Publications

2025

Woods P, Speth DR, Laso-Pérez R, Utter D, Ruff SE, Orphan V “Convergence and horizontal gene transfer drive the evolution of anaerobic methanotrophy in ‘Candidatus Methanovorans’” accepted at Science Advances 11, adg5232. https://www.science.org/doi/10.1126/sciadv.adq5232

Jiang Q, Cao L, Han Y, Li S, Zhao R, Zhang X, Ruff SE, Zhao Z, Peng J, Liao J, Zhu B, Wang M, Lin X, Dong X (2025) “Cold seeps are hotspots of deep-sea nitrogen-loss driven by microorganisms across 21 phyla” Nature Communications, 16, 1646. https://www.nature.com/articles/s41467-025-56774-1

Simon S, Soares RA, Bornemann TLV, Lange A, Griesdorn L, Fuentes A, Dieckmann M, Krok BA, Ruff SE, Hügler M, Moraru C, Probst AJ “Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing” ISME Communications, 5, ycaf041. https://doi.org/10.1093/ismeco/ycaf041

Hinkle JE, Chanton JP, Moynihan MA, Ruff SE, Teske A (2025) “Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq)” Frontiers in Microbiology, 15, 1491488. https://doi.org/10.3389/fmicb.2024.1491488

2024

Ruff SE, Hrabe de Angelis I, Mullis M, Payet JP, Magnabosco C, Lloyd KG, Sheik CS, Steen AD, Shipunova A, Morozov A, Kiel Reese B, Bradley J, Huber J, Probst A, Morrison H, Sogin ML, Ladau J, Colwell F (2024) “A global comparison of surface and subsurface microbiomes reveals large scale biodiversity gradients, and a marine-terrestrial divide” Science Advances, 10, adq0645. https://www.science.org/doi/10.1126/sciadv.adq0645

Ruff SE, Schwab L, Vidal E, Hemingway JD, Kraft B, Murali R (2024) ”Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments” FEMS Microbiology Ecology, 100, fiae132. https://academic.oup.com/femsec/article/100/11/fiae132/7778282

Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, Ruff SE, Edgcomb V, Hatzenpichler R (2024) “Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal” PLoS Biology, 22, e3002638. https://doi.org/10.1371/journal.pbio.3002638

               Commentary by Stoy and Ratcliff: https://doi.org/10.1371/journal.pbio.3002695

Jiang X, Gallager S, Pedrosa Pàmies R, Ruff SE, Liu Z (2024) “Laboratory-Simulated Photoirradiation Reveals Strong Resistance of Primary Macroplastics to Weathering” Environ Sci Technol, 58, 14775-14785. https://doi.org/10.1021/acs.est.3c09891

               Journal cover article: https://pubs.acs.org/toc/esthag/58/33

Zhang Y, McCarthy L, Ruff SE, Elhaik E “Microbiome Geographic Population Structure (mGPS) Detects Fine-Scale Geography” Genome Biology and Evolution, 16, evae209.  https://academic.oup.com/gbe/article/16/11/evae209/7814710            

Highest altimetric of all GBE articles of similar age, picked up by 15+ news outlets

Schiebel R, Aardema HM, Calleja ML, Dragoneas A, Heins L, Hrabe de Angelis IC, Pöhlker C, Slagter H, […], Ruff SE, Schmitt M, Schmitter J, Silva P, Smart S, Sörgel M, Stoll B, Su H, Vogt M, Wald T, Weber B, Weber J, Weis U, Amann R, Arístegui Ruiz J, Dittmar T, González Dávila M, Pöschl U, Haug GH (2024) “Probing the open ocean with the research sail yacht Eugen Seibold for climate geochemistry” Journal of Geophysical Research: Atmospheres, 129, 1-34. https://doi.org/10.1029/2023JD040581

2023

Pérez Castro S, Peredo E, Mason O, Vineis J, Bowen J, Mortazavi B, Ganesh A, Ruff SE, Paul BG, Giblin A, Cardon Z (2023) “Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes” (accepted at Applied and Environmental Microbiology). https://journals.asm.org/doi/10.1128/aem.00988-23

Ruff SE, Baker BJ (2023) “Editorial: Rising stars in hydrothermal vents and cold seeps: 2021” Frontiers in Microbiology,14, 1297372. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1297372/full

Zhang Y, Ruff SE, Oskolkov N, Tierney B, Ryon K, Danko D, Mason CE, Elhaik E (2023) “The microbial biodiversity at the archeological site of Tel Megiddo (Israel)” Frontiers in Microbiology, 14, 1253371. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1253371/full

Harvey EL, Yang H, Castiblanco E, Coolahan M, Dallmeyer-Drennen G, Fukuda N, Greene E, Gonsalves M, Smith S, Whalen KE (2023) Quorum sensing signal disrupts viral infection dynamics in the coccolithophore Emiliania huxleyi. Aquatic Microbial Ecology, 89:75-86. https://doi.org/10.3354/ame01998 

Ruff SE, Humez P, Hrabe de Angelis I, Nightingale M, Diao M, Cho S, Connors L, Kuloyo OO, Seltzer A, Bowman S, Wankel SD, McClain CN, Mayer B, Strous M (2023) “Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems” Nature Communications, 14, 3194. https://doi.org/10.1038/s41467-023-38523-4

2022

Niu M, Deng L, Su L, Ruff SE, Yang N, Qi Q, Li J, Wang F (2022) “Methane flux shapes the methanotrophic microbiome at cold seeps of South China Sea“ Molecular Ecology, 32, 660– 679. https://doi.org/10.1111/mec.16786

Ruff SE (2022) “Editorial: Microbial Communities and Metabolisms Involved in the Degradation of Cellular and Extracellular Organic Biopolymers” Frontiers in Microbiology, 12, 802619. https://doi.org/10.3389/fmicb.2021.802619

  • The article collection to this editorial can be found here

Moynihan MA, Goodkin NF, Morgan KM, Kho PY, Lopes dos Santos A, Lauro FM, Baker DM, Martin P. (2022) “Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef.” The ISME Journal, 6, 233-46. https://doi.org/10.1038/s41396-021-01054-1

Moynihan MA, Amini S, Oalmann J, Chua JI, Tanzil JT, Fan TY Miserez, A & Goodkin NF (2022). “Crystal orientation mapping and microindentation reveal anisotropy in Porites skeletons.” Acta Biomaterialia, 151, 446-456. https://doi.org/10.1016/j.actbio.2022.08.012

Martin P, Moynihan MA, Chen S, Woo OY, Zhou Y, Nichols RS, Chang KY, Tan AS, Chen YH, Ren H and Chen M (2022). “Monsoon-driven biogeochemical dynamics in an equatorial shelf sea: Time-series observations in the Singapore Strait.” Estuarine, Coastal and Shelf Science, 270, p.107855. https://doi.org/10.1016/j.ecss.2022.107855

2021

Klein S, Frazier V, Readdean T, Lucas E, Diaz-Jimenez EP, Sogin M, Ruff SE, Echeverri K (2021) „Common environmental pollutants negatively affect development and regeneration in the sea anemone Nematostella vectensis holobiont.” Frontiers in Ecology and Evolution, 9, 786037. https://doi.org/10.3389/fevo.2021.786037

Pérez Castro S, 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, 15, 3480-3497. https://doi.org/10.1038/s41396-021-01026-5

Teske A, Wegener G, Chanton JP, White D, MacGregor B, Hoer D, de Beer D, Zhuang G, Saxton MA, Joye SB, Lizarralde D, Soule SA, Ruff SE. (2021) “Microbial communities under distinct thermal and geochemical regimes in axial and off- axis sediments of Guaymas Basin.” Frontiers in Microbiology, 12, 633649. https://www.frontiersin.org/articles/10.3389/fmicb.2021.633649/full

Souza FFC, Mathai PP, Pauliquevis T,, Balsanelli E, Pedrosa FO, Souza EM, Baura VA, Monteiro RA, Cruz LM, Souza RAF, Andreae MO, Barbosa CGG; Hrabe de Angelis I, Sánchez-Parra B, Pӧhlker C, Weber B, Ruff SE, Reis RA, Godoi RHM, Sadowsky MJ, Huergo LF. (2021) “Influence of Seasonality on the Aerosol Microbiome of the Amazon Rainforest.” Science of the Total Environment, 760, 144092. https://www.sciencedirect.com/science/article/pii/S0048969720376233?via%3Dihub

           MBL Press Release: Seasons of the Microbiome over the Amazon Rainforest

2020

Lipson DA, Raab T, Pérez Castro S, Powell A “Organohalide respiring bacteria at the heart of anaerobic metabolism in Arctic wet tundra soils”. Applied and Environmental Microbiology, 87,e01643-20. https://aem.asm.org/content/87/3/e01643-2

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.” Proceedings of the National Academy of Sciences, 117, 11029-11037. https://www.pnas.org/content/early/2020/04/29/2002289117

MBL Press Release: Window to another World

Media coverage of the article: Phys.org / 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) https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15057

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”. Frontiers in Microbiology, 11, 1391. https://www.frontiersin.org/articles/10.3389/fmicb.2020.01391/full

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. https://link.springer.com/book/10.1007/978-3-030-34827-4

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. https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1462-2920.14929?af=R

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. https://www.sciencedirect.com/science/article/pii/S0016706119312674

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. https://environmentalmicrobiome.biomedcentral.com/track/pdf/10.1186/s40793-019-0348-0

MBL Press Release: Making “Lemonade”

Media coverage of the article: Environmental News Network / Phys.org

2019

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. https://www.frontiersin.org/articles/10.3389/fmicb.2019.00945/full

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. https://www.nature.com/articles/s41396-018-0263-1

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. https://www.nature.com/articles/s41396-019-0389-9

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. https://link.springer.com/article/10.1007/s11258-019-00912-5

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. https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.14653

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) https://www.biorxiv.org/content/10.1101/531970v1

Before 2019

For publications of the individual lab members prior to the inauguration of the RuffLab in Nov 2018 please refer to CVs and Google Scholar profiles in the People section