Articles | Volume 19, issue 16
https://doi.org/10.5194/bg-19-3757-2022
© Author(s) 2022. 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-19-3757-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
18 Aug 2022
Research article |
| 18 Aug 2022
| 18 Aug 2022
Potential contributions of nitrifiers and denitrifiers to nitrous oxide sources and sinks in China's estuarine and coastal areas
Xiaofeng Dai
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen 361005, China
Mingming Chen
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen 361005, China
Xianhui Wan
Department of Geosciences, Princeton University, Princeton, New Jersey 08544, USA
Ehui Tan
State Key Laboratory of Marine Resource Utilization in South China
Sea, Hainan University, Haikou, Hainan, 570228, China
Jialing Zeng
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen 361005, China
Nengwang Chen
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen 361005, China
Fujian Provincial Key Laboratory for Coastal Ecology and Environmental
Studies, College of the Environment and Ecology, Xiamen University, Xiamen
361005, China
Shuh-Ji Kao
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen 361005, China
State Key Laboratory of Marine Resource Utilization in South China
Sea, Hainan University, Haikou, Hainan, 570228, China
Yao Zhang
CORRESPONDING AUTHOR
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen 361005, China
Related authors
No articles found.
Weiyi Tang, Bess B. Ward, Michael Beman, Laura Bristow, Darren Clark, Sarah Fawcett, Claudia Frey, François Fripiat, Gerhard J. Herndl, Mhlangabezi Mdutyana, Fabien Paulot, Xuefeng Peng, Alyson E. Santoro, Takuhei Shiozaki, Eva Sintes, Charles Stock, Xin Sun, Xianhui S. Wan, Min N. Xu, and Yao Zhang
Earth Syst. Sci. Data, 15, 5039–5077, https://doi.org/10.5194/essd-15-5039-2023, https://doi.org/10.5194/essd-15-5039-2023, 2023
Short summary
Short summary
Nitrification and nitrifiers play an important role in marine nitrogen and carbon cycles by converting ammonium to nitrite and nitrate. Nitrification could affect microbial community structure, marine productivity, and the production of nitrous oxide – a powerful greenhouse gas. We introduce the newly constructed database of nitrification and nitrifiers in the marine water column and guide future research efforts in field observations and model development of nitrification.
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.
Emily J. Zakem, Barbara Bayer, Wei Qin, Alyson E. Santoro, Yao Zhang, and Naomi M. Levine
Biogeosciences, 19, 5401–5418, https://doi.org/10.5194/bg-19-5401-2022, https://doi.org/10.5194/bg-19-5401-2022, 2022
Short summary
Short summary
We use a microbial ecosystem model to quantitatively explain the mechanisms controlling observed relative abundances and nitrification rates of ammonia- and nitrite-oxidizing microorganisms in the ocean. We also estimate how much global carbon fixation can be associated with chemoautotrophic nitrification. Our results improve our understanding of the controls on nitrification, laying the groundwork for more accurate predictions in global climate models.
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.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
Short summary
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.
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
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.
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.
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.
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.
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
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
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
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
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
Biodiversity and Ecosystem Function: Microbial Ecology & Geomicrobiology
Microbial methane formation in deep aquifers associated with the sediment burial history at a coastal site
Impact of metabolism and temperature on 2H ∕ 1H fractionation in lipids of the marine bacterium Shewanella piezotolerans WP3
Maximum summer temperatures predict the temperature adaptation of Arctic soil bacterial communities
Aqueous system-level processes and prokaryote assemblages in the ferruginous and sulfate-rich bottom waters of a post-mining lake
Abundances and morphotypes of the coccolithophore Emiliania huxleyi in southern Patagonia compared to neighbouring oceans and Northern Hemisphere fjords
Determining the hierarchical order by which the variables of sampling period, dust outbreak occurrence, and sampling location can shape the airborne bacterial communities in the Mediterranean basin
The water column of the Yamal tundra lakes as a microbial filter preventing methane emission
Bioerosion and fungal colonization of the invasive foraminiferan Amphistegina lobifera in a Mediterranean seagrass meadow
Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove
Deep maxima of phytoplankton biomass, primary production and bacterial production in the Mediterranean Sea
Haplo-diplontic life cycle expands coccolithophore niche
The composition of endolithic communities in gypcrete is determined by the specific microhabitat architecture
Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences
Cryptic roles of tetrathionate in the sulfur cycle of marine sediments: microbial drivers and indicators
Lake mixing regime selects apparent methane oxidation kinetics of the methanotroph assemblage
The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth)
The pH-based ecological coherence of active canonical methanotrophs in paddy soils
Biogeographical distribution of microbial communities along the Rajang River–South China Sea continuum
Microbial community composition and abundance after millennia of submarine permafrost warming
Cold-water corals and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz) – living on the edge
Ecophysiological characteristics of red, green, and brown strains of the Baltic picocyanobacterium Synechococcus sp. – a laboratory study
Factors controlling the community structure of picoplankton in contrasting marine environments
Community composition and seasonal changes of archaea in coarse and fine air particulate matter
Microbial community structure in the western tropical South Pacific
Ecophysiological characterization of early successional biological soil crusts in heavily human-impacted areas
Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)
Plant n-alkane production from litterfall altered the diversity and community structure of alkane degrading bacteria in litter layer in lowland subtropical rainforest in Taiwan
Revisiting chlorophyll extraction methods in biological soil crusts – methodology for determination of chlorophyll a and chlorophyll a + b as compared to previous methods
Divergence of dominant factors in soil microbial communities and functions in forest ecosystems along a climatic gradient
Uncovering biological soil crusts: carbon content and structure of intact Arctic, Antarctic and alpine biological soil crusts
Antagonistic effects of drought and sand burial enable the survival of the biocrust moss Bryum argenteum in an arid sandy desert
Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic Sea
Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia
Effects of temperature on the composition and diversity of bacterial communities in bamboo soils at different elevations
Development of bacterial communities in biological soil crusts along a revegetation chronosequence in the Tengger Desert, northwest China
Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments
Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico)
Archive of bacterial community in anhydrite crystals from a deep-sea basin provides evidence of past oil-spilling in a benthic environment in the Red Sea
Mechanisms of Trichodesmium demise within the New Caledonian lagoon during the VAHINE mesocosm experiment
Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids
Effect of light on photosynthetic efficiency of sequestered chloroplasts in intertidal benthic foraminifera (Haynesina germanica and Ammonia tepida)
Seasonal and size-dependent variations in the phytoplankton growth and microzooplankton grazing in the southern South China Sea under the influence of the East Asian monsoon
Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest
Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China
Redox regime shifts in microbially mediated biogeochemical cycles
Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs
Microbial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota
Diversity and seasonal dynamics of airborne archaea
Methanotrophic activity and diversity of methanotrophs in volcanic geothermal soils at Pantelleria (Italy)
Genotyping an Emiliania huxleyi (prymnesiophyceae) bloom event in the North Sea reveals evidence of asexual reproduction
Taiki Katayama, Reo Ikawa, Masaru Koshigai, and Susumu Sakata
Biogeosciences, 20, 5199–5210, https://doi.org/10.5194/bg-20-5199-2023, https://doi.org/10.5194/bg-20-5199-2023, 2023
Short summary
Short summary
Methane produced by microorganisms in subsurface environments may account for a large fraction of global natural gas reserves. To understand how microbial methane is produced during sediment burial history, we examined methane-bearing aquifers in which temperature and salinity increase with depth. Geochemical and microbiological analyses showed that microbial methane is produced at depth, where microbial activity is stimulated by the increased temperature, and subsequently migrates upwards.
Xin Chen, Weishu Zhao, Liang Dong, Huahua Jian, Lewen Liang, Jing Wang, and Fengping Wang
Biogeosciences, 20, 1491–1504, https://doi.org/10.5194/bg-20-1491-2023, https://doi.org/10.5194/bg-20-1491-2023, 2023
Short summary
Short summary
Here, we studied the effects of metabolism and growth temperature on 2H/1H fractionation between fatty acids and growth water (εFA/water) by Shewanella piezotolerans WP3. Our results show that the εFA/water values display considerable variations for cultures grown on different substrates. Combined with metabolic model analysis, our results indicate that the central metabolic pathways exert a fundamental effect on the hydrogen isotope composition of lipids in heterotrophs.
Ruud Rijkers, Mark Dekker, Rien Aerts, and James T. Weedon
Biogeosciences, 20, 767–780, https://doi.org/10.5194/bg-20-767-2023, https://doi.org/10.5194/bg-20-767-2023, 2023
Short summary
Short summary
Bacterial communities in the soils of the Arctic region decompose soil organic matter to CO2 from a large carbon pool. The amount of CO2 released is likely to increase under future climate conditions. Here, we study how temperature sensitive the growth of soil bacterial communties is for 12 sampling sites in the sub to high Arctic. We show that the optimal growth temperature varies between 23 and 34 °C and is influenced by the summer temperature.
Daniel A. Petrash, Ingrid M. Steenbergen, Astolfo Valero, Travis B. Meador, Tomáš Pačes, and Christophe Thomazo
Biogeosciences, 19, 1723–1751, https://doi.org/10.5194/bg-19-1723-2022, https://doi.org/10.5194/bg-19-1723-2022, 2022
Short summary
Short summary
We spectroscopically evaluated the gradients of dissolved C, N, S, Fe and Mn in a newly formed redox-stratified lake. The lake features an intermediate redox state between nitrogenous and euxinic conditions that encompasses vigorous open sulfur cycling fuelled by the reducible Fe and Mn stocks of the anoxic sediments. This results in substantial bottom water loads of dissolved iron and sulfate. Observations made in this ecosystem have relevance for deep-time paleoceanographic reconstructions.
Francisco Díaz-Rosas, Catharina Alves-de-Souza, Emilio Alarcón, Eduardo Menschel, Humberto E. González, Rodrigo Torres, and Peter von Dassow
Biogeosciences, 18, 5465–5489, https://doi.org/10.5194/bg-18-5465-2021, https://doi.org/10.5194/bg-18-5465-2021, 2021
Short summary
Short summary
Coccolithophores are important unicellular algae with a calcium carbonate covering that might be affected by ongoing changes in the ocean due to absorption of CO2, warming, and melting of glaciers. We used the southern Patagonian fjords as a natural laboratory, where chemical conditions are naturally highly variable. One variant of a widespread coccolithophore species can tolerate these conditions, suggesting it is highly adaptable, while others were excluded, suggesting they are less adaptable.
Riccardo Rosselli, Maura Fiamma, Massimo Deligios, Gabriella Pintus, Grazia Pellizzaro, Annalisa Canu, Pierpaolo Duce, Andrea Squartini, Rosella Muresu, and Pietro Cappuccinelli
Biogeosciences, 18, 4351–4367, https://doi.org/10.5194/bg-18-4351-2021, https://doi.org/10.5194/bg-18-4351-2021, 2021
Short summary
Short summary
The bacteria carried by winds over the island of Sardinia in the Mediterranean Sea were collected, and their identities were investigated by reading DNA sequences. The sampling period was the factor that most determined the airborne species composition as its role was stronger than that of dust-carrying storms and of the geographical position of the sampling station. The bacteria found when the sampling was performed in September had more species variety than those collected in May.
Alexander Savvichev, Igor Rusanov, Yury Dvornikov, Vitaly Kadnikov, Anna Kallistova, Elena Veslopolova, Antonina Chetverova, Marina Leibman, Pavel A. Sigalevich, Nikolay Pimenov, Nikolai Ravin, and Artem Khomutov
Biogeosciences, 18, 2791–2807, https://doi.org/10.5194/bg-18-2791-2021, https://doi.org/10.5194/bg-18-2791-2021, 2021
Short summary
Short summary
Microbial processes of the methane cycle were studied in four lakes of the central part of the Yamal Peninsula in an area of continuous permafrost: two large, deep lakes and two small and shallow ones. It was found that only small, shallow lakes contributed significantly to the overall diffusive methane emissions from the water surface during the warm summer season. The water column of large, deep lakes on Yamal acted as a microbial filter preventing methane emissions into the atmosphere.
Martin Vohník
Biogeosciences, 18, 2777–2790, https://doi.org/10.5194/bg-18-2777-2021, https://doi.org/10.5194/bg-18-2777-2021, 2021
Short summary
Short summary
Amphistegina lobifera (Foraminifera) has colonized the Mediterranean through the Suez Canal, often forming thick sediments altering the invaded environments. Little is known about postmortem fate of its shells, so I investigated their turnover in the rhizosphere of the dominant Mediterranean seagrass. Most were bioeroded, likely by cyanobacteria and algae but not fungi occurring in the seagrass roots. Bioerosion may counterbalance accumulation of A. lobifera shells in the seabed substrate.
Carolina Oliveira de Santana, Pieter Spealman, Vânia Maria Maciel Melo, David Gresham, Taíse Bomfim de Jesus, and Fabio Alexandre Chinalia
Biogeosciences, 18, 2259–2273, https://doi.org/10.5194/bg-18-2259-2021, https://doi.org/10.5194/bg-18-2259-2021, 2021
Short summary
Short summary
This study highlights the influence of
tidal zonationon the prokaryotic sediment communities of a pristine mangrove forest. We observed that the variability in environmental factors between tidal zones results in differences in structure, diversity, and the potential function of prokaryotic populations. This suggests that further work is needed in determining the role tidal microhabitat biodiversity has in mangroves.
Emilio Marañón, France Van Wambeke, Julia Uitz, Emmanuel S. Boss, Céline Dimier, Julie Dinasquet, Anja Engel, Nils Haëntjens, María Pérez-Lorenzo, Vincent Taillandier, and Birthe Zäncker
Biogeosciences, 18, 1749–1767, https://doi.org/10.5194/bg-18-1749-2021, https://doi.org/10.5194/bg-18-1749-2021, 2021
Short summary
Short summary
The concentration of chlorophyll is commonly used as an indicator of the abundance of photosynthetic plankton (phytoplankton) in lakes and oceans. Our study investigates why a deep chlorophyll maximum, located near the bottom of the upper, illuminated layer develops in the Mediterranean Sea. We find that the acclimation of cells to low light is the main mechanism involved and that this deep maximum represents also a maximum in the biomass and carbon fixation activity of phytoplankton.
Joost de Vries, Fanny Monteiro, Glen Wheeler, Alex Poulton, Jelena Godrijan, Federica Cerino, Elisa Malinverno, Gerald Langer, and Colin Brownlee
Biogeosciences, 18, 1161–1184, https://doi.org/10.5194/bg-18-1161-2021, https://doi.org/10.5194/bg-18-1161-2021, 2021
Short summary
Short summary
Coccolithophores are important calcifying phytoplankton with an overlooked life cycle. We compile a global dataset of marine coccolithophore abundance to investigate the environmental characteristics of each life cycle phase. We find that both phases contribute to coccolithophore abundance and that their different environmental preference increases coccolithophore habitat. Accounting for the life cycle of coccolithophores is thus crucial for understanding their ecology and biogeochemical impact.
María Cristina Casero, Victoria Meslier, Jocelyne DiRuggiero, Antonio Quesada, Carmen Ascaso, Octavio Artieda, Tomasz Kowaluk, and Jacek Wierzchos
Biogeosciences, 18, 993–1007, https://doi.org/10.5194/bg-18-993-2021, https://doi.org/10.5194/bg-18-993-2021, 2021
Short summary
Short summary
Endolithic microhabitats have been described as the last refuge for life in arid and hyper-arid deserts where life has to deal with harsh environmental conditions, such as those in the Atacama Desert. In this work, three different endolithic microhabitats occurring in gypcrete rocks of the Atacama Desert are characterized, using both microscopy and molecular techniques, to show if the architecture of each microhabitat has an influence on the microbial communities inhabiting each of them.
Jeffrey M. Dick, Miao Yu, and Jingqiang Tan
Biogeosciences, 17, 6145–6162, https://doi.org/10.5194/bg-17-6145-2020, https://doi.org/10.5194/bg-17-6145-2020, 2020
Short summary
Short summary
Many natural environments differ in their range of salt concentration (salinity). We developed a metric for the number of water molecules in formation reactions of different proteins and found that it decreases between freshwater and marine systems and also in laboratory experiments with increasing salinity. These results demonstrate a new type of link between geochemical conditions and the chemical composition of microbial communities that can be useful for models of microbial adaptation.
Subhrangshu Mandal, Sabyasachi Bhattacharya, Chayan Roy, Moidu Jameela Rameez, Jagannath Sarkar, Tarunendu Mapder, Svetlana Fernandes, Aditya Peketi, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 17, 4611–4631, https://doi.org/10.5194/bg-17-4611-2020, https://doi.org/10.5194/bg-17-4611-2020, 2020
Short summary
Short summary
Potential roles of polythionates as key sulfur cycle intermediates are less appreciated, apparently because, in most of the natural environments, they do not accumulate to easily detectable levels. Our exploration of the eastern Arabian Sea sediment horizons revealed microbe-mediated production and redox transformations of tetrathionate to be important modules of the in situ sulfur cycle, even as high biotic and abiotic reactivity of this polythionate keeps it hidden from geochemical detection.
Magdalena J. Mayr, Matthias Zimmermann, Jason Dey, Bernhard Wehrli, and Helmut Bürgmann
Biogeosciences, 17, 4247–4259, https://doi.org/10.5194/bg-17-4247-2020, https://doi.org/10.5194/bg-17-4247-2020, 2020
Massimiliano Molari, Felix Janssen, Tobias R. Vonnahme, Frank Wenzhöfer, and Antje Boetius
Biogeosciences, 17, 3203–3222, https://doi.org/10.5194/bg-17-3203-2020, https://doi.org/10.5194/bg-17-3203-2020, 2020
Short summary
Short summary
Industrial-scale mining of deep-sea polymetallic nodules will remove nodules in large areas of the sea floor. We describe community composition of microbes associated with nodules of the Peru Basin. Our results show that nodules provide a unique ecological niche, playing an important role in shaping the diversity of the benthic deep-sea microbiome and potentially in element fluxes. We believe that our findings are highly relevant to expanding our knowledge of the impact associated with mining.
Jun Zhao, Yuanfeng Cai, and Zhongjun Jia
Biogeosciences, 17, 1451–1462, https://doi.org/10.5194/bg-17-1451-2020, https://doi.org/10.5194/bg-17-1451-2020, 2020
Short summary
Short summary
We show that soil pH is a key factor in selecting distinct phylotypes of methanotrophs in paddy soils. Type II methanotrophs dominated the methane oxidation in low-pH soils, while type I methanotrophs were more active in high-pH soils. This pH-based niche differentiation of active methanotrophs appeared to be independent of nitrogen fertilization, but the inhibition of type II methanotrophic rate in low-pH soils by the fertilization might aggravate the emission of methane from paddy soils.
Edwin Sien Aun Sia, Zhuoyi Zhu, Jing Zhang, Wee Cheah, Shan Jiang, Faddrine Holt Jang, Aazani Mujahid, Fuh-Kwo Shiah, and Moritz Müller
Biogeosciences, 16, 4243–4260, https://doi.org/10.5194/bg-16-4243-2019, https://doi.org/10.5194/bg-16-4243-2019, 2019
Short summary
Short summary
Microbial community composition and diversity in freshwater habitats are much less studied compared to marine and soil communities. This study presents the first assessment of microbial communities of the Rajang River, the longest river in Malaysia, expanding our knowledge of microbial ecology in tropical regions. Areas surrounded by oil palm plantations showed the lowest diversity and other signs of anthropogenic impacts included the presence of CFB groups as well as probable algal blooms.
Julia Mitzscherling, Fabian Horn, Maria Winterfeld, Linda Mahler, Jens Kallmeyer, Pier P. Overduin, Lutz Schirrmeister, Matthias Winkel, Mikhail N. Grigoriev, Dirk Wagner, and Susanne Liebner
Biogeosciences, 16, 3941–3958, https://doi.org/10.5194/bg-16-3941-2019, https://doi.org/10.5194/bg-16-3941-2019, 2019
Short summary
Short summary
Permafrost temperatures increased substantially at a global scale, potentially altering microbial assemblages involved in carbon mobilization before permafrost thaws. We used Arctic Shelf submarine permafrost as a natural laboratory to investigate the microbial response to long-term permafrost warming. Our work shows that millennia after permafrost warming by > 10 °C, microbial community composition and population size reflect the paleoenvironment rather than a direct effect through warming.
Blanca Rincón-Tomás, Jan-Peter Duda, Luis Somoza, Francisco Javier González, Dominik Schneider, Teresa Medialdea, Esther Santofimia, Enrique López-Pamo, Pedro Madureira, Michael Hoppert, and Joachim Reitner
Biogeosciences, 16, 1607–1627, https://doi.org/10.5194/bg-16-1607-2019, https://doi.org/10.5194/bg-16-1607-2019, 2019
Short summary
Short summary
Cold-water corals were found at active sites in Pompeia Province (Gulf of Cádiz). Since seeped fluids are harmful for the corals, we approached the environmental conditions that allow corals to colonize carbonates while seepage occurs. As a result, we propose that chemosynthetic microorganisms (i.e. sulfide-oxidizing bacteria and AOM-related microorganisms) play an important role in the colonization of the corals at these sites by feeding on the seeped fluids and avoiding coral damage.
Sylwia Śliwińska-Wilczewska, Agata Cieszyńska, Jakub Maculewicz, and Adam Latała
Biogeosciences, 15, 6257–6276, https://doi.org/10.5194/bg-15-6257-2018, https://doi.org/10.5194/bg-15-6257-2018, 2018
Short summary
Short summary
The present study describes responses of picocyanobacteria (PCY) physiology to different environmental conditions. The cultures were grown under 64 combinations of temperature, irradiance in a photosynthetically active spectrum (PAR), and salinity. The results show that each strain of Baltic Synechococcus sp. behaves differently in respective environmental scenarios. The study develops the knowledge on bloom-forming PCY and reasons further research on the smallest size fraction of phytoplankton.
Jose Luis Otero-Ferrer, Pedro Cermeño, Antonio Bode, Bieito Fernández-Castro, Josep M. Gasol, Xosé Anxelu G. Morán, Emilio Marañon, Victor Moreira-Coello, Marta M. Varela, Marina Villamaña, and Beatriz Mouriño-Carballido
Biogeosciences, 15, 6199–6220, https://doi.org/10.5194/bg-15-6199-2018, https://doi.org/10.5194/bg-15-6199-2018, 2018
Short summary
Short summary
The effect of inorganic nutrients on planktonic assemblages has been traditionally assessed by looking at concentrations rather than fluxes of nutrient supply. However, in near-steady-state systems such as subtropical gyres, nitrate concentrations are kept close to the detection limit due to phytoplankton uptake. Our results, based on direct measurements of nitrate diffusive fluxes, support the key role of nitrate supply in controlling the structure of marine picoplankton communities.
Jörn Wehking, Daniel A. Pickersgill, Robert M. Bowers, David Teschner, Ulrich Pöschl, Janine Fröhlich-Nowoisky, and Viviane R. Després
Biogeosciences, 15, 4205–4214, https://doi.org/10.5194/bg-15-4205-2018, https://doi.org/10.5194/bg-15-4205-2018, 2018
Short summary
Short summary
Archaea as a third domain of life play an important role in soils and marine environments. Although archaea have been found in air as a part of the atmospheric bioaerosol, little is known about their atmospheric dynamics due to their low number and challenging analysis.
Here we present a DNA-based study of airborne archaea, show seasonal dynamics, and discuss anthropogenic influences on the diversity, composition, and abundances of airborne archaea.
Nicholas Bock, France Van Wambeke, Moïra Dion, and Solange Duhamel
Biogeosciences, 15, 3909–3925, https://doi.org/10.5194/bg-15-3909-2018, https://doi.org/10.5194/bg-15-3909-2018, 2018
Short summary
Short summary
We report the distribution of major nano- and pico-plankton groups in the western tropical South Pacific. We found microbial community structure to be typical of highly stratified regions of the open ocean, with significant contributions to total biomass by picophytoeukaryotes, and N2 fixation playing a central role in regulating ecosystem processes. Our results also suggest a reduction in the importance of predation in regulating bacteria populations under nutrient-limited conditions.
Michelle Szyja, Burkhard Büdel, and Claudia Colesie
Biogeosciences, 15, 1919–1931, https://doi.org/10.5194/bg-15-1919-2018, https://doi.org/10.5194/bg-15-1919-2018, 2018
Short summary
Short summary
Ongoing human impact transforms habitats into surfaces lacking higher vegetation. Here, biological soil crusts (BSCs) provide ecosystem services like soil creation and carbon uptake. To understand the functioning of these areas, we examined the physiological capability of early successional BSCs. We found features enabling BSCs to cope with varying climatic stresses. BSCs are important carbon fixers independent of the dominating organism. We provide baseline data for modeling carbon fluxes.
Petr Kotas, Hana Šantrůčková, Josef Elster, and Eva Kaštovská
Biogeosciences, 15, 1879–1894, https://doi.org/10.5194/bg-15-1879-2018, https://doi.org/10.5194/bg-15-1879-2018, 2018
Short summary
Short summary
The soil microbial properties were investigated along altitudinal gradients in the Arctic. Systematic altitudinal shift in MCS resulting in high F / B ratios at the most elevated sites was observed. The changes in composition, size and activity of microbial communities were mainly controlled through the effect of vegetation on edaphic properties and by bedrock chemistry. The upward migration of vegetation due to global warming will likely diminish the spatial variability in microbial properties.
Tung-Yi Huang, Bing-Mu Hsu, Wei-Chun Chao, and Cheng-Wei Fan
Biogeosciences, 15, 1815–1826, https://doi.org/10.5194/bg-15-1815-2018, https://doi.org/10.5194/bg-15-1815-2018, 2018
Short summary
Short summary
The n-alkane in litterfall and the microbial community in litter layer in different habitats of lowland subtropical rainforest were studied. We revealed that the plant vegetation of forest not only dominated the n-alkane input of habitats but also governed the diversity of microbial community of litter layer. In this study, we found that the habitat which had high n-alkane input induced a shift of relative abundance toward phylum of Actinobacteria and the growth of alkB gene contained bacteria.
Jennifer Caesar, Alexandra Tamm, Nina Ruckteschler, Anna Lena Leifke, and Bettina Weber
Biogeosciences, 15, 1415–1424, https://doi.org/10.5194/bg-15-1415-2018, https://doi.org/10.5194/bg-15-1415-2018, 2018
Short summary
Short summary
In our study we analyzed the efficiency of different chlorophyll extraction solvents and investigated the effect of different preparatory steps to determine the optimal extraction method for biological soil crusts. Based on our results we confirm a DMSO-based chlorophyll extraction method without grinding pretreatment and suggest to insert an intermediate shaking step for complete chlorophyll extraction.
Zhiwei Xu, Guirui Yu, Xinyu Zhang, Nianpeng He, Qiufeng Wang, Shengzhong Wang, Xiaofeng Xu, Ruili Wang, and Ning Zhao
Biogeosciences, 15, 1217–1228, https://doi.org/10.5194/bg-15-1217-2018, https://doi.org/10.5194/bg-15-1217-2018, 2018
Short summary
Short summary
Forest types with specific soil conditions supported the development of distinct soil microbial communities with variable functions. Our results indicate that the main controls on soil microbes and functions vary across forest ecosystems in different climatic zones. This information will add value to the modeling of microbial processes and will contribute to carbon cycling on a large scale.
Patrick Jung, Laura Briegel-Williams, Anika Simon, Anne Thyssen, and Burkhard Büdel
Biogeosciences, 15, 1149–1160, https://doi.org/10.5194/bg-15-1149-2018, https://doi.org/10.5194/bg-15-1149-2018, 2018
Short summary
Short summary
Arctic, Antarctic and alpine biological soil crusts (BSCs) are formed by adhesion of soil particles to cyanobacteria. BSCs influence ecosystems services like soil erodibility and chemical cycles. In cold environments degradation rates are low and BSCs increase soil organic carbon through photosynthesis, whereby these soils are considered as CO2 sinks. This work provides a novel method to visualize BSCs with a focus on cyanobacteria and their contribution to soil organic carbon.
Rongliang Jia, Yun Zhao, Yanhong Gao, Rong Hui, Haotian Yang, Zenru Wang, and Yixuan Li
Biogeosciences, 15, 1161–1172, https://doi.org/10.5194/bg-15-1161-2018, https://doi.org/10.5194/bg-15-1161-2018, 2018
Short summary
Short summary
Why can biocrust moss survive and flourish in these habitats when stressed simultaneously by drought and sand burial? A field experiment was conducted to assess the combined effects of the two stressors on Bryum argenteum within biocrust. The two stressors did not exacerbate the single negative effects; their mutually antagonistic effect on the physiological vigor of B. argenteum was found, and it provided an opportunity for it to overcome the two co-occurring stressors in arid sandy ecosystems.
Johanna Maltby, Lea Steinle, Carolin R. Löscher, Hermann W. Bange, Martin A. Fischer, Mark Schmidt, and Tina Treude
Biogeosciences, 15, 137–157, https://doi.org/10.5194/bg-15-137-2018, https://doi.org/10.5194/bg-15-137-2018, 2018
Short summary
Short summary
The activity and environmental controls of methanogenesis (MG) within the sulfate-reducing zone (0–30 cm below the seafloor) were investigated in organic-rich sediments of the seasonally hypoxic Eckernförde Bay, SW Baltic Sea. MG activity was mostly linked to non-competitive substrates. The major controls identified were organic matter availability, C / N, temperature, and O2 in the water column, revealing higher rates in warm, stratified, hypoxic seasons compared to colder, oxygenated seasons.
Rebecca Elizabeth Cooper, Karin Eusterhues, Carl-Eric Wegner, Kai Uwe Totsche, and Kirsten Küsel
Biogeosciences, 14, 5171–5188, https://doi.org/10.5194/bg-14-5171-2017, https://doi.org/10.5194/bg-14-5171-2017, 2017
Short summary
Short summary
In this study we show increasing organic matter (OM) content on ferrihydrite surfaces enhances Fe reduction by the model Fe reducer S. oneidensis and a microbial consortia extracted from peat. Similarities in reduction rates between S. oneidensis and the consortia suggest electron shuttling dominates in OM-rich soils. Community profile analyses showed enrichment of fermenters with pure ferrihydrite, whereas OM–mineral complexes favored enrichment of Fe-reducing Desulfobacteria and Pelosinus sp.
Yu-Te Lin, Zhongjun Jia, Dongmei Wang, and Chih-Yu Chiu
Biogeosciences, 14, 4879–4889, https://doi.org/10.5194/bg-14-4879-2017, https://doi.org/10.5194/bg-14-4879-2017, 2017
Short summary
Short summary
We evaluated the bacterial composition and diversity of bamboo soils sampled at different elevations and incubated at different temperatures. Soil respiration was greater at higher elevation and temperature. Soil bacterial structure and diversity showed variable under different incubation times and temperatures. Increases in temperature increased soil respiration and consumption of soil soluble carbon and nitrogen, thus influencing the bacterial diversity and structure at different elevations.
Lichao Liu, Yubing Liu, Peng Zhang, Guang Song, Rong Hui, Zengru Wang, and Jin Wang
Biogeosciences, 14, 3801–3814, https://doi.org/10.5194/bg-14-3801-2017, https://doi.org/10.5194/bg-14-3801-2017, 2017
Short summary
Short summary
We studied the development process of bacterial community structure of biological soil crusts (BSCs) along a revegetation chronosequence by Illumina MiSeq sequencing in the Tengger Desert. Our results indicated (1) a shift of bacterial composition related to their function in the crust development process; (2) bacterial diversity and richness consistent with the recovery phase of soil properties; and (3) bacteria as key contributors to the BSC succession process.
Sophie L. Nixon, Jon P. Telling, Jemma L. Wadham, and Charles S. Cockell
Biogeosciences, 14, 1445–1455, https://doi.org/10.5194/bg-14-1445-2017, https://doi.org/10.5194/bg-14-1445-2017, 2017
Short summary
Short summary
Despite their permanently cold and dark characteristics, subglacial environments (glacier ice–sediment interface) are known to harbour active microbial communities. However, the role of microbial iron cycling in these environments is poorly understood. Here we show that subglacial sediments harbour active iron-reducing microorganisms, and they appear to be cold-adapted. These results may have important implications for global biogeochemical iron cycling and export to marine ecosystems.
Estelle Couradeau, Daniel Roush, Brandon Scott Guida, and Ferran Garcia-Pichel
Biogeosciences, 14, 311–324, https://doi.org/10.5194/bg-14-311-2017, https://doi.org/10.5194/bg-14-311-2017, 2017
Short summary
Short summary
Endoliths are a prominent bioerosive component of intertidal marine habitats, traditionally thought to be formed by a few cyanobacteria, algae and fungi. Using molecular techniques, however, we found that endoliths from Mona Island, Puerto Rico, were of high diversity, well beyond that reported in traditional studies. We also found evidence for substrate specialization, in that closely related cyanobacteria seem to have diversified to specialize recurrently to excavate various mineral substrates
Yong Wang, Tie Gang Li, Meng Ying Wang, Qi Liang Lai, Jiang Tao Li, Zhao Ming Gao, Zong Ze Shao, and Pei-Yuan Qian
Biogeosciences, 13, 6405–6417, https://doi.org/10.5194/bg-13-6405-2016, https://doi.org/10.5194/bg-13-6405-2016, 2016
Short summary
Short summary
Mild eruption of hydrothermal solutions on deep-sea benthic floor can produce anhydrite crystal layers, where microbes are trapped and preserved for a long period of time. These embedded original inhabitants will be biomarkers for the environment when the hydrothermal eruption occurred. This study discovered a thick anhydrite layer in a deep-sea brine pool in the Red Sea. Oil-degrading bacteria were revealed in the crystals with genomic and microscopic evidence.
Dina Spungin, Ulrike Pfreundt, Hugo Berthelot, Sophie Bonnet, Dina AlRoumi, Frank Natale, Wolfgang R. Hess, Kay D. Bidle, and Ilana Berman-Frank
Biogeosciences, 13, 4187–4203, https://doi.org/10.5194/bg-13-4187-2016, https://doi.org/10.5194/bg-13-4187-2016, 2016
Short summary
Short summary
The marine cyanobacterium Trichodesmium spp. forms massive blooms important to carbon and nitrogen cycling in the oceans that often collapse abruptly. We investigated a Trichodesmium bloom in the lagoon waters of New Caledonia to specifically elucidate the cellular processes mediating the bloom decline. We demonstrate physiological, biochemical, and genetic evidence for nutrient and oxidative stress that induced a genetically controlled programmed cell death (PCD) pathway leading to bloom demise.
Lotta Purkamo, Malin Bomberg, Riikka Kietäväinen, Heikki Salavirta, Mari Nyyssönen, Maija Nuppunen-Puputti, Lasse Ahonen, Ilmo Kukkonen, and Merja Itävaara
Biogeosciences, 13, 3091–3108, https://doi.org/10.5194/bg-13-3091-2016, https://doi.org/10.5194/bg-13-3091-2016, 2016
Short summary
Short summary
The microbial communities of up to 2.3 km depth of Precambrian crystalline bedrock fractures share features with serpenization-driven microbial communities in alkaline springs and subsurface aquifers. This study suggests that phylotypes belonging to Burkholderiales and Clostridia are possible "keystone microbial species" in Outokumpu deep biosphere. Many of the keystone species belong to the rare biosphere with low abundance but a wide range of carbon substrates and a capacity for H2 oxidation.
Thierry Jauffrais, Bruno Jesus, Edouard Metzger, Jean-Luc Mouget, Frans Jorissen, and Emmanuelle Geslin
Biogeosciences, 13, 2715–2726, https://doi.org/10.5194/bg-13-2715-2016, https://doi.org/10.5194/bg-13-2715-2016, 2016
Short summary
Short summary
Some benthic foraminifera can incorporate chloroplasts from microalgae. We investigated chloroplast functionality of two benthic foraminifera (Haynesina germanica & Ammonia tepida) exposed to different light levels. Only H. germanica was capable of using the kleptoplasts, showing net oxygen production. Chloroplast functionality time was longer in darkness (2 weeks) than at high light (1 week). Kleptoplasts are unlikely to be completely functional, thus requiring continuous chloroplast resupply.
L. Zhou, Y. Tan, L. Huang, Z. Hu, and Z. Ke
Biogeosciences, 12, 6809–6822, https://doi.org/10.5194/bg-12-6809-2015, https://doi.org/10.5194/bg-12-6809-2015, 2015
Short summary
Short summary
We observed that phytoplankton biomass and growth rate (μ), microzooplankton grazing rate (m), and coupling (correlation) between the μ and m significantly varied between the summer and winter, and microzooplankton selectively grazed more on the larger-sized phytoplankton, and a low grazing impact on phytoplankton (m/μ < 50%) in the SSCS. The salient seasonal variations in μ and m, and their coupling were closely related to environmental variables under the influence of the East Asian monsoon.
A. M. Womack, P. E. Artaxo, F. Y. Ishida, R. C. Mueller, S. R. Saleska, K. T. Wiedemann, B. J. M. Bohannan, and J. L. Green
Biogeosciences, 12, 6337–6349, https://doi.org/10.5194/bg-12-6337-2015, https://doi.org/10.5194/bg-12-6337-2015, 2015
Short summary
Short summary
Fungi in the atmosphere can affect precipitation by nucleating the formation of clouds and ice. This process is important over the Amazon rainforest where precipitation is limited by the types and amount of airborne particles. We found that the total and metabolically active fungi communities were dominated by different taxonomic groups, and the active community unexpectedly contained many lichen fungi, which are effective at nucleating ice.
W. Y. Dong, X. Y. Zhang, X. Y. Liu, X. L. Fu, F. S. Chen, H. M. Wang, X. M. Sun, and X. F. Wen
Biogeosciences, 12, 5537–5546, https://doi.org/10.5194/bg-12-5537-2015, https://doi.org/10.5194/bg-12-5537-2015, 2015
Short summary
Short summary
We examined how N and P addition influenced soil microbial community composition and enzyme activities in subtropical China. The results showed that C and N cycling enzymes were more sensitive to nutrient additions than P cycling enzymes and Gram-positive bacteria were most closely related to soil nutrient cycling enzymes. Combined additions of N and P fertilizer are recommended to promote soil fertility and microbial activity in this kind of plantation.
T. Bush, I. B. Butler, A. Free, and R. J. Allen
Biogeosciences, 12, 3713–3724, https://doi.org/10.5194/bg-12-3713-2015, https://doi.org/10.5194/bg-12-3713-2015, 2015
Short summary
Short summary
Despite their global importance, redox reactions mediated by microorganisms are often crudely represented in biogeochemical models. We show that including the dynamics of microbial growth in such a model can cause sudden shifts between redox states in response to an environmental change. We identify the conditions required for these redox regime shifts, and predict that they are likely in the modern day sulfur and nitrogen cycles, and potentially the iron cycle in the ancient ocean.
P. K. Gao, G. Q. Li, H. M. Tian, Y. S. Wang, H. W. Sun, and T. Ma
Biogeosciences, 12, 3403–3414, https://doi.org/10.5194/bg-12-3403-2015, https://doi.org/10.5194/bg-12-3403-2015, 2015
Short summary
Short summary
Microbial communities in injected water are expected to have a significant influence on those of reservoir strata in long-term water-flooding petroleum reservoirs. We thereby investigated the similarities and differences in microbial communities in water samples collected from the wellhead and downhole of injection wells, and from production wells in a homogeneous reservoir and a heterogeneous reservoir using high-throughput sequencing.
V. Marteinsson, A. Klonowski, E. Reynisson, P. Vannier, B. D. Sigurdsson, and M. Ólafsson
Biogeosciences, 12, 1191–1203, https://doi.org/10.5194/bg-12-1191-2015, https://doi.org/10.5194/bg-12-1191-2015, 2015
Short summary
Short summary
Colonization of life on Surtsey has been observed systematically since the formation of the island. Microbial colonization and the influence of associate vegetation and birds on viable counts of environmental bacteria at the surface of the Surtsey was explored for the first time in diverse surface soils. Also, hot subsurface samples deep in the centre of this volcanic island were collected. Both uncultivated bacteria and archaea were found in the subsurface samples collected below 145 m.
J. Fröhlich-Nowoisky, C. Ruzene Nespoli, D. A. Pickersgill, P. E. Galand, I. Müller-Germann, T. Nunes, J. Gomes Cardoso, S. M. Almeida, C. Pio, M. O. Andreae, R. Conrad, U. Pöschl, and V. R. Després
Biogeosciences, 11, 6067–6079, https://doi.org/10.5194/bg-11-6067-2014, https://doi.org/10.5194/bg-11-6067-2014, 2014
Short summary
Short summary
We have investigated the presence of archaea as well as their amoA gene diversity in aerosol particles collected over 1 year in central Europe and found that, within the 16S and amoA gene, Thaumarchaeota prevail and experience a diversity peak in fall, while only few Euryarchaeota were detected primarily in spring. We also compared the results with airborne archaea from Cape Verde and observe that the proportions of Euryarchaeota seem to be enhanced in coastal air compared to continental air.
A. L. Gagliano, W. D'Alessandro, M. Tagliavia, F. Parello, and P. Quatrini
Biogeosciences, 11, 5865–5875, https://doi.org/10.5194/bg-11-5865-2014, https://doi.org/10.5194/bg-11-5865-2014, 2014
S. A. Krueger-Hadfield, C. Balestreri, J. Schroeder, A. Highfield, P. Helaouët, J. Allum, R. Moate, K. T. Lohbeck, P. I. Miller, U. Riebesell, T. B. H. Reusch, R. E. M. Rickaby, J. Young, G. Hallegraeff, C. Brownlee, and D. C. Schroeder
Biogeosciences, 11, 5215–5234, https://doi.org/10.5194/bg-11-5215-2014, https://doi.org/10.5194/bg-11-5215-2014, 2014
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.
Babbin, A. R., Bianchi, D., Jayakumar, A., and Ward, B. B.: Rapid nitrous
oxide cycling in the suboxic ocean, Science, 348, 1127–1129,
https://doi.org/10.1126/science.aaa8380, 2015.
Bange, H. W., Rapsomanik, S., and Andreae, M. O.: Nitrous oxide in coastal
waters, Global Biogeochem. Cy., 10, 197–207, https://doi.org/10.1029/95GB03834,
1996.
Barnes, J. and Upstill-Goddard, R. C.: N2O seasonal distributions and
air-sea exchange in UK estuaries: Implications for the tropospheric N2O
source from European coastal waters, J. Geophys. Res.-Biogeo.,
116, G01006, https://doi.org/10.1029/2009JG001156, 2011.
Beaulieu, J. J., Tank, J. L., Hamilton, S. K., Wollheim, W. M., Hall, R. O.,
Mulholland, P. J., Peterson, B. J., Ashkenas, L. R., Cooper, L. W., Dahm, C.
N., Dodds, W. K., Grimm, N. B., Johnson, S. L., McDowell, W. H., Poole, G.
C., Maurice Valett, H., Arango, C. P., Bernot, M. J., Burgin, A. J.,
Crenshaw, C. L., Helton, A. M., Johnson, L. T., O'Brien, J. M., Potter, J.
D., Sheibley, R. W., Sobota, D. J., and Thomas, S. M.: Nitrous oxide emission
from denitrification in stream and river networks, P. Natl. Acad. Sci. USA, 108, 214–219, https://doi.org/10.1073/pnas.1011464108, 2011.
Beman, J. M., Popp, B. N., and Francis, C.: 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.2008.33, 2008.
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.
Bertagnolli, A. D., Konstantinidis, K. T., and Stewart, F. J.:
Non-denitrifier nitrous oxide reductases dominate marine biomes, Environ.
Microbiol. Rep., 12, 681–692, https://doi.org/10.1111/1758-2229.12879, 2020.
Blackmer, A. M. and Bremner, J. M.: Inhibitory effect of nitrate on reduction of
N2O to N2 by soil microorganisms, Soil Biol Biochem.,
10, 187–191, https://doi.org/10.1016/0038-0717(78)90095-0, 1978.
Blum, J. M., Su, Q., Ma, Y., Valverde-Pérez, B., Domingo-Félez, C.,
Jensen, M. M., and Smets, B. F.: The pH dependency of N-converting enzymatic
processes, pathways and microbes: effect on net N2O production,
Environ. Microbiol., 20, 1623–1640, https://doi.org/10.1111/1462-2920.14063, 2018.
Braker, G., Zhou, J., Wu, L., Devol, A. H., and Tiedje, J. M.: Nitrite
reductase genes (nirK and nirS) as functional markers to investigate diversity of
denitrifying bacteria in Pacific northwest marine sediment communities,
Appl. Environ. Microbiol., 66, 2096–2104,
2000.
Brase, L., Bange, H. W., Lendt, R., Sanders, T., and Dähnke, K.: High
resolution measurements of nitrous oxide (N2O) in the Elbe estuary,
Front. Mar. Sci., 4, 162, https://doi.org/10.3389/fmars.2017.00162, 2017.
Cao, W., Hong, H., and Yue, S.: Modelling agricultural nitrogen contributions
to the Jiulong River estuary and coastal water, Glob. Planet. Change, 47, 111–121, https://doi.org/10.1016/j.gloplacha.2004.10.006, 2005.
Capella-Gutiérrez, S., Silla-Martínez, J. M., and Gabaldón, T.:
trimAl: A tool for automated alignment trimming in large-scale phylogenetic
analyses, Bioinformatics, 25, 1972–1973,
https://doi.org/10.1093/bioinformatics/btp348, 2009.
Carey, C. J., Dove, N. C., Beman, J. M., Hart, S. C., and Aronson, E. L.:
Meta-analysis reveals ammonia-oxidizing bacteria respond more strongly to
nitrogen addition than ammonia-oxidizing archaea, Soil Biol. Biochem., 99,
158–166, https://doi.org/10.1016/j.soilbio.2016.05.014, 2016.
Castellano-Hinojosa, A., Correa-Galeote, D., Carrillo, P., Bedmar, E. J., and
Medina-Sánchez, J. M.: Denitrification and biodiversity of denitrifiers
in a High-Mountain Mediterranean Lake, Front. Microbiol., 8, 1911,
https://doi.org/10.3389/fmicb.2017.01911, 2017.
Chee-Sanford, J. C., Connor, L., Krichels, A., Yang, W. H., and Sanford, R. A.: Hierarchical detection of diverse Clade II (atypical) nosZ genes using new primer sets for classical- and multiplex PCR array applications, J. Microbiol. Methods., 172, 105908, https://doi.org/10.1016/j.mimet.2020.105908, 2020.
Chen, C. A., Wang, S., Lu, X., Zhang, S., Lui, H., Tseng, H., Wang, B., and
Huang, H.: Hydrogeochemistry and greenhouse gases of the Pearl River, its
estuary and beyond, Quaternary Int., 186, 79–90,
https://doi.org/10.1016/j.quaint.2007.08.024, 2008.
Chen, C. T. A.: Chemical and physical fronts in the Bohai, Yellow and East
China seas, J. Mar. Syst., 78, 394–410,
https://doi.org/10.1016/j.jmarsys.2008.11.016, 2009.
Codispoti, L. A. and Christensen, J. P.: Nitrification, denitrification and
nitrous oxide cycling in the eastern tropical South Pacific ocean, Mar.
Chem., 16, 277–300, https://doi.org/10.1016/0304-4203(85)90051-9,
1985.
Cole, J. J. and Caraco, N. F.: Emissions of nitrous oxide (N2O) from a
tidal, freshwater river, the Hudson River, New York, Environ. Sci. Technol.,
35, 991–996, https://doi.org/10.1021/es0015848, 2001.
Cui, P., Chen, Z., Zhao, Q., Yu, Z., Yi, Z., Liao, H., and Zhou, S.:
Hyperthermophilic composting significantly decreases N2O emissions by
regulating N2O-related functional genes, Bioresour. Technol., 272,
433–441, https://doi.org/10.1016/j.biortech.2018.10.044, 2019.
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.
De Wilde, H. P. J. and De Bie, M. J. M.: Nitrous oxide in the Schelde
estuary: Production by nitrification and emission to the atmosphere, Mar.
Chem., 69, 203–216, https://doi.org/10.1016/S0304-4203(99)00106-1, 2000.
Domeignoz-Horta1, L. A., AyméSpor, D. B., Breuil, M.-C.,
Florian Bizouard1, J. L., and L. P.: The diversity of the N2O reducers
matters for the N2O : N2 denitrification end-product ratio across an
annual and a perennial cropping system, Front. Microbiol., 6, 971,
https://doi.org/10.3389/fmicb.2015.00971, 2015.
Edgar, R. C.: Search and clustering orders of magnitude faster than BLAST,
Bioinformatics, 26, 2460–2461, 2010.
Fayazbakhsh, K., Abedian, A., Manshadi, B. D., and Khabbaz, R. S.:
Introducing a novel method for materials selection in mechanical design
using Z-transformation in statistics for normalization of material
properties, Mater. Des., 30, 4396–4404,
https://doi.org/10.1016/j.matdes.2009.04.004, 2009.
Fish, J. A., Chai, B., Wang, Q., Sun, Y., Brown, C. T., Tiedje, J. M., and Cole, J. R.: FunGene: the functional gene pipeline and repository [data set], Front. Microbiol., 4, 291, https://doi.org/10.3389/fmicb.2013.00291, 2013.
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.
Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263–2287, https://doi.org/10.5194/bg-17-2263-2020, 2020.
Garnier, J., Cébron, A., Tallec, G., Billen, G., Sebilo, M., and
Martinez, A.: Nitrogen behaviour and nitrous oxide emission in the tidal
Seine River estuary (France) as influenced by human activities in the
upstream watershed, Biogeochemistry, 77, 305–326,
https://doi.org/10.1007/s10533-005-0544-4, 2006.
Graf, D. R., Jones, C. M., and Hallin, S.: Intergenomic comparisons highlight
modularity of the denitrification pathway and underpin the importance of
community structure for N2O emissions, PLoS ONE,
9, e114118,
https://doi.org/10.1371/journal.pone.0114118, 2014.
Hallin, S., Philippot, L., Löf, F. E., Sanford, R. A., and Jones, C. M.:
Genomics and ecology of novel N2O-Reducing microorganisms, Trends
Microbiol., 26, 43–55, https://doi.org/10.1016/j.tim.2017.07.003, 2018.
He, B., Dai, M., Zhai, W., Guo, X., and Wang, L.: Hypoxia in the upper
reaches of the Pearl River Estuary and its maintenance mechanisms: A
synthesis based on multiple year observations during 2000–2008, Mar. Chem.,
167, 13–24, https://doi.org/10.1016/j.marchem.2014.07.003, 2014.
Henry, S., Bru, D., Stres, B., Hallet, S., and Philippot, L.: Quantitative
detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of
the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils, Appl. Environ.
Microbiol., 72, 5181–5189, https://doi.org/10.1128/AEM.00231-06, 2006.
Hink, L., Gubry-Rangin, C., Nicol, G. W., and Prosser, J. I.: The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions, ISME J., 12, 1084–1093, 2018.
Hornek, R., Pommerening-Roser, A., Koops, H. P., Farnleitner, A. H., Kreuzinger, N., Kirschner, A., and Mach, R.L.: Primers containing universal bases reduce multiple amoA gene specific DGGE band patterns when analysing the diversity of beta-ammonia oxidizers in the environment, J. Microbiol. Methods., 66, 147–155, 2006.
Hou, L., Xie, X., Wan, X., Kao, S. J., Jiao, N., and Zhang, Y.: Niche
differentiation of ammonia and nitrite oxidizers along a salinity gradient
from the Pearl River estuary to the South China Sea, Biogeosciences, 15,
5169–5187, https://doi.org/10.5194/bg-15-5169-2018, 2018.
Ji, Q., Buitenhuis, E., Suntharalingam, P., Sarmiento, J. L., and Ward, B.
B.: Global nitrous oxide production determined by oxygen sensitivity of
nitrification and denitrification, Global Biogeochem. Cy., 32,
1790–1802, https://doi.org/10.1029/2018GB005887, 2018a.
Ji, Q., Frey, C., Sun, X., Jackson, M., Lee, Y., Jayakumar, A., Jeffrey, C.,
and Ward, B. B.: Nitrogen and oxygen availabilities control water column
nitrous oxide production during seasonal anoxia in the Chesapeake Bay,
Biogeosciences, 15, 6127–6138, https://doi.org/10.5194/bg-15-6127-2018, 2018b.
Jones, C. M., Stres, B., Rosenquist, M., and Hallin, S.: Phylogenetic
analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes
reveal a complex evolutionary history for denitrification, Mol. Biol. Evol.
25, 1955–1966, https://doi.org/10.1093/molbev/msn146, 2008.
Jones, C. M., Graf, D. R. H., Bru, D., Philippot, L., and Hallin, S.: The
unaccounted yet abundant nitrous oxide-reducing microbial community: a
potential nitrous oxide sink, ISME J. 7, 417–26,
https://doi.org/10.1038/ismej.2012.125, 2013.
Jones, C. M., Spor, A., Brennan, F. P., Breuil, M., Bru, D., Lemanceau, P., Griffiths, B., Hallin, S., and Philippot, L.: Recently identified microbial guild mediates soil N2O sink
capacity, Nat. Clim. Change, 4, 801–805, https://doi.org/10.1038/nclimate2301, 2014.
Kato, S., Shibuya, T., Takaki, Y., Hirai, M., Nunoura, T., and Suzuki, K.: Genome-enabled metabolic reconstruction of dominant chemosynthetic colonizers in deep-sea massive sulfide deposits, Environ. Microbiol., 20, 862–877, https://doi.org/10.1111/1462-2920.14032, 2018.
Katoh, K. and Standley, D. M.: MAFFT multiple sequence alignment software
version 7: Improvements in performance and usability, Mol. Biol. Evol.,
30, 772–780, https://doi.org/10.1093/molbev/mst010, 2013.
Kester, R. A., De Boer, W., and Laanbroek, H. J.: Production of NO and
N2O by pure cultures of nitrifying and denitrifying bacteria during
changes in aeration, Appl. Environ. Microbiol., 63, 3872–3877,
1997.
Lam, P., Jensen, M. M., Lavik, G., McGinnis, D. F., Müller, B.,
Schubert, C. J., Amann, R., Thamdrup, B., and Kuypers, M. M. M.: Linking
crenarchaeal and bacterial nitrification to anammox in the Black Sea, P.
Natl. Acad. Sci. USA, 104, 7104–7109, https://doi.org/10.1073/pnas.0611081104,
2007.
Laperriere, S. M., Nidzieko, N. J., Fox, R. J., Fisher, A. W., and Santoro,
A. E.: Observations of variable ammonia oxidation and nitrous oxide flux in
a eutrophic estuary, Estuar. Coast., 42, 33–44,
https://doi.org/10.1007/s12237-018-0441-4, 2019.
Lee, J. A. and Francis, C. A.: Spatiotemporal characterization of San
Francisco Bay denitrifying communities: a comparison of nirK and nirS diversity and
abundance, Microb. Ecol., 73, 271–284, https://doi.org/10.1007/s00248-016-0865-y,
2017.
Li, J., Nedwell, D. B., Beddow, J., Dumbrell, A. J., McKew, B. A., Thorpe,
E. L., and Whitby, C.: amoA gene abundances and nitrification potential rates
suggest that benthic ammonia-oxidizing bacteria and not archaea dominate N
cycling in the Colne estuary, United Kingdom, Appl. Environ. Microbiol.,
81, 159–165, https://doi.org/10.1128/AEM.02654-14, 2015.
Lin, H., Dai, M., Kao, S. J., Wang, L., Roberts, E., Yang, J., Huang, T., and He, B.: Spatiotemporal variability of nitrous oxide in a large eutrophic estuarine system: The Pearl River Estuary, China, Mar. Chem., 182, 14–24, 2016.
Lin, J., Chen, N., Wang, F., Huang, Z., Zhang, X., and Liu, L.: Urbanization
increased river nitrogen export to western Taiwan Strait despite increased
retention by nitrification and denitrification, Ecol. Indic., 109, 105756,
https://doi.org/10.1016/j.ecolind.2019.105756, 2020.
Löscher, C. R., Kock, A., Könneke, M., Laroche, J., Bange, H. W.,
and Schmitz, R. A.: Production of oceanic nitrous oxide by ammonia-oxidizing
archaea, Biogeosciences, 9, 2419–2429, https://doi.org/10.5194/bg-9-2419-2012, 2012.
Lycus, P., Soriano-Laguna, M. J., Kjos, M., Richardson, D. J., Gates, A. J., Milligan, D. A., Frostegårda, Å., Bergausta, L., and Bakken, L. R.: A bet-hedging strategy for denitrifying bacteria curtails their release
of N2O, P. Natl. Acad. Sci. USA, 115, 11820–11825,
https://doi.org/10.1073/pnas.1805000115, 2018.
Ma, L., Lin, H., Xie, X., Dai, M., and Zhang, Y.: Major role of
ammonia-oxidizing bacteria in N2O production in the Pearl River
estuary, Biogeosciences, 16, 4765–4781, https://doi.org/10.5194/bg-16-4765-2019, 2019.
Magalhães, C., Bano, N., Wiebe, W. J., Bordalo, A. A., and Hollibaugh, J. T.: Dynamics of nitrous oxide reductase genes (nosZ) in intertidal rocky biofilms and sediments of the Douro River Estuary (Portugal), and their relation to N-biogeochemistry, Microb. Ecol., 55, 259–269, 2008.
Marchant, H. K., Ahmerkamp, S., Lavik, G., Tegetmeyer, H. E., Graf, J.,
Klatt, J. M., Holtappels, M., Walpersdorf, E., and Kuypers, M. M. M.:
Denitrifying community in coastal sediments performs aerobic and anaerobic
respiration simultaneously, ISME J. 11, 1799–1812,
https://doi.org/10.1038/ismej.2017.51, 2017.
Martens-Habbena, W. and Stahl, D. A.: Nitrogen metabolism and kinetics of
ammonia-oxidizing archaea, Methods Enzymol., 496, 465–487,
https://doi.org/10.1016/B978-0-12-386489-5.00019-1, 2011.
Marzadri, A., Dee, M. M., Tonina, D., Bellin, A., and Tank, J. L.: Role of
surface and subsurface processes in scaling N2O emissions along
riverine networks, P. Natl. Acad. Sci. USA, 114, 4330–4335,
https://doi.org/10.1073/pnas.1617454114, 2017.
Massana, R., Murray, A. E., Preston, C. M., and DeLong, E. F.: Vertical
distribution and phylogenetic characterization of marine planktonic archaea
in the Santa Barbara Channel, Appl. Environ. Microbiol., 63, 50–56,
https://doi.org/10.1128/aem.63.1.50-56.1997, 1997.
McElroy, M. B., Elkins, J. W., Wofsy, S. C., Kolb, C. E., Durán, A. P., and Kaplan, W. A.: Production and release of N2O from the Potomac Estuary, Limnol. Oceanogr., 23, 1168–1182, https://doi.org/10.4319/lo.1978.23.6.1168, 1978.
Meinhardt, K. A., Stopnisek, N., Pannu, M. W., Strand, S. E., Fransen, S.
C., Casciotti, K. L., and Stahl, D. A.: Ammonia-oxidizing bacteria are the
primary N2O producers in an ammonia-oxidizing archaea dominated
alkaline agricultural soil, Environ. Microbiol., 20, 2195–2206,
https://doi.org/10.1111/1462-2920.14246, 2018.
Molina, V., Belmar, L., and Ulloa, O.: High diversity of ammonia-oxidizing
archaea in permanent and seasonal oxygen-deficient waters of the Eastern
South Pacific, Environ. Microbiol., 12, 2450–2465,
https://doi.org/10.1111/1462-2920.14246, 2010.
Mosier, A. C. and Francis, C. A.: Denitrifier abundance and activity across
the San Francisco Bay estuary, Environ. Microbiol Rep., 2, 667–676,
https://doi.org/10.1111/j.1758-2229.2010.00156.x, 2010.
Mullins, T. D., Britschgi, T. B., Krest, R. L., and Giovannoni, S. J.: Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities, Limnol. Oceanogr., 40, 148–158, 1995.
Nakai, R., Nishijima, M., Tazato, N., Handa, Y., Karray, F., Sayadi, S.,
Isoda, H., and Naganuma, T.: Oligoflexus tunisiensis gen. nov., sp. nov., a Gram-negative, aerobic,
filamentous bacterium of a novel proteobacterial lineage, and description of
Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov, Int. J. Syst. Evol. Microbiol, 64,
3353–3359, https://doi.org/10.1099/ijs.0.060798-0, 2014.
Nevison, C., Butler, J. H., and Elkins, J. W.: Global distribution of
N2O and the ΔN2O-AOU yield in the subsurface ocean, Global
Biogeochem. Cy., 17, 1–18, https://doi.org/10.1029/2003GB002068, 2003.
Palacin-Lizarbe, C., Camarero, L., Hallin, S., Jones, C., Caliz, J.,
Casamayor, E. O., and Catalan, J.: The DNRA-denitrification dichotomy
differentiates nitrogen transformation pathways in mountain lake benthic
habitats, Front. Microbiol., 10, 1229, https://doi.org/10.3389/FMICB.2019.01229, 2019.
Park, B. J., Park, S. J., Yoon, D. N., Schouten, S., Damsté, J. S. S., and Rhee, S. K.: Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria, Appl. Environ. Microb., 76, 7575–87, 2010.
Philippot, L.: Loss in microbial diversity affects nitrogen cycling in soil,
ISME J., 11, 1609–1619, 2013.
Pike, N.: Using false discovery rates for multiple comparisons in ecology and evolution, Methods Ecol. Evol., 2, 278–282, 2011.
Price, M. N., Dehal, P. S., and Arkin, A. P.: FastTree 2 – Approximately
maximum-likelihood trees for large alignments, PLoS One 5, 9490,
https://doi.org/10.1371/journal.pone.0009490, 2010.
Xu, J., Wang, Y., Wang, Q., and Yin, J.: Nitrous oxide
concentration and nitrification and denitrification in Zhujiang River
Estuary, China. J. Environ. Sci., 18, 122–130, 2005.
Qu, Z., Bakken, L. R., Molstad, L., Frostegård, Å., and Bergaust, L.
L.: Transcriptional and metabolic regulation of denitrification in
Paracoccus denitrificans allows low but significant activity of nitrous
oxide reductase under oxic conditions, Environ. Microbiol., 18, 2951–2963,
https://doi.org/10.1111/1462-2920.13128, 2016.
R Core Team: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, https://www.R-project.org/ (last access: 5 July 2019), Vienna, Austria, 2017.
Ravishankara, A. R., Daniel, J. S., and Portmann, R. W.: Nitrous oxide
(N2O): The dominant ozone-depleting substance emitted in the 21st
century, Science, 326, 123–125, https://doi.org/10.1126/science.1176985, 2009.
Rissanen, A. J., Tiirola, M., and Ojala, A.: Spatial and temporal variation
in denitrification and in the denitrifier community in a boreal lake, Aquat.
Microbiol. Ecol., 64, 27–40, https://doi.org/10.3354/ame01506, 2011.
Riya, S., Takeuchi, Y., Zhou, S., Terada, A., and Hosomi, M.: Nitrous oxide
production and mRNA expression analysis of nitrifying and denitrifying
bacterial genes under floodwater disappearance and fertilizer application,
Environ. Sci. Pollut. Res., 24, 15852–15859,
https://doi.org/10.1007/s11356-017-9231-y, 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. Microb., 63, 4704-4712, 1997.
Rowley, G., Sullivan, M. J., Appia-Ayme, C., Gates, A. J., and Richardson, D.
J.: Copper control of bacterial nitrous oxide emission and its impact on
vitamin B12-dependent metabolism, P. Natl. Acad. Sci. USA, 110,
19926–19931, https://doi.org/10.1073/pnas.1314529110, 2013.
Sanford, R. A., Wagner, D. D., Wu, Q. Z., Chee-Sanford, J. C., Thomas, S.
H., Cruz-Garcia, C., Rodriguez, G., Massol-Deya, A., Krishnani, K. K.,
Ritalahti, K. M., Nissen, S., Konstantinidis, K. T., and Loffler, F. E.:
Unexpected nondenitrifier nitrous oxide reductase gene diversity and
abundance in soils, P. Natl. Acad. Sci. USA, 109, 19709–19714,
https://doi.org/10.1073/Pnas.1211238109, 2012.
Santoro, A. E., Buchwald, C., McIlvin, M. R., and Casciotti, K. L.: Isotopic
Signature of N2O Produced by Marine Ammonia-Oxidizing Archaea, Science,
333, 1282–1285, https://doi.org/10.1126/science.1208239, 2011.
Senbayram, M., Budai, A., Bol, R., Chadwick, D., Marton, L., Gündogan,
R., and Wu, D.: Soil NO
Shaw, L. J., Nicol, G. W., Smith, Z., Fear, J., Prosser, J. I., and Baggs,
E. M.: Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway,
Environ. Microbiol., 8, 214–222, https://doi.org/10.1111/j.1462-2920.2005.00882.x,
2006.
Silvennoinen, H., Liikanen, A., Torssonen, J., Florian Stange, C., and
Martikainen, P. J.: Denitrification and nitrous oxide effluxes in boreal,
eutrophic river sediments under increasing nitrate load: A laboratory
microcosm study, Biogeochemistry, 91, 105–116,
https://doi.org/10.1007/s10533-008-9262-z, 2008.
Smith, C. J., Nedwell, D. B., Dong, L. F., and Osborn, A. M.: Diversity and
abundance of nitrate reductase genes (narG and napA), nitrite reductase genes
(nirS and nrfA), and their transcripts in estuarine sediments, Appl. Environ.
Microbiol., 73, 3612–3622, https://doi.org/10.1128/AEM.02894-06, 2007.
Solomon, S. D., Qin, D., Manning, M., Chen, Z., Marquis, M., Averyt, K., Tignor, M., and Miller, H. L.: Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC), Cambridge Univ. Press, Cambridge, 996 pp., UK, 2007.
Song, D., Zhang, G., Li, P., and Liu, S.: Distribution and fluxes of nitrous
oxide in the Bohai Sea in summer, Adv. Mar. Sci., 2, 13–21,
https://doi.org/10.12677/ams.2015.22003, 2015.
Song, K., Suenaga, T., Hamamoto, A., Satou, K., Riya, S., Hosomi, M., and
Terada, A.: Abundance, transcription levels and phylogeny of bacteria
capable of nitrous oxide reduction in a municipal wastewater treatment
plant, J. Biosci. Bioeng., 118, 289–297,
https://doi.org/10.1016/j.jbiosc.2014.02.028, 2014.
Stieglmeier, M., Mooshammer, M., Kitzler, B., Wanek, W.,
Zechmeister-Boltenstern, S., Richter, A., and Schleper, C.: Aerobic nitrous
oxide production through N-nitrosating hybrid formation in ammonia-oxidizing
archaea, ISME J., 8, 1135–1146, https://doi.org/10.1038/ismej.2013.220, 2014.
Sun, X., Jayakumar, A., and Ward, B. B.: Community composition of nitrous
oxide consuming bacteria in the oxygen minimum zone of the Eastern Tropical
South Pacific, Front. Microbiol., 8, 1183,
https://doi.org/10.3389/fmicb.2017.01183, 2017.
Sun, X., Jayakumar, A., Tracey, J. C., Wallace, E.,
Kelly, C. L., Casciotti, K. L., and Ward, B. B.: Microbial N2O consumption
in and above marine N2O production hotspots, ISME J., 15, 1434–1444,
https://doi.org/10.1038/s41396-020-00861-2, 2021.
Thompson, K. A.: Abundance, activity and community structure of nitrifier and denitrifier communities in Agro-Ecosystems, PhD thesis, Land Resource Science, University of Guelph, Guelph, Ontario, Canada, 184 pp., 2016.
Wang, L., Zheng, B., Nan, B., and Hu, P.: Diversity of bacterial community
and detection of nirS- and nirK-encoding denitrifying bacteria in sandy intertidal
sediments along Laizhou Bay of Bohai Sea, China, Mar. Pollut. Bull.,
88, 215–223, https://doi.org/10.1016/j.marpolbul.2014.09.002, 2014.
Wang, L., Zhang, G., Zhu, Z., Li, J., Liu, S., Ye, W., and Han, Y.:
Distribution and sea-to-air flux of nitrous oxide in the East China Sea
during the summer of 2013, Cont. Shelf Res., 123, 99–110,
https://doi.org/10.1016/j.csr.2016.05.001, 2016.
Wang, Y., Guo, J., Vogt, R.D., Mulder, J., Wang, J., and Zhang, X.: Soil pH as the chief modifier for regional nitrous oxide emissions: new evidence and implications for global estimates and mitigation, Glob. Change Biol., 24, e617–e626, 2017.
Wei, W., Isobe, K., Nishizawa, T., Zhu, L., Shiratori, Y., Ohte, N., Koba,
K., Otsuka, S., and Senoo, K.: Higher diversity and abundance of denitrifying
microorganisms in environments than considered previously, ISME J., 9,
1954–1965, https://doi.org/10.1038/ismej.2015.9, 2015.
Wittorf, L., Roger, F., Alsterberg, C., Gamfeldt, L., Hulth, S., Sundback,
K., Jones, C. M., and Hallin, S.: Habitat diversity and type govern potential
nitrogen loss by denitrification in coastal sediments and differences in
ecosystem-level diversities of disparate N2O reducing communities, FEMS
Microbiol. Ecol. 96, 1–9, https://doi.org/10.1093/femsec/fiaa091, 2020.
Wrage, N., Velthof, G. L., Van Beusichem, M. L., and Oenema, O.: Role of
nitrifier denitrification in the production of nitrous oxide, Soil Biol.
Biochem. 33, 1723–1732, https://doi.org/10.1016/S0038-0717(01)00096-7, 2001.
Wu, J., Chen, N., Hong, H., Lu, T., Wang, L., and Chen, Z.: Direct
measurement of dissolved N2 and denitrification along a subtropical
river-estuary gradient, China. Mar. Pollut. Bull., 66, 125–134,
https://doi.org/10.1016/j.marpolbul.2012.10.020, 2013.
Yamagishi, H., Westley, M. B., Popp, B. N., Toyoda, S., Yoshida, N.,
Watanabe, S., Koba, K., and Yamanaka, Y.: Role of nitrification and
denitrification on the nitrous oxide cycle in the eastern tropical North
Pacific and Gulf of California, J. Geophys. Res., 112, 1–15,
https://doi.org/10.1029/2006JG000227, 2007.
Yan, W., Yang, L., Wang, F., Wang, J., and Ma, P.: Riverine N2O
concentrations, exports to estuary and emissions to atmosphere from the
Changjiang River in response to increasing nitrogen loads, Global
Biogeochem. Cy., 26, GB4006, https://doi.org/10.1029/2010GB003984, 2012.
Yan, X., Wan, X. S., Liu, L., Xu, M. N., Tan, E., Zheng, Z., Zou, W., Tian,
L., Li, D. W., Trull, T. W., and Kao, S. J.: Biogeochemical dynamics in a
eutrophic tidal estuary revealed by isotopic compositions of multiple
nitrogen species, J. Geophys. Res.-Biogeo., 124,
1849–1864, https://doi.org/10.1029/2018JG004959, 2019.
Yan, X., Zhai, W., Hong, H., Li, Y., and Guo, W.:
Distribution, fluxes and decadal changes of nutrients in the Jiulong River
Estuary, Southwest Taiwan Strait, Chinese Sci. Bull. 57, 2307–2318,
https://doi.org/10.1007/s11434-012-5084-4, 2012.
Yao, Y., Tian, H., Shi, H., Pan, S., Xu, R., Pan, N., and Canadell, J. G.:
Increased global nitrous oxide emissions from streams and rivers in the
Anthropocene, Nat. Clim. Change, 10, 138–142,
https://doi.org/10.1038/s41558-019-0665-8, 2020.
Yoon, S., Nissen, S., Park, D., Sanford, R. A., and Löffler, F. E.: Nitrous oxide reduction kinetics distinguish bacteria harboring clade I versus clade II NosZ, Appl. Environ. Microb., 82, 3793–3800, 2016.
Zhan, L., Chen, L., Zhang, J., and Zheng, A.: Distribution of N2O in the Jiulongjiang River Estuary and estimation of its air-sea flux during winter, Journal of Oceanography in Taiwan Strait, 30, 189–195, https://doi.org/10.3969/J.ISSN.1000-8160.2011.02.006, 2011. (in Chinese).
Zhang, G., Zhang, J., Ren, J., Li, J., and Liu, S.: Distributions and
sea-to-air fluxes of methane and nitrous oxide in the North East China Sea
in summer, Mar. Chem., 110, 42–55, https://doi.org/10.1016/j.marchem.2008.02.005,
2008.
Zhang, G., Zhang, J., Liu, S., Ren, J., and Zhao, Y.: Nitrous
oxide in the Changjiang (Yangtze River) Estuary and its adjacent marine
area: Riverine input, sediment release and atmospheric fluxes,
Biogeosciences, 7, 3505–3516, https://doi.org/10.5194/bg-7-3505-2010, 2010.
Zhang, J.: Biogeochemistry of Chinese estuarine and coastal waters:
nutrients, trace metals and biomarkers, J. Mater. Cycl. Waste Manag.,
3, 65–76, https://doi.org/10.1007/s10113-001-0039-3, 2002.
Zhang, Y., Xie, X., Jiao, N., Hsiao, S. S. Y., and Kao, S. J.: Diversity and
distribution of amoA-type nitrifying and nirS-type denitrifying microbial
communities in the Yangtze River estuary, Biogeosciences, 11, 2131–2145,
https://doi.org/10.5194/bg-11-2131-2014, 2014.
Zhao, S., Wang, Q., Zhou, J., Yuan, D., and Zhu, G.: Linking abundance and
community of microbial N2O-producers and N2O-reducers with
enzymatic N2O production potential in a riparian zone, Sci. Total
Environ., 642, 1090–1099, https://doi.org/10.1016/J.SCITOTENV.2018.06.110, 2018.
Zheng, Z. Z., Wan, X., Xu, M. N., Hsiao, S. S. Y., Zhang, Y., Zheng, L. W.,
Wu, Y., Zou, W., and Kao, S. J.: Effects of temperature and particles on
nitrification in a eutrophic coastal bay in southern China, J. Geophys. Res.-Biogeo., 122, 2325–2337, https://doi.org/10.1002/2017JG003871, 2017.
Zhu, Z. Y., Zhang, J., Wu, Y., Zhang, Y. Y., Lin, J., and Liu, S. M.:
Hypoxia off the Changjiang (Yangtze River) Estuary: Oxygen depletion and
organic matter decomposition, Mar. Chem., 125, 108–116,
https://doi.org/10.1016/j.marchem.2011.03.005, 2011.
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.
This study revealed the distinct distribution patterns of six key microbial functional genes and...
Altmetrics
Final-revised paper
Preprint