In revision

Lipson DA, Raab T, Pérez Castro S, Powell A “Organohalide respiring bacteria at the heart of anaerobic metabolism in Arctic we tundra soils” (in revision)

Esch EH, Pérez Castro S, Lipson DA, Cleland EE “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 SE, Dong X, Ellefson ED, Li C, Brooks JM, Bernard BB, Hubert CJR (2020) “Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres.” (in press at Proceedings of the National Academy of Sciences, USA)

MBL Press Release: Window to another World

Media coverage of the article: / Environmental News Network / Science Daily / EurekAlert

Wang Y, Wegener G, Ruff SE, Wang F (2020) “Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in archaea” (in press at Environmental Microbiology)

Richter-Heitmann T, Hofner B, Krah F-Z, Sikorski J, Wüst PK, Bunk B, Huang S, Regan KM, Berner D, Boeddinghaus RS, Marhan S, Prati D, Kandeler E, Overmann J, Friedrich MW “Stochastic dispersal rather than deterministic selection explains the spatio-temporal distribution of soil bacteria in a temperate grassland” (accepted at Frontiers in Microbiology)

Ruff SE “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 SE, Cahill A, Connors L, Zorz JK, Nightingale M, Mayer B, Strous M (2020) “Methane oxidation and methanotroph population dynamics in groundwater mesocosms.” Environmental Microbiology, 22, 1222-1237.

Pérez Castro S, Esch EH, Eviner VT, Cleland EE, Lipson DA (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


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.


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