Submitted or in revision

Wang, Y.; Wegener, G.; Ruff, S. E.; Wang, F. “Anaerobic alkane oxidation in methyl/alkyl-coenzyme M reductase containing archaea.” (submitted)

Esch E.H.; Pérez Castro, S.; Lipson, D.A.;Cleland, E.E. “Invasion alters decomposition responses to drought through differential above- and below- ground sensitivity to microbial and microclimate influences.” (in revision)

Published or accepted


Chakraborty, A.; Ruff, S. E.; Dong, X.; Ellefson, E. D.; Li, C.; Brooks, J. M.; Bernard, B. B.; Hubert, C. J. R. “Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres.” (in press at Proceedings of the National Academy of Sciences, USA)

Ruff, S. E.; “Microbial communities and metabolisms at hydrocarbon seeps.” Chapter in Book: “Marine Hydrocarbon Seeps – Microbiology and Biogeochemistry of a Global Marine Habitat”; Book Series: Springer Oceanography, Eds. Teske, A.; Carvalho, V.

Kuloyo, O.; Ruff, S. E.; Cahill, A.; Connors, L.; Zorz, J. K.; Nightingale, M.; Mayer, B.; Strous, M. “Methane oxidation and methanotroph population dynamics in groundwater mesocosms.” (accepted at Environmental Microbiology)

Pérez Castro, S.; Esch E.H.; Eviner V.T.; Cleland, E.E.; Lipson, D.A. (2020) “Exotic herbaceous species interact with severe drought to alter soil N cycling in a semi-arid shrubland.” Geoderma, 361:114111.

Bhatnagar S, Cowley ES, Kopf SH, Pérez Castro S, Kearney S, Dawson SC, Hanselmann K, Ruff SE. (2020) “Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom.” Environmental Microbiome, 15:3.

MBL Press Release: Making “Lemonade”

Media coverage of the article: Environmental News Network /


Cramm MA, Chakraborty A, Li C, Ruff SE, Barker Jørgensen B, Hubert CRJ (2019) “Freezing tolerance of thermophilic bacterial endospores in marine sediments.” Frontiers in Microbiology, 10:945.

Ruff SE, Felden J, Marcon Y, Knittel K, Ramette A, Boetius A. (2019) Disturbance and recovery of methanotrophic communities at a deep-sea mud volcano.” The ISME Journal, 13, 197-213.

Media coverage of the article: EurekAlert / Informationsdienst Wissenschaft / Phys.Org / GIT Laborportal / Naturschutz / VBIO

Pérez Castro S, Cleland EE, Wagner R, Al Sawad R, Lipson DA. (2019) “Soil microbial responses to drought and exotic plants shift carbon metabolism.” The ISME Journal.

Puritty CE, Esch E, Pérez Castro S, Ryan EM, Lipson DA,Cleland EE. (2019) “Drought in Southern California coastal sage scrub reduces herbaceous biomass of exotic species more than native species, but exotic growth recovers quickly when drought ends.” Plant Ecology, 220, 151-169.

Goldmann K, Boeddinghaus RS, Klemmer S, Regan KM, Heintz-Buschart A, Fischer M, Prati D, Piepho H-P, Berner D, Marhan S, Kandeler E, Buscot F, Wubet T. (2019) “Unraveling spatio-temporal variability of arbuscular mycorrhiza fungi in a temperate grassland plot.” Environmental Microbiology.

Fiore-Donno AM, Richter-Heitman T, Degrune F, Dumack K, Regan KM, Marhan S, Boeddinghaus RS, Rillig MC, Friedrich MW, Kandeler E, Bonkowski M. (2019) “Environmental selection and spatiotemporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland.” (in press at Frontiers in Microbiology)


Saad S, Bhatnagar S, Tegetmeyer HE, Geelhoed J, Strous M, Ruff SE. (2017) “Transient exposure to oxygen and nitrate reveals ecophysiology of benthic microbial populations.” Environmental Microbiology, 19, 4866-4881.

Cahill A, Steelman C, Forde O, Kuloyo O, Ruff SE, Mayer B, Mayer KU, Strous M, Ryan C, Cherry J. (2017) “Methane Mobility and Fate in Groundwater Determined from a Controlled Release Field Experiment.” Nature Geoscience, 10, 289-294.

Media coverage of the article: Science DailyRD Mag / Resilience / CanTech LetterThe Tyee


Ruff SE, Kuhfuss H, Wegener G, Lott C, Ramette A, Wiedling J, Knittel K, Weber M. (2016) “Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy.” Frontiers in Microbiology, 7:374.

Media coverage of the article: Il Tirreno Blog / Il Tirreno Video

Regan K, Stempfhuber B, Schloter M, Rasche F, Prati D, Philippot L, Boeddinghaus RS, Kandeler E, Marhan S. (2016) “Spatial and temporal dynamics of nitrogen fixing, nitrifying and denitrifying microbes in an unfertilized grassland soil.” Soil Biology & Biochemistry,

Stempfhuber B, Richter-Heitmann T, Regan KM, Kölbl A, Wüst PK, Marhan S, Sikorski J, Overmann J, Friedrich MW, Kandeler E, Schloter M. (2016) “Spatial interaction of archaeal ammonia-oxidizing bacteria in an unfertilized grassland soil.” Frontiers in Microbiology, 6:1567.

Klaus VH, Boch S, Boeddinghaus RS, Hölzel N, Kandeler E, Marhan S, Oelmann Y, Prati D, Regan KM, Schmitt B, Sorkau E, Kleinebecker T. (2016) “Temporal and small-scale variation in grassland productivity, biomass quality and nutrient limitation.” Plant Ecology.


Ruff SE, Biddle J, Teske A, Knittel K, Boetius A, Ramette A. (2015) “Global dispersion and local diversification of the methane seep microbiome.” Proceedings of the National Academy of Sciences USA, 113, 4015-4020.

Media coverage of the article: (radio interview in german) / Der Standard / Nature Education / Science Daily / Newswise / Deepwave Blog


Ruff SE, Probandt D, Zinkann A-C, Iversen M, Klaas C, Würzberg L, Rödiger-Krombholz N, Wolf-Gladrow D, Amann R, Knittel K. (2014) “Indications for algae-degrading benthic microbial communities in deep-sea sediments along the Antarctic Polar Front.” Deep-Sea Research Part II, 108, 6- 16.

Regan K, Nunan N, Boeddinghaus RS , Baumgartner V, Berner D, Boch S, Oelmann Y, Overmann J, Prati D, Schloter M, Schmitt B, Sorkau E, Steffens M, Kandeler E, Marhan S. (2014) “Seasonal controls on grassland microbial biogeography: Are they governed by plants, abiotic properties or both?” Soil Biology & Biochemistry, 71: 21-30.


Ruff, SE, Arnds J, Knittel K, Amann R, Wegener G, Ramette A, Boetius A. (2013) “Microbial communities of marine methane seeps at Hikurangi margin (New Zealand).” PLoS ONE, 8. e72627