Article
Microbiology
Jorge R. Osman, Yang Wang, Chloe Jaubert, Tuyet-Nga Nguyen, Gustavo R. Fernandes, Michael S. DuBow
Summary: In desert-like areas of eastern Utah, bacterial community composition is significantly influenced by pH and organic matter concentration, with Proteobacteria and Gemmatimonadetes being the predominant phyla in high-altitude desert soils. The relative abundance of these phyla is correlated with soil pH and organic matter concentration, suggesting their importance in shaping bacterial community structure in these environments.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Geosciences, Multidisciplinary
Yu-Te Lin, William B. Whitman, David C. Coleman, Shih-Hao Jien, Hsueh-Ching Wang, Chih-Yu Chiu
Summary: The study found significant differences in bacterial community composition between coniferous forest and grassland soils at the treeline, with correlations to soil pH, organic C, and C/N. Historical vegetation types also had a significant impact on the abundance of certain bacterial groups.
Article
Microbiology
Christina Karmisholt Overgaard, Ke Tao, Sha Zhang, Bent Tolstrup Christensen, Zuzana Blahovska, Simona Radutoiu, Simon Kelly, Morten Kam Dahl Dueholm
Summary: Intensive agricultural systems have positive effects on supporting the growing human population, but the excessive use of mineral fertilizers and pesticides may have negative impacts on nutrient cycles and biodiversity. Harnessing the beneficial relationships between plants and plant-associated rhizobacteria can increase nutrient-use efficiency and provide pathogen resistance. Analyzing the plant-associated microbiota using high-throughput sequencing can lead to improved taxonomic classification and identification of new plant-associated microbes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Environmental Sciences
Mikolaj Dziurzynski, Adrian Gorecki, Julia Pawlowska, Lukasz Istel, Przemyslaw Decewicz, Piotr Golec, Michal Styczynski, Krzysztof Poszytek, Anna Rokowska, Dorota Gorniak, Lukasz Dziewit
Summary: Arctic soils have unique microbial ecosystems and provide opportunities for studying microbial ecology and evolution. A combination of culture-dependent and culture-independent approaches revealed a cultivation bias in studies of cold-active microorganisms. A novel protocol combining a culture-dependent approach, metabarcoding, next-generation sequencing, and genomic data reuse was developed to obtain psychrotolerant, multi-metal-resistant strains with potential biotechnological applications.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Gian Maria Niccolo Benucci, Ehsan R. Toosi, Fan Yang, Terence L. Marsh, Gregory M. Bonito, Alexandra Kravchenko
Summary: Microbial communities are the primary decomposers of carbon in soil, but the effects of soil structure, management type, moisture content, and plant species on this process are not well understood. The diversity and composition of leaf microbiomes were significantly influenced by soil structure, management type, plant species, moisture content, and pore sizes. Understanding these factors is important for environmental sustainability and evaluating changes in ecosystem functions.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Soil Science
Yang Wang, Yu Hong, Yulu Tian, Guiquan Tian, Jinghui Zhang, Huawu Wu, Yan Bai, Jingmei Qian
Summary: Soil water availability is a critical limitation for soil respiration and ecosystem functions in biological soil crusts of arid ecosystems. A 3-year field experiment in a desert shrub in northwestern China revealed that increased rainfall led to an increase in microbial biomass carbon and nitrogen, while soil organic carbon, total nitrogen, pH, and biological thickness remained relatively stable. Water addition significantly altered the bacterial community composition, with Actinobacteria increasing and Bacteroidetes and Cyanobacteria decreasing in abundance. The effects of soil physiochemical properties and bacterial community composition on soil respiration varied, with soil physiochemical properties having a larger impact.
Article
Ecology
Nicholas V. Travanty, Edward L. Vargo, Charles S. Apperson, Loganathan Ponnusamy
Summary: The long-standing association between insects and microorganisms plays a crucial role in the success of social insect groups. In this study, the bacterial microbiomes in soils with and without red imported fire ants were characterized, revealing significant differences in bacterial community structures. Red imported fire ants were found to have a notable impact on soil microbial communities, with differences in abundance of certain taxa and distinct bacterial compositions in worker ants compared to nest soils.
Article
Immunology
Yu Hao, Zhi Zeng, Xian Peng, Ping Ai, Qi Han, Biao Ren, Mingyun Li, Haohao Wang, Xinxuan Zhou, Xuedong Zhou, Yue Ma, Lei Cheng
Summary: This study established a microbiome-based risk screening tool for nasopharyngeal carcinoma (NPC). The tool is non-invasive, simple, low-cost, and has a high accuracy. It can be used for early detection and risk screening of NPC.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biology
Aleksei O. Zverev, Oksana N. Kurchak, Olga V. Orlova, Olga P. Onishchuk, Arina A. Kichko, Aleksander V. Eregin, Aleksey N. Naliukhin, Aleksandr G. Pinaev, Evgeny E. Andronov
Summary: Crop rotation is an effective method for restoring soil fertility. This study aims to assess the microbiological effects of crop rotation and develop long-term crop rotation schemes that consider the microbiological effects. Short-term experiments were conducted with different plant combinations, and it was found that both primary and secondary crops significantly influenced the microbial composition of soil communities.
Article
Immunology
Jingjie Song, Zhenzhen Tang, Xueqing Zhao, Yanqiong Yin, Xiangyong Li, Fushou Chen, Aidong Chen, Ying Liu
Summary: The red imported fire ants (RIFA) are an invasive species that has rapidly expanded its invasion in China, resulting in negative effects on soil microbial communities and ecosystem function. The study found significant differences in microbial community structure and function among different samples, indicating that RIFA invasion can significantly alter soil microbial composition and ultimately affect ecosystem function. Effective management strategies are urgently needed to mitigate the negative impact of invasive species on native ecosystems.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Evgeny Abakumov, Aleksei Zverev, Evgeny Andronov, Timur Nizamutdinov
Summary: Technogenic processes and agrodevelopment cause significant changes in soil properties. Next-generation sequencing allows detailed investigation of soil microbial composition and functions. This study explored the taxonomic diversity of natural and anthropogenically disturbed soils in Russia using next-generation sequencing. It was found that microbial communities in disturbed soils differ from natural and agrogenic soils, indicating the sensitivity of microbial communities as indicators of human impact on soil.
APPLIED SCIENCES-BASEL
(2023)
Article
Medicine, General & Internal
Raquel Rodriguez-Garcia, Maria Angeles Rodriguez-Esteban, Jonathan Fernandez-Suarez, Ana Morilla, Enrique Garcia-Carus, Mauricio Telenti, Carlos Morales, Guillermo Muniz Albaiceta, Javier Fernandez
Summary: The study demonstrates that 16S rDNA tissue PCR provides complementary information for the diagnosis of IE, especially when blood cultures are negative, with a higher reliability in identifying pathogens.
Article
Ecology
Jan-Hendrik Keet, Allan G. Ellis, Cang Hui, Ana Novoa, Johannes J. Le Roux
Summary: The study found that invasive nitrogen-fixing Australian Acacia trees altered soil chemistry and function in South Africa's Core Cape Subregion, increasing levels of nitrogen, carbon, and pH, as well as influencing the composition of soil bacterial communities.
Article
Agronomy
Mohamed Hassan Korkar, Mahmoud Magdy, Samah Mohamed Rizk, Yosur Gamal Fiteha, Aiman Hanafy Atta, Mohamed Abdel-Salam Rashed
Summary: The study using metabarcoding techniques analyzed the bacterial profile of soil samples in Egypt and discovered differences in rhizosphere bacteria between agricultural land and reclaimed land. The findings provide important insights into the significance of rhizosphere microbiome and the potential use of microbial-based biofertilizers.
Article
Ecology
Loren Billet, Stephane Pesce, Fabrice Martin-Laurent, Marion Devers-Lamrani
Summary: The application of organic amendment, such as manure, to agricultural soil can lead to the transfer of bacterial pathogens and antibiotic-resistant bacteria. This study investigated the invasion of manure-borne bacteria into amended soil and found that the invasion was still observable 1 month after the soil amendment. Additionally, exposure to the antibiotic sulfamethazine was found to enhance the invasion ability of some manure-borne bacteria.
Article
Plant Sciences
P. E. Courty, M. Buee, J. J. T. Tech, D. Brule, Y. Colin, J. H. J. Leveau, S. Uroz
Correction
Biotechnology & Applied Microbiology
S. Uroz, P. Oger
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2019)
Article
Multidisciplinary Sciences
Pierre Plassart, Nicolas Chemidlin Prevost-Boure, Stephane Uroz, Samuel Dequiedt, Dorothy Stone, Rachel Creamer, Robert I. Griffiths, Mark J. Bailey, Lionel Ranjard, Philippe Lemanceau
SCIENTIFIC REPORTS
(2019)
Article
Environmental Sciences
Yannick Colin, Marta Goberna, Miguel Verdu, Jose A. Navarro-Cano
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2019)
Review
Plant Sciences
Stephane Uroz, Pierre Emmanuel Courty, Phil Oger
TRENDS IN PLANT SCIENCE
(2019)
Article
Microbiology
Richard Splivallo, Maryam Vandatzadeh, Jose G. Macia-Vicente, Virginie Molinier, Martina Peter, Simon Egli, Stephane Uroz, Francesco Paolocci, Aurelie Deveau
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Marta Goberna, Alicia Montesinos-Navarro, Alfonso Valiente-Banuet, Yannick Colin, Alicia Gomez-Fernandez, Santiago Donat, Jose A. Navarro-Cano, Miguel Verdu
MOLECULAR ECOLOGY RESOURCES
(2019)
Article
Multidisciplinary Sciences
O. Nicolitch, M. Feucherolles, J-L Churin, L. Fauchery, M-P Turpault, S. Uroz
SCIENTIFIC REPORTS
(2019)
Article
Ecology
Yannick Colin, Thierry Berthe, Noelie Molbert, Elodie Guigon, Anne-Laure Vivant, Fabrice Alliot, Sylvie Collin, Aurelie Goutte, Fabienne Petit
Summary: The study found that urbanization primarily affects the microbial communities associated with fish skin, with less impact on the gut microbiota. The skin microbiota of fish in urbanized areas exhibited significant changes in structure and composition, possibly due to greater environmental pressures.
Article
Environmental Sciences
Axel Aigle, Yannick Colin, Rayan Bouchali, Emilie Bourgeois, Romain Marti, Sebastien Ribun, Laurence Marjolet, Adrien C. M. Pozzi, Boris Misery, Celine Colinon, Claire Bernardin-Souibgui, Laure Wiest, Didier Blaha, Wessam Galia, Benoit Cournoyer
Summary: The study investigated the relationship between the distribution patterns of tpm gene in urban deposits and chemical pollutants, revealing a significant correlation; tpm-harboring bacteria showed distinctive community patterns in polluted urban deposits, with associations to different concentrations of priority pollutants over time and location.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Ecology
Y. Colin, M-P Turpault, L. Fauchery, M. Buee, S. Uroz
Summary: The composition of mineral-associated fungal communities was found to be influenced by forest plant cover in different types of forests, and there was also variation between different types of minerals.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yannick Colin, Noelie Molbert, Thierry Berthe, Simon Agostini, Fabrice Alliot, Beatriz Decenciere, Alexis Millot, Aurelie Goutte, Fabienne Petit
Summary: This study experimentally investigated the effects of Polycyclic Aromatic Hydrocarbons (PAHs) exposure and infection by a common intestinal parasite on the gut microbial flora of a freshwater fish. The results showed that the parasitic infection had a greater impact on the gut bacterial diversity and composition than PAH exposure. Furthermore, significant changes in the abundance of major bacterial phyla were observed, which correlated with the host's infection status.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Laura C. Kelly, Damian W. Rivett, Eva Pakostova, Simon Creer, Tom Cotterell, D. Barrie Johnson
Summary: The study investigates the influence of substratum mineralogy on microbial community composition in an abandoned sulfide ore mine system. The results show that the mineralogy of both primary and secondary minerals is correlated with prokaryotic community structure. It is also found that there is high variability in the abundance of acidophilic bacteria taxa in the samples, and previously unreported bacterial taxa are present in the extreme acidic mine environments. These findings offer insights into the biodiversity drivers in extremely acidic mine environments.
MICROBIOLOGICAL RESEARCH
(2023)
Article
Marine & Freshwater Biology
Yannick Colin, Caroline Arcanjo, Claire Da Costa, Anne-Laure Vivant, Gauthier Tremolet, Nathalie Giusti-Petrucciani, Aurelie Duflot, Joelle Forget-Leray, Thierry Berthe, Celine Boulange-Lecomite
Summary: Chemical contamination is a common threat to biota in estuarine and coastal ecosystems, particularly trace metals which can accumulate and negatively impact small invertebrates like zooplankton. It has been hypothesized that metal exposure could also affect the zooplankton microbiota, leading to further impairment of host fitness. To test this hypothesis, copepods were exposed to dissolved copper and their transcriptomic changes and microbiota alteration were assessed. The study found minimal gene expression differences in the copper-treated copepods compared to the controls, but significant changes in the taxonomic diversity and composition of the microbiota. These findings highlight the importance of considering the microbial component when evaluating the vulnerability of zooplankton to metal stress.
AQUATIC TOXICOLOGY
(2023)
Article
Geosciences, Multidisciplinary
Yannick Colin, Rayan Bouchali, Laurence Marjolet, Romain Marti, Florian Vautrin, Jeremy Voisin, Emilie Bourgeois, Veronica Rodriguez-Nava, Didier Blaha, Thierry Winiarski, Florian Mermillod-Blondin, Benoit Cournoyer
HYDROLOGY AND EARTH SYSTEM SCIENCES
(2020)