Article
Environmental Sciences
Jing Chen, Shuo Zhao, Yating Gan, Jing Wu, Jingcheng Dai, Dazhong Yan
Summary: DDT contamination inhibits soil ammonia oxidation, but it recovers over time. DDT affects the diversity and community composition of ammonia-oxidizing archaea, but has no significant effect on ammonia-oxidizing bacteria.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biotechnology & Applied Microbiology
H. M. Tang, X. P. Xiao, C. Li, L. H. Shi, K. K. Cheng, L. Wen, W. Y. Li, K. Wang
Summary: The study found that abundance of AOB and AOA increased under organic N conditions, and different short-term organic manure N input treatments altered the diversity of soil AOB and AOA communities. Soil microbial community and specific N-utilizing microbial groups were significantly affected by practices of organic manure N input.
JOURNAL OF APPLIED MICROBIOLOGY
(2021)
Article
Biodiversity Conservation
Weifang Hu, Mianrun Chen, Xue Lan, Guoliang Li, Bin Wang, Dong Yao Sun, Xianbiao Lin
Summary: This study found significant shifts in potential ammonia oxidation rates (PARs) and gene abundances of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) along different salinity gradients. The PARs were higher under high salinity conditions, and the AOB gene abundance was greater than AOA under moderate and high salinity. This has important implications for nitrogen cycling in estuarine sediments.
ECOLOGICAL INDICATORS
(2022)
Article
Biodiversity Conservation
Tong-tong Liu, Hong Yang
Summary: Research on ammonia-oxidizing microorganisms (AOM) in Lake Taihu sediment revealed that although the total abundance of ammonia-oxidizing bacteria (AOB) surpassed that of ammonia-oxidizing archaea (AOA), active AOA showed a closer correlation with the potential nitrification rate. The active transcription abundance of AOM generally decreased with increasing depth, especially for AOA, while the total abundance of AOM varied little. The community structures of AOA and AOB changed significantly with depth, with Group I.1a and Nitrosomonas as predominant clusters, respectively.
ECOLOGICAL INDICATORS
(2021)
Article
Microbiology
Anna N. Rasmussen, Christopher A. Francis
Summary: Ammonia-oxidizing archaea (AOA) play a crucial role in the transformation of ammonia in aquatic environments worldwide, especially in nutrient-rich coastal and estuarine waters like San Francisco Bay. A study found a significant AOA bloom in the southern part of San Francisco Bay, which coincided with high nitrite concentrations. Analysis of AOA genomes revealed their streamlined structure and specific genomic characteristics. These findings provide important insights into the understanding of AOA blooms.
Article
Environmental Sciences
Shishi He, Zhirong Zhao, Zhichao Tian, Chi Xu, Yuan Liu, Da He, Yinghui Zhang, Maosheng Zheng
Summary: This study analyzed activated sludge samples from municipal and industrial wastewater treatment plants and found that comammox bacteria were more abundant than ammonia-oxidizing bacteria and ammonia-oxidizing archaea in municipal plants, while this trend did not hold true for industrial plants. Furthermore, a higher diversity of comammox bacteria was found in municipal samples. This study provides important insights into the abundance and diversity of comammox bacteria in municipal and refinery wastewater treatment systems.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Agronomy
Xingjia He, Sen Li, Fengzhi Wu
Summary: Intercropping has a significant impact on soil properties and microbial communities, with different intercropping systems affecting ammonia-oxidizing microorganisms differently in different seasons. Soil physicochemical state, PNR, AOA and AOB communities were significantly altered by intercropping, with seasonal variation playing a greater role in shaping the community structures.
Article
Environmental Sciences
Xia Jia, Yunfeng Gao, Xiaodi Li, Yonghua Zhao, Lu Wang, Chunyan Zhang
Summary: This study investigated the impacts of elevated CO2 and cadmium levels on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings. The results showed that elevated CO2 combined with Cd pollution generally stimulated nitrification enzyme activities and influenced bacterial community structures.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Chemistry, Multidisciplinary
Limin Fan, Liping Qiu, Gengdong Hu, Chao Song, Shunlong Meng, Dandan Li, Jiazhang Chen
Summary: This study investigated ammonia-oxidizing bacterial communities in water and surface sediments of three tilapia ponds and found that the abundance and diversity of these bacterial communities were influenced by monthly variations in the water and sediment differences among the ponds. The main factors affecting the bacterial communities in the water were total nitrogen, nitrate, total phosphorus, and sulphate, while total phosphorus was the main influencing factor in the sediments.
APPLIED SCIENCES-BASEL
(2022)
Article
Soil Science
Shishi He, Yuanwei Li, Hongbin Mu, Zhirong Zhao, Jiawen Wang, Shufeng Liu, Zhenli Sun, Maosheng Zheng
Summary: This study highlights the important role of local ammonium concentration in affecting the ecological niche differentiation of comammox and canonical ammonia-oxidizing prokaryotes. The results show growth differences between CAOB and AOA, with CAOB favoring oligotrophic environments and being more tolerant to a broader range of ammonium concentrations.
APPLIED SOIL ECOLOGY
(2021)
Article
Soil Science
Haiyang Liu, Hangwei Hu, Xing Huang, Tida Ge, Yongfu Li, Zhenke Zhu, Xingmei Liu, Wenfeng Tan, Zhongjun Jia, Hongjie Di, Jianming Xu, Yong Li
Summary: Chemoautotrophic canonical ammonia-oxidizers play a significant role in autotrophic nitrification during the mineralization of organic substances with low C/N ratios in paddy soils, as shown by N-15 tracing and DNA-SIP techniques.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Soil Science
Yongxin Lin, Hang-Wei Hu, Guiping Ye, Jianbo Fan, Weixin Ding, Zi-Yang He, Yong Zheng, Ji-Zheng He
Summary: The meta-analysis of laboratory incubation studies with 1-octyne as the nitrification inhibitor shows that AOB play a more dominant role in soil nitrification in cropland than in wetland soils, indicating a major role of AOB in acidic soil nitrification. Moreover, the reduction of nitrification rate by 1-octyne is greater in soils incubated in slurry and with nitrogen additions, suggesting AOB's importance in nitrification in global acidic soils.
Article
Plant Sciences
Li Chen, Rong Bo Zheng, Jun Qin Gao, Ming Hua Song, Xue Lian Guo
Summary: The study found that yak excreta application significantly affects the composition of ammonia-oxidizing bacteria communities and nitrification response in meadow marsh soil and marsh soil. Additionally, urease and catalase activities play important roles in influencing the structure of AOB communities.
JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION
(2021)
Article
Agricultural Engineering
Jun-Gyu Park, Beom Lee, Tae-Young Heo, A-In Cheon, Hang-Bae Jun
Summary: This study analyzed the community structure and function of nitrification microorganisms in nitrogen removal processes, revealing higher quantities of ammonia-oxidizing archaea in the oxidation ditch compared to A2/O, with complete ammonia oxidizers only found in the former. The longer retention times in the oxidation ditch process were more effective in promoting the proliferation of novel nitrifying microorganisms and nitrogen removal.
BIORESOURCE TECHNOLOGY
(2021)
Article
Microbiology
Di Wu, Xiao-Ling Wang, Xi-Xia Zhu, Hai-Hong Wang, Wei Liu, Lin Qi, Peng Song, Ming-Ming Zhang, Wei Zhao
Summary: The coexistence of ammonia-oxidizing bacterial strain in rhizosphere soil of Italian ryegrass increases its regrowth by regulating the delivery and concentration of cytokinins.
Article
Multidisciplinary Sciences
Simon Ramondenc, Damien Eveillard, Lionel Guidi, Fabien Lombard, Benoit Delahaye
SCIENTIFIC REPORTS
(2020)
Article
Chemistry, Medicinal
Alison E. Murray, Nicole E. Avalon, Lucas Bishop, Karen W. Davenport, Erwan Delage, Armand E. K. Dichosa, Damien Eveillard, Mary L. Higham, Sofia Kokkaliari, Chien-Chi Lo, Christian S. Riesenfeld, Ryan M. Young, Patrick S. G. Chain, Bill J. Baker
Article
Microbiology
Ulysse Guyet, Ngoc A Nguyen, Hugo Dore, Julie Haguait, Justine Pittera, Mael Conan, Morgane Ratin, Erwan Corre, Gildas Le Corguille, Loraine Brillet-Gueguen, Mark Hoebeke, Christophe Six, Claudia Steglich, Anne Siegel, Damien Eveillard, Frederic Partensky, Laurence Garczarek
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Microbiology
Alison E. Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kaempfer, Konstantinos T. Konstantinidis, Christopher E. Lane, R. Thane Papke, Donovan H. Parks, Ramon Rossello-Mora, Matthew B. Stott, Iain C. Sutcliffe, J. Cameron Thrash, Stephanus N. Venter, William B. Whitman, Silvia G. Acinas, Rudolf Amann, Karthik Anantharaman, Jean Armengaud, Brett J. Baker, Roman A. Barco, Helge B. Bode, Eric S. Boyd, Carrie L. Brady, Paul Carini, Patrick S. G. Chain, Daniel R. Colman, Kristen M. DeAngelis, Maria Asuncion de los Rios, Paulina Estrada-de los Santos, Christopher A. Dunlap, Jonathan A. Eisen, David Emerson, Thijs J. G. Ettema, Damien Eveillard, Peter R. Girguis, Ute Hentschel, James T. Hollibaugh, Laura A. Hug, William P. Inskeep, Elena P. Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G. Lloyd, Frank E. Lffler, Thulani P. Makhalanyane, Duane P. Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedros-Alio, Alexander J. Probst, Theo H. M. Smits, Andrew D. Steen, Emma T. Steenkamp, Anja Spang, Frank J. Stewart, James M. Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Brian P. Hedlund, Anna-Louise Reysenbach
NATURE MICROBIOLOGY
(2020)
Article
Environmental Sciences
Clarisse Lemonnier, Morgan Perennou, Damien Eveillard, Antonio Fernandez-Guerra, Aude Leynaert, Louis Marie, Hilary G. Morrison, Laurent Memery, Christine Paillard, Lois Maignien
FRONTIERS IN MARINE SCIENCE
(2020)
Article
Microbiology
Hugo Dore, Gregory K. Farrant, Ulysse Guyet, Julie Haguait, Florian Humily, Morgane Ratin, Frances D. Pitt, Martin Ostrowski, Christophe Six, Loraine Brillet-Gueguen, Mark Hoebeke, Antoine Bisch, Gildas Le Corguille, Erwan Corre, Karine Labadie, Jean-Marc Aury, Patrick Wincker, Dong Han Choi, Jae Hoon Noh, Damien Eveillard, David J. Scanlan, Frederic Partensky, Laurence Garczarek
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Seaver Wang, Weiyi Tang, Erwan Delage, Scott Gifford, Hannah Whitby, Aridane G. Gonzalez, Damien Eveillard, Helene Planquette, Nicolas Cassar
Summary: The variation in microbial cycling of nutrients and carbon in the ocean is found to be an emergent property of complex planktonic communities, with a focus on the diversity and distribution of nitrogen fixing marine diazotrophs. Research shows a negative relationship between eukaryotic diversity and nitrogen fixation, with high rates of nitrogen fixation occurring at sites with high abundances of mixotrophic stramenopiles.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Simon M. Dittami, Enrique Arboleda, Jean-Christophe Auguet, Arite Bigalke, Enora Briand, Paco Cardenas, Ulisse Cardini, Johan Decelle, Aschwin H. Engelen, Damien Eveillard, Claire M. M. Gachoni, Sarah M. Griffiths, Tilmann Harder, Ehsan Kayal, Elena Kazamia, Francois H. Lathier, Monica Medina, Ezequiel M. Marzinelli, Teresa Maria Morganti, Laura Nunez Pons, Soizic Prado, Jose Pintado, Mahasweta Saha, Marc-Andre selosse, Derek Skillings, Willem Stock, Shinichi Sunagawa, Eve Toulza, Alexey Vorobev, Catherine Leblanc, Fabrice Not
Summary: Host-microbe interactions are crucial in marine ecosystems, and the holobiont concept suggests that a host and its associated microbiota should be studied together to understand their biology, ecology, and evolution. Deeper understanding of these complex systems requires further technological and conceptual advances.
Article
Multidisciplinary Sciences
Yajuan Lin, Carly Moreno, Adrian Marchetti, Hugh Ducklow, Oscar Schofield, Erwan Delage, Michael Meredith, Zuchuan Li, Damien Eveillard, Samuel Chaffron, Nicolas Cassar
Summary: This study investigates how interannual variability in sea-ice conditions impacts biodiversity and biological carbon fluxes in the Western Antarctic Peninsula using a 5-year DNA metabarcoding dataset. The results indicate that sea-ice extent is a dominant factor influencing eukaryotic plankton community composition, biodiversity, and net community production, with species richness and evenness decreasing with an increase in sea surface temperature. The study concludes that eukaryotic plankton diversity and carbon cycling in the Western Antarctic Peninsula are strongly linked to sea-ice conditions.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, Charlotte Nef, Mathieu Ardyna, Ahmed A. Zayed, Pedro C. Junger, Pierre E. Galand, Connie Lovejoy, Alison E. Murray, Hugo Sarmento, Silvia G. Acinas, Marcel Babin, Daniele Iudicone, Olivier Jaillon, Eric Karsenti, Patrick Wincker, Lee Karp-Boss, Matthew B. Sullivan, Chris Bowler, Colomban de Vargas, Damien Eveillard
Summary: Using Tara Oceans sampling, a global ocean cross-domain plankton co-occurrence network was identified and niche modeling was used to assess its vulnerabilities to environmental change. The results showed that the plankton interactome self-organized latitudinally into marine biomes and was more connected poleward. These findings provide baseline approaches to assess community structure and organismal interactions under climate scenarios, while identifying plausible plankton bioindicators for monitoring climate change in the ocean.
Article
Ecology
Antoine Regimbeau, Marko Budinich, Abdelhalim Larhlimi, Juan Jose Pierella Karlusich, Olivier Aumont, Laurent Memery, Chris Bowler, Damien Eveillard
Summary: This study proposes a new conceptual niche called metabolic niche, which resumes the whole metabolic capabilities of an organism, and explores the key genes essential for the metabolic niche through statistical analysis.
Article
Multidisciplinary Sciences
Simon A. Schroeter, Damien Eveillard, Samuel Chaffron, Johanna Zoppi, Bernd Kampe, Patrick Lohmann, Nico Jehmlich, Martin von Bergen, Carlos Sanchez-Arcos, Georg Pohnert, Martin Taubert, Kirsten Kuesel, Gerd Gleixner
Summary: The study reveals that functions within decomposer communities are redundantly distributed under different types of litter sources, but their relative expressions are rapidly optimized to address specific litter properties. Furthermore, the decomposer community may be influenced by DOM containing natural antibiotics, leading to specialization towards specific litter sources and decomposition states.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Guillermo Dominguez-Huerta, Ahmed A. Zayed, James M. Wainaina, Jiarong Guo, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Mohamed Mohssen, Olivier Zablocki, Eric Pelletier, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Tara Oceans Coordinators, Chris Bowler, Damien Eveillard, Lionel Guidi, Eric Karsenti, Jens H. Kuhn, Hiroyuki Ogata, Patrick Wincker, Alexander Culley, Samuel Chaffron, Matthew B. Sullivan
Summary: This study reveals patterns and predictors of marine RNA virus diversity and identifies their ecological impacts on marine ecosystems. The research also highlights unexpectedly high polar ecological interactions.
Review
Microbiology
Andre Abreu, Etienne Bourgois, Adam Gristwood, Romain Trouble, Silvia G. Acinas, Peer Bork, Emmanuel Boss, Chris Bowler, Marko Budinich, Samuel Chaffron, Colomban de Vargas, Tom O. Delmont, Damien Eveillard, Lionel Guidi, Daniele Iudicone, Stephanie Kandels, Helene Morlon, Fabien Lombard, Rainer Pepperkok, Juan Jose Pierella Karlusich, Gwenael Piganeau, Antoine Regimbeau, Guilhem Sommeria-Klein, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker, Olivier Zablocki, Detlev Arendt, Josipa Bilic, Robert Finn, Edith Heard, Brendan Rouse, Jessica Vamathevan, Raffaella Casotti, Ibon Cancio, Michael Cunliffe, Anne Emmanuelle Kervella, Wiebe H. C. F. Kooistra, Matthias Obst, Nicolas Pade, Deborah M. Power, Ioulia Santi, Tatiana Margo Tsagaraki, Jan Vanaverbeke
Summary: Studying the ocean microbiome is crucial for ocean governance, addressing climate change and pollution, and achieving multiple Sustainable Development Goals. Microbes play essential roles in marine ecology, participating in nutrient cycles, carbon dioxide removal, and supporting marine food webs. Technological advances have allowed for a better understanding of the taxonomic and functional diversity of the global ocean microbiome. Understanding and protecting the ocean microbiome can contribute to addressing environmental and societal challenges.
NATURE MICROBIOLOGY
(2022)
Correction
Microbiology
Alison E. Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kampfer, Konstantinos T. Konstantinidis, Christopher E. Lane, R. Thane Papke, Donovan H. Parks, Ramon Rossello-Mora, Matthew B. Stott, Iain C. Sutcliffe, J. Cameron Thrash, Stephanus N. Venter, William B. Whitman, Silvia G. Acinas, Rudolf I. Amann, Karthik Anantharaman, Jean Armengaud, Brett J. Baker, Roman A. Barco, Helge B. Bode, Eric S. Boyd, Carrie L. Brady, Paul Carini, Patrick S. G. Chain, Daniel R. Colman, Kristen M. DeAngelis, Maria Asuncion de los Rios, Paulina de los Santos, Christopher A. Dunlap, Jonathan A. Eisen, David Emerson, Thijs J. G. Ettema, Damien Eveillard, Peter R. Girguis, Ute Hentschel, James T. Hollibaugh, Laura A. Hug, William P. Inskeep, Elena P. Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G. Lloyd, Frank E. Loffler, Thulani P. Makhalanyane, Duane P. Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedros-Alio, Alexander J. Probst, Theo H. M. Smits, Andrew D. Steen, Emma T. Steenkamp, Anja Spang, Frank J. Stewart, James M. Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Pablo Yarza, Brian P. Hedlund, Anna-Louise Reysenbach
Summary: An amended version of this paper has been published and is accessible via a link at the top of the page.
NATURE MICROBIOLOGY
(2021)