Anne Dekas is a geomicrobiologist interested in how microbial life affects the chemistry and climate of our planet today and throughout time. She obtained her PhD in Geobiology at the California Institute of Technology in 2013, and her AB in Earth and Planetary Sciences at Harvard University in 2004. She joined the Earth System Science Department at Stanford University as an assistant professor in September 2015.
Assistant Professor, Earth System Science
Assistant Professor, Earth System Science, Stanford University (2015 - Present)
Lawrence Postdoctoral Fellow, Lawrence Livermore National Laboratory (2013 - 2015)
NSF Graduate Research Fellow, Geological and Planetary Sciences, California Institute of Technology (2006 - 2009)
Technical Assistant, Planetary Protection Group, Jet Propulsion Laboratory (2005 - 2006)
Honors & Awards
Early Career Investigator in Marine Microbial Ecology and Evolution Award, Simons Foundation (2017-2020)
Outstanding Poster Presentation Award, Lawrence Livermore National Laboratory Poster Symposium (2014)
Lawrence Postdoctoral Fellowship, Lawrence Livermore National Laboratory (2013-2015)
Outstanding Oral Presentation, Southern California Geobiology Symposium (2009)
Tech Brief Award, NASA Jet Propulsion Laboratory (2009)
Graduate Research Fellowship, National Science Foundation (2006-2009)
Harvard College Award, Harvard University (2002, 2003)
John Harvard Award, Harvard University (2001)
Boards, Advisory Committees, Professional Organizations
Member, American Geophysical Union (2008 - Present)
Member, International Society for Microbial Ecology (2008 - Present)
PhD, California Institute of Technology, Geological and Planetary Sciences, Geobiology (2013)
AB, Harvard University, Earth and Planetary Sciences, Biogeochemistry (2004)
Current Research and Scholarly Interests
Environmental microbiology, deep-sea microbial ecology, marine biogeochemistry
- Fundamentals of Geobiology
ESS 205, GEOLSCI 205 (Aut)
Independent Studies (1)
- Graduate Research
ESS 400 (Aut, Win, Spr, Sum)
- Graduate Research
Prior Year Courses
- Life at the Extremes: From the Deep Sea to Deep Space
EARTHSYS 36N (Aut)
- Techniques in Environmental Microbiology
ESS 210 (Spr)
- Life at the Extremes: From the Deep Sea to Deep Space
EARTHSYS 36N (Aut)
- Techniques in Environmental Microbiology
ESS 210 (Spr)
- Topics in Earth System Science
ESS 301 (Spr)
- Life at the Extremes: From the Deep Sea to Deep Space
High-quality genome sequences of uncultured microbes by assembly of read clouds.
Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20*) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which were complete (>90% complete, <5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.
View details for DOI 10.1038/nbt.4266
View details for PubMedID 30320765
Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading.
Nitrogen fixation, the biological conversion of N2 to NH3 , is critical to alleviating nitrogen limitation in many marine ecosystems. To date, few measurements exist of N2 fixation in deep-sea sediments. Here, we conducted >400 bottle incubations with sediments from methane seeps, whale falls, and background sites off the western coast of the United States from 600 to 2893 m water depth to investigate the potential rates, spatial distribution, and biological mediators of benthic N2 fixation. We found that N2 fixation was widespread, yet heterogeneously distributed with sediment depth at all sites. In some locations, rates exceeded previous measurements by >10X, and provided up to 31% of the community anabolic growth requirement for nitrogen. Diazotrophic activity appeared to be inhibited by pore water ammonium: N2 fixation was only observed if incubation ammonium concentrations were ≤25 muM, and experimental additions of ammonium reduced diazotrophy. In seep sediments, N2 fixation was dependent on CH4 and coincident with sulfate reduction, consistent with previous work showing diazotrophy by microorganisms mediating sulfate-coupled methane oxidation. However, the pattern of diazotrophy was different in whale fall and associated reference sediments, where it was largely unaffected by CH4 , suggesting catabolically different diazotrophs at these sites. This article is protected by copyright. All rights reserved.
View details for DOI 10.1111/1462-2920.14342
View details for PubMedID 29968367
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
2018; 150: 41-56
View details for DOI 10.1016/j.dsr2.2018.03.001
Early-career scientists explore newly discovered methane seeps
View details for DOI 10.1029/2017EO068011
Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses
2016; 10 (3): 678-692
To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5'-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no (15)NH4(+) assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active 'free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. (15)N2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, (15)N2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced (15)N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations.
View details for DOI 10.1038/ismej.2015.145
View details for Web of Science ID 000370472500013
View details for PubMedID 26394007
View details for PubMedCentralID PMC4817681
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.
View details for DOI 10.1038/ncomms10476
View details for Web of Science ID 000369019300004
View details for PubMedID 26814032
Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea
2014; 16 (10): 3012-3029
Nitrogen (N2) fixation was investigated at Mound 12, Costa Rica, to determine its spatial distribution and biogeochemical controls in deep-sea methane seep sediment. Using (15)N2 tracer experiments and isotope ratio mass spectrometry analysis, we observed that seep N2 fixation is methane-dependent, and that N2 fixation rates peak in a narrow sediment depth horizon corresponding to increased abundance of aggregates of anaerobic methanotrophic archaea (ANME-2) and sulfate-reducing bacteria (SRB). Using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS), we directly measured (15)N2 uptake by ANME-2/SRB aggregates (n = 26) and observed maximum (15)N incorporation within ANME-2-dominated areas of the aggregates, consistent with previous analyses. NanoSIMS analysis of single cells (n = 34) from the same microcosm experiment revealed no (15)N2 uptake. Together, these observations suggest that ANME-2, and possibly physically associated SRB, mediate the majority of new nitrogen production within the seep ecosystem. ANME-2 diazotrophy was observed while in association with members of two distinct orders of SRB: Desulfobacteraceae and Desulfobulbaceae. The rate of N2 fixation per unit volume biomass was independent of the identity of the associated SRB, aggregate size and morphology. Our results show that the distribution of seep N2 fixation is heterogeneous, laterally and with depth in the sediment, and is likely influenced by chemical gradients affecting the abundance and activity of ANME-2/SRB aggregates.
View details for DOI 10.1111/1462-2920.12247
View details for Web of Science ID 000343867700002
View details for PubMedID 24107237
Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane
2014; 8 (1): 150-163
Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps; however, the ecophysiology of these different symbiotic associations has not been examined. Here, we applied a combination of molecular, geochemical and Fluorescence in situ hybridization (FISH) coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations (Eel River Basin, Hydrate Ridge and Costa Rican Margin seeps) to investigate the distribution and physiology of a newly identified subgroup of the Desulfobulbaceae (seepDBB) found in consortia with ANME-2c archaea, and compared these with the more commonly observed associations between the same ANME partner and the Desulfobacteraceae (DSS). FISH analyses revealed aggregates of seepDBB cells in association with ANME-2 from both environmental samples and laboratory incubations that are distinct in their structure relative to co-occurring ANME/DSS consortia. ANME/seepDBB aggregates were most abundant in shallow sediment depths below sulfide-oxidizing microbial mats. Depth profiles of ANME/seepDBB aggregate abundance revealed a positive correlation with elevated porewater nitrate relative to ANME/DSS aggregates in all seep sites examined. This relationship with nitrate was supported by sediment microcosm experiments, in which the abundance of ANME/seepDBB was greater in nitrate-amended incubations relative to the unamended control. FISH-NanoSIMS additionally revealed significantly higher (15)N-nitrate incorporation levels in individual aggregates of ANME/seepDBB relative to ANME/DSS aggregates from the same incubation. These combined results suggest that nitrate is a geochemical effector of ANME/seepDBB aggregate distribution, and provides a unique niche for these consortia through their utilization of a greater range of nitrogen substrates than the ANME/DSS.
View details for DOI 10.1038/ismej.2013.147
View details for Web of Science ID 000328605200015
View details for PubMedID 24008326
Polyphosphate Storage during Sporulation in the Gram-Negative Bacterium Acetonema longum
JOURNAL OF BACTERIOLOGY
2013; 195 (17): 3940-3946
Using electron cryotomography, we show that the Gram-negative sporulating bacterium Acetonema longum synthesizes high-density storage granules at the leading edges of engulfing membranes. The granules appear in the prespore and increase in size and number as engulfment proceeds. Typically, a cluster of 8 to 12 storage granules closely associates with the inner spore membrane and ultimately accounts for ∼7% of the total volume in mature spores. Energy-dispersive X-ray spectroscopy (EDX) analyses show that the granules contain high levels of phosphorus, oxygen, and magnesium and therefore are likely composed of polyphosphate (poly-P). Unlike the Gram-positive Bacilli and Clostridia, A. longum spores retain their outer spore membrane upon germination. To explore the possibility that the granules in A. longum may be involved in this unique process, we imaged purified Bacillus cereus, Bacillus thuringiensis, Bacillus subtilis, and Clostridium sporogenes spores. Even though B. cereus and B. thuringiensis contain the ppk and ppx genes, none of the spores from Gram-positive bacteria had granules. We speculate that poly-P in A. longum may provide either the energy or phosphate metabolites needed for outgrowth while retaining an outer membrane.
View details for DOI 10.1128/JB.00712-13
View details for Web of Science ID 000323047900016
View details for PubMedID 23813732
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, VOL 486, PART A
2011; 486: 281-305
Growing appreciation for the biogeochemical significance of uncultured microorganisms is changing the focus of environmental microbiology. Techniques designed to investigate microbial metabolism in situ are increasingly popular, from mRNA-targeted fluorescence in situ hybridization (FISH) to the "-omics" revolution, including metagenomics, transcriptomics, and proteomics. Recently, the coupling of FISH with nanometer-scale secondary ion mass spectrometry (NanoSIMS) has taken this movement in a new direction, allowing single-cell metabolic analysis of uncultured microbial phylogenic groups. The main advantage of FISH-NanoSIMS over previous noncultivation-based techniques to probe metabolism is its ability to directly link 16S rRNA phylogenetic identity to metabolic function. In the following chapter, we describe the procedures necessary to identify nitrogen-fixing microbes within marine sediment via FISH-NanoSIMS, using our work on nitrogen fixation by uncultured deep-sea methane-consuming archaea as a case study.
View details for DOI 10.1016/B978-0-12-381294-0.00012-2
View details for Web of Science ID 000286404100012
View details for PubMedID 21185440
Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia
2009; 326 (5951): 422-426
Nitrogen-fixing (diazotrophic) microorganisms regulate productivity in diverse ecosystems; however, the identities of diazotrophs are unknown in many oceanic environments. Using single-cell-resolution nanometer secondary ion mass spectrometry images of 15N incorporation, we showed that deep-sea anaerobic methane-oxidizing archaea fix N2, as well as structurally similar CN-, and share the products with sulfate-reducing bacterial symbionts. These archaeal/bacterial consortia are already recognized as the major sink of methane in benthic ecosystems, and we now identify them as a source of bioavailable nitrogen as well. The archaea maintain their methane oxidation rates while fixing N2 but reduce their growth, probably in compensation for the energetic burden of diazotrophy. This finding extends the demonstrated lower limits of respiratory energy capable of fueling N2 fixation and reveals a link between the global carbon, nitrogen, and sulfur cycles.
View details for DOI 10.1126/science.1178223
View details for Web of Science ID 000270818600052
View details for PubMedID 19833965
Bacillus canaveralius sp nov., an alkali-tolerant bacterium isolated from a spacecraft assembly facility
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
2009; 59: 2015-2019
Two Gram-positive, rod-shaped, alkali-tolerant (pH 10.5), endospore-forming bacteria (strains KSC SF8bT and KSC SF10a) were isolated from surfaces within the Payload Hazardous Servicing Facility, where robotic spacecraft are assembled and tested before launch, at the Kennedy Space Center at Cape Canaveral. Based on 16S rRNA gene sequence similarities, these strains were shown to belong to the family Bacillaceae and the genus Bacillus. The highest 16S rRNA gene sequence similarity was approximately 97.5%, observed between the novel strains and Bacillus selenatarsenatis SF-1T. Several phenotypic characteristics, such as growth with 10% NaCl and assimilation of melibiose and lactose, were useful in the discrimination of this novel species from the closely related alkali-tolerant species Bacillus firmus and B. selenatarsenatis. DNA-DNA hybridization studies revealed reassociation values of less than 45% between strain KSC SF8bT and its closest genotypic neighbours. The combination of unique phenotypic and genotypic characteristics allowed the differentiation of these alkali- and halotolerant spore-forming strains from related Bacillus species, and a novel species, Bacillus canaveralius sp. nov., is proposed. The type strain is KSC SF8bT (=ATCC BAA-1493T=MTCC 8908T).
View details for DOI 10.1099/ijs.0.009167-0
View details for Web of Science ID 000271435400027
View details for PubMedID 19567559
Diverse syntrophic partnerships from-deep-sea methane vents revealed by direct cell capture and metagenomics
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2008; 105 (19): 7052-7057
Microorganisms play a fundamental role in the cycling of nutrients and energy on our planet. A common strategy for many microorganisms mediating biogeochemical cycles in anoxic environments is syntrophy, frequently necessitating close spatial proximity between microbial partners. We are only now beginning to fully appreciate the diversity and pervasiveness of microbial partnerships in nature, the majority of which cannot be replicated in the laboratory. One notable example of such cooperation is the interspecies association between anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. These consortia are globally distributed in the environment and provide a significant sink for methane by substantially reducing the export of this potent greenhouse gas into the atmosphere. The interdependence of these currently uncultured microbes renders them difficult to study, and our knowledge of their physiological capabilities in nature is limited. Here, we have developed a method to capture select microorganisms directly from the environment, using combined fluorescence in situ hybridization and immunomagnetic cell capture. We used this method to purify syntrophic anaerobic methane oxidizing ANME-2c archaea and physically associated microorganisms directly from deep-sea marine sediment. Metagenomics, PCR, and microscopy of these purified consortia revealed unexpected diversity of associated bacteria, including Betaproteobacteria and a second sulfate-reducing Deltaproteobacterial partner. The detection of nitrogenase genes within the metagenome and subsequent demonstration of (15)N(2) incorporation in the biomass of these methane-oxidizing consortia suggest a possible role in new nitrogen inputs by these syntrophic assemblages.
View details for DOI 10.1073/pnas.0711303105
View details for Web of Science ID 000255921200048
View details for PubMedID 18467493
Microbial burden and diversity of commercial airline cabin air during short and long durations of travel
2008; 2 (5): 482-497
Total microbial burden and diversity associated with commercial airliner cabin air was assessed by molecular methods in 125 air samples from the business-class sections of 16 domestic and international flights. Viable microbial burden within these cabin air parcels constituted only 1-10% of the total microbial population and ranged from below detection limits to 1.2 x 10(4) cells m(-3) as determined with a validated ATP-based technology. Cultivable bacterial diversity was almost entirely limited to Gram-positive bacteria such as Staphylococcus and Bacillus. In contrast, cloning and sequencing 16S rRNA gene directly from the samples without cultivation indicated a significantly broader diversity, as sequences representing more than 100 species, and encompassing 12 classes of bacteria, were retrieved in varying abundance. Sequences of proteobacterial and Gram-positive lineage were retrieved most frequently (58% and 31% of all clone sequences, respectively), with Gram-positive and alpha-proteobacterial sequences dominating international flight samples and beta- and gamma-proteobacterial sequences comprising the largest portion of those retrieved from domestic flights. Significant differences in bacterial load and diversity were noted between samples obtained on domestic and international flights. The disparities observed in microbial abundance and diversity further underscore the immense value of state-of-the art molecular assays in augmenting traditional culture-based techniques.
View details for DOI 10.1038/ismej.2008.11
View details for Web of Science ID 000255974500004
View details for PubMedID 18256704
Molecular bacterial community analysis of clean rooms where spacecraft are assembled
FEMS MICROBIOLOGY ECOLOGY
2007; 61 (3): 509-521
Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha- and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments .
View details for DOI 10.1111/j.1574-6941.2007.00360.x
View details for Web of Science ID 000248961900011
View details for PubMedID 17655710
Isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2007; 73 (8): 2600-2611
In assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. Several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. Due to their proximity to spacefaring objects, these bacteria pose a considerable risk for forward contamination of extraterrestrial sites. Samples collected from four geographically distinct National Aeronautics and Space Administration clean rooms were challenged with UV-C irradiation, 5% hydrogen peroxide, heat shock, pH extremes (pH 3.0 and 11.0), temperature extremes (4 degrees C to 65 degrees C), and hypersalinity (25% NaCl) prior to and/or during cultivation as a means of selecting for extremotolerant bacteria. Culture-independent approaches were employed to measure viable microbial (ATP-based) and total bacterial (quantitative PCR-based) burdens. Intracellular ATP concentrations suggested a viable microbial presence ranging from below detection limits to 10(6) cells/m(2). However, only 0.1 to 55% of these viable cells were able to grow on defined culture medium. Isolated members of the Bacillaceae family were more physiologically diverse than those reported in previous studies, including thermophiles (Geobacillus), obligate anaerobes (Paenibacillus), and halotolerant, alkalophilic species (Oceanobacillus and Exiguobacterium). Non-spore-forming microbes (alpha- and beta-proteobacteria and actinobacteria) exhibiting tolerance to the selected stresses were also encountered. The multiassay cultivation approach employed herein enhances the current understanding of the physiological diversity of bacteria housed in these clean rooms and leads us to ponder the origin and means of translocation of thermophiles, anaerobes, and halotolerant alkalophiles into these environments.
View details for DOI 10.1128/AEM.03007-06
View details for Web of Science ID 000246542400023
View details for PubMedID 17308177
High-mass triple systems: The classical Cepheid Y Carinae
2005; 130 (2): 789-793
View details for Web of Science ID 000230721600034