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
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
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
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
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
Preeyaporn Pornkulwat, Eakalak Khan, Sorawit Powtongsook, Wuttichai Mhuantong, Chamorn Chawengkijwanich, Tawan Limpiyakorn
Summary: This study comprehensively investigated the impacts of ammonia and salinity on culturing nitrifying microorganisms and successfully formulated nitrifying cultures for different recirculating aquaculture system (RAS) types. The findings suggest that cultures prepared at low ammonia loading rates are most suitable for various RAS types, while cultures prepared at high ammonia loading rates are dominated by nitrifying microorganisms with low substrate affinity.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Ecology
K. Scarlett, S. Denman, D. R. Clark, J. Forster, E. Vanguelova, N. Brown, C. Whitby
Summary: The health of oak trees is influenced by the abundance of ammonia-oxidizing bacteria (AOB) in the soil, with a positive correlation between AOB abundance and soil pH. In contrast, there is no clear relationship between the abundance of archaea (AOA) and tree health. The ratio of soil carbon to nitrogen (C:N) is a key factor influencing denitrifier abundance, with correlations with AOB regardless of tree health.
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
Microbiology
Jonathan Rodriguez, Seemanti Chakrabarti, Eunkyung Choi, Nisreen Shehadeh, Samantha Sierra-Martinez, Jun Zhao, Willm Martens-Habbena
Summary: The discovery of ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing (comammox) bacteria in terrestrial ecosystems highlights their important role in nitrification. A nutrient-limited enrichment strategy was found to favor the growth of comammox bacteria with high affinity and yield. Direct enrichment from soil and nutrient-limited sub-cultivation consistently yielded high enrichments of Nitrosocosmicus-affiliated AOA associated with multiple canonical nitrite-oxidizing Nitrospira strains.
FRONTIERS IN MICROBIOLOGY
(2022)
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
Biotechnology & Applied Microbiology
Elizabeth French, Jessica A. Kozlowski, Annette Bollmann
Summary: The study found that ammonia-oxidizing archaea are more abundant in systems with low ammonium availabilities, while ammonia-oxidizing bacteria are more abundant when ammonium availability increases. Population dynamics of ammonia oxidizers may shift in response to changes in ammonium concentrations.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Environmental Sciences
Hang Ding, Mingzhi Zhou, Yuchun Wang, Mingming Hu, Jie Wen, Shanze Li, Yufei Bao, Jianwei Zhao
Summary: This study investigated the vertical niche differentiation of CMX Nitrospira bacteria (NB) in the soils of different water-level fluctuation zones in the Three Gorges Reservoir region. The results showed that the abundance and diversity of CMX NB varied with different zones and depths. Total nitrogen and total carbon were found to have significant effects on the community structure of CMX NB, and the artificial restoration of the zones also influenced its niche differentiation.
ENVIRONMENTAL SCIENCES EUROPE
(2022)
Article
Soil Science
Zhen Zhen, Gaoyang Li, Yijie Chen, Ting Wei, Huijun Li, Fengcheng Huang, Yongxiang Huang, Lei Ren, Yanqiu Liang, Dayi Zhang, Zhong Lin, Zhe Li
Summary: Plantations of saline-alkali tolerant rice in coastal areas are proposed to improve rice yield and ensure food security. This study investigated the effects of saline-alkali tolerant rice cultivation on the nitrification process in coastal solonchaks. The results showed that the abundance and nitrification rates of AOA and AOB decreased with increasing salinity, but increased significantly in the rice rhizosphere. Saline-alkali tolerant rice cultivation enhanced the nitrification process of the soil by increasing the nitrification contribution of AOB.
APPLIED SOIL ECOLOGY
(2023)
Article
Environmental Sciences
Xi Zhang, Ying Jiao, Bingxue Wang, Xintong Xu, Yubing Dong, Zhengqin Xiong
Summary: Soil nitrification, driven by ammonia-oxidizing microorganisms, is a crucial source of nitrous oxide (N2O) and nitric oxide (NO). Biochar amendment and climate warming can regulate soil nitrification, but their effects on different aged biochars and temperature combinations remain unclear.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
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
Ecology
Colin T. Bates, Arthur Escalas, Jialiang Kuang, Lauren Hale, Yuan Wang, Don Herman, Erin E. Nuccio, Xiaoling Wan, Amrita Bhattacharyya, Ying Fu, Renmao Tian, Gangsheng Wang, Daliang Ning, Yunfeng Yang, Liyou Wu, Jennifer Pett-Ridge, Malay Saha, Kelly Craven, Eoin L. Brodie, Mary Firestone, Jizhong Zhou
Summary: A study conducted in southern Oklahoma, USA, analyzed the impacts of cultivating Switchgrass on soil greenhouse gases, chemistry, and microbial communities over 17 months. Results showed significant changes in soil carbon stocks and greenhouse gas fluxes, particularly on highly degraded lands.
Article
Ecology
Man-Young Jung, Christopher J. Sedlacek, K. Dimitri Kits, Anna J. Mueller, Sung-Keun Rhee, Linda Hink, Graeme W. Nicol, Barbara Bayer, Laura Lehtovirta-Morley, Chloe Wright, Jose R. de la Torre, Craig W. Herbold, Petra Pjevac, Holger Daims, Michael Wagner
Summary: This study characterized the ammonia oxidation kinetic properties of 12 AOA, finding that Nitrosocosmicus species have the lowest affinity for ammonia and total ammonium among all characterized AOA. The substrate affinity of ammonia oxidizers is correlated with their cell surface area to volume ratios, and ammonia-not ammonium-is the substrate for the ammonia monooxygenase enzyme of AOA and comammox, which is similar to AOB.
Correction
Multidisciplinary Sciences
Bram W. Stone, Junhui Li, Benjamin J. Koch, Steven J. Blazewicz, Paul Dijkstra, Michaela Hayer, Kirsten S. Hofmockel, Xiao-Jun Allen Liu, Rebecca L. Mau, Ember M. Morrissey, Jennifer Pett-Ridge, Egbert Schwartz, Bruce A. Hungate
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Bram W. Stone, Junhui Li, Benjamin J. Koch, Steven J. Blazewicz, Paul Dijkstra, Michaela Hayer, Kirsten S. Hofmockel, Xiao-Jun Allen Liu, Rebecca L. Mau, Ember M. Morrissey, Jennifer Pett-Ridge, Egbert Schwartz, Bruce A. Hungate
Summary: The fate of soil carbon depends on microbial processes, and different microbial taxa have individualistic effects on carbon fluxes. Nutrient amendment diminishes bacterial functional diversity, consolidating carbon flow through fewer bacterial taxa. Mapping carbon flow through different microbial taxa is crucial in developing taxon-sensitive soil carbon models.
NATURE COMMUNICATIONS
(2021)
Article
Environmental Sciences
Eric W. Slessarev, Oliver A. Chadwick, Noah W. Sokol, Erin E. Nuccio, Jennifer Pett-Ridge
Summary: This study shows that rock weathering can influence the abundance of poorly crystalline minerals and organic carbon in soil, but this influence is limited by weathering rates and climatic conditions in geographic regions. The geological source in soil has a certain impact on organic carbon storage.
Review
Environmental Sciences
Peter M. Kopittke, Asmeret Asefaw Berhe, Yolima Carrillo, Timothy R. Cavagnaro, Deli Chen, Qing-Lin Chen, Mercedes Roman Dobarco, Feike A. Dijkstra, Damien J. Field, Michael J. Grundy, Ji-Zheng He, Frances C. Hoyle, Ingrid Kogel-Knabner, Shu Kee Lam, Petra Marschner, Cristina Martinez, Alex B. McBratney, Eve McDonald-Madden, Neal W. Menzies, Luke M. Mosley, Carsten W. Mueller, Daniel V. Murphy, Uffe N. Nielsen, Anthony G. O'Donnell, Elise Pendall, Jennifer Pett-Ridge, Cornelia Rumpel, Iain M. Young, Budiman Minasny
Summary: Healthy soils play a crucial role in planetary survivability, providing not only calories but also other essential functions. However, intensive agriculture is rapidly degrading soils and diminishing their capacity to deliver vital functions, highlighting the need to focus on the multiple functions of soils for long-term human welfare and the survivability of the planet.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2022)
Article
Engineering, Environmental
Janghyuk Lee, Rachel Hestrin, Erin E. Nuccio, Keith D. Morrison, Christina E. Ramon, Ty J. Samo, Jennifer Pett-Ridge, Sonny S. Ly, Ted A. Laurence, Peter K. Weber
Summary: This study developed a label-free multiphoton nonlinear imaging approach to visualize microorganisms in soil and roots, providing contrast and chemical information. The method successfully imaged fungi and bacteria structures in the soil and roots, holding significant promise for soil science research.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Biodiversity Conservation
Craig R. See, Adrienne B. Keller, Sarah E. Hobbie, Peter G. Kennedy, Peter K. Weber, Jennifer Pett-Ridge
Summary: This article questions the assumption that microbial redistribution of carbon into non-rhizosphere soils is minimal, arguing that fungal redistribution plays a significant role. The analysis demonstrates that the omission of the hyphosphere overlooks key mechanisms for mineral-associated organic matter formation in bulk soils.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Biodiversity Conservation
Alicia M. Purcell, Michaela Hayer, Benjamin J. Koch, Rebecca L. Mau, Steven J. Blazewicz, Paul Dijkstra, Michelle C. Mack, Jane C. Marks, Ember M. Morrissey, Jennifer Pett-Ridge, Rachel L. Rubin, Egbert Schwartz, Natasja C. van Gestel, Bruce A. Hungate
Summary: Soil carbon storage is crucial for global climate, with microbial growth rates sensitive to temperature, showing diverse responses among taxa. Long-term experimental warming reduced soil microbial growth rates, with varied response magnitude among taxa but consistent direction of reduced growth. The study suggests that aggregate microbial responses may be adequate for climate modeling, and highlights the importance of indirect effects of warming on soil microbes.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Soil Science
Christina Fossum, Katerina Y. Estera-Molina, Mengting Yuan, Donald J. Herman, Ilexis Chu-Jacoby, Peter S. Nico, Keith D. Morrison, Jennifer Pett-Ridge, Mary K. Firestone
Summary: Plant-fixed carbon moves into soil within days and becomes associated with the mineral fraction of the soil within weeks. While most plant carbon cycles rapidly within a year, a significant proportion persists in the soil for longer than 2 years. Our 2-year field study reveals the rapid movement of plant carbon into the heavy fraction of soil, followed by the evolution of the chemical forms of organic carbon in the heavy fraction.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Correction
Microbiology
Anneliek M. ter Horst, Christian Santos-Medellin, Jackson W. Sorensen, Laura A. Zinke, Rachel M. Wilson, Eric R. Johnston, Gareth Trubl, Jennifer Pett-Ridge, Steven J. Blazewicz, Paul J. Hanson, Jeffrey P. Chanton, Christopher W. Schadt, Joel E. Kostka, Joanne B. Emerson
Article
Soil Science
Sungeun Lee, Jackson W. Sorensen, Robin L. Walker, Joanne B. Emerson, Graeme W. Nicol, Christina Hazard
Summary: The pH of soil significantly influences viral communities, with 99% of viral operational taxonomic units restricted to specific pH levels. Analysis of viromes from various soil systems showed that viral clusters from acidic and neutral pH soils were more associated with those from specific pH levels, indicating that soil pH plays a key role in structuring viral communities locally and globally.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Editorial Material
Microbiology
James Prosser
Summary: This article introduces a series of articles on important questions, hypotheses, and theories in microbial ecology. It highlights the significance of asking questions and proposing hypotheses as scientists, and emphasizes the importance of scientific aims. The current global issues surrounding climate crisis, pandemics, and antibiotic resistance underscore the urgent need for a deeper understanding of microbial ecology and the importance of effectively communicating the definition, power, and limitations of science to a wider audience.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Sungeun Lee, Ella T. Sieradzki, Graeme W. Nicol, Christina Hazard
Summary: This study investigated the characteristics of viruses infecting autotrophic AOA using DNA stable-isotope probing and metagenomic analysis. The findings suggest that virus infection of AOA may be a common process during nitrification, with the potential to influence host physiology and activity.
