pelikan, C., Watzka, M., Richter, A., Noel, A., Hubert, C.R.J., Rattei, T.M Hofmann, T., Herbold, C.W., Loy, A. DNA-foraging bacteria in the seafloor. bioRxiv 528695, (2019) doi:10.1101/528695

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. Chakraborty, A., Ellefson, E., Li, C., Gittins, D., Brooks, J.M., Bernard, B.B., Hubert, C.R.J. Thermophilic endospores associated with migrated thermogenic hydrocarbons in deep Gulf of Mexico marine sediments. ISME J 12, 1895–1906 (2018) doi:10.1038/s41396-018-0108-y

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. Bell, E., Blake, L.I., Sherry, A., Head, I.M., Hubert, C.R.J. Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities. Environmental Microbiology 20, 1134-1147 (2018) doi:10.1111/1462-2920.14056

2017

  1. Dolfing, J., Hubert, C.R.J. Using Thermodynamics to Predict the Outcomes of Nitrate-Based Oil Reservoir Souring Control Interventions. Front Microbiol 8, 2575 (2017) doi:10.3389/fmicb.2017.02575

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Wehrmann, L.M., Riedinger, N., Brunner, B., Kamyshny A., Hubert, C.R.J., Herbert, L.C., Brüchert, V., Jørgensen, B.B.,Ferdelman, T.G., Formolo, M.J. Iron-controlled oxidative sulfur cycling recorded in the distribution and isotopic composition of sulfur species in glacially influenced fjord sediments of west Svalbard. Chemical Geology 466, 678-695 (2017) doi:10.1016/j.chemgeo.2017.06.013

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Rosa de Rezende, J., Hubert, C.R.J., Røy, H., Kjeldsen, K.U., Jørgensen, B.B. Estimating the abundance of endospores of sulfate-reducing bacteria in environmental samples by inducing germination and exponential growth. Geomicrobiology Journal 34, 338-345 (2017) doi:10.1080/01490451.2016.1190805

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. Robador, A., Müller, A., Sawicka, J., Berry, D., Hubert, C.R.J., et al. Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments. ISME J 10, 796–809 (2016) doi:10.1038/ismej.2015.157

  4. McCann, C.M., Wade, M.J., Gray, N.D., Roberts, J.A., Hubert, C.R.J., Graham D.W. Microbial communities in a high arctic polar desert landscape. Front Microbiol 7, 419 (2016) doi:10.3389/fmicb.2016.00419

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. Schimak, M., Kleiner, M., Wetzel, S., Liebeke, M., Dubilier, N., Fuchs, B. 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. Tan, B., Jane Fowler, S., Abu Laban, N., Dong, X., Sensen, C.W., Foght, J., Gieg, L.M. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. ISME J 9, 2028-2045 (2015) doi:10.1038/ismej.2015.22.

  3. Sayavedra, L., Kleiner, M., Ponnudurai, R., 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. Abu Laban, N., Dao, A., and Foght, J. DNA Stable-Isotope Probing of Oil Sands Tailings Pond Enrichment cultures Reveals Different Key Players for Toluene Degradation Under methanogenic and Sulfidogenic Conditions. FEMS Microbial Ecology 91, (2015) doi:10.1093/femsec/fiv039

  11. 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.

  12. O'sullivan, L.A., Roussel, E.G., Weightman, A.J., Webster, G., Hubert, C.R.J., Bell, E., Head, I., Sass, H., Parkes, R.J. Survival of Desulfotomaculum spores from estuarine sediments after serial autoclaving and high-temperature exposure. ISME J 9, 922-933 (2015) doi:10.1038/ismej.2014.190

  13. 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

  14. Abu Laban, N., Tan, B., Dao, A., and Foght, J. Draft Genome Sequence of Uncultivated Desulfosporosinus sp. Strain Tol-M, Obtained by Stable Isotope Probing Using [13C6] Toluene. Genome Announcements 3, e10422-14 (2015) doi:10.1128/genomeA.01422-14

  15. Abu Laban, N., Tan, B., Dao, A., and Foght, J. Draft Genome Sequence of Uncultivated Toluene-Degrading Desulfobulbaceae Bacterium Tol-SR, Obtained by Stable Isotope Probing Using [13C6] Toluene. Genome Announcements 3, e10423-14 (2015) doi:10.1128/genomeA.01423-14

  16. 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. Abu Laban, N., Semple, K., Dao, A., and Foght, J. Biodegradation of C7 and C8 iso-Alkanes under Methanogenic Conditions. Environmental Microbiology, (2014) doi:10.1111/1462-2920.12643

  4. 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

  5. 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.

  6. Tan, B., Charchunk, R., Li, C., Nesbø, C., Abu Laban, N., and Foght, J. Draft Genome Sequence of Uncultivated Firmicutes (Peptococcaceae SCADC) Single Cells Sorted from Methanogenic Alkane-Degrading Cultures. Genome Announcements 2, e00909-14 (2014) doi:10.1128/genomeA.00909-14

  7. 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

  8. 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

  9. Müller, A.L., Rosa De Rezende, J., Hubert, C.R.J., Kjeldsen, K.U., Lagkouvardos, I., Berry, D., Jørgensen, B.B., Loy, A. Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents. ISME J 8, 1153-1165 (2014) doi:10.1038/ismej.2013.225

  10. 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

  11. 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

  12. 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