Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation

Zhibo Shao; Yangchun Xu; Hua Wang; Weicheng Luo; Lice Wang; Yuhong Huang; Nona Sheila R. Agawin; Ayaz Ahmed; Mar Benavides; Mikkel Bentzon-Tilia; Ilana Berman-Frank; Hugo Berthelot; Isabelle C. Biegala; Mariana B. Bif; Antonio Bode; Sophie Bonnet; Deborah A. Bronk; Mark V. Brown; Lisa Campbell; Douglas G. Capone; Edward J. Carpenter; Nicolas Cassar; Bonnie X. Chang; Dreux Chappell; Yuh-ling Lee Chen; Matthew J. Church; Francisco M. Cornejo-Castillo; Amália Maria Sacilotto Detoni; Scott C. Doney; Cecile Dupouy; Marta Estrada; Camila Fernandez; Bieito Fernández-Castro; Debany Fonseca-Batista; Rachel A. Foster; Ken Furuya; Nicole Garcia; Kanji Goto; Jesús Gago; Mary R. Gradoville; M. Robert Hamersley; Britt A. Henke; Cora Hörstmann; Amal Jayakumar; Zhibing Jiang; Shuh-Ji Kao; David M. Karl; Leila R. Kittu; Angela N. Knapp; Sanjeev Kumar; Julie LaRoche; Hongbin Liu; Jiaxing Liu; Caroline Lory; Carolin R. Löscher; Emilio Marañón; Lauren F. Messer; Matthew M. Mills; Wiebke Mohr; Pia H. Moisander; Claire Mahaffey; Robert Moore; Beatriz Mouriño-Carballido; Margaret R. Mulholland; Shin-ichiro Nakaoka; Joseph A. Needoba; Eric J. Raes; Eyal Rahav; Teodoro Ramírez-Cárdenas; Christian Furbo Reeder; Lasse Riemann; Virginie Riou; Julie C. Robidart; Vedula V. S. S. Sarma; Takuya Sato; Himanshu Saxena; Corday Selden; Justin R. Seymour; Dalin Shi; Takuhei Shiozaki; Arvind Singh; Rachel E. Sipler; Jun Sun; Koji Suzuki; Kazutaka Takahashi; Yehui Tan; Weiyi Tang; Jean-Éric Tremblay; Kendra Turk-Kubo; Zuozhu Wen; Angelicque E. White; Samuel T. Wilson; Takashi Yoshida; Jonathan P. Zehr; Run Zhang; Yao Zhang; Ya-Wei Luo

doi:10.5194/essd-15-3673-2023

Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N₂ fixation

Zhibo Shao, Yangchun Xu, Hua Wang, Weicheng Luo, Lice Wang, Yuhong Huang, Nona Sheila R. Agawin, Ayaz Ahmed, Mar Benavides, Mikkel Bentzon-Tilia, Ilana Berman-Frank, Hugo Berthelot, Isabelle C. Biegala, Mariana B. Bif, Antonio Bode, Sophie Bonnet, Deborah A. Bronk, Mark V. Brown, Lisa Campbell, Douglas G. CaponeEdward J. Carpenter, Nicolas Cassar, Bonnie X. Chang, Dreux Chappell, Yuh-ling Lee Chen, Matthew J. Church, Francisco M. Cornejo-Castillo, Amália Maria Sacilotto Detoni, Scott C. Doney, Cecile Dupouy, Marta Estrada, Camila Fernandez, Bieito Fernández-Castro, Debany Fonseca-Batista, Rachel A. Foster, Ken Furuya, Nicole Garcia, Kanji Goto, Jesús Gago, Mary R. Gradoville, M. Robert Hamersley, Britt A. Henke, Cora Hörstmann, Amal Jayakumar, Zhibing Jiang, Shuh-Ji Kao, David M. Karl, Leila R. Kittu, Angela N. Knapp, Sanjeev Kumar, Julie LaRoche, Hongbin Liu, Jiaxing Liu, Caroline Lory, Carolin R. Löscher, Emilio Marañón, Lauren F. Messer, Matthew M. Mills, Wiebke Mohr, Pia H. Moisander, Claire Mahaffey, Robert Moore, Beatriz Mouriño-Carballido, Margaret R. Mulholland, Shin-ichiro Nakaoka, Joseph A. Needoba, Eric J. Raes, Eyal Rahav, Teodoro Ramírez-Cárdenas, Christian Furbo Reeder, Lasse Riemann, Virginie Riou, Julie C. Robidart, Vedula V. S. S. Sarma, Takuya Sato, Himanshu Saxena, Corday Selden, Justin R. Seymour, Dalin Shi, Takuhei Shiozaki, Arvind Singh, Rachel E. Sipler, Jun Sun, Koji Suzuki, Kazutaka Takahashi, Yehui Tan, Weiyi Tang, Jean-Éric Tremblay, Kendra Turk-Kubo, Zuozhu Wen, Angelicque E. White, Samuel T. Wilson, Takashi Yoshida, Jonathan P. Zehr, Run Zhang, Yao Zhang, Ya-Wei Luo^*

^*Corresponding author for this work

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Abstract

Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N₂ fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N₂ fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N₂ fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr⁻¹; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr⁻¹ (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr⁻¹). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr⁻¹), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr⁻¹). Moreover, version 2 estimates the N₂ fixation rate in the Indian Ocean to be 35±14 Tg N yr⁻¹, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N₂ fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N₂ bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022).

Original language	English
Journal	Earth System Science Data
Volume	15
Issue number	8
Pages (from-to)	3673-3709
Number of pages	37
ISSN	1866-3508
DOIs	https://doi.org/10.5194/essd-15-3673-2023
Publication status	Published - 2023

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Shao, Z., Xu, Y., Wang, H., Luo, W., Wang, L., Huang, Y., Agawin, N. S. R., Ahmed, A., Benavides, M., Bentzon-Tilia, M., Berman-Frank, I., Berthelot, H., Biegala, I. C., Bif, M. B., Bode, A., Bonnet, S., Bronk, D. A., Brown, M. V., Campbell, L., ... Luo, Y-W. (2023). Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N₂ fixation. Earth System Science Data, 15(8), 3673-3709. https://doi.org/10.5194/essd-15-3673-2023

@article{7237ef23f48f4301a99ef464e27eb71a,

title = "Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation",

abstract = "Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr−1 (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr−1). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr−1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr−1). Moreover, version 2 estimates the N2 fixation rate in the Indian Ocean to be 35±14 Tg N yr−1, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N2 bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022).",

author = "Zhibo Shao and Yangchun Xu and Hua Wang and Weicheng Luo and Lice Wang and Yuhong Huang and Agawin, {Nona Sheila R.} and Ayaz Ahmed and Mar Benavides and Mikkel Bentzon-Tilia and Ilana Berman-Frank and Hugo Berthelot and Biegala, {Isabelle C.} and Bif, {Mariana B.} and Antonio Bode and Sophie Bonnet and Bronk, {Deborah A.} and Brown, {Mark V.} and Lisa Campbell and Capone, {Douglas G.} and Carpenter, {Edward J.} and Nicolas Cassar and Chang, {Bonnie X.} and Dreux Chappell and Chen, {Yuh-ling Lee} and Church, {Matthew J.} and Cornejo-Castillo, {Francisco M.} and Detoni, {Am{\'a}lia Maria Sacilotto} and Doney, {Scott C.} and Cecile Dupouy and Marta Estrada and Camila Fernandez and Bieito Fern{\'a}ndez-Castro and Debany Fonseca-Batista and Foster, {Rachel A.} and Ken Furuya and Nicole Garcia and Kanji Goto and Jes{\'u}s Gago and Gradoville, {Mary R.} and Hamersley, {M. Robert} and Henke, {Britt A.} and Cora H{\"o}rstmann and Amal Jayakumar and Zhibing Jiang and Shuh-Ji Kao and Karl, {David M.} and Kittu, {Leila R.} and Knapp, {Angela N.} and Sanjeev Kumar and Julie LaRoche and Hongbin Liu and Jiaxing Liu and Caroline Lory and L{\"o}scher, {Carolin R.} and Emilio Mara{\~n}{\'o}n and Messer, {Lauren F.} and Mills, {Matthew M.} and Wiebke Mohr and Moisander, {Pia H.} and Claire Mahaffey and Robert Moore and Beatriz Mouri{\~n}o-Carballido and Mulholland, {Margaret R.} and Shin-ichiro Nakaoka and Needoba, {Joseph A.} and Raes, {Eric J.} and Eyal Rahav and Teodoro Ram{\'i}rez-C{\'a}rdenas and Reeder, {Christian Furbo} and Lasse Riemann and Virginie Riou and Robidart, {Julie C.} and Sarma, {Vedula V. S. S.} and Takuya Sato and Himanshu Saxena and Corday Selden and Seymour, {Justin R.} and Dalin Shi and Takuhei Shiozaki and Arvind Singh and Sipler, {Rachel E.} and Jun Sun and Koji Suzuki and Kazutaka Takahashi and Yehui Tan and Weiyi Tang and Jean-{\'E}ric Tremblay and Kendra Turk-Kubo and Zuozhu Wen and White, {Angelicque E.} and Wilson, {Samuel T.} and Takashi Yoshida and Zehr, {Jonathan P.} and Run Zhang and Yao Zhang and Ya-Wei Luo",

year = "2023",

doi = "10.5194/essd-15-3673-2023",

language = "English",

volume = "15",

pages = "3673--3709",

journal = "Earth System Science Data",

issn = "1866-3508",

publisher = "Copernicus GmbH",

number = "8",

}

Shao, Z, Xu, Y, Wang, H, Luo, W, Wang, L, Huang, Y, Agawin, NSR, Ahmed, A, Benavides, M, Bentzon-Tilia, M, Berman-Frank, I, Berthelot, H, Biegala, IC, Bif, MB, Bode, A, Bonnet, S, Bronk, DA, Brown, MV, Campbell, L, Capone, DG, Carpenter, EJ, Cassar, N, Chang, BX, Chappell, D, Chen, YL, Church, MJ, Cornejo-Castillo, FM, Detoni, AMS, Doney, SC, Dupouy, C, Estrada, M, Fernandez, C, Fernández-Castro, B, Fonseca-Batista, D, Foster, RA, Furuya, K, Garcia, N, Goto, K, Gago, J, Gradoville, MR, Hamersley, MR, Henke, BA, Hörstmann, C, Jayakumar, A, Jiang, Z, Kao, S-J, Karl, DM, Kittu, LR, Knapp, AN, Kumar, S, LaRoche, J, Liu, H, Liu, J, Lory, C, Löscher, CR, Marañón, E, Messer, LF, Mills, MM, Mohr, W, Moisander, PH, Mahaffey, C, Moore, R, Mouriño-Carballido, B, Mulholland, MR, Nakaoka, S, Needoba, JA, Raes, EJ, Rahav, E, Ramírez-Cárdenas, T, Reeder, CF, Riemann, L, Riou, V, Robidart, JC, Sarma, VVSS, Sato, T, Saxena, H, Selden, C, Seymour, JR, Shi, D, Shiozaki, T, Singh, A, Sipler, RE, Sun, J, Suzuki, K, Takahashi, K, Tan, Y, Tang, W, Tremblay, J-É, Turk-Kubo, K, Wen, Z, White, AE, Wilson, ST, Yoshida, T, Zehr, JP, Zhang, R, Zhang, Y & Luo, Y-W 2023, 'Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N₂ fixation', Earth System Science Data, vol. 15, no. 8, pp. 3673-3709. https://doi.org/10.5194/essd-15-3673-2023

TY - JOUR

T1 - Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation

AU - Shao, Zhibo

AU - Xu, Yangchun

AU - Wang, Hua

AU - Luo, Weicheng

AU - Wang, Lice

AU - Huang, Yuhong

AU - Agawin, Nona Sheila R.

AU - Ahmed, Ayaz

AU - Benavides, Mar

AU - Bentzon-Tilia, Mikkel

AU - Berman-Frank, Ilana

AU - Berthelot, Hugo

AU - Biegala, Isabelle C.

AU - Bif, Mariana B.

AU - Bode, Antonio

AU - Bonnet, Sophie

AU - Bronk, Deborah A.

AU - Brown, Mark V.

AU - Campbell, Lisa

AU - Capone, Douglas G.

AU - Carpenter, Edward J.

AU - Cassar, Nicolas

AU - Chang, Bonnie X.

AU - Chappell, Dreux

AU - Chen, Yuh-ling Lee

AU - Church, Matthew J.

AU - Cornejo-Castillo, Francisco M.

AU - Detoni, Amália Maria Sacilotto

AU - Doney, Scott C.

AU - Dupouy, Cecile

AU - Estrada, Marta

AU - Fernandez, Camila

AU - Fernández-Castro, Bieito

AU - Fonseca-Batista, Debany

AU - Foster, Rachel A.

AU - Furuya, Ken

AU - Garcia, Nicole

AU - Goto, Kanji

AU - Gago, Jesús

AU - Gradoville, Mary R.

AU - Hamersley, M. Robert

AU - Henke, Britt A.

AU - Hörstmann, Cora

AU - Jayakumar, Amal

AU - Jiang, Zhibing

AU - Kao, Shuh-Ji

AU - Karl, David M.

AU - Kittu, Leila R.

AU - Knapp, Angela N.

AU - Kumar, Sanjeev

AU - LaRoche, Julie

AU - Liu, Hongbin

AU - Liu, Jiaxing

AU - Lory, Caroline

AU - Löscher, Carolin R.

AU - Marañón, Emilio

AU - Messer, Lauren F.

AU - Mills, Matthew M.

AU - Mohr, Wiebke

AU - Moisander, Pia H.

AU - Mahaffey, Claire

AU - Moore, Robert

AU - Mouriño-Carballido, Beatriz

AU - Mulholland, Margaret R.

AU - Nakaoka, Shin-ichiro

AU - Needoba, Joseph A.

AU - Raes, Eric J.

AU - Rahav, Eyal

AU - Ramírez-Cárdenas, Teodoro

AU - Reeder, Christian Furbo

AU - Riemann, Lasse

AU - Riou, Virginie

AU - Robidart, Julie C.

AU - Sarma, Vedula V. S. S.

AU - Sato, Takuya

AU - Saxena, Himanshu

AU - Selden, Corday

AU - Seymour, Justin R.

AU - Shi, Dalin

AU - Shiozaki, Takuhei

AU - Singh, Arvind

AU - Sipler, Rachel E.

AU - Sun, Jun

AU - Suzuki, Koji

AU - Takahashi, Kazutaka

AU - Tan, Yehui

AU - Tang, Weiyi

AU - Tremblay, Jean-Éric

AU - Turk-Kubo, Kendra

AU - Wen, Zuozhu

AU - White, Angelicque E.

AU - Wilson, Samuel T.

AU - Yoshida, Takashi

AU - Zehr, Jonathan P.

AU - Zhang, Run

AU - Zhang, Yao

AU - Luo, Ya-Wei

PY - 2023

Y1 - 2023

N2 - Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr−1 (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr−1). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr−1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr−1). Moreover, version 2 estimates the N2 fixation rate in the Indian Ocean to be 35±14 Tg N yr−1, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N2 bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022).

AB - Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr−1 (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr−1). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr−1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr−1). Moreover, version 2 estimates the N2 fixation rate in the Indian Ocean to be 35±14 Tg N yr−1, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N2 bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022).

U2 - 10.5194/essd-15-3673-2023

DO - 10.5194/essd-15-3673-2023

M3 - Journal article

SN - 1866-3508

VL - 15

SP - 3673

EP - 3709

JO - Earth System Science Data

JF - Earth System Science Data

IS - 8

ER -