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
Agronomy
Lei Cui, Dongpo Li, Zhijie Wu, Yan Xue, Yuchao Song, Furong Xiao, Lili Zhang, Ping Gong, Ke Zhang
Summary: The application of nitrification inhibitors (NIs) can effectively reduce nitrogen (N) loss by delaying the nitrification process through influencing the growth of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in different soils.
Article
Soil Science
Sandipan Samaddar, Jaak Truu, Poulami Chatterjee, Kristjan Oopkaup, Marika Truu, Kiyoon Kim, Sookjin Kim, Radomir Schmidt, Aritra Roy Choudhury, Jeongyun Choi, Tongmin Sa
Summary: This study found that long-term application of inorganic nitrogen fertilizers selectively enriched certain AOA lineages, with inorganic nitrogen favoring an increase in abundance of Nitrososphaera lineage. The distinct response of two AOA lineages to different nitrogen management practices further supported the concept of habitat partitioning in paddy soil ecosystems.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2021)
Article
Biodiversity Conservation
Di Liang, G. Philip Robertson
Summary: The long-term contribution of nitrification to nitrous oxide (N2O) emissions as well as the proportion of N2O derived from nitrification in different ecosystems remains uncertain, with actual values likely to be lower than estimated due to low N2O yields in cultured nitrifiers and competing sinks for available NH4+.
GLOBAL CHANGE BIOLOGY
(2021)
Article
Microbiology
Hao Liu, Peng Zhou, Shunyan Cheung, Yanhong Lu, Hongbin Liu, Hongmei Jing
Summary: Coastal upwelling affects temperature, salinity and inorganic nutrients in the water column, leading to changes in microbial populations and their metabolic activities. This study investigated the impact of eastern Hainan upwelling on ammonia-oxidizing archaea (AOA) through genetic analysis and measurement of ammonia oxidation rate. The findings suggest that coastal upwelling significantly influences AOA community and ammonia oxidation rate, and should be considered in future assessment of global nitrogen budgets and biogeochemical nitrogen cycles.
Article
Soil Science
Konrad Egenolf, Philipp Schad, Ashly Arevalo, Daniel Villegas, Jacobo Arango, Hannes Karwat, Georg Cadisch, Frank Rasche
Summary: Brachiaria humidicola (syn. Urochloa humidicola) has been recognized for controlling soil nitrification through releasing nitrification inhibitors (NI), termed as biological nitrification inhibition (BNI), which can reduce net nitrification rates by 50 to 85%. Adjustment of soil pH and microbial background has little influence on BNI performance, while the decrease in net nitrification rates mainly depends on microbial N immobilization and efficient plant N uptake.
BIOLOGY AND FERTILITY OF SOILS
(2022)
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
Engineering, Environmental
Helin Wang, Ping Li, Xiaohan Liu, Jing Zhang, Lisa Y. Stein, Ji-Dong Gu
Summary: This study investigated the influence of reactive oxygen species (ROS) on ammonia-oxidizing microorganisms (AOMs) in redox-fluctuating aquifers through field investigation and in-lab verification. The results showed that ROS played an important role in regulating AOMs, with ammonia-oxidizing archaea dominating in aquifers with lower ROS levels, and ammonia-oxidizing bacteria and heterotrophic nitrifying aerobic bacteria predominating in areas with higher ROS levels.
Article
Agronomy
Yubing Dong, Xintong Xu, Junqian Zhang, Ying Jiao, Bingxue Wang, Chenyuan Wang, Zhengqin Xiong
Summary: This study investigated the emission characteristics and relative contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and other microbial processes to nitrous oxide (N2O) production in greenhouse vegetable fields in the middle and lower reaches of the Yangtze River. The results showed that the ammonia oxidation process is the dominant contributor to N2O production, regardless of soil pH. AOA-driven N2O emission rates were consistently higher than AOB-driven rates, and both were positively correlated with soil pH.
Article
Soil Science
Ting Lan, Mengxiao Li, Xiaoqian He, Ouping Deng, Wei Zhou, Ling Luo, Guangdeng Chen, Shu Yuan, Jing Ling, Min Zeng, Xuesong Gao
Summary: An aerobic N-15 microcosmic experiment was conducted to compare the inhibitory effects of the biological nitrification inhibitor (BNI), methyl 3-(4-hydroxyphenyl) propionate (MHPP) and the synthetic nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on the gross nitrification rate and the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in contrasting soils. The results showed that the two inhibitors had different effects on nitrification rates and the response of AOB to the inhibitors was more sensitive.
BIOLOGY AND FERTILITY OF SOILS
(2022)
Article
Multidisciplinary Sciences
Ronnakrit Rattanasriampaipong, Yi Ge Zhang, Ann Pearson, Brian P. Hedlund, Shuang Zhang
Summary: Archaeal membrane lipids, specifically the GDGTs, can be used to reconstruct ancient temperatures and provide insights into the ecology and evolution of marine ammonia-oxidizing archaea (AOA). The study identified thermal and nonthermal behaviors of GDGTs, which can be used as indicators of environmental temperature. The distribution of GDGTs in AOA cultures and shallow water samples followed a temperature-dependent trend, while deep water samples showed a nonthermal behavior. Statistical analysis revealed long-term trends in GDGT-2/GDGT-3 ratios, suggesting a suppression of deep water marine AOA during greenhouse climates in the Mesozoic and early Cenozoic periods.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Soil Science
Jun Xie, Zifang Wang, Ying Wang, Shujiang Xiang, Ziyi Xiong, Ming Gao
Summary: Fertilization and soil environmental factors play a role in the niche differentiation of ammonia-oxidizing microorganisms and affect the ammonia-oxidation process. In this study, the effect of manure, chemical fertilizer, and manure combined with biochar on soil properties and the abundance, diversity, and structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the rhizosphere were investigated. The results showed that chemical fertilizer and manure combined with biochar increased the potential nitrification rate (PNR) and AOA amoA gene abundance, while manure combined with biochar decreased PNR and AOA amoA gene abundance. The population structure of AOA and AOB was influenced by pH, available phosphorus, carbon-to-nitrogen ratio, soil moisture content, nitrate nitrogen, and ammonium nitrogen in the rhizosphere. The ammonia oxidation process in the acid purple soil was dominated by AOA in the presence of chemical fertilizer and pig manure combined with rice husk biochar.
APPLIED SOIL ECOLOGY
(2023)
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
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
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
Ecology
Yong-Feng Wang, Ji-Dong Gu, Richard P. Dick, Wei Han, Hui-Xiao Yang, Huan-Qin Liao, Yi Zhou, Han Meng
Summary: Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are key players in the nitrogen cycle in a coastal ecosystem, with variations in abundance, diversity, and community structures observed across different sites. Agricultural activities appear to have an influence on the nitrifiers, particularly affecting AOB abundance and diversity in farmland areas.
Article
Biotechnology & Applied Microbiology
Yong-Hui Li, Ji-Dong Gu
Summary: Water plays a crucial role in the initiation of microbial colonization and subsequent biodeterioration processes in cultural heritage materials. The different types of water in materials, along with characteristics like porosity and pore connectivity, affect microbial growth and biodeterioration. Managing water is a fundamental strategy to prevent long-term damage to cultural heritage.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2022)
Article
Biotechnology & Applied Microbiology
Shuang Zhang, Jian Yang, Boyu Dong, Jiani Yang, Hong Pan, Weidong Wang, Lei Yan, Ji-Dong Gu
Summary: A microbial consortium BYQ enriched from a spring in the Wudalianchi volcanic area showed high-efficiency Fe(II) oxidation and leaching of PCBs. Acidithiobacillus spp. dominated the community regardless of subculturing and bioleaching conditions, and jarosite formation was observed during bioleaching.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2022)
Article
Environmental Sciences
Xinghua Ding, Wensheng Lan, Aixin Yan, Yiliang Li, Yoko Katayama, Ji-Dong Gu
Summary: The study conducted a metadata analysis on the microbial sequencing data available from NCBI database to determine the diversity, biodeterioration potential, and functionality of stone microbiomes on world cultural heritage sites under different climatic conditions. The microbial communities on stone monuments were found to be associated with climate types, with stone monuments in dry climates showing higher diversity. Functions related to photosynthesis and UV resistance were identified in different climate types. The research highlighted the diverse and self-sustaining nature of these stone-dwelling microbiomes, driven by energy metabolism and biomass accumulation, with biochemical reactions of nitrogen and sulfur cycles being predominant.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Environmental Sciences
Shanshan Meng, Tao Peng, Xiaobo Liu, Amit Pratush, Hui Wang, Tongwang Huang, Ji-Dong Gu, Zhong Hu
Summary: Mangroves serve as important reservoirs of unclassified Archaea, and the distribution and functional genes of archaeal communities involved in the nitrogen cycle were found to be influenced by total nitrogen, total carbon, and nitrate concentrations. Selective Archaea, especially Crenarchaeota and Euryarchaeota, play a major role in nitrogen cycling in mangroves, particularly in nitrification.
GEOMICROBIOLOGY JOURNAL
(2022)
Editorial Material
Ecology
Xiaobo Liu, Jin-Long Yang, Daniel Rittschof, James S. Maki, Ji-Dong Gu
Summary: Biofouling has significant impacts on the environment, economy, and society. Effective strategies for addressing biofouling should incorporate sustainability concepts and focus on disrupting attachment of organisms or developing innovative surfaces to remove fouling organisms. Other viable options, including eco-friendly antifouling chemicals, should also be considered.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Engineering, Environmental
Ling-Dong Shi, Xiyang Dong, Zongbao Liu, Yuchun Yang, Jih-Gaw Lin, Meng Li, Ji-Dong Gu, Li-Zhong Zhu, He-Ping Zhao
Summary: The diversity of both microorganisms and viruses in activated sludge of wastewater treatment plants plays a crucial role in controlling microbial dynamics and metabolisms. This study reveals the presence of unknown viral genera in activated sludge, indicating an unexplored reservoir for new viruses and viral diversity. The study also shows that viruses can enhance the performance of activated sludge by encoding auxiliary metabolic genes (AMGs) involved in biodegradation, but can also facilitate the spread of antibiotic resistance genes (ARGs) among microorganisms. Overall, this study highlights the mixed blessing of viruses in wastewater treatment plants and their impact on biochemical processes.
Article
Biochemical Research Methods
Joon-Yong Lee, Hugh D. Mitchell, Meagan C. Burnet, Ruonan Wu, Sarah C. Jenson, Eric D. Merkley, Ernesto S. Nakayasu, Carrie D. Nicora, Janet K. Jansson, Kristin E. Burnum-Johnson, Samuel H. Payne
Summary: Metaproteomics is increasingly used for high-throughput characterization of proteins in complex environments, and the creation of a sample-specific protein sequence database is crucial for accurate analysis. This study presents a de novo peptide sequencing approach to identify sample composition directly from metaproteomic data, using a deep learning model trained on diverse bacteria. The results demonstrate the potential of this method as an alternative and complementary approach to construct sample-specific protein databases, particularly in the absence of matched metagenomes.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Environmental Sciences
Ling Luo, Dahang Deng, Xin Zhao, Hairong Hu, Xinyi Li, Jidong Gu, Yan He, Gang Yang, Ouping Deng, Yinlong Xiao
Summary: This study found that nanoparticles nZVI and nZnO can promote the abundance of tetracycline resistance genes in sediment, but nZVI and bacterial communities can also reduce tetracycline resistance gene abundance when tetracycline is present. The findings are important for understanding the role of nanoparticles in promoting and reducing antibiotic resistance genes in the environment.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Biotechnology & Applied Microbiology
Jing Chen, Zhichao Zhou, Ji-Dong Gu
Summary: This study investigated the diversity and abundance of n-damo bacteria in vegetated and non-vegetated sediments of a subtropical mangrove wetland. The results showed that the seasonal changes and vegetation had significant impacts on the n-damo bacterial community. The study further revealed that NH4+ and NH4+/NO2- were important factors influencing the diversity of n-damo bacteria in mangrove wetland sediments.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2022)
Article
Multidisciplinary Sciences
Ruonan Wu, Clyde A. Smith, Garry W. Buchko, Ian K. Blaby, David Paez-Espino, Nikos C. Kyrpides, Yasuo Yoshikuni, Jason E. McDermott, Kirsten S. Hofmockel, John R. Cort, Janet K. Jansson
Summary: Metagenomics has revealed the presence of auxiliary metabolic genes (AMGs) in soil viral genomes, and this study provides evidence that these AMGs actually produce functional proteins that can metabolize chitin. The crystal structure of a soil viral AMG product, which exhibits chitosanase activity, has been determined, providing insights into substrate specificity and enzyme mechanism. These findings support the idea that soil viruses contribute auxiliary functions to their hosts.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
Janet K. Jansson, Ruonan Wu
Summary: Soil viruses play important roles in soil ecology and are influenced by climate change, which affects their diversity and ecology.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Microbiology
Ruonan Wu, Eric M. Bottos, Vincent G. Danna, James C. Stegen, Janet K. Jansson, Michelle R. Davison
Summary: Arctic permafrost thawing leads to the emergence of RNA viruses that target eukaryotic hosts and pose potential threats to humans, animals, and plants. This study identifies a diverse RNA viral community in thawed permafrost samples, showing distinct compositions compared to other habitats. The detection of potential pathogens highlights the importance of environmental reservoirs for RNA viral pathogens, particularly in the context of the ongoing COVID-19 pandemic. Understanding viral-host interactions and the ecological roles of RNA viruses in thawed permafrost is crucial.
Editorial Material
Immunology
Tingtao Chen, Ruonan Wu, Lei Cheng, Qinping Liao, Zhangran Chen
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Green & Sustainable Science & Technology
Ruonan Wu, Gareth Trubl, Neslihan Tas, Janet K. Jansson
Summary: Due to global climate change, the Arctic is presently experiencing unprecedented warming, leading to the thawing of permafrost and consequential impacts on human health and the environment. The limited understanding of microorganisms and viruses in permafrost hinders the assessment of their potential risks to humans, animals, and plants.