Articles | Volume 17, issue 23
https://doi.org/10.5194/bg-17-6017-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-17-6017-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
03 Dec 2020
Research article |
| 03 Dec 2020
| 03 Dec 2020
New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem
Yanhong Lu
SZU–HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
Shunyan Cheung
Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
Ling Chen
State Key Laboratory of Marine Environmental Science, Xiamen
University, Xiamen, China
Shuh-Ji Kao
State Key Laboratory of Marine Environmental Science, Xiamen
University, Xiamen, China
Xiaomin Xia
Key Laboratory of Tropical Marine Bio-resources and Ecology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
Jianping Gan
SZU–HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
Minhan Dai
State Key Laboratory of Marine Environmental Science, Xiamen
University, Xiamen, China
Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
Related authors
No articles found.
Yuye Han, Zvi Steiner, Zhimian Cao, Di Fan, Junhui Chen, Jimin Yu, and Minhan Dai
EGUsphere, https://doi.org/10.5194/egusphere-2024-3492, https://doi.org/10.5194/egusphere-2024-3492, 2024
Short summary
Short summary
Coccolithophore calcite accounts for a major fraction of particulate inorganic carbon (PIC) standing stocks in the western North Pacific, with a markedly higher contribution in the oligotrophic subtropical gyre than in the Kuroshio-Oyashio transition region, which highlights the importance of coccolithophores for PIC production in the pelagic ocean. We also found extensive dissolution of coccolithophore calcite in the oversaturated shallow waters primarily driven by microbial metabolic activity.
Michael Morando, Jonathan Magasin, Shunyan Cheung, Matthew M. Mills, Jonathan P. Zehr, and Kendra A. Turk-Kubo
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2024-163, https://doi.org/10.5194/essd-2024-163, 2024
Revised manuscript accepted for ESSD
Short summary
Short summary
Nitrogen is crucial in ocean food webs, but only some microbes can fix N2 gas into a bioavailable form. Most are known only by their nifH gene sequence. We created a software workflow for nifH data and ran it on 865 ocean samples, producing a database that captures the global diversity of N2-fixing marine microbes and the environmental factors that influence them. The workflow and DB can standardize analyses on past and future nifH datasets to enable insights into marine microbial communities.
Yanmin Wang, Xianghui Guo, Guizhi Wang, Lifang Wang, Tao Huang, Yan Li, Zhe Wang, and Minhan Dai
EGUsphere, https://doi.org/10.5194/egusphere-2023-3155, https://doi.org/10.5194/egusphere-2023-3155, 2024
Preprint archived
Short summary
Short summary
This study reports higher nutrient release in fish farming system compared to river inputs and other sources with implications for coastal environment. DIN and DIP variation in Sansha Bay are dominated by mariculture activity relative to river input during spring. The N/P budget shows that 52.8 ± 4.7 % of DIN and 33.0 ± 3.7 % of DIP released from fish feeds exceeded other nutrient inputs. Co-culture strategies (e.g., of fish, kelp and oysters) allow effective mitigation of environmental impacts.
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, and Ya-Wei Luo
Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023, https://doi.org/10.5194/essd-15-3673-2023, 2023
Short summary
Short summary
N2 fixation by marine diazotrophs is an important bioavailable N source to the global ocean. This updated global oceanic diazotroph database increases the number of in situ measurements of N2 fixation rates, diazotrophic cell abundances, and nifH gene copy abundances by 184 %, 86 %, and 809 %, respectively. Using the updated database, the global marine N2 fixation rate is estimated at 223 ± 30 Tg N yr−1, which triplicates that using the original database.
Wenfeng Lai and Jianping Gan
Ocean Sci., 19, 1107–1121, https://doi.org/10.5194/os-19-1107-2023, https://doi.org/10.5194/os-19-1107-2023, 2023
Short summary
Short summary
Our study shows a high-resolution regional atmospheric model improves near-surface wind and air temperature simulation, resulting in improved circulation and hydrographic simulations in the Pearl River estuary. High-resolution wind forcing is critical for coastal circulation and cross-isobath transport, while high-resolution heat forcing greatly improves sea surface temperature simulation. High-resolution atmospheric forcing is essential for accurately simulating dynamic coastal ocean processes.
Yifan Ma, Kuanbo Zhou, Weifang Chen, Junhui Chen, Jin-Yu Terence Yang, and Minhan Dai
Biogeosciences, 20, 2013–2030, https://doi.org/10.5194/bg-20-2013-2023, https://doi.org/10.5194/bg-20-2013-2023, 2023
Short summary
Short summary
We distinguished particulate organic carbon (POC) export fluxes out of the nutrient-depleted layer (NDL) and the euphotic zone. The amount of POC export flux at the NDL base suggests that the NDL could be a hotspot of particle export. The substantial POC export flux at the NDL base challenges traditional concepts that the NDL was limited in terms of POC export. The dominant nutrient source for POC export fluxes should be subsurface nutrients, which was determined by 15N isotopic mass balance.
Zhixuan Wang, Guizhi Wang, Xianghui Guo, Yan Bai, Yi Xu, and Minhan Dai
Earth Syst. Sci. Data, 15, 1711–1731, https://doi.org/10.5194/essd-15-1711-2023, https://doi.org/10.5194/essd-15-1711-2023, 2023
Short summary
Short summary
We reconstructed monthly sea surface pCO2 data with a high spatial resolution in the South China Sea (SCS) from 2003 to 2020. We validate our reconstruction with three independent testing datasets and present a new method to assess the uncertainty of the data. The results strongly suggest that our reconstruction effectively captures the main features of the spatiotemporal patterns of pCO2 in the SCS. Using this dataset, we found that the SCS is overall a weak source of atmospheric CO2.
Xiaofeng Dai, Mingming Chen, Xianhui Wan, Ehui Tan, Jialing Zeng, Nengwang Chen, Shuh-Ji Kao, and Yao Zhang
Biogeosciences, 19, 3757–3773, https://doi.org/10.5194/bg-19-3757-2022, https://doi.org/10.5194/bg-19-3757-2022, 2022
Short summary
Short summary
This study revealed the distinct distribution patterns of six key microbial functional genes and transcripts related to N2O sources and sinks in four estuaries spanning the Chinese coastline, which were significantly constrained by nitrogen and oxygen concentrations, salinity, temperature, and pH. The community structure of the nosZ clade II was distinctly different from those in the soil and marine OMZs. Denitrification may principally control the N2O emissions patterns across the estuaries.
Yangyang Zhao, Khanittha Uthaipan, Zhongming Lu, Yan Li, Jing Liu, Hongbin Liu, Jianping Gan, Feifei Meng, and Minhan Dai
Biogeosciences, 18, 2755–2775, https://doi.org/10.5194/bg-18-2755-2021, https://doi.org/10.5194/bg-18-2755-2021, 2021
Short summary
Short summary
In situ oxygen consumption rates were estimated for the first time during destruction of coastal hypoxia as disturbed by a typhoon and its reinstatement in the South China Sea off the Pearl River estuary. The reinstatement of summer hypoxia was rapid with a comparable timescale with that of its initial disturbance from frequent tropical cyclones, which has important implications for better understanding the intermittent nature of coastal hypoxia and its prediction in a changing climate.
Siqi Wu, Moge Du, Xianhui Sean Wan, Corday Selden, Mar Benavides, Sophie Bonnet, Robert Hamersley, Carolin R. Löscher, Margaret R. Mulholland, Xiuli Yan, and Shuh-Ji Kao
Biogeosciences Discuss., https://doi.org/10.5194/bg-2021-104, https://doi.org/10.5194/bg-2021-104, 2021
Preprint withdrawn
Short summary
Short summary
Nitrogen (N2) fixation is one of the most important nutrient sources to the ocean. Here, we report N2 fixation in the deep, dark ocean in the South China Sea via a highly sensitive new method and elaborate controls, showing the overlooked importance of N2 fixation in the deep ocean. By global data compilation, we also provide an easy measured basic parameter to estimate deep N2 fixation. Our study may help to expand the area limit of N2 fixation studies and better constrain global N2 fixation.
Guizhi Wang, Samuel S. P. Shen, Yao Chen, Yan Bai, Huan Qin, Zhixuan Wang, Baoshan Chen, Xianghui Guo, and Minhan Dai
Earth Syst. Sci. Data, 13, 1403–1417, https://doi.org/10.5194/essd-13-1403-2021, https://doi.org/10.5194/essd-13-1403-2021, 2021
Short summary
Short summary
This study reconstructs a complete field of summer sea surface partial pressure of CO2 (pCO2) over the South China Sea (SCS) with a 0.5° resolution in the period of 2000–2017 using the scattered underway pCO2 observations. The spectral optimal gridding method was used in this reconstruction with empirical orthogonal functions computed from remote sensing data. Our reconstructed data show that the rate of sea surface pCO2 increase in the SCS is 2.4 ± 0.8 µatm yr-1 during 2000–2017.
Hiu Suet Kung and Jianping Gan
Ocean Sci., 16, 1095–1110, https://doi.org/10.5194/os-16-1095-2020, https://doi.org/10.5194/os-16-1095-2020, 2020
Short summary
Short summary
Based on a well-validated ocean circulation model, we found that near-inertial oscillations (NIOs) and near-inertial kinetic energy (KEni) varied distinctly during forcing and relaxation stages of tropical cyclone (TC) forcing, and the horizontal and vertical transport of KEni was largely modulated by the velocity and vorticity of the jet in the semi-enclosed South China Sea (SCS). This study enriches our understanding of the spatial–temporal variability of NIOs in the frequently TC-affected SCS.
Juan Yao, Juying Wang, Hongbin Liu, and Kedong Yin
Biogeosciences Discuss., https://doi.org/10.5194/bg-2020-188, https://doi.org/10.5194/bg-2020-188, 2020
Preprint withdrawn
Short summary
Short summary
Our study finds that winds appear to be a dominant regulating force on the formation of hypoxia in the Pearl River estuarine waters. The wind speed > 6 m/s appears to a threshold above which the water column stratification is destroyed and the formation of bottom hypoxia is interrupted. The frequency of such the above-threshold wind events decreases significantly, implying that climate change induced variability in wind speeds can exasperate the coastal formation of bottom hypoxia in the region.
Li Ma, Hua Lin, Xiabing Xie, Minhan Dai, and Yao Zhang
Biogeosciences, 16, 4765–4781, https://doi.org/10.5194/bg-16-4765-2019, https://doi.org/10.5194/bg-16-4765-2019, 2019
Short summary
Short summary
The major microbial process producing N2O in estuarine ecosystems remains controversial. Combining the concentrations and isotopic compositions of N2O, distributions and transcript levels of ammonia-oxidizing bacterial and archaeal amoA and denitrifier nirS genes, and in situ incubation estimates of nitrification rates and N2O production rates, we clarified that ammonia-oxidizing bacteria contributed the major part in N2O production in the upper Pearl River estuary despite their low abundance.
Lei Hou, Xiabing Xie, Xianhui Wan, Shuh-Ji Kao, Nianzhi Jiao, and Yao Zhang
Biogeosciences, 15, 5169–5187, https://doi.org/10.5194/bg-15-5169-2018, https://doi.org/10.5194/bg-15-5169-2018, 2018
Short summary
Short summary
The niche differentiation of ammonia and nitrite oxidizers is controversial because they display disparate patterns in different environments. Combining molecular and nitrification rate analyses, our study clarified that water mass mixing and the substrate availability primarily regulated the niche differentiation of nitrifier populations along a salinity gradient. The nitrifier populations may have specific adaptations to different substrate conditions through their ecological strategies.
Li Luo, Shuh-Ji Kao, Hongyan Bao, Huayun Xiao, Hongwei Xiao, Xiaohong Yao, Huiwang Gao, Jiawei Li, and Yangyang Lu
Atmos. Chem. Phys., 18, 6207–6222, https://doi.org/10.5194/acp-18-6207-2018, https://doi.org/10.5194/acp-18-6207-2018, 2018
Mianrun Chen, Dongyoung Kim, Hongbin Liu, and Chang-Keun Kang
Biogeosciences, 15, 2055–2073, https://doi.org/10.5194/bg-15-2055-2018, https://doi.org/10.5194/bg-15-2055-2018, 2018
Short summary
Short summary
The trophic preference (i.e., food resources and trophic levels) of different copepod groups was assessed along a salinity gradient in the temperate estuarine Gwangyang Bay of Korea, based on a seasonal investigation of taxonomic results in 2015 and stable isotope analysis incorporating multiple linear regression models. Our results depict a simple energy flow of the planktonic food web of Gwangyang Bay.
Guizhi Wang, Shuling Wang, Zhangyong Wang, Wenping Jing, Yi Xu, Zhouling Zhang, Ehui Tan, and Minhan Dai
Biogeosciences, 15, 997–1009, https://doi.org/10.5194/bg-15-997-2018, https://doi.org/10.5194/bg-15-997-2018, 2018
Short summary
Short summary
Time-series observations of nutrients and 228Ra, a groundwater discharge tracer, were carried out from spring to neap tide in the Luhuitou fringing reef at Sanya Bay in the South China Sea. Nitrate, phosphate, and silicate in the water column showed greater diurnal variation during the spring tide. Biological processes predominantly controlled the composition of nutrients, but there was less of an impact in the spring tide due to groundwater discharge in this reef system.
Xin Lin, Ruiping Huang, Yan Li, Futian Li, Yaping Wu, David A. Hutchins, Minhan Dai, and Kunshan Gao
Biogeosciences, 15, 551–565, https://doi.org/10.5194/bg-15-551-2018, https://doi.org/10.5194/bg-15-551-2018, 2018
Short summary
Short summary
We examine the effects of elevated CO2 on bacterioplankton community during a mesocosm experiment in subtropical, eutrophic coastal waters in southern China. We found that the elevated CO2 hardly altered the network structure of the bacterioplankton taxa present with high abundance but appeared to reassemble the community network of taxa with low abundance. Results suggest that the bacterioplankton community in this subtropical, high-nutrient coastal environment is insensitive to elevated CO2.
Yangyang Lu, Zuozhu Wen, Dalin Shi, Mingming Chen, Yao Zhang, Sophie Bonnet, Yuhang Li, Jiwei Tian, and Shuh-Ji Kao
Biogeosciences, 15, 1–12, https://doi.org/10.5194/bg-15-1-2018, https://doi.org/10.5194/bg-15-1-2018, 2018
Short summary
Short summary
We investigated the light response of field Trichodesmium N2 fixation and net dissolved nitrogen release behavior. Our results suggest that N2 fixation was a function of light intensity, and the light requirement of Trichodesmium nitrogen fixation was high relative to its photosynthetic light demand. Meanwhile, light is a crucial parameter driving the physiological state of Trichodesmium, which subsequently determined the C / N metabolism and net dissolved nitrogen release.
Jianzhong Su, Minhan Dai, Biyan He, Lifang Wang, Jianping Gan, Xianghui Guo, Huade Zhao, and Fengling Yu
Biogeosciences, 14, 4085–4099, https://doi.org/10.5194/bg-14-4085-2017, https://doi.org/10.5194/bg-14-4085-2017, 2017
Short summary
Short summary
We provide direct and quantitative assessments showing the marine organic matter from eutrophication-induced primary production dominated oxygen consumption in the hypoxic zone, while the terrestrially sourced organic matter also significantly contributed to the formation and maintenance of hypoxia in the lower Pearl River Estuary (PRE) and the adjacent coastal water.
Xiang Gong, Wensheng Jiang, Linhui Wang, Huiwang Gao, Emmanuel Boss, Xiaohong Yao, Shuh-Ji Kao, and Jie Shi
Biogeosciences, 14, 2371–2386, https://doi.org/10.5194/bg-14-2371-2017, https://doi.org/10.5194/bg-14-2371-2017, 2017
Short summary
Short summary
The subsurface chlorophyll maximum layer (SCML) forms near the nitracline. By incorporating a piecewise function for the approximate Gaussian vertical profile of chlorophyll, we derive analytical solutions of a specified nutrient–phytoplankton model. Nitracline depth is deeper than SCML depth, and a thinner SCML corresponds to a steeper nitracline. A higher light attenuation coefficient leads to a shallower but steeper nitracline. Nitracline steepness is independent of surface light intensity.
Tsung-Yu Lee, Li-Chin Lee, Jr-Chuan Huang, Shih-Hao Jien, Thomas Hein, Franz Zehetner, Shuh-Ji Kao, and Fuh-Kwo Shiah
Biogeosciences Discuss., https://doi.org/10.5194/bg-2017-105, https://doi.org/10.5194/bg-2017-105, 2017
Revised manuscript not accepted
Min Nina Xu, Yanhua Wu, Li Wei Zheng, Zhenzhen Zheng, Huade Zhao, Edward A. Laws, and Shuh-Ji Kao
Biogeosciences, 14, 1021–1038, https://doi.org/10.5194/bg-14-1021-2017, https://doi.org/10.5194/bg-14-1021-2017, 2017
Short summary
Short summary
To resolve multiple N transformation rates, we proposed an innovative “isotope matrix method” to simultaneously derive rates for multiple transformations. This method was designed specifically for incubations in the euphotic zone under simulated in situ light conditions and minimized potential biases caused by non-targeted processes. The method facilitates simple post hoc analysis of data and can be used to probe specific effects of environmental factors on the rates of interactive N processes.
Xiaobo Jin, Chuanlian Liu, Alex J. Poulton, Minhan Dai, and Xianghui Guo
Biogeosciences, 13, 4843–4861, https://doi.org/10.5194/bg-13-4843-2016, https://doi.org/10.5194/bg-13-4843-2016, 2016
Short summary
Short summary
The vertical structure of the coccolithophore community in the water column was controlled by trophic conditions, which were regulated by mesoscale eddies across the South China Sea basin. Three key species (Emiliania huxleyi, Gephyrocapsa oceanica, Florisphaera profunda) contributed roughly half of the surface ocean coccolith-calcite concentrations. E. huxleyi coccolith length is influenced by light and nutrients through the regulation of growth rates.
Hongbin Liu and Chih-Jung Wu
Biogeosciences, 13, 4767–4775, https://doi.org/10.5194/bg-13-4767-2016, https://doi.org/10.5194/bg-13-4767-2016, 2016
Short summary
Short summary
The transport of organic C from the surface to the deep ocean by sinking particles composed of remains of dead cells and zooplankton fecal pellets can reduce the atmospheric CO2. Study of the effect of the silica content of diatoms, one of the most important primary products, on the production, degradation and sinking of its fecal pellets provides a better understanding of the complexity and variability of the planktonic food web and its implication on the vertical flux of C in the global ocean.
Jr-Chuan Huang, Tsung-Yu Lee, Teng-Chiu Lin, Thomas Hein, Li-Chin Lee, Yu-Ting Shih, Shuh-Ji Kao, Fuh-Kwo Shiah, and Neng-Huei Lin
Biogeosciences, 13, 1787–1800, https://doi.org/10.5194/bg-13-1787-2016, https://doi.org/10.5194/bg-13-1787-2016, 2016
Short summary
Short summary
The mean riverine DIN export of 49 watersheds in Taiwan is ∼ 3800 kg N km−2 yr−1, 18 times the global average. The mean riverine DIN export ratio is 0.30–0.51, which is much higher than the average of 0.20–0.25 of large rivers around the world, indicating excessive N input relative to ecosystem retention capacity. The DIN export ratio is positively related to agriculture input, and levels of human disturbance and watersheds with high DIN export ratios are likely at advanced stages of N excess.
Shuh-Ji Kao, Tzu-Ling Chiang, Da-Wei Li, Yi-Chia Hsin, Li-Wei Zheng, Jin-Yu Terence Yang, Shih-Chieh Hsu, Chau-Ron Wu, and Minhan Dai
Clim. Past Discuss., https://doi.org/10.5194/cp-2015-167, https://doi.org/10.5194/cp-2015-167, 2016
Preprint withdrawn
Short summary
Short summary
A 3-D model was run for the South China Sea to explore the effects of sea level drop and monsoon wind intensity on glacial patterns of circulation and ventilation. Winter northeasterly monsoon wind intensity governs the volume transport of Kuroshio intrusion through the Luzon Strait, subsequently, the water exchange rate and the mean residence time of water body of the SCS.
L. Luo, X. H. Yao, H. W. Gao, S. C. Hsu, J. W. Li, and S. J. Kao
Atmos. Chem. Phys., 16, 325–341, https://doi.org/10.5194/acp-16-325-2016, https://doi.org/10.5194/acp-16-325-2016, 2016
Short summary
Short summary
Concentrations and depositions of various nitrogen species of water-soluble fraction in aerosols were observed during spring over the eastern China seas and northwestern Pacific Ocean. Results revealed nitrogen deposition associated with the sea fog weather was 6 times higher than that of spring supply from the Yangtze River to the ECS shelf. The DON emission had occurred most likely during sea spray. Weather conditions modulate the nitrogen exchange at the ocean-atmosphere boundary.
X.-H. Guo, W.-D. Zhai, M.-H. Dai, C. Zhang, Y. Bai, Y. Xu, Q. Li, and G.-Z. Wang
Biogeosciences, 12, 5495–5514, https://doi.org/10.5194/bg-12-5495-2015, https://doi.org/10.5194/bg-12-5495-2015, 2015
Short summary
Short summary
We report the most comprehensive data set of surface seawater pCO2 and air-sea CO2 fluxes in the East China Sea (ECS) based on 24 surveys conducted in 2006-2011. We categorized the ECS into five different domains characterized by different physics and biogeochemistry to better characterize the seasonality of the pCO2 dynamics and to better constrain the CO2 flux. The annual average CO2 influx into the entire ECS shelf was 6.9+/-4.0 mmol m-2 d-1, about twice the global average in an ocean margin.
H. Jing, E. Rocke, L. Kong, X. Xia, H. Liu, and M. R. Landry
Biogeosciences Discuss., https://doi.org/10.5194/bgd-12-13483-2015, https://doi.org/10.5194/bgd-12-13483-2015, 2015
Manuscript not accepted for further review
Short summary
Short summary
Photosynthetic Dinoflagellates predominated in the surface, while potential parasitic Dinoflagellates and Ciliates dominated in the OMZ and deeper water in Costa Rica Dome. Total and active protists in the anoxic core were distinct from those in others depths. Reduced community diversity and presence of parasitic/symbiotic trophic lifestyles in the suboxic/anoxic OMZ suggests that oxygen deficiency could cause a change of protist community and the associated microbial food web as well.
Y.-T. Shih, T.-Y. Lee, J.-C. Huang, S.-J. Kao, K.-K. Liu, and F.-J. Chang
Hydrol. Earth Syst. Sci. Discuss., https://doi.org/10.5194/hessd-12-449-2015, https://doi.org/10.5194/hessd-12-449-2015, 2015
Revised manuscript not accepted
Short summary
Short summary
This study combines the observed riverine DIN (dissolved inorganic nitrogen) export and the controlling factors (land-use, population and discharge) to inversely estimate the effective DIN yield factors for individual land-use and per capita loading. Those estimated DIN yield factors can extrapolate all possible combinations of land-use, discharge, and population density, demonstrating the capability for scenario assessment.
K.-K. Liu, C.-K. Kang, T. Kobari, H. Liu, C. Rabouille, and K. Fennel
Biogeosciences, 11, 7061–7075, https://doi.org/10.5194/bg-11-7061-2014, https://doi.org/10.5194/bg-11-7061-2014, 2014
Short summary
Short summary
This paper provides background info on the East China Sea, Japan/East Sea and South China Sea and highlights major findings in the special issue on their biogeochemical conditions and ecosystem functions. The three seas are subject to strong impacts from human activities and/or climate forcing. Because these continental margins sustain arguably some of the most productive marine ecosystems in the world, changes in these stressed ecosystems may threaten the livelihood of a large human population.
Z. Cao, M. Dai, W. Evans, J. Gan, and R. Feely
Biogeosciences, 11, 6341–6354, https://doi.org/10.5194/bg-11-6341-2014, https://doi.org/10.5194/bg-11-6341-2014, 2014
T.-Y. Lee, Y.-T. Shih, J.-C. Huang, S.-J. Kao, F.-K. Shiah, and K.-K. Liu
Biogeosciences, 11, 5307–5321, https://doi.org/10.5194/bg-11-5307-2014, https://doi.org/10.5194/bg-11-5307-2014, 2014
S.-C. Hsu, G.-C. Gong, F.-K. Shiah, C.-C. Hung, S.-J. Kao, R. Zhang, W.-N. Chen, C.-C. Chen, C. C.-K. Chou, Y.-C. Lin, F.-J. Lin, and S.-H. Lin
Atmos. Chem. Phys. Discuss., https://doi.org/10.5194/acpd-14-21433-2014, https://doi.org/10.5194/acpd-14-21433-2014, 2014
Revised manuscript has not been submitted
K. Suzuki, A. Hattori-Saito, Y. Sekiguchi, J. Nishioka, M. Shigemitsu, T. Isada, H. Liu, and R. M. L. McKay
Biogeosciences, 11, 2503–2517, https://doi.org/10.5194/bg-11-2503-2014, https://doi.org/10.5194/bg-11-2503-2014, 2014
N. Jiao, Y. Zhang, K. Zhou, Q. Li, M. Dai, J. Liu, J. Guo, and B. Huang
Biogeosciences, 11, 2465–2475, https://doi.org/10.5194/bg-11-2465-2014, https://doi.org/10.5194/bg-11-2465-2014, 2014
Y. Zhang, X. Xie, N. Jiao, S. S.-Y. Hsiao, and S.-J. Kao
Biogeosciences, 11, 2131–2145, https://doi.org/10.5194/bg-11-2131-2014, https://doi.org/10.5194/bg-11-2131-2014, 2014
S. S.-Y. Hsiao, T.-C. Hsu, J.-w. Liu, X. Xie, Y. Zhang, J. Lin, H. Wang, J.-Y. T. Yang, S.-C. Hsu, M. Dai, and S.-J. Kao
Biogeosciences, 11, 2083–2098, https://doi.org/10.5194/bg-11-2083-2014, https://doi.org/10.5194/bg-11-2083-2014, 2014
C. Guo, H. Liu, L. Zheng, S. Song, B. Chen, and B. Huang
Biogeosciences, 11, 1847–1862, https://doi.org/10.5194/bg-11-1847-2014, https://doi.org/10.5194/bg-11-1847-2014, 2014
J.-Y. T. Yang, S.-C. Hsu, M. H. Dai, S. S.-Y. Hsiao, and S.-J. Kao
Biogeosciences, 11, 1833–1846, https://doi.org/10.5194/bg-11-1833-2014, https://doi.org/10.5194/bg-11-1833-2014, 2014
S.-J. Kao, R. G. Hilton, K. Selvaraj, M. Dai, F. Zehetner, J.-C. Huang, S.-C. Hsu, R. Sparkes, J. T. Liu, T.-Y. Lee, J.-Y. T. Yang, A. Galy, X. Xu, and N. Hovius
Earth Surf. Dynam., 2, 127–139, https://doi.org/10.5194/esurf-2-127-2014, https://doi.org/10.5194/esurf-2-127-2014, 2014
Y.-F. Tseng, J. Lin, M. Dai, and S.-J. Kao
Biogeosciences, 11, 409–423, https://doi.org/10.5194/bg-11-409-2014, https://doi.org/10.5194/bg-11-409-2014, 2014
C.-C. Lai, Y.-W. Fu, H.-B. Liu, H.-Y. Kuo, K.-W. Wang, C.-H. Lin, J.-H. Tai, G. T. F. Wong, K.-Y. Lee, T.-Y. Chen, Y. Yamamoto, M.-F. Chow, Y. Kobayashi, C.-Y. Ko, and F.-K. Shiah
Biogeosciences, 11, 147–156, https://doi.org/10.5194/bg-11-147-2014, https://doi.org/10.5194/bg-11-147-2014, 2014
A. Q. Han, M. H. Dai, J. P. Gan, S.-J. Kao, X. Z. Zhao, S. Jan, Q. Li, H. Lin, C.-T. A. Chen, L. Wang, J. Y. Hu, L. F. Wang, and F. Gong
Biogeosciences, 10, 8159–8170, https://doi.org/10.5194/bg-10-8159-2013, https://doi.org/10.5194/bg-10-8159-2013, 2013
T.-C. Hsu and S.-J. Kao
Biogeosciences, 10, 7847–7862, https://doi.org/10.5194/bg-10-7847-2013, https://doi.org/10.5194/bg-10-7847-2013, 2013
W.-D. Zhai, M.-H. Dai, B.-S. Chen, X.-H. Guo, Q. Li, S.-L. Shang, C.-Y. Zhang, W.-J. Cai, and D.-X. Wang
Biogeosciences, 10, 7775–7791, https://doi.org/10.5194/bg-10-7775-2013, https://doi.org/10.5194/bg-10-7775-2013, 2013
K.-K. Liu, L.-W. Wang, M. Dai, C.-M. Tseng, Y. Yang, C.-H. Sui, L. Oey, K.-Y. Tseng, and S.-M. Huang
Biogeosciences, 10, 7449–7462, https://doi.org/10.5194/bg-10-7449-2013, https://doi.org/10.5194/bg-10-7449-2013, 2013
C. Du, Z. Liu, M. Dai, S.-J. Kao, Z. Cao, Y. Zhang, T. Huang, L. Wang, and Y. Li
Biogeosciences, 10, 6419–6432, https://doi.org/10.5194/bg-10-6419-2013, https://doi.org/10.5194/bg-10-6419-2013, 2013
N. N. Chang, J. C. Shiao, G. C. Gong, S. J. Kao, and C. H. Hsieh
Biogeosciences Discuss., https://doi.org/10.5194/bgd-10-1051-2013, https://doi.org/10.5194/bgd-10-1051-2013, 2013
Revised manuscript not accepted
Related subject area
Biogeochemistry: Environmental Microbiology
Effects of surface water interactions with karst groundwater on microbial biomass, metabolism, and production
Overview: Global change effects on terrestrial biogeochemistry at the plant–soil interface
Ideas and perspectives: Microorganisms in the air through the lenses of atmospheric chemistry and microphysics
Changes in diazotrophic community structure associated with Kuroshio succession in the northern South China Sea
Technical note: A comparison of methods for estimating coccolith mass
Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments
Characteristics of bacterial and fungal communities and their associations with sugar compounds in atmospheric aerosols at a rural site in northern China
Responses of globally important phytoplankton species to olivine dissolution products and implications for carbon dioxide removal via ocean alkalinity enhancement
Differentiation of cognate bacterial communities in thermokarst landscapes: implications for ecological consequences of permafrost degradation
A multi-phase biogeochemical model for mitigating earthquake-induced liquefaction via microbially induced desaturation and calcium carbonate precipitation
Phosphorus regulates ectomycorrhizal fungi biomass production in a Norway spruce forest
Reallocation of elemental content and macromolecules in the coccolithophore Emiliania huxleyi to acclimate to climate change
Abrasion of sedimentary rocks as a source of hydrogen peroxide and nutrients to subglacial ecosystems
Nitrous oxide (N2O) synthesis by the freshwater cyanobacterium Microcystis aeruginosa
Interdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcing
Depth-related patterns in microbial community responses to complex organic matter in the western North Atlantic Ocean
Assessing the influence of ocean alkalinity enhancement on a coastal phytoplankton community
Eddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North Atlantic
Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif
Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)
Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forest
Physiological control on carbon isotope fractionation in marine phytoplankton
Implementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decomposition
Impact of dust addition on the microbial food web under present and future conditions of pH and temperature
Fractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sediments
Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean
Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin
Disturbance triggers non-linear microbe–environment feedbacks
Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern Ocean
Microbial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communities
Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments
Spatiotemporal patterns of N2 fixation in coastal waters derived from rate measurements and remote sensing
Biotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implications
Potential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteria
Microbial functional signature in the atmospheric boundary layer
Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics
Reviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pump
Salinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)
On giant shoulders: how a seamount affects the microbial community composition of seawater and sponges
Spatial variations in sedimentary N-transformation rates in the North Sea (German Bight)
Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge
Co-occurrence of Fe and P stress in natural populations of the marine diazotroph Trichodesmium
Senescence as the main driver of iodide release from a diverse range of marine phytoplankton
Reviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scale
Deep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic sponges
Inducing the attachment of cable bacteria on oxidizing electrodes
Bacterial degradation activity in the eastern tropical South Pacific oxygen minimum zone
Macromolecular fungal ice nuclei in Fusarium: effects of physical and chemical processing
Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica
Comprehensive characterization of an aspen (Populus tremuloides) leaf litter sample that maintained ice nucleation activity for 48 years
Adrian Barry-Sosa, Madison K. Flint, Justin C. Ellena, Jonathan B. Martin, and Brent C. Christner
Biogeosciences, 21, 3965–3984, https://doi.org/10.5194/bg-21-3965-2024, https://doi.org/10.5194/bg-21-3965-2024, 2024
Short summary
Short summary
This study examined springs in north central Florida focusing on how interactions between the surface and subsurface affected the properties of groundwater microbes. We found that microbes reproduced at rates that greatly exceed those documented for any other aquifer. Although the groundwater discharged to spring runs contains low concentrations of nutrients, our results indicate that microbes have access to sources of energy and produce new cells at rates similar to surface waterbodies.
Lucia Fuchslueger, Emily Francesca Solly, Alberto Canarini, and Albert Carles Brangarí
Biogeosciences, 21, 3959–3964, https://doi.org/10.5194/bg-21-3959-2024, https://doi.org/10.5194/bg-21-3959-2024, 2024
Short summary
Short summary
This overview of the special issue “Global change effects on terrestrial biogeochemistry at the plant–soil interface” features empirical, conceptual and modelling-based studies and outlines key findings on plant responses to elevated CO2; soil organism responses to warming; impacts on soil organic carbon, nitrogen and mineral nutrient cycling; and water level changes affecting greenhouse gas emissions, from the Arctic to the tropics, which are crucial for deciphering feedbacks to global change.
Barbara Ervens, Pierre Amato, Kifle Aregahegn, Muriel Joly, Amina Khaled, Tiphaine Labed-Veydert, Frédéric Mathonat, Leslie Nuñez López, Raphaëlle Péguilhan, and Minghui Zhang
EGUsphere, https://doi.org/10.5194/egusphere-2024-2377, https://doi.org/10.5194/egusphere-2024-2377, 2024
Short summary
Short summary
Atmospheric microorganisms are a small fraction of Earth's microbiome, with bacteria being a significant part. Aerosolized bacteria are airborne for a few days encountering unique chemical and physical conditions affecting stress levels and survival. We explore chemical and microphysical conditions bacteria encounter, highlighting potential nutrient and oxidant limitations and diverse effects by pollutants, which may ultimately impact the microbiome's role in global ecosystems and biodiversity.
Han Zhang, Guangming Mai, Weicheng Luo, Meng Chen, Ran Duan, and Tuo Shi
Biogeosciences, 21, 2529–2546, https://doi.org/10.5194/bg-21-2529-2024, https://doi.org/10.5194/bg-21-2529-2024, 2024
Short summary
Short summary
We report taxon-specific biogeography of N2-fixing microbes (diazotrophs) driven by Kuroshio intrusion (Kl) into the South China Sea. We show that the composition and distribution of distinct diazotrophic taxa shift with Kl-induced variations in physicochemical parameters of seawater and that Kl shapes diazotrophic community primarily as a stochastic process. This study thus has implications for the distribution of diazotrophs in a future warming ocean, as Kls are projected to intensify.
Celina Rebeca Valença, Luc Beaufort, Gustaaf Marinus Hallegraeff, and Marius Nils Müller
Biogeosciences, 21, 1601–1611, https://doi.org/10.5194/bg-21-1601-2024, https://doi.org/10.5194/bg-21-1601-2024, 2024
Short summary
Short summary
Coccolithophores contribute to the global carbon cycle and their calcite structures (coccoliths) are used as a palaeoproxy to understand past oceanographic conditions. Here, we compared three frequently used methods to estimate coccolith mass from the model species Emiliania huxleyi and the results allow for a high level of comparability between the methods, facilitating future comparisons and consolidation of mass changes observed from ecophysiological and biogeochemical studies.
Ralf Conrad and Peter Claus
Biogeosciences, 21, 1161–1172, https://doi.org/10.5194/bg-21-1161-2024, https://doi.org/10.5194/bg-21-1161-2024, 2024
Short summary
Short summary
Knowledge of carbon isotope fractionation is important for the assessment of the pathways involved in the degradation of organic matter. Formate is an important intermediate during this process. It was mainly converted to carbon dioxide and acetate both in the presence and absence of sulfate. Methane was only a minor product and was mainly formed from the acetate. The acetate was depleted in the heavy carbon atom relative to formate, while the carbon dioxide was enriched.
Mutong Niu, Shu Huang, Wei Hu, Yajie Wang, Wanyun Xu, Wan Wei, Qiang Zhang, Zihan Wang, Donghuan Zhang, Rui Jin, Libin Wu, Junjun Deng, Fangxia Shen, and Pingqing Fu
Biogeosciences, 20, 4915–4930, https://doi.org/10.5194/bg-20-4915-2023, https://doi.org/10.5194/bg-20-4915-2023, 2023
Short summary
Short summary
Sugar compounds in air can trace the source of bioaerosols that affect public health and climate. In rural north China, we observed increased fungal activity at night and less variable bacterial community diversity. Certain night-increasing sugar compounds were more closely related to fungi than bacteria. The fungal community greatly influenced sugar compounds, while bacteria played a limited role. Caution is advised when using sugar compounds to trace airborne microbes, particularly bacteria.
David A. Hutchins, Fei-Xue Fu, Shun-Chung Yang, Seth G. John, Stephen J. Romaniello, M. Grace Andrews, and Nathan G. Walworth
Biogeosciences, 20, 4669–4682, https://doi.org/10.5194/bg-20-4669-2023, https://doi.org/10.5194/bg-20-4669-2023, 2023
Short summary
Short summary
Applications of the mineral olivine are a promising means to capture carbon dioxide via coastal enhanced weathering, but little is known about the impacts on important marine phytoplankton. We examined the effects of olivine dissolution products on species from three major phytoplankton groups: diatoms, coccolithophores, and cyanobacteria. Growth and productivity were generally either unaffected or stimulated, suggesting the effects of olivine on key phytoplankton are negligible or positive.
Ze Ren, Shudan Ye, Hongxuan Li, Xilei Huang, and Luyao Chen
Biogeosciences, 20, 4241–4258, https://doi.org/10.5194/bg-20-4241-2023, https://doi.org/10.5194/bg-20-4241-2023, 2023
Short summary
Short summary
Permafrost thaw initiates thermokarst landscape formation, resulting in distinct new habitats, including degraded permafrost soil, thermokarst lake sediments, and lake water. These distinct habitats harbored differentiated bacterial communities that originated from the same source, differing in diversity, assembly mechanisms, and environmental influences. The results imply ecological consequences of permafrost degradation in the face of further climate change.
Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
Biogeosciences, 20, 2903–2917, https://doi.org/10.5194/bg-20-2903-2023, https://doi.org/10.5194/bg-20-2903-2023, 2023
Short summary
Short summary
Earthquake-induced soil liquefaction poses a significant global threat. Microbially induced desaturation and precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bacteria-driven ground improvement technique under existing structures. We developed a next-generation biogeochemical model to understand and predict the behavior of MIDP in the natural environment to design field-based hazard mitigation treatments.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
Short summary
Short summary
In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
Yong Zhang, Yong Zhang, Shuai Ma, Hanbing Chen, Jiabing Li, Zhengke Li, Kui Xu, Ruiping Huang, Hong Zhang, Yonghe Han, and Jun Sun
Biogeosciences, 20, 1299–1312, https://doi.org/10.5194/bg-20-1299-2023, https://doi.org/10.5194/bg-20-1299-2023, 2023
Short summary
Short summary
We found that increasing light intensity compensates for the negative effects of low phosphorus (P) availability on cellular protein and nitrogen contents. Reduced P availability, increasing light intensity, and ocean acidification act synergistically to increase cellular contents of carbohydrate and POC and the allocation of POC to carbohydrate. These regulation mechanisms in Emiliania huxleyi could provide vital information for evaluating carbon cycle in marine ecosystems under global change.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943, https://doi.org/10.5194/bg-20-929-2023, https://doi.org/10.5194/bg-20-929-2023, 2023
Short summary
Short summary
Microbial ecosystems have been found in all subglacial environments sampled to date. Yet, little is known of the sources of energy and nutrients that sustain these microbial populations. This study shows that crushing of sedimentary rocks, which contain organic carbon, carbonate and sulfide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
Biogeosciences, 20, 687–693, https://doi.org/10.5194/bg-20-687-2023, https://doi.org/10.5194/bg-20-687-2023, 2023
Short summary
Short summary
We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749, https://doi.org/10.5194/bg-19-5729-2022, https://doi.org/10.5194/bg-19-5729-2022, 2022
Short summary
Short summary
We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631, https://doi.org/10.5194/bg-19-5617-2022, https://doi.org/10.5194/bg-19-5617-2022, 2022
Short summary
Short summary
Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399, https://doi.org/10.5194/bg-19-5375-2022, https://doi.org/10.5194/bg-19-5375-2022, 2022
Short summary
Short summary
Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219, https://doi.org/10.5194/bg-19-5199-2022, https://doi.org/10.5194/bg-19-5199-2022, 2022
Short summary
Short summary
Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Sania Arif, Heiko Nacke, Elias Schliekmann, Andreas Reimer, Gernot Arp, and Michael Hoppert
Biogeosciences, 19, 4883–4902, https://doi.org/10.5194/bg-19-4883-2022, https://doi.org/10.5194/bg-19-4883-2022, 2022
Short summary
Short summary
The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654, https://doi.org/10.5194/bg-19-4639-2022, https://doi.org/10.5194/bg-19-4639-2022, 2022
Short summary
Short summary
The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726, https://doi.org/10.5194/bg-19-3713-2022, https://doi.org/10.5194/bg-19-3713-2022, 2022
Short summary
Short summary
Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Karen M. Brandenburg, Björn Rost, Dedmer B. Van de Waal, Mirja Hoins, and Appy Sluijs
Biogeosciences, 19, 3305–3315, https://doi.org/10.5194/bg-19-3305-2022, https://doi.org/10.5194/bg-19-3305-2022, 2022
Short summary
Short summary
Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
Short summary
Short summary
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
Short summary
Short summary
Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546, https://doi.org/10.5194/bg-18-6533-2021, https://doi.org/10.5194/bg-18-6533-2021, 2021
Short summary
Short summary
Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422, https://doi.org/10.5194/bg-18-5397-2021, https://doi.org/10.5194/bg-18-5397-2021, 2021
Short summary
Short summary
A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222, https://doi.org/10.5194/bg-18-5203-2021, https://doi.org/10.5194/bg-18-5203-2021, 2021
Short summary
Short summary
Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Hager, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
Short summary
Short summary
Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749, https://doi.org/10.5194/bg-18-3733-2021, https://doi.org/10.5194/bg-18-3733-2021, 2021
Short summary
Short summary
Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342, https://doi.org/10.5194/bg-18-3331-2021, https://doi.org/10.5194/bg-18-3331-2021, 2021
Short summary
Short summary
Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106, https://doi.org/10.5194/bg-18-2091-2021, https://doi.org/10.5194/bg-18-2091-2021, 2021
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871, https://doi.org/10.5194/bg-18-1857-2021, https://doi.org/10.5194/bg-18-1857-2021, 2021
Short summary
Short summary
In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, https://doi.org/10.5194/bg-18-1067-2021, 2021
Short summary
Short summary
Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095, https://doi.org/10.5194/bg-17-6081-2020, https://doi.org/10.5194/bg-17-6081-2020, 2020
Short summary
Short summary
The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374, https://doi.org/10.5194/bg-17-4355-2020, https://doi.org/10.5194/bg-17-4355-2020, 2020
Short summary
Short summary
This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778, https://doi.org/10.5194/bg-17-3757-2020, https://doi.org/10.5194/bg-17-3757-2020, 2020
Short summary
Short summary
Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732, https://doi.org/10.5194/bg-17-3723-2020, https://doi.org/10.5194/bg-17-3723-2020, 2020
Short summary
Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486, https://doi.org/10.5194/bg-17-3471-2020, https://doi.org/10.5194/bg-17-3471-2020, 2020
Short summary
Short summary
Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van
Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851, https://doi.org/10.5194/bg-17-2839-2020, https://doi.org/10.5194/bg-17-2839-2020, 2020
Short summary
Short summary
The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519, https://doi.org/10.5194/bg-17-2499-2020, https://doi.org/10.5194/bg-17-2499-2020, 2020
Short summary
Short summary
Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551, https://doi.org/10.5194/bg-17-2537-2020, https://doi.org/10.5194/bg-17-2537-2020, 2020
Short summary
Short summary
Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471, https://doi.org/10.5194/bg-17-2453-2020, https://doi.org/10.5194/bg-17-2453-2020, 2020
Short summary
Short summary
Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533, https://doi.org/10.5194/bg-17-1507-2020, https://doi.org/10.5194/bg-17-1507-2020, 2020
Short summary
Short summary
Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245, https://doi.org/10.5194/bg-17-1231-2020, https://doi.org/10.5194/bg-17-1231-2020, 2020
Short summary
Short summary
Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607, https://doi.org/10.5194/bg-17-597-2020, https://doi.org/10.5194/bg-17-597-2020, 2020
Short summary
Short summary
Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230, https://doi.org/10.5194/bg-17-215-2020, https://doi.org/10.5194/bg-17-215-2020, 2020
Short summary
Short summary
Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659, https://doi.org/10.5194/bg-16-4647-2019, https://doi.org/10.5194/bg-16-4647-2019, 2019
Short summary
Short summary
A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128, https://doi.org/10.5194/bg-16-4113-2019, https://doi.org/10.5194/bg-16-4113-2019, 2019
Short summary
Short summary
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
Yalda Vasebi, Marco E. Mechan Llontop, Regina Hanlon, David G. Schmale III, Russell Schnell, and Boris A. Vinatzer
Biogeosciences, 16, 1675–1683, https://doi.org/10.5194/bg-16-1675-2019, https://doi.org/10.5194/bg-16-1675-2019, 2019
Short summary
Short summary
Ice nucleation particles (INPs) help ice form at temperatures as high as −4 °C and contribute to the formation of precipitation. Leaf litter contains a high concentration of INPs, but the organisms that produce them are unknown. Here, we cultured two bacteria and one fungus from leaf litter that produce INPs similar to those found in leaf litter. This suggests that leaf litter may be an important habitat of these organisms and supports a role of these organisms as producers of atmospheric INPs.
Cited articles
Abell, G. C. J., Revill, A. T., Smith, C., Bissett, A. P., Volkman, J. K., and Robert, S. S.: Archaeal ammonia oxidizers and nirS-type denitrifiers dominate
sediment nitrifying and denitrifying populations in a subtropical macrotidal
estuary, ISME J., 4, 286–300,
https://doi.org/10.1038/ismej.2009.105, 2010.
Agarwala, R., Barrett, T., Beck, J., Benson, D. A., Bollin, C., Bolton, E.,
Bourexis, D., Brister, J. R., Bryant, S. H., Canese, K., Cavanaugh, M.,
Charowhas, C., Clark, K., Dondoshansky, I., Feolo, M., Fitzpatrick, L., Funk, K.,
Geer, L. Y., Gorelenkov, V., Graeff, A., Hlavina, W., Holmes, B., Johnson, M.,
Kattman, B., Khotomlianski, V., Kimchi, A., Kimelman, M., Kimura, M., Kitts, P.,
Klimke, W., Kotliarov, A., Krasnov, S., Kuznetsov, A., Landrum, M. J., Landsman,
D., Lathrop, S., Lee, J. M., Leubsdorf, C., Lu, Z. Y., Madden, T. L.,
Marchler-Bauer, A., Malheiro, A., Meric, P., Karsch-Mizrachi, I., Mnev, A.,
Murphy, T., Orris, R., Ostell, J., O'Sullivan, C., Palanigobu, V., Panchenko, A. R., Phan, L., Pierov, B., Pruitt, K. D., Rodarmer, K., Sayers, E. W., Schneider,
V., Schoch, C. L., Schuler, G. D., Sherry, S. T., Siyan, K., Soboleva, A.,
Soussov, V., Starchenko, G., Tatusova, T. A., Thibaud-Nissen, F., Todorov, K.,
Trawick, B. W., Vakatov, D., Ward, M., Yaschenko, E., Zasypkin, A., and Zbicz, K.: Database resources of the National Center for Biotechnology Information,
Nucl. Acids Res., 46, 8–13,
https://doi.org/10.1093/nar/gkx1095, 2018.
Alves, R. J. E., Minh, B. Q., Urich, T., von Haeseler, A., and Schleper, C.:
Unifying the global phylogeny and environmental distribution of
ammonia-oxidising archaea based on amoA genes, Nat. Commun., 9, 1517,
https://doi.org/10.1038/s41467-018-03861-1, 2018.
Beman, J. M., Popp, B. N., and Francis, C. A.: Molecular and biogeochemical
evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of
California, ISME J., 2, 429–441,
https://doi.org/10.1038/ismej.2007.118, 2008.
Beman, J. M., Popp, B. N., and Alford, S. E.: Quantification of ammonia
oxidation rates and ammonia-oxidizing archaea and bacteria at high
resolution in the Gulf of California and eastern tropical North Pacific
Ocean, Limnol. Oceanogr., 57, 711–726,
https://doi.org/10.4319/lo.2012.57.3.0711, 2012.
Bernhard, A. E. and Bollmann, A.: Estuarine nitrifiers: New players,
patterns and processes, Estuar. Coast. Shelf Sci., 88, 1–11,
https://doi.org/10.1016/j.ecss.2010.01.023, 2010.
Bernhard, A. E., Landry, Z. C., Blevins, A., de la Torre, J. R., Giblin, A. E.,
and Stahl, D. A.: Abundance of ammonia-oxidizing archaea and bacteria along
an estuarine salinity gradient in relation to potential nitrification rates,
Appl. Environ. Microbiol., 76, 1285–1289,
https://doi.org/10.1128/Aem.02018-09, 2010.
Blainey, P. C., Mosier, A. C., Potanina, A., Francis, C. A., and Quake, S. R.:
Genome of a Low-salinity ammonia-oxidizing archaeon determined by
single-cell and metagenomic analysis, PLoS One, 6, e16626,
https://doi.org/10.1371/journal.pone.0016626, 2011.
Bristow, L. A., Dalsgaard, T., Tiano, L., Mills, D. B., Bertagnolli, A. D.,
Wright, J. J., Hallam, S. J., Ulloa, O., Canfield, D. E., Revsbech, N. P., and Thamdrup, B.: Ammonium and nitrite oxidation at nanomolar oxygen
concentrations in oxygen minimum zone waters, P. Natl. Acad. Sci. USA,
113, 10601–10606, https://doi.org/10.1073/pnas.1600359113, 2016.
Caffrey, J. M., Bano, N., Kalanetra, K., and Hollibaugh, J. T.: Ammonia
oxidation and ammonia-oxidizing bacteria and archaea from estuaries with
differing histories of hypoxia, ISME J., 1, 660–662,
https://doi.org/10.1038/ismej.2007.79, 2007.
Campbell, L. G., Thrash, J. C., Rabalais, N. N., and Mason, O. U.: Extent of
the annual Gulf of Mexico hypoxic zone influences microbial community
structure, PLoS One, 14, e0209055, https://doi.org/10.1371/journal.pone.0209055, 2019.
Casciotti, K. L., Sigman, D. M., Hastings, M. G., Bohlke, J. K., and Hilkert,
A.: Measurement of the oxygen isotopic composition of nitrate in seawater
and freshwater using the denitrifier method, Anal. Chem., 74, 4905–4912, https://doi.org/10.1021/ac020113w, 2002.
Cheung, S., Mak, W., Xia, X. M., Lu, Y. H., Cheung, Y. Y., and Liu, H. B.:
Overlooked genetic diversity of ammonia oxidizing archaea lineages in the
global oceans, J. Geophys. Res.-Biogeo., 124, 1799–1811,
https://doi.org/10.1029/2018jg004636, 2019.
Dai, M. Guo, H.,
Zhai, W., Yuan, L., Wang, B., Wang, L., Cai, P., Tang, T., and Cai, W.-J.:
Oxygen depletion in the upper reach of
the Pearl River estuary during a winter drought, Mar. Chem., 102, 159–169, https://doi.org/10.1016/j.marchem.2005.09.020, 2006.
Dai, M., Wang, L., Guo, X., Zhai, W., Li, Q., He, B., and Kao, S.-J.: Nitrification and inorganic nitrogen distribution in a large perturbed river/estuarine system: the Pearl River Estuary, China, Biogeosciences, 5, 1227–1244, https://doi.org/10.5194/bg-5-1227-2008, 2008.
Damashek, J., Casciotti, K. L., and Francis, C. A.: Variable nitrification
rates across environmental gradients in turbid, nutrient-rich estuary waters
of San Francisco Bay, Estuar. Coast., 39, 1050–1071,
https://doi.org/10.1007/s12237-016-0071-7, 2016.
Elling, F. J., Konneke, M., Mussmann, M., Greve, A., and Hinrichs, K. U.:
Influence of temperature, pH, and salinity on membrane lipid composition and
TEX86 of marine planktonic thaumarchaeal isolates, Geochim. Cosmochim. Ac.,
171, 238–255, https://doi.org/10.1016/j.gca.2015.09.004, 2015.
Erguder, T. H., Boon, N., Wittebolle, L., Marzorati, M., and Verstraete, W. :
Environmental factors shaping the ecological niches of ammonia-oxidizing
archaea, FEMS Microbiol Rev., 33, 855–869,
https://doi.org/10.1111/j.1574-6976.2009.00179.x, 2009.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and Oakley, B. B.: Ubiquity and diversity of ammonia-oxidizing archaea in water columns and
sediments of the ocean, P. Natl. Acad. Sci. USA, 102, 14683–14688, https://doi.org/10.1073/pnas.0506625102, 2005.
Hallam, S. J., Mincer, T. J., Schleper, C., Preston, C. M., Roberts, K.,
Richardson, P. M., and DeLong, E. F.: Pathways of carbon assimilation and
ammonia oxidation suggested by environmental genomic analyses of marine
Crenarchaeota, PLoS Biol., 4, 520–536,
https://doi.org/10.1371/journal.pbio.0040095, 2006.
Happel, E. Bartl, I., Voss, M., and Riemann, L.: Extensive nitrification and
active ammonia oxidizers in two contrasting coastal systems of the Baltic
Sea, Environ. Microbiol., 20, 2913–2926, https://doi.org/10.1111/1462-2920.14293, 2018.
Harrison, P. J., Yin, K. D., Lee, J. H. W., Gan, J. P., and Liu, H. B.:
Physical-biological coupling in the Pearl River Estuary, Cont. Shelf Res.,
28, 1405–1415, https://doi.org/10.1016/j.csr.2007.02.011, 2008.
Hsiao, S. S.-Y., Hsu, T.-C., Liu, J.-w., Xie, X., Zhang, Y., Lin, J., Wang, H., Yang, J.-Y. T., Hsu, S.-C., Dai, M., and Kao, S.-J.: Nitrification and its oxygen consumption along the turbid Chang Jiang River plume, Biogeosciences, 11, 2083–2098, https://doi.org/10.5194/bg-11-2083-2014, 2014.
Jing, H. M., Cheung, S. Y., Xia, X. M., Suzuki, K., Nishioka, J., and Liu, H. B.: Geographic distribution of ammonia-oxidizing archaea along the Kuril
Islands in the western subarctic Pacific, Front. Microbiol., 8, 1247,
https://doi.org/10.3389/fmicb.2017.01247, 2017.
Kahle, D. and Wickham, H.: ggmap: Spatial Visualization with ggplot2, The R
J., 51, 144–161, 2013.
Kitzinger, K., Padilla, C. C., Marchant, H. K., Hach, P. F., Herbold, C. W.,
Kidane, A. T., Konneke, M., Littmann, S., Mooshammer, M., Niggemann, J., Petrov,
S., Richter, A., Stewart, F., Wagner, M., Kuypers, M. M. M., and Bristow, L. A.:
Cyanate and urea are substrates for nitrification by Thaumarchaeota in the
marine environment, Nat. Microbiol., 4, 234–243,
https://doi.org/10.1038/s41564-018-0316-2, 2019.
Knapp, A. N., Sigman, D. M., and Lipschultz, F.: N isotopic composition of
dissolved organic nitrogen and nitrate at the Bermuda Atlantic time-series
study site, Global Biogeochem. Cy., 19, GB1018,
https://doi.org/10.1029/2004gb002320, 2005.
Konneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., and Stahl, D. A.: Isolation of an autotrophic ammonia-oxidizing
marine archaeon, Nature, 437, 543–546,
https://doi.org/10.1038/nature03911, 2005.
Letunic, I. and Bork, P.: Interactive tree of life (iTOL) v3: an online
tool for the display and annotation of phylogenetic and other trees, Nucleic
Acids Res., 44, 242–245, https://doi.org/10.1093/nar/gkw290,
2016.
Lipschultz, F., Wofsy, S. C., and Fox, L. E.: Nitrogen-metabolism of the
eutrophic Delaware River ecosystem, Limnol. Oceanogr., 31, 701–716, https://doi.org/10.4319/lo.1986.31.4.0701, 1986.
Liu, H. B., Jing, H. M., Wong, T. H. C., and Chen, B. Z.: Co-occurrence of
phycocyanin- and phycoerythrin-rich Synechococcus in subtropical estuarine and coastal
waters of Hong Kong, Environ. Microbiol. Rep., 6, 90–99,
https://doi.org/10.1111/1758-2229.12111, 2014.
Logares, R., Audic, S., Bass, D., Bittner, L., Boutte, C., Christen, R., Claverie,
J. M., Decelle, J., Dolan, J. R., Dunthorn, M., Edvardsen, B., Gobet, A.,
Kooistra, W. H. C. F., Mahe, F., Not, F., Ogata, H., Pawlowski, J., Pernice, M.,
C., Romac, S., Shalchian-Tabrizi, K., Simon, N., Stoeck, T., Santini, S., Siano,
R., Wincker, P., Zingone, A., Richards, T. A., de Vargas, C., and Massana, R.:
Patterns of rare and abundant marine microbial eukaryotes, Curr. Biol.,
24, 813–821, https://doi.org/10.1016/j.cub.2014.02.050, 2014.
Lu, Y. H., Xia, X. M., Cheung, S. Y., Jing, H. M., and Liu, H. B.:
Differential distribution and determinants of ammonia oxidizing archaea
sublineages in the oxygen minimum zone off Costa Rica, Microorganisms, 7, 453,
https://doi.org/10.3390/microorganisms7100453, 2019.
Lu, Z. M., Gan, J. P., Dai, M. H., Liu, H. B., and Zhao, X. Z.: Joint effects
of extrinsic biophysical fluxes and intrinsic hydrodynamics on the formation
of hypoxia west off the Pearl River Estuary, J. Geophys. Res.-Ocean,
123, 6241–6259, https://doi.org/10.1029/2018jc014199, 2018.
Magalhaes, C. M., Machado, A., and Bordalo, A. A.: Temporal variability in
the abundance of ammonia-oxidizing bacteria vs. archaea in sandy sediments
of the Douro River estuary, Portugal, Aquat. Microb. Ecol., 56, 13–23, https://doi.org/10.3354/ame01313, 2009.
Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R., and Stahl, D. A.: Ammonia oxidation kinetics determine niche separation of nitrifying
Archaea and Bacteria, Nature, 461, 976–979,
https://doi.org/10.1038/nature08465, 2009.
Moin, N. S., Nelson, K. A., Bush, A., and Bernhard, A. E.: Distribution and
diversity of archaeal and bacterial ammonia oxidizers in salt marsh
sediments, Appl. Environ. Microbiol., 75, 7461–7468,
https://doi.org/10.1128/Aem.01001-09, 2009.
Mosier, A. C. and Francis, C. A.: Relative abundance and diversity of
ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary,
Environ. Microbiol., 10, 3002–3016,
https://doi.org/10.1111/j.1462-2920.2008.01764.x, 2008.
Mosier, A. C. and Francis C. A.: Determining the distribution of marine
and coastal ammonia-oxidizing archaea and bacteria using a quantitative
approach, Meth. Enzymol., 486, 205–221,
https://doi.org/10.1016/S0076-6879(11)86009-X, 2011.
Oksanen, J., Blanchet, F. G., Friendly, Kindt, M. R., Legendre, P., McGlinn, D.,
Minchin, P. R., O'Hara, R. B., Simpson, G. L., Solymos, P. M., Stevens, H. H.,
Szoecs E., and Wagner, H.: vegan: Community Ecology Package, R package
version 2.5-6, availabe at: https://CRAN.R-project.org/package (last access: 19 September 2020), 2019.
Pai, S. C., Tsau, Y. J., and Yang, T. I.: pH and buffering capacity problems
involved in the determination of ammonia in saline water using the
indophenol blue spectrophotometric method, Anal. Chim. Ac., 434, 209–216, https://doi.org/10.1016/S0003-2670(01)00851-0, 2001.
Pakulski, J. D., Benner, R., Amon, R., Eadie, B., and Whitledge, T.: Community
metabolism and nutrient cycling in the Mississippi River Plume – Evidence
for intense nitrification at intermediate salinities, Mar. Ecol. Prog. Ser.,
117, 207–218, https://doi.org/10.3354/meps117207, 1995.
Peng, X. F., Jayakumar, A., and Ward, B. B.: Community composition of
ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen
minimum zones, Front. Microbiol., 4, 177, https://doi.org/10.3389/fmicb.2013.00177, 2013.
Qian, W., Gan, J. P., Liu, J. W., He, B. Y., Lu, Z. M., Guo, X. H., Wang, D. L.,
Guo, L. G., Huang, T., and Dai, M. H.: Current status of emerging hypoxia in
a eutrophic estuary: The lower reach of the Pearl River Estuary, China,
Estuar. Coast. Shelf S., 205, 58–67,
https://doi.org/10.1016/j.ecss.2018.03.004, 2018.
Qin, W., Amin, S. A., Martens-Habbena, W., Walker, C. B., Urakawa, H., Devol, A.
H., Ingalls, A. E., Moffett, J. W., Armbrust, E. V., and Stahl, D. A.: Marine
ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide
ecotypic variation, P. Natl. Acad. Sci. USA, 111, 12504–12509.
https://doi.org/10.1073/pnas.1324115111, 2014.
Qin, W., Carlson, L. T., Armbrust, E. V., Devol, A. H., Moffett, J. W., Stahl, D.
A., and Ingalls, A. E.: Confounding effects of oxygen and temperature on the
TEX86 signature of marine Thaumarchaeota, P. Natl. Acad. Sci. USA,
112, 10979–10984, https://doi.org/10.1073/pnas.1501568112, 2015.
Qin, W., Meinhardt, K. A., Moffett, J. W., Devol, A. H., Armbrust, E. V.,
Ingalls, A. E., and Stahl, D. A.: Influence of oxygen availability on the
activities of ammonia-oxidizing archaea, Environ. Microbiol. Rep.,
9, 250–256, https://doi.org/10.1111/1758-2229.12525, 2017.
Rotthauwe, J. H., Witzel, K. P., and Liesack, W.: The ammonia monooxygenase
structural gene amoA as a functional marker: Molecular fine-scale analysis of
natural ammonia-oxidizing populations, Appl. Environ. Microbiol.,
63, 4704–4712, 1997.
Sampou, P. and Kemp, W. N.: Factors regulating phytoplankton community
respiration in Chesapeake Bay, Mar. Ecol. Prog. Ser., 110, 249–258,
https://doi.org/10.3354/meps110249, 1994.
Santoro, A. E., Francis, C. A., de Sieyes, N. R., and Boehm, A. B.: Shifts in
the relative abundance of ammonia-oxidizing bacteria and archaea across
physicochemical gradients in a subterranean estuary, Environ. Microbiol.,
10, 1068–1079, https://doi.org/10.1111/j.1462-2920.2007.01547.x,
2008.
Santoro, A. E., Dupont, C. L., Richter, R. A., Craig, M. T., Carini, P., McIlvin,
M. R., Yang, Y., Orsi, W. D., Moran, D. M., and Saito, M. A.: Genomic and
proteomic characterization of Candidatus Nitrosopelagicus brevis: An ammonia-oxidizing archaeon from the
open ocean, P. Natl. Acad. Sci. USA, 112, 1173–1178,
https://doi.org/10.1073/pnas.1416223112, 2015.
Santoro, A. E., Saito, M. A., Goepfert, T. J., Lamborg, C. H., Dupont, C. L., and DiTullio, G. R.: Thaumarchaeal ecotype distributions across the
equatorial Pacific Ocean and their potential roles in nitrification and
sinking flux attenuation, Limnol. Oceanogr., 62, 1984–2003,
https://doi.org/10.1002/lno.10547, 2017.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M.,
Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C.
J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J., and Weber, C. F.: Introducing mothur: Open-Source, Platform-Independent, Community-Supported
Software for describing and comparing microbial communities, Appl. Environ.
Microbiol., 75, 7537–7541, https://doi.org/10.1128/Aem.01541-09,
2009.
Seyler, L. M., McGuinness, L. M., and Kerkhof, L. J.: Crenarchaeal
heterotrophy in salt marsh sediments, ISME J., 8, 1534–1543, https://doi.org/10.1038/ismej.2014.15, 2014.
Seyler, L. M., McGuinness, L. R., Gilbert, J. A., Biddle, J. F., Gong, D. L.,
and Kerkhof, L. J.: Discerning autotrophy, mixotrophy and heterotrophy in
marine TACK archaea from the North Atlantic, FEMS Microbiol. Ecol., 94, fiy014,
https://doi.org/10.1093/femsec/fiy014, 2018.
Seyler, L. M., Tuorto, S., McGuinness, L. R., Gong, D. L., and Kerkhof, L. J.:
Bacterial and archaeal specific-predation in the North Atlantic Basin,
Front. Mar. Sci., 6, 555, https://doi.org/10.3389/fmars.2019.00555, 2019.
Sigman, D. M., Casciotti, K. L., Andreani, M., Barford, C., Galanter, M., and Bohlke, J. K.: A
bacterial method for the nitrogen isotopic analysis of nitrate in seawater
and freshwater, Anal. Chem., 73, 4145–4153,
https://doi.org/10.1021/ac010088e, 2001.
Smith, J. M., Damashek, J., Chavez, F. P., and Francis, C. A.: Factors
influencing nitrification rates and the abundance and transcriptional
activity of ammonia-oxidizing microorganisms in the dark northeast Pacific
Ocean, Limnol. Oceanogr., 61, 596–609, https://doi.org/10.1002/lno.10235,
2016.
Vaulot, D., Courties, C., and Partensky, F.: A simple method to preserve
oceanic phytoplankton for Flow Cytometric Analyses, Cytometry, 10, 629–635, https://doi.org/10.1002/cyto.990100519, 1989.
Wankel, S. D., Mosier, A. C., Hansel, C. M., Paytan, A., and Francis, C. A.:
Spatial variability in nitrification rates and ammonia-oxidizing microbial
communities in the agriculturally impacted Elkhorn Slough Estuary,
California, Appl. Environ. Microbiol., 77, 269–280,
https://doi.org/10.1128/Aem.01318-10, 2011.
Ward, B. B.: Nitrification and ammonification in aquatic systems, Life
Support Biosph. Sci., 3, 25–29, 1996.
Welschmeyer, N. A.: Fluorometric analysis of Chlorophyll-a in the presence
of Chlorophyll-B and pheopigments, Limnol. Oceanogr., 39, 1985–1992, https://doi.org/10.4319/lo.1994.39.8.1985, 1994.
Wickham, H.: ggplot2: Elegant graphics for data analysis, Springer-Verlag
New York, USA, 2016.
Wu, R. N., Meng, H., Wang, Y. F., Lan, W. S., and Gu, J. D.: A more
comprehensive community of ammonia-oxidizing archaea (AOA) revealed by
genomic DNA and RNA analyses of amoA gene in subtropical acidic Forest Soils,
Microbiol. Ecol., 74, 910–922,
https://doi.org/10.1007/s00248-017-1045-4, 2017.
Xu, J., Jing, H. M., Kong, L. L., Sun, M. M., Harrison, P. J., and Liu, H. B.:
Effect of seawater-sewage cross-transplants on bacterial metabolism and
diversity, Microbiol. Ecol., 66, 60–72,
https://doi.org/10.1007/s00248-013-0207-2, 2013.
Yool, A., Martin, A. P., Fernandez, C., and Clark, D. R.: The significance of
nitrification for oceanic new production, Nature, 447, 999–1002,
https://doi.org/10.1038/nature05885, 2007.
Zhao, H. T.: Evolution of the Pearl River Estuary, China Ocean Press,
Beijing, China, 1990 (in Chinese).
Zhao, Y. Y., Liu, J., Uthaipan, K., Song, X., Xu, Y., He, B. Y., Liu, H.,
Gan, J. P., and Dai, M. H.: Dynamics of inorganic carbon and pH in a large
subtropical continental shelf system: Interaction between eutrophication,
hypoxia, and ocean acidification, Limnol. Oceanogr., 65, 1359–1379,
https:/.doi.org/10.1002/lmo.11393, 2020.
Short summary
Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Through a comprehensive investigation, we observed differential niche partitioning among diverse...
Altmetrics
Final-revised paper
Preprint