Santoro Alyson

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Santoro

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Alyson

ORCID

0000-0003-2503-8219

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Nitrogen cycling in the secondary nitrite maximum of the eastern tropical North Pacific off Costa Rica

(John Wiley & Sons, 2015-12-15) Buchwald, Carolyn ; Santoro, Alyson E. ; Stanley, Rachel H. R. ; Casciotti, Karen L.

Nitrite is a central intermediate in the marine nitrogen cycle and represents a critical juncture where nitrogen can be reduced to the less bioavailable N2 gas or oxidized to nitrate and retained in a more bioavailable form. We present an analysis of rates of microbial nitrogen transformations in the oxygen deficient zone (ODZ) within the eastern tropical North Pacific Ocean (ETNP). We determined rates using a novel one-dimensional model using the distribution of nitrite and nitrate concentrations, along with their natural abundance nitrogen (N) and oxygen (O) isotope profiles. We predict rate profiles for nitrate reduction, nitrite reduction, and nitrite oxidation throughout the ODZ, as well as the contributions of anammox to nitrite reduction and nitrite oxidation. Nitrate reduction occurs at a maximum rate of 25 nM d−1 at the top of the ODZ, at the same depth as the maximum rate of nitrite reduction, 15 nM d−1. Nitrite oxidation occurs at maximum rates of 10 nM d−1 above the secondary nitrite maximum, but also in the secondary nitrite maximum, within the ODZ. Anammox contributes to nitrite oxidation within the ODZ but cannot account for all of it. Nitrite oxidation within the ODZ that is not through anammox is also supported by microbial gene abundance profiles. Our results suggest the presence of nitrite oxidation within the ETNP ODZ, with implications for the distribution and physiology of marine nitrite-oxidizing bacteria, and for total nitrogen loss in the largest marine ODZ.
Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

(John Wiley & Sons, 2017-04-05) Santoro, Alyson E. ; Saito, Mak A. ; Goepfert, Tyler J. ; Lamborg, Carl H. ; Dupont, Christopher L. ; DiTullio, Giacomo R.

Thaumarchaea are among the most abundant microbial groups in the ocean, but controls on their abundance and the distribution and metabolic potential of different subpopulations are poorly constrained. Here, two ecotypes of ammonia-oxidizing thaumarchaea were quantified using ammonia monooxygenase (amoA) genes across the equatorial Pacific Ocean. The shallow, or water column “A” (WCA), ecotype was the most abundant ecotype at the depths of maximum nitrification rates, and its abundance correlated with other biogeochemical indicators of remineralization such as NO3 : Si and total Hg. Metagenomes contained thaumarchaeal genes encoding for the catalytic subunit of the urease enzyme (ureC) at all depths, suggesting that members of both WCA and the deep, water column “B” (WCB) ecotypes may contain ureC. Coupled urea hydrolysis-ammonia oxidation rates were similar to ammonia oxidation rates alone, suggesting that urea could be an important source of ammonia for mesopelagic ammonia oxidizers. Potential inducement of metal limitation of both ammonia oxidation and urea hydrolysis was demonstrated via additions of a strong metal chelator. The water column inventory of WCA was correlated with the depth-integrated abundance of WCB, with both likely controlled by the flux of sinking particulate organic matter, providing strong evidence of vertical connectivity between the ecotypes. Further, depth-integrated amoA gene abundance and nitrification rates were correlated with particulate organic nitrogen flux measured by contemporaneously deployed sediment traps. Together, the results refine our understanding of the controls on thaumarchaeal distributions in the ocean, and provide new insights on the relationship between material flux and microbial communities in the mesopelagic.
Roadmap Towards Communitywide Intercalibration and Standardization of Ocean Nucleic Acids ‘Omics Measurements

(Woods Hole Oceanographic Institution, 2022-03) Berube, Paul M. ; Gifford, Scott M. ; Hurwitz, Bonnie ; Jenkins, Bethany D. ; Marchetti, Adrian ; Santoro, Alyson E.

In January 2020, the US Ocean Carbon & Biogeochemistry (OCB) Project Office funded the Ocean Nucleic Acids 'omics Intercalibration and Standardization workshop held at the University of North Carolina in Chapel Hill. Thirty-two participants from across the US, along with guests from Canada and France, met to develop a framework for standardization and intercalibration (S&I) of ocean nucleic acid ‘omics (na’omics) approaches (i.e., amplicon sequencing, metagenomics and metatranscriptomics). During the three-day workshop, participants discussed numerous topics, including: a) sample biomass collection and nucleic acid preservation for downstream analysis, b) extraction protocols for nucleic acids, c) addition of standard reference material to nucleic acid isolation protocols, d) isolation methods unique to RNA, e) sequence library construction, and f ) integration of bioinformatic considerations. This report provides a summary of these and other topics covered during the workshop and a series of recommendations for future S&I activities for na’omics approaches.
Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys.

(Wiley, 2019-11-19) Weber, Laura ; Gonzalez‐Díaz, Patricia ; Armenteros, Maickel ; Ferrer, Víctor M. ; Bretos, Fernando ; Bartels, Erich ; Santoro, Alyson E. ; Apprill, Amy

There are a few baseline reef‐systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected ‘crown jewel’ offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta‐diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.
Enrichment and characterization of ammonia-oxidizing archaea from the open ocean : phylogeny, physiology and stable isotope fractionation

( 2011-03-14) Santoro, Alyson E. ; Casciotti, Karen L.

Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the north Pacific Ocean that have been maintained in laboratory culture for over three years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S rRNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and cDNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonium (NH4 +) to nitrite (NO2 -). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15εNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15εNH3 ranged from 13- 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15εNH3 is similar.
N2O concentrations from San Pedro Ocean Time-series (SPOT) measured between 2014 to 2016

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-08-20) Santoro, Alyson ; Capone, Douglas G.

N2O concentrations from San Pedro Ocean Time-series (SPOT) measured between 2014 to 2016. Water samples were collected using a Niskin bottle rosette equipped with a CTD. N₂O concentrations were measured using a headspace equilibration method and analyzed on a SRI Greenhouse Gas Monitoring Gas Chromatograph. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/774571
Dissolved nitrite and ammonium concentration data from R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011 in the Eastern Tropical South Pacific

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-05-07) Casciotti, Karen L. ; Santoro, Alyson E. ; Knapp, Angela N.

Dissolved nitrite ([NO2-]) and ammonium ([NH4+]) concentration data were collected on two cruises in the Eastern Tropical South Pacific. Data from R/V Atlantis (AT15-61) cruise collected in Jan-Feb 2010 and data from R/V Melville (MV1104) cruise collected in Mar-Apr 2011 as part of the Microbial Nitrification project. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/820165
Processed CTD data from cruises R/V Atlantis (AT15-61) in Jan-Feb 2010 and R/V Melville (MV1104) in Mar-Apr 2011 in the Eastern Tropical South Pacific

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-05-07) Casciotti, Karen L. ; Capone, Douglas G. ; Santoro, Alyson E. ; Berelson, William M. ; Knapp, Angela N.

Processed CTD data from cruises R/V Atlantis (AT15-61) in Jan-Feb 2010 and R/V Melville (MV1104) in Mar-Apr 2011 in the Eastern Tropical South Pacific For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/827861
R/V Falkor 160115 CTD log from the ProteOMZ expedition in the Central Pacfic during 2016 (ProteOMZ project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-03-26) Saito, Mak A. ; Santoro, Alyson

R/V Falkor 160115 CTD log from the ProteOMZ expedition in the Central Pacfic during 2016 (ProteOMZ project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/708458
Ammonia oxidation, nitrite oxidation, and nitrate reduction rates from R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011 in the Eastern Tropical South Pacific

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-05-07) Casciotti, Karen L. ; Santoro, Alyson E.

Ammonia oxidation, nitrite oxidation, and nitrate reduction rates from cruises R/V Atlantis (AT15-61) in Jan-Feb 2010 and R/V Melville (MV1104) in Mar-Apr 2011 in the Eastern Tropical South Pacific For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/826782
Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011.

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-05-07) Casciotti, Karen L. ; Santoro, Alyson E.

Water column amoA and Nitrospina-like 16S rRNA gene abundances from qPCR in the Eastern Tropical South Pacific using seawater collected on R/V Atlantis (AT15-61) cruise in Jan-Feb 2010 and R/V Melville (MV1104) cruise in Mar-Apr 2011. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/826781
Primary production from the San Pedro Ocean Time-series (SPOT) measured between 2014 to 2016

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-08-20) Santoro, Alyson ; Capone, Douglas G.

Primary production from the San Pedro Ocean Time-series (SPOT) measured between 2014 to 2016. Water samples were collected using a Niskin bottle rosette equipped with a CTD. Rates of primary production were measured by quantifying the rate of CO2 fixation via H¹³CO₃ uptake. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/821539
Event log from R/V Falkor cruise 160115 on the ProteOMZ expedition in the Central Pacific during 2016 (ProteOMZ project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-03-26) Saito, Mak A. ; Santoro, Alyson

R/V Falkor 160115 event log from the ProteOMZ expedition in the Central Pacific during 2016. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/708384
Nitrous oxide concentrations from the R/V Falkor expedition FK160115 in the Central Pacific from January to February 2016

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-06-08) Laperriere, Sarah Marie ; Santoro, Alyson E.

Dissolved N2O concentrations from were measured in discrete samples on a research expedition to the Equatorial Pacific. Water samples were collected using a 24 bottle Niskin rosette equipped with a CTD. N₂O concentrations were measured using a headspace equilibration method and analyzed on a SRI Greenhouse Gas Monitoring Gas Chromatograph. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/775849
Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification.

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-06-07) Dupont, Christopher ; Santoro, Alyson

Nitrosopelagicus brevis CN25 and U25 were grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/739636
Measured Nutrients from the San Pedro Ocean Time-series (SPOT) station

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-04-04) Capone, Douglas G. ; Santoro, Alyson E.

This dataset includes nutrients measured at the San Pedro Ocean Time-series (SPOT) station from September 2014 to July 2016. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/773564
Ammonia and urea-derived-N oxidation rates measured using 15N additions from San Pedro Ocean Time-series (SPOT) measured between 2014 to 2016

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-08-20) Santoro, Alyson ; Capone, Douglas G.

Ammonia and urea-derived-N oxidation rates measured using 15N additions from San Pedro Ocean Time-series (SPOT) measured between 2014 to 2016. Water samples were collected using a Niskin bottle rosette equipped with a CTD. Rates of water column ammonia and urea-derived-N oxidation were measured from bottle incubations. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/774602
Complete genome sequences of two phylogenetically distinct Nitrospina strains isolated from the Atlantic and Pacific Oceans

(American Society for Microbiology, 2022-05-02) Bayer, Barbara ; Kellom, Matthew ; Valois, Frederica ; Waterbury, John B. ; Santoro, Alyson E.

The complete genome sequences of two chemoautotrophic nitrite-oxidizing bacteria of the genus Nitrospina are reported. Nitrospina gracilis strain Nb-211 was isolated from the Atlantic Ocean, and Nitrospina sp. strain Nb-3 was isolated from the Pacific Ocean. We report two highly similar ~3.07-Mbp genome sequences that differ by the presence of ferric iron chelator (siderophore) biosynthesis genes.
Oxygen isotopic composition of nitrate and nitrite produced by nitrifying cocultures and natural marine assemblages

(Association for the Sciences of Limnology and Oceanography, 2012-09) Buchwald, Carolyn ; Santoro, Alyson E. ; McIlvin, Matthew R. ; Casciotti, Karen L.

The δ18O value of nitrate produced during nitrification (δ18ONO3,nit) was measured in experiments designed to mimic oceanic conditions, involving cocultures of ammonia-oxidizing bacteria or ammonia-oxidizing archaea and nitrite-oxidizing bacteria, as well as natural marine assemblages. The estimates of ranged from −1.5‰ ± 0.1‰ to +1.3‰ ± 1.4‰ at δ18O values of water (H2O) and dissolved oxygen (O2) of 0‰ and 24.2‰ vs. Vienna Standard Mean Ocean Water, respectively. Additions of 18O-enriched H2O allowed us to evaluate the effects of oxygen (O) isotope fractionation and exchange on . Kinetic isotope effects for the incorporation of O atoms were the most important factors for setting overall values relative to the substrates (O2 and H2O). These isotope effects ranged from +10‰ to +22‰ for ammonia oxidation (O2 plus H2O incorporation) and from +1‰ to +27‰ for incorporation of H2O during nitrite oxidation. values were also affected by the amount and duration of nitrite accumulation, which permitted abiotic O atom exchange between nitrite and H2O. Coculture incubations where ammonia oxidation and nitrite oxidation were tightly coupled showed low levels of nitrite accumulation and exchange (3% ± 4%). These experiments had values of −1.5‰ to +0.7‰. Field experiments had greater accumulation of nitrite and a higher amount of exchange (22% to 100%), yielding an average value of +1.9‰ ± 3.0‰. Low levels of biologically catalyzed exchange in coculture experiments may be representative of nitrification in much of the ocean where nitrite accumulation is low. Abiotic oxygen isotope exchange may be important where nitrite does accumulate, such as oceanic primary and secondary nitrite maxima.
US National BioGeoSCAPES Workshop Report

(Woods Hole Oceangraphic Institution, 2023-01-09) Twining, Benjamin S. ; Saito, Mak A. ; Santoro, Alyson E. ; Marchetti, Adrian ; Levine, Naomi M.

BioGeoSCAPES (BGS) is an international program being developed to understand controls on ocean productivity and metabolism by integrating systems biology (‘omics) and biogeochemistry (Figure 1). To ensure global input into the design of the BGS Program, countries interested in participating were tasked with holding an organizing meeting to discuss the country-specific research priorities. A United States BGS planning meeting, sponsored by the Ocean Carbon & Biogeochemistry (OCB) Project Office, was convened virtually November 10-12, 2021. The objectives of the meeting were to communicate the planning underway by international partners, engage the US community to explore possible national contributions to such a program, and build understanding, support, and momentum for US efforts towards BGS. The meeting was well-attended, with 154 participants and many fruitful discussions that are summarized in this document. Key outcomes from the meeting were the identification of additional programs and partners for BGS, a prioritization of measurements requiring intercalibration, and the development of a consensus around key considerations to be addressed in a science plan. Looking forward, the hope is that this workshop will serve as the foundation for future US and international discussions and planning for a BGS program, enabled by NSF funding for an AccelNet project (AccelNet - Implementation: Development of an International Network for the Study of Ocean Metabolism and Nutrient Cycles on a Changing Planet (BioGeoSCAPES)), beginning in 2022.

Santoro Alyson

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