Article
Environmental Sciences
Judith Riedo, Aya Yokota, Barbara Walther, Nora Bartolome, Marcel G. A. van der Heijden, Thomas D. Bucheli, Florian Walder
Summary: Pesticides are essential in modern agriculture but can cause widespread contamination of the environment, including soils. It is important to assess the risk posed by pesticide contamination thoroughly. This study measured and compared the bioavailable and total concentrations of three fungicides in soils and evaluated their effects on microbial markers.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Agronomy
Rong Zhong, Zhaolan Zi, Peiru Wang, Hafeez Noor, Aixia Ren, Yongkang Ren, Min Sun, Zhiqiang Gao
Summary: In a 5-year field experiment in the Loess Plateau, China, the effects of long-term fallow tillage on soil microbial community structure and winter wheat yield were evaluated. Results showed that no-tillage and subsoiling tillage methods significantly improved soil moisture and organic carbon contents, as well as the diversity of microbial community. Deep plowing increased the metabolic functional diversity of bacteria and fungi. Both subsoiling tillage and deep plowing increased the yield of winter wheat, with deep plowing having the best effect.
Article
Plant Sciences
Lei Liu, Wei Lin, Li Zhang, Xuexiao Tang, Yue Liu, Siren Lan, Shusheng Wang, Yan Zhou, Xiaochou Chen, Ling Wang, Xiang Chen, Lijin Guo
Summary: The relationship between Rhododendron simsii and its soil microbial community under heat stress was investigated in this study. It was found that heat stress altered the physiological characteristics of the plant, soil physicochemical properties, and soil microbial community structure. These changes were correlated with the availability of soil available nitrogen and suggest that the soil microbial community may play a crucial role in plant resistance to heat stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Engineering, Environmental
Sara Gallego, Jose Maria Esbri, Juan Antonio Campos, Jesus Daniel Peco, Fabrice Martin-Laurent, Pablo Higueras
Summary: Mining activities can cause long-lasting residue pollution in the surrounding environment. A study on a 100 year-old mine showed that potentially toxic elements have ecotoxicological impacts on microbial activity and diversity. Furthermore, assessing the relationship between physicochemical properties and microbial diversity and activity can help stakeholders define appropriate management strategies.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Review
Oncology
Nicholas Bradley Larson, Ann L. Oberg, Alex A. Adjei, Liguo Wang
Summary: Next-generation sequencing (NGS) technologies, widely used in cancer research, generate vast and diverse data that require sophisticated computational methods and bioinformatics expertise. This review provides background details of NGS technology and basic bioinformatics concepts for clinicians interested in cancer research applications, with a focus on DNA-based approaches. It introduces principles of library preparation, alignment, variant calling, variant annotations, and NGS applications for other molecular data types. The review also discusses the utility of NGS methods in NSCLC research and study design considerations for leveraging NGS technologies in clinical care.
JOURNAL OF THORACIC ONCOLOGY
(2023)
Article
Agronomy
Chengyu Xu, Yulin Li, Xue Hu, Qian Zang, Hengyang Zhuang, Lifen Huang
Summary: Organic cultivation improves soil physicochemical properties, enhances soil enzyme activity, and alters soil microbial diversity and bacterial abundance compared to conventional cultivation.
Article
Biochemistry & Molecular Biology
Sanjay Joshi, Hadia Awan, Priyanka Paul, Ran Tian, Sharyn E. Perry
Summary: AGL15, a member of the MADS-domain transcription factor family, primarily accumulates in plant embryos and promotes plant regeneration. Through the use of different technological platforms, researchers have identified an interaction between AGL15 and the brassinosteroid hormone signaling pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Microbiology
Maria Luisa Castrejon-Godinez, Efrain Tovar-Sanchez, Leticia Valencia-Cuevas, Marcos Eduardo Rosas-Ramirez, Alexis Rodriguez, Patricia Mussali-Galante
Summary: Glyphosate is a widely used broad-spectrum herbicide in agriculture since the 1970s, with increasing levels particularly due to the introduction of glyphosate-resistant crops in the 1990s. Its presence in the environment and potential adverse effects on human health have raised concerns. Bioremediation is suggested as a suitable alternative for treating glyphosate pollution, with microorganisms showing potential for herbicide biodegradation. Further research is needed to understand the mechanisms employed by the microorganisms to counteract glyphosate exposure effects.
Article
Immunology
Ing-Kit Lee, Jen-Ping Chang, Wen-Chi Huang, Chien -Hsiang Tai, Huang-Tu Wu, Chih-Hung Chi
Summary: This study demonstrates the significant advantage of NGS technology in detecting microorganisms in septic patients, especially for microorganisms that are currently difficult or impossible to culture. Combining NGS and BC analyses can increase the positivity rate of detection.
JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION
(2022)
Article
Immunology
Esther Benamu, Kiran Gajurel, Jill N. Anderson, Tullia Lieb, Carlos A. Gomez, Hon Seng, Romielle Aquino, Desiree Hollemon, David K. Hong, Timothy A. Blauwkamp, Mickey Kertesz, Lily Blair, Paul L. Bollyky, Bruno C. Medeiros, Steven Coutre, Simona Zompi, Jose G. Montoya, Stan Deresinski
Summary: This study evaluated the ability of Karius microbial cell-free DNA sequencing test (KT) to identify infectious etiologies in patients with febrile neutropenia (FN) and its impact on antimicrobial treatment. The results showed that KT was able to detect organisms that were not identified by conventional microbiological tests, and it had the potential to improve the diagnosis and optimize the antimicrobial therapy for FN.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Medical Laboratory Technology
Bennett Oh Vic Shum, Carel Jacobus Pretorius, Letitia Min Fen Sng, Ilya Henner, Paulette Barahona, Emre Basar, Jim McGill, Urs Wilgen, Anna Zournazi, Lilian Downie, Natalie Taylor, Liam Cheney, Sylvania Wu, Natalie Angela Twine, Denis Carolin Bauer, Gerald Francis Watts, Akash Navilebasappa, Kishore Rajagopal Kumar, Jacobus Petrus Johannes Ungerer, Glenn Bennett
Summary: The study found that newborn screening can be expanded using targeted gene sequencing (TGS), which is a feasible and cost-effective method. The TGS assay had a high sensitivity (>99%) and specificity (100%) with a turnaround time of 7 to 10 days and a maximum batch size of 1536 samples. This approach can increase the number of conditions screened and improve the effectiveness of newborn screening programs.
CLINICAL CHEMISTRY
(2023)
Article
Immunology
Joshua A. Hill, Sudeb C. Dalai, David K. Hong, Asim A. Ahmed, Carine Ho, Desiree Hollemon, Lily Blair, Joyce Maalouf, Jacob Keane-Candib, Terry Stevens-Ayers, Michael Boeckh, Timothy A. Blauwkamp, Cynthia E. Fisher
Summary: The study evaluated the performance of plasma microbial cell-free DNA sequencing (mcfDNA-Seq) test for diagnosing pulmonary invasive mold infections (IMIs) after hematopoietic cell transplant (HCT). The mcfDNA-Seq test showed moderate sensitivity and high specificity, positive predictive value (PPV), and negative predictive value (NPV) for pulmonary IMI, especially for non-Aspergillus species after HCT.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Ecology
Laura Vega, Jesus Jaimes, Duvan Morales, David Martinez, Lissa Cruz-Saavedra, Marina Munoz, Juan David Ramirez
Summary: This study examined the microbial communities in urban recreational lakes and a contaminated stream in Bogota, Colombia, revealing the presence of various pathogens that may pose a risk to citizen's health. The study highlights the importance of monitoring microbial communities in recreational waters as indicators of contamination and potential public health threats.
Article
Biotechnology & Applied Microbiology
Raphael Rodriguez, Yamuna Krishnan
Summary: This article reviews the historical development of next-generation sequencing chemistry, highlighting the significant impact of the underlying chemical principles on biology.
NATURE BIOTECHNOLOGY
(2023)
Article
Environmental Sciences
Zografina Mavriou, Ioanna Alexandropoulou, Paraschos Melidis, Dimitrios G. Karpouzas, Spyridon Ntougias
Summary: The study demonstrated successful treatment of fludioxonil-rich wastewater using an immobilized cell bioreactor, achieving consistently high removal efficiency above 96%. Twelve transformation products were identified during fludioxonil degradation, with the main pathway involving hydroxylation, carbonylation, and defluorination. High-throughput sequencing revealed changes in bacterial community composition towards advanced degradation-capable taxa under reduced hydraulic retention times.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Environmental Sciences
Asma Ben Salem, Hanene Chaabane, Tessnime Ghazouani, Pierluigi Caboni, Valentina Coroneo, Marion Devers, Jeremie Beguet, Fabrice Martin-Laurent, Sami Fattouch
Summary: A bacterial strain S. rubidaea ABS 10 was found in a Tunisian soil that can dissipate chlorpyrifos and accelerate its degradation in both non-sterile and sterile soil.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Soil Science
Sara Gallego, Yvonne Bigott, Arnaud Mounier, Ayme Spor, Peter Schroder, Fabrice Martin-Laurent
Summary: This study assessed the effects of wastewater irrigation on the colonization, diversity, and composition of arbuscular mycorrhizal fungal (AMF) in lettuce roots. It found that neither the wastewater nor the concentration of spiked PPCPs had an impact on the root-associated AMF community.
BIOLOGY AND FERTILITY OF SOILS
(2022)
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.
Editorial Material
Microbiology
Aurelie Cebron, Dimitrios Georgios Karpouzas, Fabrice Martin-Laurent, Soizic Morin, Carmen Palacios, Mechthild Schmitt-Jansen
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Patrick Hohener, Delphine Guers, Laure Malleret, Ouassim Boukaroum, Fabrice Martin-Laurent, Jeremy Masbou, Sylvain Payraudeau, Gwenael Imfeld
Summary: The transfer of pesticides from agricultural soils to food and drinking water is a major health concern. This review focuses on the use of multi-elemental compound-specific isotope analysis to study the sources and transformations of pesticides in agricultural soils. Advanced extraction and purification techniques as well as analytical techniques for measuring stable isotope composition of pesticides are discussed. A unique dataset of isotopic compositions of various pesticides and isotope fractionation values for different compounds is reported, providing insights into the mechanisms of pesticide transformation.
ENVIRONMENTAL CHEMISTRY LETTERS
(2022)
Article
Environmental Sciences
Johannes Wirsching, Benedikt Wimmer, Franziska Ditterich, Johanna Schloegl, Fabrice Martin-Laurent, Carolin Huhn, Stefan Haderlein, Ellen Kandeler, Christian Poll
Summary: Glyphosate and its metabolite AMPA are frequently detected in European agricultural topsoils. This study found that shrinkage cracks occurring after dry periods could facilitate GLP transport to greater depths where subsoil conditions slow further microbial degradation. The degradation pathway to AMPA dominated, and degradation mainly occurred in Gram+- bacteria.
ENVIRONMENTAL POLLUTION
(2022)
Article
Environmental Sciences
Yvonne Bigott, Sara Gallego, Nicola Montemurro, Marie-Christine Breuil, Sandra Perez, Antonios Michas, Fabrice Martin-Laurent, Peter Schroeder
Summary: This study assessed the uptake and metabolization of pharmaceuticals and personal care products (PPCPs) from treated wastewater into lettuce, as well as the impact on root-associated bacteria. The results showed that lettuce irrigated with treated wastewater had higher PPCP concentrations. Furthermore, irrigation with wastewater significantly affected microbial diversity and the structure and composition of root-associated bacteria.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Evangelia S. Papadopoulou, Eleftheria Bachtsevani, Christina V. Papazlatani, Constantina Rousidou, Antonios Brouziotis, Eleni Lampronikou, Myrto Tsiknia, Sotirios Vasileiadis, Ioannis Ipsilantis, Urania Menkissoglu-Spiroudi, Constantinos Ehaliotis, Laurent Philippot, Graeme W. Nicol, Dimitrios G. Karpouzas
Summary: Nitrification inhibitors (NIs) have been used in agriculture for over 40 years, but little is known about their activity on different groups of ammonia-oxidizing microorganisms (AOM) and their effects on off-target soil microorganisms. In this study, the researchers compared the efficacy of a novel NI, quinone imine (QI), with established NIs. The results showed that the effectiveness of NIs varied across soils with different pH, and QI significantly affected prokaryotic and fungal diversity. These findings highlight the need for novel NI strategies and the importance of monitoring their impact on off-target soil microorganisms for sustainable use of nitrogen fertilizers and soil ecosystem functioning.
MICROBIOLOGY SPECTRUM
(2022)
Article
Environmental Sciences
Clemence Thiour-Mauprivez, Franck Emmanuel Dayan, Hugo Terol, Marion Devers, Christophe Calvayrac, Fabrice Martin-Laurent, Lise Barthelmebs
Summary: This study investigated the effects of agronomical doses of beta-triketone herbicides on soil bacterial strains, and found that different strains exhibited varying responses to the herbicides and different molecules had varying inhibitory effects. Molecular docking analysis revealed different binding potentials between the herbicides and bacterial HPPD. The results suggest that these herbicides may impact the HPPD enzymatic activity of non-target microorganisms.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Wiktoria Maj, Giorgia Pertile, Magdalena Frac
Summary: Soil-borne Neosartorya spp. are highly resilient fungi that can excrete mycotoxins and have great resistance to high temperatures. They easily transfer between soil and crops, posing a threat to horticulture and food production. Despite being a cause of spoilage in fruit produce, juices, and pulps, these fungi can also participate in carbon transformation, sequestration, and plant protection in drought conditions. The taxonomical controversy surrounding Neosartorya spp. and its resemblance to its anamorph leads to uncertain data in research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Sarah Huet, Sana Romdhane, Marie-Christine Breuil, David Bru, Arnaud Mounier, Ayme Spor, Laurent Philippot
Summary: We manipulated soil microbial communities and found that interactions between microorganisms play a crucial role in determining their fitness and soil functions. Our study highlights the importance of density-dependent interactions in microbial community assembly and demonstrates the potential of manipulating microbial communities for soil ecosystem restoration.
Article
Plant Sciences
Emma Mortier, Arnaud Mounier, Jonathan Kreplak, Fabrice Martin-Laurent, Ghislaine Recorbet, Olivier Lamotte
Summary: Under agroforestry practices, inter-specific facilitation between tree rows and cultivated alleys occurs when plants increase the growth of their neighbors especially under nutrient limitation. Owing to a coarse root architecture limiting soil inorganic phosphate (Pi) uptake, walnut trees (Juglans spp.) exhibit dependency on soil-borne symbiotic arbuscular mycorrhizal fungi that extend extra-radical hyphae beyond the root Pi depletion zone. To investigate the benefits of mycorrhizal walnuts in alley cropping, we experimentally simulated an agroforestry system in which walnut rootstocks RX1 (J. regia x J. microcarpa) were connected or not by a common mycelial network (CMN) to maize plants grown under two contrasting Pi levels. Mycorrhizal colonization parameters showed that the inoculum reservoir formed by inoculated walnut donor saplings allowed the mycorrhization of maize recipient roots. Relative to non-mycorrhizal plants and whatever the Pi supply, CMN enabled walnut saplings to access maize Pi fertilization residues according to significant increases in biomass, stem diameter, and expression of JrPHT1;1 and JrPHT1;2, two mycorrhiza-inducible phosphate transporter candidates here identified by phylogenic inference of orthologs. In the lowest Pi supply, stem height, leaf Pi concentration, and biomass of RX1 were significantly higher than in non-mycorrhizal controls, showing that mycorrhizal connections between walnut and maize roots alleviated Pi deficiency in the mycorrhizal RX1 donor plant. Under Pi limitation, maize recipient plants also benefited from mycorrhization relative to controls, as inferred from larger stem diameter and height, biomass, leaf number, N content, and Pi concentration. Mycorrhization-induced Pi uptake generated a higher carbon cost for donor walnut plants than for maize plants by increasing walnut plant photosynthesis to provide the AM fungus with carbon assimilate. Here, we show that CMN alleviates Pi deficiency in co-cultivated walnut and maize plants, and may therefore contribute to limit the use of chemical P fertilizers in agroforestry systems.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Jennifer Hellal, Lise Barthelmebs, Annette Berard, Aurelie Cebron, Giulia Cheloni, Simon Colas, Cristiana Cravo-Laureau, Caroline De Clerck, Nicolas Gallois, Marina Hery, Fabrice Martin-Laurent, Jean Martins, Soizic Morin, Carmen Palacios, Stephane Pesce, Agnes Richaume, Stephane Vuilleumier
Summary: Environmental pollution is a major challenge faced by humanity, and microorganisms play crucial roles in the degradation, transformation, and transfer of pollutants. Microbial ecotoxicology is an expanding research area that aims to understand the interactions between pollutants and microorganisms. This perspective paper provides an overview of the research challenges in microbial ecotoxicology and highlights areas where further efforts are needed.
FEMS MICROBIOLOGY ECOLOGY
(2023)
