Publications

2024

Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity
Achberger, Amanda M., Rose Jones, John Jamieson, Charles P. Holmes II, Florence Schubotz, et al. 2024. "Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity." Nature Microbiology. 10.1038/s41564-024-01599-9

Microbial Proxies for Anoxic Microsites Vary with Management and Partially Explain Soil Carbon Concentration
Lacroix, Emily M., Anna Gomes, Gabby Barratt Heitmann, Dylan Schuler, Anne E. Dekas, et al. 2024. "Microbial Proxies for Anoxic Microsites Vary with Management and Partially Explain Soil Carbon Concentration." Environmental Science & Technology. 10.1021/acs.est.4c01882

Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant inorganic carbon fixation by heterotrophs
Meyer, Nicolette R., Yuki Morono, and Anne E. Dekas. 2024. "Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant inorganic carbon fixation by heterotrophs." Applied and Environmental Microbiology. 10.1128/aem.00446-24

Fervidibacter sacchari and universal polysaccharide metabolism in the Armatimonadota
Nou, Nancy O., Jonathan K. Covington, Dengxun Lai, Xavier Mayali, Cale O. Seymour, et. al. 2024. "Fervidibacter sacchari and universal polysaccharide metabolism in the Armatimonadota." Accepted at Nature Communications.
 

Autochthonous carbon loading of macroalgae stimulates benthic biological nitrogen fixation rates in shallow coastal marine sediments
Raut, Yubin, Casey R. Barr, Emily R. Paris, Bennett J. Kapili, Anne E. Dekas, and Douglas G. Capone. 2024. "Autochthonous carbon loading of macroalgae stimulates benthic biological nitrogen fixation rates in shallow coastal marine sediments." Frontiers in Microbiology. 10.3389/fmicb.2023.1312843

2023

Single-cell view of deep-sea microbial activity and intracommunity heterogeneity
Arandia-Gorostidi, Nestor, Alma Parada, Anne E. Dekas. 2023. “Single-cell view of deep-sea microbial activity and intracommunity heterogeneity.” The ISME Journal. 10.1038/s41396-022-01324-6
 

Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring
Buessecker, Steffen P., Grayson L. Chadwick, Melanie E. Quan, Brian P. Hedlund, Jeremy A. Dodsworth, and Anne E. Dekas. 2023. "Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring." ISME Journal. 10.1038/s41396-023-01472-3

Silicate biomineralization of sediment- and carbonate-hosted anaerobic methane-oxidizing consortia and implications for microbial fossil preservation
Osorio-Rodriguez, Daniela, Kyle S. Metcalfe, Shawn E. McGlynn, Hang Yu, Anne E. Dekas, et al. 2023. "Silicate biomineralization of sediment- and carbonate-hosted anaerobic methane-oxidizing consortia and implications for microbial fossil preservation." Proceedings of the National Academy of Sciences. 10.1073/pnas.2302156120

Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota
Parada, Alma E., Xavier Mayali, Peter Weber, Jessica Wollard, Alyson Santoro, et al. 2023. “Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota.” Environmental Microbiology. 10.1111/1462-2920.16299

Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity
Paris, Emily R., Nestor Arandia-Gorostidi, Benjamin Klempay, Jeff S. Bowman, Alexandra Pontefract, et. al. 2023. "Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity." Science Advances. 10.1126/sciadv.adj3594

2022

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea
Buessecker, Steffen, Marike Palmer, Dengxun Lai, Joshua Dimapilis, Xavier Mayali, et al. 2022. “An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea.” Nature Communications. 10.1038/s41467-022-31452-8

Contributions of anoxic microsites to soil carbon protection across soil textures
Lacroix, Emily M., Janica Mendillo, Anna Gomes, Anne Dekas, and Scott Fendorf. 2022. “Contributions of anoxic microsites to soil carbon protection across soil textures.” Geoderma. 10.1016/j.geoderma.2022.116050
 

Rates and physicochemical drivers of microbial anabolic activity in deep‐sea sediments and implications for deep time
Meyer, Nicolette, Alma E. Parada, Bennett J. Kapili, Julian L. Fortney, and Anne E. Dekas. 2022. “Rates and physicochemical drivers of microbial anabolic activity in deep‐sea sediments and implications for deep time.” Environmental Microbiology. 10.1111/1462-2920.16183

Cold Seeps on the Passive Northern US Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea
Semler, Amanda C., Julian L. Fortney, Robinson W. Fulweiler, Anne E. Dekas. 2022.“Cold Seeps on the Passive Northern US Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.” Applied and Environmental Microbiology. 10.1128/aem.00468-22

Comparison of Microbial Profiling and Tracer Testing for the Characterization of Injector-Producer Interwell Connectivities
Zhang, Yuran, Anne E. Dekas, Adam J. Hawkins, John Carlo Primo, Oxana Gorbatenko, et al. 2022. “Comparison of Microbial Profiling and Tracer Testing for the Characterization of Injector-Producer Interwell Connectivities.” Water. 10.3390/w14182921

Geological activity shapes the microbiome in deep-subsurface aquifers by advection
Zhang, Yuran, Roland N Horne, Adam J Hawkins, John Carlo Primo, Oxana Gorbatenko, et. al. 2022. “Geological activity shapes the microbiome in deep-subsurface aquifers by advection.” Proceedings of the National Academy of Sciences. 10.1073/pnas.2113985119
Scientific American feature

2021

Quantifying Microbial Activity In Situ: the Link between Cells and Cycles
Dekas, Anne E. 2021. “Quantifying Microbial Activity In Situ: the Link between Cells and Cycles.” mSystems. 10.1128/mSystems.00758-21


 

PPIT: an R package for inferring microbial taxonomy from nifH sequences
Kapili, Bennett J. and Anne E. Dekas. 2021. “PPIT: an R package for inferring microbial taxonomy from nifH sequences.” Bioinformatics. 10.1093/bioinformatics/btab100

 

Characterizing the “fungal shunt”: Parasitic fungi on diatoms affect carbon flow and bacterial communities in aquatic microbial food webs
Klawonn, Isabell, Silke Van den Wyngaert, Alma E. Parada, Nestor Arandia-Gorostidi, Martin J. Whitehouse, et al. 2021. “Characterizing the “fungal shunt”: Parasitic fungi on diatoms affect carbon flow and bacterial communities in aquatic microbial food webs.” Proceedings of the National Academy of Sciences. 10.1073/pnas.2102225118
Discover Magazine feature

Microbial diversity and activity in Southern California salterns and bitterns: analogues for remnant ocean worlds
Klempay, Benjamin, Nestor Arandia-Gorostidi, Anne E. Dekas, Douglas H. Bartlett, Christopher E. Carr, et al. 2021. “Microbial diversity and activity in Southern California salterns and bitterns: analogues for remnant ocean worlds.” Environmental Microbiology. 10.1111/1462-2920.15440

NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single-cell rates of microbial activity
Meyer, Nicolette R., Julian L. Fortney, and Anne E. Dekas. 2021. “NanoSIMS sample preparation decreases isotope enrichment: magnitude, variability and implications for single-cell rates of microbial activity.” Environmental Microbiology. 10.1111/1462-2920.15264

DNA Tracer Transport Through Porous Media—The Effect of DNA Length and Adsorption
Zhang, Yuran., Marshall B. Hartung, Adam J. Hawkins, Anne E. Dekas, Kewen Li, et al. 2021. “DNA Tracer Transport Through Porous Media—The Effect of DNA Length and Adsorption.” Water Resources Research. 10.1029/2020WR028382
 

2020

Evidence for Phylogenetically and Catabolically Diverse Active Diazotrophs in Deep-Sea Sediment
Kapili, Bennett J., Samuel E. Barnett, Daniel H. Buckley, and Anne E. Dekas. 2020. “Evidence for Phylogenetically and Catabolically Diverse Active Diazotrophs in Deep-Sea Sediment.” The ISME Journal. 10.1038/s41396-019-0584-8
 

Microbial Community Composition in Deep‐Subsurface Reservoir Fluids Reveals Natural Interwell Connectivity
Zhang, Yuran, Anne E. Dekas, Adam J. Hawkins, Alma E. Parada, Oxana Gorbatenko, et al. 2020. “Microbial Community Composition in Deep‐Subsurface Reservoir Fluids Reveals Natural Interwell Connectivity.” Water Resources Research. 10.1029/2019WR025916

2019

Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-Isotope NanoSIP
Dekas, Anne E., Alma E. Parada, Xavier Mayali, Jed A. Fuhrman, Jessica Wollard, et al. 2019. “Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-Isotope NanoSIP.” Frontiers in Microbiology. 10.3389/fmicb.2019.02682

2018

High-quality genome sequences of uncultured microbes by assembly of read clouds
Bishara, Alex, Eli L. Moss, Mikhail Kolmogorov, Alma E. Parada, Ziming Weng, et al. 2018. “High-quality genome sequences of uncultured microbes by assembly of read clouds.” Nature Biotechnology. 10.1038/nbt.4266
 

Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading
Dekas, Anne E., David A. Fike, Grayson L. Chadwick, Abigail Green-Saxena, Julian Fortney, et al. 2018. “Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading.” Environmental Microbiology. 10.1111/1462-2920.14342

Characterization of benthic biogeochemistry and ecology at three methane seep sites on the Northern U.S. Atlantic margin
McVeigh, Doreen, Adam Skarke, Anne Dekas, Chiara Borrelli, W.-L. Hong, et al. 2018. “Characterization of benthic biogeochemistry and ecology at three methane seep sites on the Northern U.S. Atlantic margin.” Deep Sea Research Part II: Topical Studies in Oceanography. 10.1016/j.dsr2.2018.03.001

2017

Early-career scientists explore newly discovered methane seeps
Dekas, Anne E. and Adam Skarke. 2017. “Early-career scientists explore newly discovered methane seeps.” Eos. 10.1029/2017EO068011


 

2016

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses
Dekas, Anne E., Stephanie A. Connon, Grayson L. Chadwick, Elizabeth Trembath-Reichert, and Victoria J. Orphan. 2016. “Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses.” The ISME Journal. 10.1038/ismej.2015.145

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
Eloe-Fadrosh, Emiley A., David Paez-Espino, Jessica Jarett, Peter F. Dunfield, Brian P. Hedlund, et al. 2016. “Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.” Nature Communications. 10.1038/ncomms10476

2014

Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea
Dekas, Anne E., Grayson L. Chadwick, Marshall W. Bowles, Samantha B. Joye, and Victoria J. Orphan. 2014. “Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea.” Environmental Microbiology. 10.1111/1462-2920.12247

Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane
Green-Saxena, A., A. E. Dekas, N. F. Dalleska, and V. J. Orphan. 2014. “Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane.” The ISME Journal. 10.1038/ismej.2013.147
 

2013

Polyphosphate Storage during Sporulation in the Gram-Negative Bacterium Acetonema longum
Tocheva, Elitza I., Anne E. Dekas, Shawn E. McGlynn, Dylan Morris, Victoria J. Orphan, et al. 2013. “Polyphosphate Storage during Sporulation in the Gram-Negative Bacterium Acetonema Longum.” Journal of Bacteriology. 10.1128/JB.00712-13

2011

Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence in situ Hybridization Coupled to Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS)
Dekas, Anne E., and Victoria J. Orphan. 2011. “Chapter 12 – Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence in situ Hybridization Coupled to Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS).” Methods in Enzymology: Research on Nitrification and Related Processes, Part A. 10.1016/B978-0-12-381294-0.00012-2

2009

Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia
Dekas, Anne E., Rachel S. Poretsky, and Victoria J. Orphan. 2009. “Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia.” Science. 10.1126/science.1178223
 

Bacillus canaveralius sp. nov., an alkali-tolerant bacterium isolated from a spacecraft assembly facility
Newcombe, David, Anne Dekas, Shanmugam Mayilraj, and Kasthuri Venkateswaran. 2009. “Bacillus canaveralius sp. nov., an alkali-tolerant bacterium isolated from a spacecraft assembly facility.” International Journal of Systematic and Evolutionary Microbiology. 10.1099/ijs.0.009167-0

2008

Microbial burden and diversity of commercial airline cabin air during short and long durations of travel
Osman, Shariff, Myron T. La Duc, Anne Dekas, David Newcombe, and Kasthuri Venkateswaran. 2008. “Microbial burden and diversity of commercial airline cabin air during short and long durations of travel.” The ISME Journal. 10.1038/ismej.2008.11

Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics
Pernthaler, Annelie, Anne E. Dekas, C. Titus Brown, Shana K. Goffredi, Tsegereda Embaye, et al. 2008. “Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics.” Proceedings of the National Academy of Sciences. 10.1073/pnas.0711303105

2007

Isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments
La Duc, Myron T., Anne Dekas, Shariff Osman, Christine Moissl, David Newcombe, et al. 2007. “Isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments.” Applied and Environmental Microbiology. 10.1128/AEM.03007-06

Molecular bacterial community analysis of clean rooms where spacecraft are assembled
Moissl, Christine, Shariff Osman, Myron T. La Duc, Anne Dekas, Eoin Brodie, et al. 2007. “Molecular bacterial community analysis of clean rooms where spacecraft are assembled.” FEMS Microbiology Ecology. 10.1111/j.1574-6941.2007.00360.x

2005

High-Mass Triple Systems: The Classical Cepheid Y Carinae
Evans, N. R., K. G. Carpenter, R. Robinson, F. Kienzle, and A. E. Dekas. 2005. “High-Mass Triple Systems: The Classical Cepheid Y Carinae.” Astronomical Journal. 10.1086/430458