Publications

A list of all publications of the Department of Environmental Microbiology.

  1. 2024

    1. 65. Haluska AA, Röhler K, Fabregat-Palau J, Alexandrino DAM, Abramov S, Thompson KJ, et al. Complementary Field and Laboratory Batch Studies to Quantify Generation Rates of Perfluoroalkyl Acids in a Contaminated Agricultural Topsoil with Unknown Precursors. 2024;44:61–75.
    2. 64. Peña-Montenegro TD, Kleindienst S, Allen AE, Eren AM, Mccrow JP, Arnold J, et al. Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant. Applied and environmental microbiology. 2024;90:e01083–24.
    3. 63. Langarica-Fuentes A, Straub D, Wimmer B, Thompson K, Nahnsen S, Huhn C, et al. Subtle microbial community changes despite rapid glyphosate degradation in microcosms with four German agricultural soils. Applied soil ecology. 2024;198:105381.
    4. 62. Vogel AL, Thompson KJ, Straub D, Musat F, Gutierrez T, Kleindienst S. Genetic redundancy in the naphthalene - degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations. FEMS microbiology ecology. 2024;100:fiae060.
    5. 61. Fang X, Blanco AEC, Christl I, Le Bars M, Straub D, Kleindienst S, et al. Simultaneously decreasing arsenic and cadmium in rice by soil sulfate and limestone amendment under intermittent flooding. Environmental pollution. 2024;347:123786.

  2. 2023

    1. 60. Peña-Montenegro TD, Kleindienst S, Allen AE, Eren AM, Mccrow JP, Sánchez-Calderón JD, et al. Species-specific responses of marine bacteria to environmental perturbation. ISME communications. 2023;3:99.
    2. 59. Vogel AL, Thompson KJ, Kleindienst S, Zarfl C. Dosage concentration and pulsing frequency affect the degradation efficiency in simulated bacterial polycyclic aromatic hydrocarbon-degrading cultures. Environmental science and pollution research. 2023;30:59813–25.
    3. 58. Lu L, Rughöft S, Straub D, Joye SBB, Kappler A, Kleindienst S. Rhamnolipid Biosurfactants Enhance Microbial Oil Biodegradation in Surface Seawater from the North Sea. ACS ES & T water. 2023;3:2255–66.
    4. 57. Vogel AL, Thompson KJ, App CB, Gutierrez T, Löffler FE, Kleindienst S. Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation. Frontiers in microbiology. 2023;14.
    5. 56. Wimmer B, Langarica-Fuentes A, Schwarz E, Kleindienst S, Huhn C, Pagel H. Mechanistic modeling indicates rapid glyphosate dissipation and sorption-driven persistence of its metabolite AMPA in soil. Journal of environmental quality. 2023;52:393–405.

  3. 2022

    1. 55. Abramov SM, Straub D, Tejada J, Grimm L, Schädler F, Bulaev, et al. Biogeochemical Niches of Fe-Cycling Communities Influencing Heavy Metal Transport along the Rio Tinto, Spain. Applied and environmental microbiology. 2022;88:e02290–21.
    2. 54. Le AV, Straub D, Planer-Friedrich B, Hug SJ, Kleindienst S, Kappler A. Microbial communities contribute to the elimination of As, Fe, Mn, and NH4+ from groundwater in household sand filters. The science of the total environment. 2022;838:156496.
    3. 53. Patzner MS, Kainz N, Lundin E, Barczok M, Smith C, Herndon E, et al. Seasonal Fluctuations in Iron Cycling in Thawing Permafrost Peatlands. Environmental science & technology. 2022;56:4620–31.
    4. 52. Patzner MS, Logan M, McKenna AM, Young RB, Zhou Z, Joss H, et al. Microbial iron cycling during palsa hillslope collapse promotes greenhouse gas emissions before complete permafrost thaw. Communications earth & environment. 2022;3:76.
    5. 51. Huang Y-M, Jakus N, Straub D, Konstantinidis KT, Blackwell N, Kappler A, et al. ‘Candidatus ferrigenium straubiae’ sp. nov., ‘Candidatus ferrigenium bremense’ sp. nov., ‘Candidatus ferrigenium altingense’ sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae. Systematic and applied microbiology. 2022;45:126306.

  4. 2021

    1. 50. Pfeiffer S, Kappler A, Haderlein SB, Schmidt C, Byrne JM, Kleindienst S, et al. A biogeochemical–hydrological framework for the role of redox-active compounds in aquatic systems. Nature geoscience. 2021;14:264–72.
    2. 49. Yang Z, Sun T, Kleindienst S, Straub D, Kretzschmar R, Angenent LT, et al. A coupled function of biochar as geobattery and geoconductor leads to stimulation of microbial Fe(III) reduction and methanogenesis in a paddy soil enrichment culture. Soil biology and biochemistry. 2021;163:108446.
    3. 48. Huang Y-M, Straub D, Kappler A, Smith N, Blackwell N, Kleindienst S. A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction. Microbial physiology. 2021;31:280–95.
    4. 47. Glodowska M, Schneider M, Eiche E, Kontny A, Neumann T, Straub D, et al. Fermentation, methanotrophy and methanogenesis influence sedimentary Fe and As dynamics in As-affected aquifers in Vietnam. The science of the total environment. 2021;779:146501.
    5. 46. Jakus N, Blackwell N, Straub D, Kappler A, Kleindienst S. Presence of Fe(II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by an Fe(II)-oxidizing Gallionellaceae sp. FEMS microbiology ecology. 2021;97:fiab145.
    6. 45. Pienkowska A, Glodowska M, Mansor M, Buchner D, Straub D, Kleindienst S, et al. Isotopic Labeling Reveals Microbial Methane Oxidation Coupled to Fe(III) Mineral Reduction in Sediments from an As-Contaminated Aquifer. Environmental science & technology letters. 2021;8:832–7.
    7. 44. Glodowska M, Stopelli E, Straub D, Thi DV, Trang OTK, Viet PH, et al. Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling. Journal of hazardous materials. 2021;407:124398.
    8. 43. Nikolova CN, Ijaz UZ, Magill C, Kleindienst S, Joye SB, Gutierrez T. Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants. Microbiome. 2021;9:191.
    9. 42. Huang Y-M, Straub D, Blackwell N, Kappler A, Kleindienst S. Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS. Applied and environmental microbiology. 2021;87:e00496–21.
    10. 41. Jakus N, Blackwell N, Osenbrück K, Straub D, Byrne JM, Wang Z, et al. Nitrate Removal by a Novel Lithoautotrophic Nitrate-Reducing, Iron(II)-Oxidizing Culture Enriched from a Pyrite-Rich Limestone Aquifer. Applied and environmental microbiology. 2021;87:e0046021.
    11. 40. Glodowska M, Schneider M, Eiche E, Kontny A, Neumann T, Straub D, et al. Microbial transformation of biogenic and abiogenic Fe minerals followed by in-situ incubations in an As-contaminated vs. non-contaminated aquifer. Environmental pollution. 2021;281:117012.

  5. 2020

    1. 39. Rughöft S, Jehmlich N, Gutierrez T, Kleindienst S. Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation. Microorganisms. 2020;9:3.
    2. 38. Gutierrez T, Kleindienst S. Uncovering Microbial Hydrocarbon Degradation Processes: The Promise of Stable Isotope Probing. In: Teske A, Carvalho V, editors. Marine Hydrocarbon Seeps : Microbiology and Biogeochemistry of a Global Marine Habitat. Springer; 2020. pp. 183–99. (Teske A, Carvalho V, editors. Springer Oceanography).
    3. 37. Glodowska M, Stopelli E, Schneider M, Rathi B, Strauber D, Lightfoot A, et al. Arsenic mobilization by anaerobic iron-dependent methane oxidation. Communications earth & environment. 2020;1:42.
    4. 36. Glodowska M, Stopelli E, Schneider M, Lightfoot A, Rathi B, Straub D, et al. Role of in Situ Natural Organic Matter in Mobilizing As during Microbial Reduction of FeIII-Mineral-Bearing Aquifer Sediments from Hanoi (Vietnam). Environmental science & technology. 2020;54:4149–59.
    5. 35. Abramov SM, Tejada J, Grimm L, Schädler F, Bulaev A, Tomaszewski EJ, et al. Role of biogenic Fe(III) minerals as a sink and carrier of heavy metals in the Rio Tinto, Spain. The science of the total environment. 2020;718:137294.
    6. 34. Kleindienst S, et al. Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes. The science of the total environment. 2020;717:137143.
    7. 33. Blackwell N, Bryce C, Straub D, Kappler A, Kleindienst S. Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments. Applied and environmental microbiology. 2020;86:e01160–20.
    8. 32. Kleindienst S, Knittel K. Anaerobic Hydrocarbon-Degrading Sulfate-Reducing Bacteria at Marine Gas and Oil Seeps. In: Teske A, Carvalho V, editors. Marine Hydrocarbon Seeps : Microbiology and Biogeochemistry of a Global Marine Habitat. Springer; 2020. pp. 21–41. (Teske A, Carvalho V, editors. Springer Oceanography).
    9. 31. Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. Frontiers in microbiology. 2020;11:550420.
    10. 30. Rughöft S, Vogel AL, Joye SB, Gutierrez T, Kleindienst S. Starvation-Dependent Inhibition of the Hydrocarbon Degrader Marinobacter sp. TT1 by a Chemical Dispersant. Journal of marine science and engineering. 2020;8:925.

  6. 2019

    1. 29. Kleindienst S, Chourey K, Chen G, Murdoch RW, Higgins SA, Iyer R, et al. Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism. Applied and environmental microbiology. 2019;85.
    2. 28. Ziervogel K, Joye SB, Kleindienst S, Malkin SY, Passow U, Steen AD, et al. Polysaccharide hydrolysis in the presence of oil and dispersants: Insights into potential degradation pathways of exopolymeric substances (EPS) from oil-degrading bacteria. Elementa. 2019;7:31.
    3. 27. Otte JM, Blackwell N, Ruser R, Kappler A, Kleindienst S, Schmidt C. N2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment. Scientific reports. 2019;9:10691.
    4. 26. Bryce C, Blackwell N, Straub D, Kleindienst S, Kappler A. Draft Genome Sequence of Chlorobium sp. Strain N1, a Marine Fe(II)-Oxidizing Green Sulfur Bacterium. Microbiology resource announcements. 2019;8:e00080–19.

  7. 2018

    1. 25. Otte JM, Blackwell N, Soos V, Rughöft S, Maisch M, Kappler A, et al. Sterilization impacts on marine sediment : are we able to inactivate microorganisms in environmental samples? FEMS microbiology ecology. 2018;94:fiy189.
    2. 24. Joye S, Kleindienst S, Peña-Montenegro D. SnapShot: Microbial Hydrocarbon Bioremediation. Cell. 2018;172:1336.
    3. 23. et al., Kleindienst S. A case study for late Archean and Proterozoic biogeochemical iron- and sulphur cycling in a modern habitat : the Arvadi Spring. Geobiology. 2018;16:353–68.
    4. 22. Bryce C, Franz-Wachtel M, Nalpas NC, Miot J, Benzerara K, Byrne JM, et al. Proteome Response of a Metabolically Flexible Anoxygenic Phototroph to Fe(II) Oxidation. Applied and environmental microbiology. 2018;84:e01166–18.
    5. 21. Tominski C, Lösekann-Behrens T, Ruecker A, Hagemann N, Kleindienst S, Mueller CW, et al. Insights into Carbon Metabolism Provided by Fluorescence In Situ Hybridization-Secondary Ion Mass Spectrometry Imaging of an Autotrophic, Nitrate-Reducing, Fe(II)-Oxidizing Enrichment Culture. Applied and environmental microbiology. 2018;84:e02166–17.
    6. 20. Bryce C, Blackwell N, Schmidt C, Otte J, Huang Y-M, Kleindienst S, et al. Microbial anaerobic Fe(II) oxidation – Ecology, mechanisms and environmental implications. Environmental microbiology. 2018;20:3462–83.
    7. 19. Otte JM, Harter J, Laufer K, Blackwell N, Straub D, Kappler A, et al. The distribution of active iron-cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients. Environmental microbiology. 2018;20:2483–99.

  8. 2017

    1. 18. Joye SB, Kleindienst S. 2. Hydrocarbon seep ecosystems. In: Kallmeyer J, editor. Life at Vents and Seeps. De Gruyter; 2017. pp. 33–52.
    2. 17. Kleindienst S, Joye SB. Global Aerobic Degradation of Hydrocarbons in Aquatic Systems. In: Rojo F, editor. Aerobic Utilization of Hydrocarbons, Oils, and Lipids. Springer; 2017. pp. 797–814. (Rojo F, editor. Handbook of Hydrocarbon and Lipid Microbiology).
    3. 16. Kleindienst S, Higgins SA, Tsementzi D, Chen G, Konstantinidis KT, Mack EE, et al. ‘Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Systematic and applied microbiology. 2017;40:150–9.
    4. 15. Chen G, Kleindienst S, Griffiths DR, Mack EE, Seger ES, Löffler FE. Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture. Environmental microbiology. 2017;19:4784–96.
    5. 14. Nordhoff M, Tominski C, Halama M, Byrne JM, Obst M, Kleindienst S, et al. Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS. Applied and environmental microbiology. 2017;83:e00752–17.

  9. 2016

    1. 13. Joye SB, Kleindienst S, Gilbert JA, Handley KM, Weisenhorn P, Overholt WA, et al. Responses of Microbial Communities to Hydrocarbon Exposures. Oceanography. 2016;29:136–49.
    2. 12. Kleindienst S, Higgins SA, Tsementzi D, Konstantinidis KT, Mack EE, Löffler FE. Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium. Microbiology resource announcements. 2016;3:e00037–16.
    3. 11. Seidel M, Kleindienst S, Dittmar T, Joye SB, Medeiros PM. Biodegradation of crude oil and dispersants in deep seawater from the Gulf of Mexico: Insights from ultra-high resolution mass spectrometry. Deep-sea research. Part 2, Topical studies in oceanography. 2016;129:108–18.
    4. 10. Kleindienst S, Grim S, Sogin M, Bracco A, Crespo-Medina M, Joye SB. Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume. The ISME journal. 2016;10:400–15.
    5. 9. Kleindienst S, et al. Reply to Prince et al.: Ability of chemical dispersants to reduce oil spill impacts remains unclear. Proceedings of the National Academy of Sciences of the United States of America. 2016;113:E1422–3.

  10. 2015

    1. 8. Kleindienst S, et al. Chemical dispersants can suppress the activity of natural oil-degrading microorganisms. Proceedings of the National Academy of Sciences of the United States of America. 2015;112:14900–5.
    2. 7. Kleindienst S, Paul JH, Joye SB. Using dispersants after oil spills: impacts on the composition and activity of microbial communities. Nature reviews : Microbiology [Internet]. 2015;13:388–96. Available from: https://www.nature.com/articles/nrmicro3452

  11. 2014

    1. 6. Kleindienst S, et al. Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps. The ISME journal. 2014;8:2029–44.

  12. 2013

    1. 5. et al., Kleindienst S. Predominant archaea in marine sediments degrade detrital proteins. Nature. 2013;496:215–8.
    2. 4. von Netzer F, Pilloni G, Kleindienst S, Krüger M, Knittel K, Gründger F, et al. Enhanced Gene Detection Assays for Fumarate-Adding Enzymes Allow Uncovering of Anaerobic Hydrocarbon Degraders in Terrestrial and Marine Systems. Applied and environmental microbiology. 2013;79:543–52.

  13. 2012

    1. 3. Graue J, Kleindienst S, Lueders T, Cypionka H, Engelen B. Identifying fermenting bacteria in anoxic tidal-flat sediments by a combination of microcalorimetry and ribosome-based stable-isotope probing. FEMS microbiology ecology. 2012;81:78–87.
    2. 2. Kleindienst S, Ramette A, Amann R, Knittel K. Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments. Environmental microbiology. 2012;14:2689–710.

  14. 2010

    1. 1. Orcutt BN, Joye SB, Kleindienst S, Knittel K, Ramette A, Reitz A, et al. Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments. Deep-sea research. Part 2, Topical studies in oceanography. 2010;57:2008–21.
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