PUBLICATIONS

2024

Kumler W. and Ingalls A.E., squallms: Squashing qualms with speedy quality assurance via lasso labeling for untargeted mass spectrometry data. JOSS

Y Zheng, B Wang, P Gao, Y Yang, B Xu, X Su, D Ning, Q Tao, Q Li, F Zhao,  D. Wang, Y. Zhang, M. Li, M. K H Winkler, A.E. Ingalls, J. Zhou, C. Zhang, D.A. Stahl, J. Jiang, W. Martens-Habbena, W. Qin. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. The ISME Journal 18 (1).

2023

Park J., Durham B.P., Key R.S., Groussman R.D., Pinedo-Gonzalez P., Hawco N.J., John S.G., Carlson M.C.G., Lindell D., Juranek L., Ferrón S., Ribalet F., Armbrust E.V., Ingalls A.E., Bundy R.M., Siderophore production and utilization by microbes in the north Pacific Ocean.

H.M. Dawson, E. Connors, N.G. Erazo, J.S. Sacks, V. Mierzejewski,  V. Mierzejewski, S.M. Rundell, L.T. Carlson, J.W. Deming, A.E. Ingalls, J.S. Bowman, J.N. Young Microbial metabolomic responses to changes in temperature and salinity along the western Antarctic Peninsula. The ISME Journal 17 (11), 2035-2046.

W. Kumler, B.J. Hazelton, A.E. Ingalls. Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics. BMC bioinformatics 24 (1), 404.

2022

Sacks J.S., Heal K.R., Boysen, A.K., Carlson, L.T., Ingalls A.E. L&O Methods.

Quantification of dissolved metabolites in environmental samples through cation-exchange solid-phase extraction paired with liquid chromatography-mass spectrometry. 

Duffy M.E., Neibauer J.A., Adams J., Lundeen R.A., Rocap G., Ingalls A.E., Fuchsman C.A., Keil R. G. Limnology and Oceanography.

Protein cycling in the eastern tropical North Pacific oxygen-deficient one: A de novo-discovery peptidomic approach. 

Durham B.P., Boysen A.K., Heal K.R., Carlson L.T., Boccamazzo R., Deodato C.R., Qin W., Cattolico R.A., Armbrust E.V., Ingalls A.E. Frontiers in Marine Science.

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton.  

Boysen A.K., Durham B.P., Kumler W., Key R.S., Heal K.R., Carlson L.T., Groussman R.D., Armbrust E.V., Ingalls A.E. Environmental Microbiology. 

Glycine Betaine uptake and metabolism in marine microbial communities.

Muratore D., Boysen A.K., Harke M.J., Becker K.W., Casey J.R., Coesel S.N., Mende D.R., Wilson S.T., Aylward F.O., Eppley J., Visolova A., Peng s., Rodriguez-Gonzalez R., Beckett S.J., Armbrust E.V., DeLong E.F., Karl D.M., White A.E., Zehr J.P., Van Mooy B.A.S., Dyhrman S.T., Ingalls A.E., Weitz J.S. Nature Ecology and Evolution.

Complex marine microbial communities partition metabolism of scarce resources over the diel cycle.

Heal, K.R., Maloney A.E., Ingalls A.E., Bundy, R. L&O Letters. 

Diverse arsenic-containing lipids in the surface ocean. 

Biller S.J., Lundeen R.A., Hmelo L.R., Becker K.W., Arellano A., Dooley K., Carlson L.T., Heal K.R., Van Mooy B.A.S., Ingalls A.E., Chisholm S. Environmental Microbiology. 

Prochlorococcus extracellular vesicles: molecular composition and adsorption to diverse microbes.  

Li F., Leu A., Poff K., Carlson L.T., Ingalls A.E., DeLong E.F. Environmental Microbiology. 

Planktonic archaeal ether lipid origins in surface waters of the North Pacific Subtropical Gyre. 

2021

Heal K.R., Durham, B.P., Boysen A.K., Carlson L.T., Qin W., Ribalet F., White A.E., Bundy R.M., Armbrust E.V., Ingalls A.E. mSystems. 

Marine community metabolomes carry fingerprints of phytoplankton community composition.  

Boysen A.K., Carlson L.T., Durham B.P., Groussman R.D., Aylward F.O., Ribalet F., Heal K.R., DeLong E.F., Armbrust E.V., Ingalls A.E. mSystems. 

Daily oscillations of particulate metabolites reflect synchronized microbial activity in the North Pacific Subtropical Gyre.  

2020

Dawson H.M., Heal K.R., Torstensson A., Carlson L.T., Ingalls A.E., Young J.N. Integrative and Comparative Biology. 

Large diversity in nitrogen and sulfur containing compatible solute profiles in polar and temperate diatoms. 

Mattes T.E., Ingalls A.E., Burke S., Morris R.M. Environmental Microbiology. 

Metabolic flexibility of SUP05 under low DO growth conditions. 

Steen A.D., Kush S., Hussain A., Cakić N., Coffinet S., Dittmar T., Fulton J., Galy V., Hinrichs K-U., Ingalls A.E., Koch B., Kujawinski E., Liu Z., Osterholz H., Rush D., Seidel M., Sepulveda J., Wakeham S.G. Frontiers in Marine Science.

Analytical and computational advances, opportunities, and challenges in marine biogeochemistry in an era of “omics.” 

Qin W., Zheng Y., Zhao F., Wang Y., Urakawa H., Martens-Habbena W., Liu H., Huang X., Zhang X., Nakagawa T., Mende D.R., Bollmann A., Wang B., Zhang Y., Amin S.A., Nielsen J.L., Mori K., Takahashi R., Armbrust E.V., Winkler M.H., Delong E.F., Li M., Lee P.H., Zhou J., Zhang C., Zhang T., Stahl. D.A., Ingalls A.E. ISME. 

Alternate strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. 

Dawson, H.M., Heal, K.R., Boysen, A.K., Carlson, L.T., Ingalls, A.E., Young, J.N. Elementa.

Potential of temperature and salinity driven shifts in diatom compatible solute concentrations to impact biogeochemical cycling within sea ice.

Zhang Y., Qin W., Hou L., Zakem E.J., Wan X, Zhao Z., Liu L., Hunt K. A., Jiao N., Kao S.J., Tang K., Xie X, Shen J., Li Y., Chen M., Dai X., Liu C., Deng W., Dai M., Ingalls A.E., Stahl D.A., Herndl G.J. PNAS.

Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean. 

2019

Lu X., Heal K.R., Ingalls A.E., Doxey A.C., Neufeld J.D. ISME Journal.

Metagenomic and chemical characterization of soil vitamin B12 production.  

Wilson S.T., Hawco N.J., Armbrust E.V., Barone B., Bjorkman K.M., Boysen A.K., Burgos M., Burrell T.J., Casey J.R., DeLong E.F., Dugenne M., Dutkiewicz S., Dyhrman S.T., Ferron S., Follows M.J., Foreman R.K., Funkey C.P., Harke M.J., Henke B.A., Hill C.N., Hynes A.M., Ingalls A.E., John O., Kelly R.L., Knapp A.N., Letelier R.M., Ribalet F., Shimabukuro E.M., Tabata R.K.S., Turk-Kubo K.A., White A.E., Zehr J.P., John S., Karl D.M. Science.

Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean. 

Wang B., Qin W., Ren Y, Zhou X., Jung M.Y., Han P., Eloe-Fadrosh E.A., Li M., Lu L., Yan X., Liu Y., Heiner C., Hall R., Martens-Habbena W., Herbold C.W., Bartlett D.H., Huang L., Ingalls A.E., Rhee S.-K., Wagner M., Stahl D.A., Jia Z. ISME J.

 Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons .

Durham B.P., Boysen A.K., Carlson L.T., Groussman R.D., Heal K.R., Cain K.R., Morales R.L., Coesel S.N., Morris R.M., Ingalls A.E., Armbrust E.V. Nature Microbiology.

Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean.  

Heal K.R., Kellogg N.A., Carlson L.T., Lionheart R.M., Ingalls A.E. Protist.

Metabolomic consequences of cobalamin scarcity in diatoms as revealed through metabolomics.  

Spietz R.L., Lundeen R.A., Zhao X., Nicastro D., Ingalls A.E., Morris R.M. Environmental Microbiology.

Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria. 

Shah V., Zhao X., Lundeen R., Ingalls A.E., Nicastro D., Morris R.M. mBio.

Morphological Plasticity in a Sulfur-Oxidizing Marine Bacterium from the SUP05 Clade Enhances Dark Carbon Fixation. 

Torstensson A, Young, J., Carlson L.T., Ingalls A.E. Deming, J.  Journal of Phycology. 

Use of exogenous glycine betaine and its precursor choline as osmoprotectants in antarctic sea-ice diatoms.  

2018

Heal K.R.*, Qin W.*, Amin S.A., Devol A. H., Moffett J.W., Armbrust E.V., Stahl D.A., Ingalls A.E. 2018. Environmental Microbiology.

Accumulation of NO2-cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the Eastern Tropical North Pacific. 

Boysen A., Heal K.R., Carlson L.T. and Ingalls A.E. 2018. Analytical Chemistry.

Best-matched internal standard normalization in liquid chromatography-mass spectrometry metabolomics applied to environmental samples. 

2017

Qin W., Amin S.A., Lundeen R.A., Heal K.R., Martens-Habbena W., Turkarslan S., Urakawa H., Costa K.C., Hendrickson E.L. Wang T., Beck D.A.C., Tequia S.M., Taub F., Holmes A.D., Lowe T.M., Moffett J.W., Devol A.H., Baliga N.S., Arp D.J., Sayavedra-Soto L.A., Hackett M., Armbrust E.V., Ingalls A.E., Stahl D.A. 2017. The ISME Journal (2018) 12, 508–519. 

Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. 

Horak R.E.A., Qin W., Bertagnolli A., Nelson A., Heal K.R., Han H., Heller M., Schauer A., Jeffrey W., Armbrust E.V., Moffett J.W., Ingalls A.E., Stahl D.A., Devol A.H. 2017. Limnology and Oceanography.  

Relative impacts of light, temperature and reactive oxygen on thaumarchaeal ammonia oxidation in the North Pacific Ocean.  

Qin W., Heal K.R., Ramdasi R., Kobelt J.N., Martens-Habbena W., Bertagnolli A., Amin S.A., Walker C.B., Urakawa H., Könneke M., Devol A.H., Moffett J.W., Armbrust E.V., Ingalls A.E., Jensen G.J., Stahl D.A. 2017. Microbiology Research.

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminogenes gen. nov., sp. nov., Nitrosopumilus oxyclinae gen. nov., sp. nov., and Nitrosopumilus ureaphilus gen. nov., sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota.  

 Qin, W., Meinhardt K.A., Moffett J.W., Devol A.H., Armbrust E.V., Ingalls A.E., Stahl D.A., 2017. Environmental Microbiology Reports. 9:250-256.

Influence of oxygen availability on the activities of ammonia-oxidizing archaea.   

Fassbender A.J., Palevsky H.I., MArtz T.D., Ingalls A.E.,  Gledhill M., Fawecett S.E., Brandes J., Aluwihare L.I., and participants of COME ABOARD and DISCO XXV. 2017. Marine Chemistry.

Perspectives on Chemical Oceanography in a changing environment: Participants of the COME ABOARD Meeting examine the field in the context of 40 years of DISCO. 

Heal K.R., Qin W., Ribalet F., Bertagnolli A.D., Coyote-Maestas W., Hmelo L.R., Moffett J. W., Devol A.H., Armbrust E.V., Stahl D.A., Ingalls A.E. 2017.   PNAS. 

Two distinct pools of B12 analogs reveal community interdependencies in the ocean.

2016

Ingalls A.E., 2016. News and Views. Nature Geosciences.

Paleoceanography: Signal from the subsurface.  

2015

French D. W*, Huguet C., Turich C., Wakeham S.G., Carlson L.T., Ingalls A.E.  2015.  Organic Geochemistry. 88: 91-112.

Spatial distributions of core and intact glycerol dialkyl glycerol tetraethers (GDGTs) in the Columbia River basin, Washington: insights into origin and implications for the BIT Index.

Qin, W., Carlson L.T., Armbrust, E. V., Devol, A. H., Moffett J. W., Stahl, D. A., Ingalls, A. E. 2015.  PNAS.

Confounding effects of oxygen and temperature on the TEX86 signature of marine thaumarchaeota.

Amin, S.S., Hmelo L.R., van Tol H., Durham B., Truxal L., Heal K., Morales R., Berthiaume C., Djunaedi B., Ingalls A.E., Parsek M., Moran MA., Armbrust E.V.  2015.  Nature. 522: 98-101. 

Interaction and signaling between a cosmopolitan phytoplankton and associated bacteria.  

Martens-Habbena W., Qin W., Horak R.E.A., Urakawa H., Schauer A.J., Moffett J.W., Armbrust E.V., Ingalls A.E., Devol A.H., Stahl D.A.  2015. Environmental Microbiology

The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by nitric oxide scavenger. 

Bridoux M. C., Neibauer J., Nunn B., Ingalls A.E., Keil R. G. 2015. J. Mar. Systems. 

Suspended marine particulate proteins in coastal and oligotrophic waters.  

2014

Heal, K.R., Carlson L.T., Devol A. H., Armbrust E.V., Moffett J.W., Stahl, D.A., Ingalls A.E., 2014. Rapid Communication in Mass Spectrometry.

Determination of four forms of vitamin B12 and other B vitamins in seawater by liquid chromatography tandem mass spectrometry. 

Qin, W, Amin, S.S., Martens-Habbena W., Urakawa H., Devol, A. H., Ingalls, A. E., Moffett, J. W., Armbrust E. V., Stahl, D. A., 2014.  

Marine ammonia-oxidizing archaea isolates display obligate mixotrophy and wide ecotypic variation. PNAS. 111(34) 12504-12509.

Urakawa H, Martens-Habbena W, Huguet C, de la Torre J, Ingalls AE, Devol AH and Stahl DA. 2014.  59(4) Limnology and Oceanography.

Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary. 

Jacquot J.E., Horak R.E.A., Amin S.A., Devol A.H., Ingalls A.E., Armbrust E.V., Stahl D.A., Moffett J.W. 2014.  Mar. Chem. 

Assessment of potential for copper limitation of ammonia oxidation by Archaea in a dynamic estuary.  

2013

Schouten S., A.E. Ingalls, and 55 other authors.  2013.  G-Cubed.

An interlaboratory study of TEX86 and BIT analyses of sediments, extracts and standard mixtures.  

Ellis, E.E., A.E. Ingalls, J.E. Richey, R.G. Keil, L.T. Truxal, G.M. Santos, S.R. Alin, and E.R.M. Druffel. 2013. Geophysical Res. Lett.

Age of riverine carbon suggests rapid export of terrestrial primary production in tropics.  

Amin S.A., Moffett J.W., Martens-Habbena W., Jacquot J., Devol A, Ingalls AE, Stahl D.A., Armbrust E.V.  2013. Limnology and Oceanography.

Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications for nitrification in the marine environment. 

Close H.C., Shah S.R., Ingalls A.E., Aaron F. Diefendorf, Eoin L. Brodie, Roberta L. Hansman, Katherine H. Freeman, Lihini I. Aluwihare, Ann Pearson.  2013. PNAS. 

Export of submicron particulate organic matter to mesopelagic depths in an oligotrophic gyre.  

Horak R.E.A, Qin W., Schauer A.J., Armbrust E.V., Ingalls A.E., Moffett J.W., Stahl D.A., Devol A.H. 2013.  The ISME Journal.

Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea. 

Pearson, A. and Ingalls A.E. 2013.  Annual Reviews in Earth and Planetary Sciences.

Assessing the use of archaeal lipids as marine environmental proxies. 

Bridoux, M.C., and A.E. Ingalls. 2013. Geobiology. 

Diatom Microfossils from Cretaceous and Eocene Sediments Contain Native Silica Precipitating Long Chain Polyamines.  

2012

Bridoux, M.C., V.V. Annenkov, R.G. Keil, and A.E. Ingalls. 2012. Org. Geochem

Widespread distribution and molecular diverstiy of diatom frustule bound aliphatic long chain polyamines (LCPAs) in marine sediments. 

Bridoux, M.C., R.G. Keil, and A.E. Ingalls. 2012. Org. Geochem.

 Analysis of natural diatom communities reveals novel insights into the diversity of long chain polyamine (LCPA) structures involved in silica precipitation. 

Ellis, E.E., R.G. Keil, A.E. Ingalls, J.E. Richey, and S.R. Alin. 2012. Journal of Geophysical Research-Biogeosciences. 

Seasonal variability in the sources of particulate organic matter of the Mekong River as discerned by elemental and lignin analyses.  

Ingalls, A.E., C. Huguet, and L.T. Truxal. 2012. Applied and Environmental Microbiology. 

Distribution of Intact and Core Membrane Lipids of Archaeal Glycerol Dialkyl Glycerol Tetraethers among Size-Fractionated Particulate Organic Matter in Hood Canal, Puget Sound.   

2011

Bridoux M., Annenko V., Menzel H., Keil R., and Ingalls A.E. 2011. Rapid Communications in Mass Spectrometry. 

A new liquid chromatography/electrospray ionization mass spectrometry method for the analysis of underivitized aliphatic long chain polyamines. 

Shevenell A., Ingalls A.E., Domack E.W., Kelly C.,  2011. Nature.

Holocene Southern Ocean surface temperature variability west of the Antarctic Peninsula.

Ingalls AE, Ellis E, McDuffee K, Keil R, dos Santos Guaciara, Druffel ERM. 2011. Analytical Chemistry. 

HPLC Purification of higher plant-derived lignin phenols for compound specific radiocarbon analysis.  

2010

Huguet C, Martens-Habbena W, Urakawa H, Truxal L, Stahl DA, Ingalls AE. 2010. Organic Geochemistry. 

Changes in intact membrane lipid content of archaeal cells may indicate metabolic status. 

Bridoux M and Ingalls AE, 2010. Marine Chemistry. 

Radiocarbon dating of diatom-bound organic compounds. 

Huguet C, Martens-Habbena W, Urakawa H, Stahl DA, Ingalls AE. 2010. Limnology and Oceanography Methods.

Comparison of extraction methods for quantitative analysis of core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs) in environmental samples.  

2009 and earlier 

Ingalls AE, Whitehead KI, Bridoux, M.  2009. Geochimica Cosmochimica Acta

Tinted windows:  the presence and identification of the UV-absorbing compounds, mycosporine-like amino acids, in the frustules of marine diatoms.

Hansman RL, Griffin S, Watson JT, Druffel ERM, Ingalls AE, Pearson A, Aluwihare LI. 2009. PNAS.

The radiocarbon signature of microbial organisms in the mesopelagic ocean. 

Schouten, S, Hopmans EC, van der Meer J, Mets A, Bard E, Bianchi TS, Diefendorf A, Escala M, Freeman KH, Furukawa Y, Huguet C, Ingalls AE, Ménot-Combes G, Nederbragt AJ, Oba M, Pearson A, Pearson EJ, Rosell-Melé A, Schaeffer P, Shah SR, Shanahan TM, Smith RW, Smittenberg R, Suzuki M, Talbot HM, Uchida M, Van Mooy BAS, Yamamoto M, Zhang Z, Sinningh Damsté J. 2009. G-Cubed

An interlaboratory study of TEX86 and BIT analysis using high performance liquid chromatography/mass spectrometry.

de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA. 2008. Environmental Microbiology. 

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol.  

Walsh E. Ingalls AE, Keil R. 2008. Limnology and Oceanography

Sources and Transport of Terrestrial Organic Matter in Vancouver Island Fjords and the Vancouver- Washington Margin:  A multiproxy approach using δ13Corg, lignin phenols and the ether lipid BIT Index.

Shevenell, A.E., Ingalls, A.E., and E.W. Domack, 2007. 

Orbital and atmospheric forcing of western Antarctic Peninsula climate in the Holocene: The TEX86 paleotemperature record of Palmer Deep.  Changing World-Online Proceedings of the 10th ISAES X, A.K. Cooper and C.R. Raymond et al., eds., USGS Open-File Report, p. 131-4p, vol. 1047. 

Ingalls AE, Liu ZF and Lee C. 2006. DSR I.

Seasonal and latitudinal trends in source and diagenesis of sinking particles in the Pacific sector of the Southern Ocean: insights from amino acids, pigments and diatom-bound organic matter.

Ingalls AE, Shah S, Hansman RL, Aluwihare LI, Santos GM, Druffel ERM, Pearson A. 2006.  PNAS.

Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon.

Ingalls AE and Pearson A. The Oceanography Society.  2005. Invited article, Oceanography.

Ten Years of Compound-Specific Radiocarbon Analysis.  

Ingalls AE, Anderson RF, Pearson A, 2004. Marine Chemistry.

Radiocarbon dating of diatom-bound organic compounds. 

Ingalls AE, Lee C and Aller RC. 2004.  

Organic matter diagenesis in shallow water carbonate sediments. Geochimica et Cosmochimica Acta.

Pearson A., Huang Z., Ingalls A. E., Romanek C., Wiegel J. Freeman K. H., Smittenberg R. H. and Zhang C.L.  2004. Applied and Environmental Microbiology

Nonmarine Crenarchaeol in Nevada Hot Springs.

Ingalls AE, Lee C and Druffel ERM. 2003.  Geochimica Cosmochimica et Acta.

Preservation of organic matter in mound-forming skeletons.  

Ingalls AE, Lee C, Hedges JI and Wakeham SG. 2003. Deep-Sea Research II. 

The role of biominerals in the sinking flux and preservation of amino acids in the Southern Ocean along 170°W

Ingalls AE, Aller RC, Lee C and Sun M-Y.  2000.  Journal of Marine Research.

The influence of macrofauna on chlorophyll-a degradation in coastal marine sediments.