Review
Engineering, Environmental
Shaoyi Xu, Xiaolong Wu, Huijie Lu
Summary: This review discusses the roles of nitrogen-cycling microorganisms in wastewater treatment, focusing on often overlooked microbes that are functionally important. Advancements in molecular technologies have enabled comprehensive studies on the application and potential of these microbes in nitrogen removal processes in wastewater treatment plants.
FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING
(2021)
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
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
Environmental Sciences
Yuyin Yang, Jianfei Chen, Jennifer Pratscher, Shuguang Xie
Summary: Methanotrophs are the main consumers of methane in lake sediments and play a key role in regulating methane flux and carbon cycling. In this study, nucleic acid stable isotope probing was used to investigate the active methanotrophic microbial community in eutrophication-affected shallow lakes. The results showed that gamma-proteobacterial methanotrophs and beta-proteobacterial methanol-utilizers were involved in methane-derived carbon assimilation, with Crenothrix being the key methane consumer. The wide distribution of Crenothrix in lake sediments and its active methane assimilation suggest its importance as a biological sink for methane in shallow lakes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
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
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
Engineering, Environmental
Guoqiang Liu, Xianwei Wu, Deyong Li, Lugao Jiang, Ju Huang, Li Zhuang
Summary: The study showed that short-term low dissolved oxygen increased N2O emissions, while long-term low DO decreased emissions by increasing the abundance of ammonia oxidizers in the ASP. Long-term low DO reduced AOB abundance but increased AOA, with AOA potentially inhibiting N2O production. The positive correlation between N2O emissions and nitrite concentration became insignificant after 80 days of low DO operation, suggesting that ASPs can reduce N2O production and CO2 emissions by operating with low DO and extended sludge age.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
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
Environmental Sciences
Feng Wang, Xiaolong Liang, Shihan Ma, Lingzhi Liu, Jingkuan Wang
Summary: The study found that ammonia-oxidizing archaea and ammonia-oxidizing bacteria had significantly higher transcriptional abundance of amoA gene in soils compared to complete ammonia oxidizers, suggesting the former may be the dominant contributors to soil nitrification. Seasonal variation and fertilization regimes substantially affected the abundance of ammonia-oxidizing microbes, with ammonia-oxidizing bacteria being less sensitive to these factors compared to ammonia-oxidizing archaea.
JOURNAL OF SOILS AND SEDIMENTS
(2021)
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
Engineering, Environmental
Bingbing Ma, Xiaojing Zhang, Aihua Gao, Chuang Ma, Yulin Hou, Zirui Zhao, Hao Hu
Summary: The CANON process was utilized for treating composting wastewater, resulting in decreased ammonia levels and increased total nitrogen removal rate. Microorganisms secreted more extracellular polymeric substances to counteract cell damage caused by harmful substances, maintaining system stability.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Engineering, Environmental
Jing Guo, Xingke Wu, Suyu Liu, Yu Zhang, Zhiqiang Cai
Summary: The current research hotspot is the use of biological methods to degrade high ammonia nitrogen wastewater. Three high-efficiency ammonia-oxidizing bacteria were isolated and purified from wastewater for constructing compound bacteria, showing promising results in degradation efficiency in a pilot test.
JOURNAL OF WATER PROCESS ENGINEERING
(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
Multidisciplinary Sciences
Soo Y. Ro, Luis F. Schachner, Christopher W. Koo, Rahul Purohit, Jonathan P. Remis, Grace E. Kenney, Brandon W. Liauw, Paul M. Thomas, Steven M. Patrie, Neil L. Kelleher, Amy C. Rosenzweig
NATURE COMMUNICATIONS
(2019)
Article
Chemistry, Multidisciplinary
Kiwon Ok, Wenjing Li, Heather M. Neu, Sharon Batelu, Timothy L. Stemmler, Maureen A. Kane, Sarah L. J. Michel
CHEMISTRY-A EUROPEAN JOURNAL
(2020)
Article
Biochemistry & Molecular Biology
Grace E. Kenney, Laura M. K. Dassama, Anastasia C. Manesis, Matthew O. Ross, Siyu Chen, Brian M. Hoffman, Amy C. Rosenzweig
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Microbiology
Jordan E. Bisanz, Paola Soto-Perez, Cecilia Noecker, Alexander A. Aksenov, Kathy N. Lam, Grace E. Kenney, Elizabeth N. Bess, Henry J. Haiser, Than S. Kyaw, Feiqiao B. Yu, Vayu M. Rekdal, Connie W. Y. Ha, Suzanne Devkota, Emily P. Balskus, Pieter C. Dorrestein, Emma Allen-Vercoe, Peter J. Turnbaugh
CELL HOST & MICROBE
(2020)
Article
Chemistry, Multidisciplinary
Molly J. McBride, Debangsu Sil, Tai L. Ng, Anne Marie Crooke, Grace E. Kenney, Christina R. Tysoe, Bo Zhang, Emily P. Balskus, Amie K. Boal, Carsten Krebs, J. Martin Bollinger
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Genetics & Heredity
Aileen Patricia Szczepanski, Zibo Zhao, Tori Sosnowski, Young Ah Goo, Elizabeth Thomas Bartom, Lu Wang
Article
Biochemistry & Molecular Biology
Yun Ji Park, Gerri M. Roberts, Rana Montaser, Grace E. Kenney, Paul M. Thomas, Neil L. Kelleher, Amy C. Rosenzweig
Summary: Methanobactins are ribosomally produced peptidic natural products that bind copper with high affinity, originating from methanotrophic bacteria to acquire copper needed for enzymatic methane oxidation. They have unique structures and provide support for the proposed role of unknown biosynthetic enzymes.
Review
Biochemistry & Molecular Biology
Courtney J. Campbell, Ashley E. Pall, Akshata R. Naik, Lindsey N. Thompson, Timothy L. Stemmler
Summary: Iron-sulfur clusters are crucial for cellular activities and the ISC pathway serves as the central mechanism for providing 2Fe-2S clusters in eukaryotes. Study of the NIAUF complex reveals insights into the coordinated mechanism of Fe-S cluster assembly.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Madhura S. Damle, Aarshi N. Singh, Stephen C. Peters, Veronika A. Szalai, Oriana S. Fisher
Summary: Research on the ycn operon in Bacillus subtilis revealed a protein, YcnI, that can interact with copper ions. Structural analysis showed a unique copper-binding site in YcnI, suggesting a possible role as a copper chaperone.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Microscopy
Tiara V. Hinton, Sharon Batelu, Noah Gleason, Timothy L. Stemmler
Summary: Fe-S clusters play crucial roles in biochemical pathways in living organisms, synthesizing through mitochondrial and cytosolic pathways in eukaryotes. Deficiency in Fe-S clusters can be detrimental to cell and organism viability.
Article
Biochemistry & Molecular Biology
Luis F. Schachner, Benjamin Des Soye, Soo Ro, Grace E. Kenney, Ashley N. Ives, Taojunfeng Su, Young Ah Goo, Michael C. Jewett, Amy C. Rosenzweig, Neil L. Kelleher
Summary: The phosphorylation of triosephosphate isomerase (TPI) enhances its activity and facilitates substrate binding to the active site. Hetero-dimerization and subunit asymmetry are key features of TPI, and tetramerization plays a crucial role in enzymatic regulation. This study highlights the importance of studying endogenous proteoforms for understanding the functional role of post-translational modifications (PTMs).
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jose A. Velilla, Matthew R. Volpe, Grace E. Kenney, Richard M. Walsh, Emily P. Balskus, Rachelle Gaudet
Summary: Colibactin, a DNA cross-linking agent produced by gut bacteria, is implicated in colorectal cancer. This study reveals that ClbP is an important catalyst for activating Colibactin, and its activity depends on its specific structure and substrate binding site.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jose A. Velilla, Grace E. Kenney, Rachelle Gaudet
Summary: Bacteria employ various strategies to protect themselves from the toxicity of antimicrobial metabolites they produce. One resistance mechanism involves the assembly and hydrolysis of a non-toxic precursor by prodrug-activating peptidases. These peptidases have different transmembrane domain (TMD) structures and substrate specificities. In addition to prodrug activation, ClbP-like proteins may also be involved in the biosynthesis or degradation of other natural products, and their association with transporters is important for the export of these products.
Review
Biochemistry & Molecular Biology
Jing Guo, Oriana S. Fisher
Summary: A large number of copper binding proteins use the cupredoxin domain to coordinate metal ions. This domain is common in a diverse group of copper binding domains. The cupredoxin fold is ideal for various purposes such as electron transfer and enzyme catalysis. The core structure remains stable upon metal binding, but variations within the coordination environment of the metal site result in different copper binding affinities and spectroscopic properties.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2022)
Article
Oncology
Qi Jin, Carlos A. Martinez, Kelly M. Arcipowski, Yixing Zhu, Blanca T. Gutierrez-Diaz, Kenneth K. Wang, Megan R. Johnson, Andrew G. Volk, Feng Wang, Jian Wu, Charles Grove, Hui Wang, Ivan Sokirniy, Paul M. Thomas, Young Ah Goo, Nebiyu A. Abshiru, Nobuko Hijiya, Sofie Peirs, Niels Vandamme, Geert Berx, Steven Goosens, Stacy A. Marshall, Emily J. Rendleman, Yoh-hei Takahashi, Lu Wang, Radhika Rawat, Elizabeth T. Bartom, Clayton K. Collings, Pieter Van Vlierberghe, Alexandros Strikoudis, Stephen Kelly, Beatrix Ueberheide, Christine Mantis, Irawati Kandela, Jean-Pierre Bourquin, Beat Bornhauser, Valentina Serafin, Silvia Bresolin, Maddalena Paganin, Benedetta Accordi, Giuseppe Basso, Neil L. Kelleher, Joseph Weinstock, Suresh Kumar, John D. Crispino, Ali Shilatifard, Panagiotis Ntziachristos
CLINICAL CANCER RESEARCH
(2019)