Article
Ecology
Akari Aizawa, Yuka Watanabe, Kaori Hashioka, Aya Kadoya, Satoru Suzuki, Takeshi Yoshimura, Isao Kudo
Summary: This study measured the ammonium oxidation rates in Mutsu Bay and found that the bottom waters had high rates of ammonium oxidation, which were mainly carried out by ammonia-oxidizing archaea. Ammonia-oxidizing bacteria were found to be attached to the sediment surface. Additionally, the study found that the ammonia-oxidizing archaea were more active than the ammonia-oxidizing bacteria based on the quantification of their copy numbers. These findings are important for understanding nitrogen cycling processes in the ocean.
REGIONAL STUDIES IN MARINE SCIENCE
(2023)
Article
Soil Science
Tharaniya Srikanthasamy, Sebastien Barot, Fulgence K. Koffi, Kevin Tambosco, Yoan Marcangeli, David Carmignac, Aya Brigitte N'Dri, Jonathan Gervaix, Julie Leloup, Xavier Le Roux, Jean-Christophe Lata
Summary: In this study, the researchers examined the influence of climate seasonality and plant cover type on the abundances and transcription levels of bacterial and archaeal nitrifiers in a savanna ecosystem for the first time. They found that different tree and grass species had contrasting effects on nitrification, with higher enzyme activity and abundances of bacterial nitrifiers under trees and lower enzyme activity and abundances of bacterial nitrifiers under grasses compared to bare soil. The study also revealed seasonal variations in the abundances and transcriptional activities of nitrifiers, with archaeal nitrifiers likely dominating nitrification in these savanna soils.
Article
Agronomy
Qinghua Li, Lin Zhao, Fei Wang, Hongmei Chen, Xiaojie Qian
Summary: This study investigates the effects of a bamboo-biochar-based fertilizer on soil N2O emissions and nitrifier and denitrifier communities in acidic soil. The results show that the fertilizer promotes soil nitrification, reduces the adverse effects of nitrogen fertilizer, and decreases N2O emissions.
Article
Marine & Freshwater Biology
Enrico Tatti, Aoife M. Duff, Anastasiia Kostrytsia, Fabien Cholet, Umer Z. Ijaz, Cindy J. Smith
Summary: The study revealed that in coastal ecosystems, both ammonia oxidizing archaea (AOA) and bacteria (AOB) play important roles in the nitrification process, with their activity levels varying in different habitats. The results also showed discrepancies between the active transcripts in situ and in laboratory experiments, indicating the influence of incubation conditions on the activity of AOA and AOB in soil-dominated environments.
ESTUARINE COASTAL AND SHELF SCIENCE
(2022)
Article
Environmental Sciences
Jiazhen Hu, Jie Wang, Shihong Yang, Suting Qi, Zewei Jiang, Huidong Dai, Jiaoyan Zhou
Summary: Evidence suggests that controlled irrigation (CI) and biochar application (BA) have an impact on soil microbial genes related to nitrogen conversion in paddy fields. The application of biochar increases the abundance of nitrogen-fixing bacteria, leading to higher levels of ammonium and nitrate in the soil. Moreover, biochar treatment also increases the microbial diversity in the paddy field. The combined use of CI and BA affects soil nitrogen content, temperature, pH, and electrical conductivity, which in turn affect microbial genes related to nitrogen transformation.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Environmental Sciences
Yu-Pin Lin, Andrianto Ansari, Rainer Ferdinand Wunderlich, Huu-Sheng Lur, Thanh Ngoc-Dan Cao, Hussnain Mukhtar
Summary: Understanding the niche segregation of AOA and AOB in ammonia oxidation and N2O production under different pH and temperature conditions is crucial for predicting N2O dynamics. Results showed that AOA and AOB occupied different niches for PAO, with soil temperature being a major determinant. N2O fluxes were higher in acidic conditions and lower in alkaline conditions, with a significant positive correlation between PAO and N2O fluxes.
Article
Environmental Sciences
Lin Zhao, Qinghua Li, Xiaojie Qian, Hongmei Chen, Fei Wang, Zhigang Yi
Summary: The study found that different concentrations of biochar-based fertilizer have varying effects on N2O emissions, with lower concentrations having a promoting effect and higher concentrations having an inhibitory effect. N2O emissions were closely related to soil pH, Rhodanobacter (nosZ), and Proteobacteria (nirK). Additionally, the sensitivity of AOA to urea was higher, while the combined application of biochar-based fertilizer significantly restored the diversity of the AOA community.
JOURNAL OF SOILS AND SEDIMENTS
(2022)
Article
Environmental Sciences
Mengyue Zhao, Xiufeng Tang, Dongyao Sun, Lijun Hou, Min Liu, Qiang Zhao, Uli Klumper, Zhexue Quan, Ji-Dong Gu, Ping Han
Summary: The recent discovery of complete ammonia oxidizers (comammox) challenges the traditional understanding of nitrification, showing that one organism can convert ammonia to nitrate. This study on nitrifying microorganisms in the Nanliu estuary demonstrates the niche specificity of different nitrifiers modulated mainly by salinity. The research also reveals a clear response by comammox Nitrospira to a wide range of simulated salinity levels.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Chris Chisholm, Hong J. Di, Keith Cameron, Andriy Podolyan, Anish Shah, Lisa Hsu, Jupei Shen
Summary: This study investigated the abundance and community composition of comammox Nitrospira across different regions of pasture-based dairy farms and different land uses within the same region. The results showed that comammox Nitrospira were most abundant under west coast dairy farm conditions and irrigated dairy farms. The abundance of comammox Nitrospira was also influenced by soil moisture and annual rainfall.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biotechnology & Applied Microbiology
Shanshan Meng, Tao Peng, Hui Wang, Tongwang Huang, Ji-Dong Gu, Zhong Hu
Summary: This study investigated the distribution and abundance of ammonia-oxidizing archaea and ammonia-oxidizing bacteria, complete ammonia oxidizers, and nitrite-oxidizing bacteria in mangrove ecosystems. The results showed that different primers had varying efficiency in detecting and characterizing specific bacterial groups in mangrove sediments. Additionally, diverse and abundant novel nitrifying bacteria were found in the mangrove sediments.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Environmental Sciences
Huijun Ye, Changyuan Tang, Yingjie Cao, Xing Li, Pinyi Huang
Summary: This study investigated the effects of AOA and AOB abundance and different environmental conditions on nitrification performance, finding that tea orchard soil had lower pH and higher nitrogen content compared to forest soil, with AOA and AOB abundance being pH-dependent in both soils. The study also observed that AOA and AOB performance was restricted by pH and the environment when pH < 4, especially in long-term fertilized farmlands.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Ecology
Xin Bai, Xiaojing Hu, Junjie Liu, Dan Wei, Ping Zhu, Xi'an Cui, Baoku Zhou, Xueli Chen, Judong Liu, Jian Jin, Xiaobing Liu, Guanghua Wang
Summary: This study investigated the contributions of different ammonia oxidizers and heterotrophic nitrifiers to nitrification potential in arable black soils and found that AOB are the dominant ammonia oxidizers contributing to nitrification.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2022)
Article
Microbiology
Haitao Wang, Alexandre Bagnoud, Rafael Ponce-Toledo, Melina Kerou, Micha Weil, Christa Schleper, Tim Urich
Summary: The newly established taxonomy for AOA based on amoA provides a finer resolution and reveals novel environmental patterns. By linking 16S rRNA gene classification to this novel taxonomy through phylogenetic congruence, it allows for the identification of specific AOA clades. This approach provides a pathway for interpreting the ecology of globally abundant AOA, especially when using 16S rRNA gene sequencing data in microbiome studies.
Article
Environmental Sciences
Shuang Liu, Jiahui Zhang, Yuchun Wang, Mingming Hu, Yufei Bao, Shanze Li, Jie Wen, Jianwei Zhao
Summary: This study investigated the distribution and abundance of complete ammonia oxidizers (comammox) in river sediments in the Three Gorges Reservoir area. The results showed that comammox clade A was dominant, and its abundance increased along the length of the river. The abundance of comammox clades A and B was positively correlated with sediment pH, indicating the importance of pH as an environmental factor for the growth of comammox bacteria.
Article
Soil Science
Yue Li, Huanhuan Wei, Mingqi Liu, Jinfeng Yang, Xiaori Han
Summary: The continuous low-dose application of biochar can indirectly increase crop yield by regulating the microbial mechanism in the nitrification process. Biochar-based fertilizer can reduce the nitrification rate compared to chemical fertilizer application.
APPLIED SOIL ECOLOGY
(2023)
Article
Ecology
Antonio Gaspar G. de Sousa, Maria Paola Tomasino, Pedro Duarte, Mar Fernandez-Mendez, Philipp Assmy, Hugo Ribeiro, Jaroslaw Surkont, Ricardo B. Leite, Jose B. Pereira-Leal, Luis Torgo, Catarina Magalhaes
Article
Microbiology
Adriana Rego, Francisco Raio, Teresa P. Martins, Hugo Ribeiro, Antonio G. G. Sousa, Joana Seneca, Mafalda S. Baptista, Charles K. Lee, S. Craig Cary, Vitor Ramos, Maria F. Carvalho, Pedro N. Leao, Catarina Magalhaes
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Microbiology
Adriana Rego, Antonio G. G. Sousa, Joao P. Santos, Francisco Pascoal, Joao Canario, Pedro N. Leao, Catarina Magalhaes
Article
Microbiology
Jorge T. Antunes, Antonio G. G. Sousa, Joana Azevedo, Adriana Rego, Pedro N. Leao, Vitor Vasconcelos
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Cell Biology
Rafael A. Paiva, Antonio G. G. Sousa, Camila Ramos, Mariana Avila, Jingtao Lilue, Tiago Paixao, Vera C. Martins
Summary: Thymus autonomy relies on double-negative 3 early thymocytes that acquire stem-cell-like properties, maintaining thymopoiesis in the absence of competent progenitors. While the transcriptional programs in autonomously functioning thymus cells are similar to those in steady state, a new cell population emerges that expresses aberrant Notch target genes, potentially leading to leukemia.
Article
Engineering, Environmental
Javier Garcia-Calleja, Thibaut Cossart, Zoyne Pedrero, Joao P. Santos, Laurent Ouerdane, Emmanuel Tessier, Vera Slaveykova, David Amouroux
Summary: Understanding the complexation of mercury (Hg) with low molecular weight (LMW) bioligands can help elucidate its speciation, and the use of isotopically labeled Hg species in cyanobacteria has provided insights into the role of intracellular biogenic ligands in the speciation of iHg and MeHg.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Cell Biology
Susana Ramos, Temitope W. Ademolue, Elisa Jentho, Qian Wu, Joel Guerra, Rui Martins, Gil Pires, Sebastian Weis, Ana Rita Carlos, Ines Mahu, Elsa Seixas, Denise Duarte, Fabienne Rajas, Silvia Cardoso, Antonio G. G. Sousa, Jingtao Lilue, Tiago Paixao, Gilles Mithieux, Fatima Nogueira, Miguel P. Soares
Summary: Malaria-associated hypoglycemia is a non-canonical resistance mechanism against Plasmodium falciparum infection, where the host reduces glycemia to starve the parasite. This hypometabolic response is triggered by labile heme, a byproduct of hemolysis, leading to illness-induced anorexia and repression of hepatic glucose production. While transient repression prevents inflammation and organ damage, sustained repression causes hypoglycemia.
Article
Plant Sciences
Chandra Shekhar Misra, Antonio G. G. Sousa, Pedro M. Barros, Anton Kermanov, Joerg D. Becker
Summary: Transcriptome analysis of sperm cells and vegetative nuclei reveals the alternative splicing landscape in the male gametophyte of Arabidopsis thaliana. The study identifies many genes involved in mRNA splicing, chromatin modification, and protein localization in both sperm cells and vegetative nuclei.
Article
Chemistry, Analytical
Thibaut Cossart, Javier Garcia-Calleja, Joao P. Santos, Elaheh Lotfi Kalahroodi, Isabelle A. M. Worms, Zoyne Pedrero, David Amouroux, Vera Slaveykova
Summary: Phytoplankton can directly and indirectly influence the biogeochemical cycling and transformations of mercury. However, the current understanding of how phytoplankton affects these processes is limited. Recent research has shown that different microalgal species and cyanobacteria contribute to the transformations and reduction of mercury, and the biomolecules released by phytoplankton also participate in abiotic reduction. However, further studies are needed to explore the underlying mechanisms and the importance of these interactions in the aquatic environment.
ENVIRONMENTAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Joao Pereira Santos, Lirie Mehmeti, Vera Slaveykova
Summary: In this study, a simple and cost-effective wet digestion method was developed for the determination of total mercury in small plankton samples. The method was optimized and validated using certified reference materials. The results showed that the method had good repeatability and accuracy in determining the mercury content in small plankton samples.
METHODS AND PROTOCOLS
(2022)
Article
Plant Sciences
Bruno Peixoto, Thiago A. Moraes, Virginie Mengin, Leonor Margalha, Ruben Vicente, Regina Feil, Melanie Hohne, Antonio G. G. Sousa, Jingtao Lilue, Mark Stitt, John E. Lunn, Elena Baena-Gonzalez
Summary: Under favorable growth conditions, SnRK1 plays a role in sucrose homeostasis and transcriptome remodeling in autotrophic tissues, and its activity is influenced by diel fluctuations in trehalose 6-phosphate (Tre6P) levels. Daily changes in Tre6P levels impact the activity of the SnRK1 protein kinase, contributing to the maintenance of sucrose homeostasis and diel patterns of gene expression.
Article
Chemistry, Multidisciplinary
Joana Costa, Antonio G. G. Sousa, Ana Carolina Carneiro, Ana Paula Mucha, C. Marisa R. Almeida, Catarina Magalhaes, Mafalda S. Baptista
Summary: The study showed that exposure to Cu NPs <50 nm in estuarine sediments promoted immediate and transient expression of key denitrification genes. Over time, gene expression and potential denitrification rates increased, but after 48 hours, expression levels were no longer different from the control group.
ENVIRONMENTAL SCIENCE-NANO
(2021)
