Article
Agronomy
Papa Mamadou Sitor Ndour, Cheikh Mbacke Barry, Diame Tine, Carla De la Fuente Canto, Mariama Gueye, Mohamed Barakat, Philippe Ortet, Wafa Achouak, Ibrahima Ndoye, Bassirou Sine, Laurent Laplaze, Thierry Heulin, Laurent Cournac
Summary: This study demonstrates that in pearl millet, the rhizosheath size is related to soil nutrient dynamics and microbiota diversity. However, it also shows that other factors shape this trait and their relative importance must be determined.
Article
Soil Science
Papa Mamadou Sitor Ndour, Christine Hatte, Wafa Achouak, Thierry Heulin, Laurent Cournac
Summary: Rhizosheath size varies significantly with crop genotype, and root exudation is one of the driving factors. Different plant sizes in rhizosheath showed distinct effects on the C input and sequestration in the soil.
Article
Multidisciplinary Sciences
C. de la Fuente Canto, M. N. Diouf, P. M. S. Ndour, M. Debieu, A. Grondin, S. Passot, A. Champion, C. Barrachina, M. Pratlong, P. Gantet, K. Assigbetse, N. Kane, P. Cubry, A. G. Diedhiou, T. Heulin, W. Achouak, Y. Vigouroux, L. Cournac, L. Laplaze
Summary: This study investigated the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi in pearl millet. The genetic control of this trait was analyzed using genome wide association (GWAS) and gene expression studies. The results showed that root exudation mainly regulates rhizosheath formation, which is under complex genetic control in pearl millet.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Tie-Yuan Liu, Nenghui Ye, Xinyu Wang, Debatosh Das, Yuxiang Tan, Xiangkai You, Mingxiu Long, Tianming Hu, Lei Dai, Jianhua Zhang, Mo-Xian Chen
Summary: The study found that the rhizocompartments of switchgrass harbor distinct and overlapping microbial communities, with low complexity in the root compartments dominated by Proteobacteria and Firmicutes. Under drought conditions, there was selective enrichment of Cyanobacteria and Bacteroidetes in rhizosheath soil, while Proteobacteria and Firmicutes were selectively depleted. The rhizosheath microbiome assembly is driven by drought stress, with ecotype-specific recruitment revealing differences in drought stress responses.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Agronomy
Ko-Hsuan Chen, Reid Longley, Gregory Bonito, Hui-Ling Liao
Summary: The improved two-step PCR approach significantly enhances sequence quantity and recovery rate, while maintaining high read quality. By incorporating synthetic barcodes independently, this method can be broadly adapted to different genomic regions and organisms of scientific interest.
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
Microbiology
Jingwen Ha, Yu Gao, Rui Zhang, Ke Li, Yijie Zhang, Xiaolei Niu, Xin Chen, Kai Luo, Yinhua Chen
Summary: The root-associated microbial communities of different cassava genotypes show significant differences in composition. Across 14 genotypes, the diversity and abundance of bacterial species in the rhizosphere were found to be higher than in the tuber endosphere.
FRONTIERS IN MICROBIOLOGY
(2021)
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
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
Microbiology
Anais Masse, Juliette Detang, Charlotte Duval, Sebastien Duperron, Anthony C. C. Woo, Isabelle Domart-Coulon
Summary: This study analyzed the composition and plasticity of bacterial communities associated with the green algae Ostreobium in response to varying salinities. The results showed that the host genotype of Ostreobium determined the structure of the bacterial community, with different genotypes having different dominant bacterial strains. The abundance of Rhizobiales also shifted in response to an increase in salinity. Additionally, a small core microbiota was found across all salinities, suggesting an important functional role in the coral holobiont.
Article
Engineering, Environmental
Riccardo Campo, Alberto Vassallo, Graziella Rabbeni, Walter Arancio, Giuseppe Gallo, Gaetano Di Bella
Summary: Reactivation of aerobic granular sludge (AGS) was applied to treat industrial slop wastewater with high salinity and hydrocarbons. Different treatment methods led to varying granulation effects and protein/polysaccharides ratio, ultimately resulting in different total petroleum hydrocarbons removal efficiencies. The presence of oil-polluted seawater-associated bacteria in the reactor cultivated with slop played a key role in the biodegradation of TPHs.
JOURNAL OF WATER PROCESS ENGINEERING
(2021)
Article
Environmental Studies
Beatrice Farda, Rihab Djebaili, Matteo Bernardi, Loretta Pace, Maddalena Del Gallo, Marika Pellegrini
Summary: Intensive agricultural practices have negative impacts on soil quality and microbial communities, as well as the occurrence of fusariosis in saffron fields. This study investigates the changes in bacterial communities induced by fusariosis and highlights the importance of understanding the interactions between intensive agricultural practices, microbial communities, and crop diseases.
Article
Agricultural Engineering
Yunxia Pan, Xuntao Zheng, Yang Xiang
Summary: The study shows that a characterized microbial consortium can efficiently degrade rice straw to produce high yields of acetic and butyric acids. Within 12 days, the rice straw lost 86.9% in weight, with degradation rates of hemicellulose, cellulose, and lignin reaching 97.1%, 86.4%, and 70.3% respectively. Metagenomic analyses revealed that glycoside hydrolases (GHs) were the largest enzyme group with lignocellulose degrading enzymes primarily found in dominant genera such as Prevotella, Cellulosilyticum, and Clostridium.
BIORESOURCE TECHNOLOGY
(2021)
Article
Microbiology
Nowreen Arefa, Ashish Kumar Sarker, Md. Ajijur Rahman
Summary: This study aimed to isolate novel antibiotic-producing bacteria (APB) from river sediments in Bangladesh, particularly targeting the genus Streptomyces. The results showed that manipulating self-protection mechanisms of APB is an effective method to discover potential sources of new antibacterial compounds with known scaffolds.
Article
Microbiology
Rihab Djebaili, Amedeo Mignini, Ilaria Vaccarelli, Marika Pellegrini, Daniela M. Spera, Maddalena Del Gallo, Anna Maria D'Alessandro
Summary: This study aimed to evaluate the suitability of Stiffe caves as a source of cyanobacteria for the production of PHAs. The results showed that the illuminated walls of the caves harbored cyanobacteria strains with good PHA-producing abilities, and the production rates could be optimized through nutritional starvation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Geosciences, Multidisciplinary
Aurelie Cambou, Bernard G. G. Barthes, Patricia Moulin, Laure Chauvin, El Hadji Faye, Dominique Masse, Tiphaine Chevallier, Lydie Chapuis-Lardy
Summary: This study used visible and near infrared diffuse reflectance spectroscopy to predict soil organic carbon, nitrogen contents, and electrical conductivity in variably salt-affected topsoils of the Sine Saloum region in Senegal. The results showed that the spectroscopy was able to accurately discriminate different soil salinity levels, and the best predictions were achieved using global and local calibration procedures with log-transformation based on salinity class.
Article
Food Science & Technology
Jim Gaffney, Dejene Girma, Ndjido Ardo Kane, Victor Llaca, Emma Mace, Nigel Taylor, Redeat Tibebu
Summary: Severe price spikes and rapid expansion of cultivated area indicate the global food supply is under severe stress. Scientific discovery and improved agricultural productivity require unencumbered access to and use of genetic sequence data. Similar to the rapid development of COVID-19 vaccines, genetic sequence data offer enormous opportunities to improve crop production, but it requires commitment, collaboration, and cooperation.
GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT
(2022)
Article
Soil Science
Tantely Razafimbelo, Alain Albrecht, Thierry Becquer, Laetitia Bernard, Tiphaine Chevallier, Amandine Erktan, Lydie Chapuis-Lardy, Jean Trap, Andry Andriamananjara, Michel Rabenarivo, Tovonarivo Rafolisy, Tovohery Rakotoson, Nandrianina Ramifehiarivo, Malatiana Razafindrakoto, Eric Blanchart
Article
Soil Science
Laura Mason, Spencer Debenport, Chelsea DeLay, Ibrahima Diedhiou, Brian McSpadden B. Gardener, Komi B. Assigbetsee, Virginia Rich, Richard P. Dick
Summary: The vulnerable agroecosystems in the Sahel of West Africa threaten food security. Intercropping with Guiera senegalensis J.F. Gmel, an indigenous shrub, has been shown to improve pearl millet yield by improving soil quality, nutrient and water availability, and harboring a distinct microbial community. This study aimed to investigate the impact of G. senegalensis on soil chemistry, enzyme activity, microbiomes, and metabolic pathways in millet root zone soils in farmers' fields.
SOIL SCIENCE SOCIETY OF AMERICA JOURNAL
(2023)
Article
Plant Sciences
Maud I. Tenaillon, Ewen Burban, Stella Huynh, Arthur Wojcik, Anne-Celine Thuillet, Domenica Manicacci, Pierre R. Gerard, Karine Alix, Harry Belcram, Amandine Cornille, Marie Brault, Rebecca Stevens, Jacques Lagnel, Catherine Dogimont, Yves Vigouroux, Sylvain Glemin
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Evolutionary Biology
Tram Vi, Yves Vigouroux, Philippe Cubry, Pierre Marraccini, Ha Viet Phan, Giang Ngan Khong, Valerie Poncet
Summary: Humans have played a significant role in spreading crops beyond their native range, creating new opportunities for hybridization. Analyzing admixed genomes can provide valuable information about the adaptive history of crops and their impact on current varietal diversity.
GENOME BIOLOGY AND EVOLUTION
(2023)
Review
Ecology
Papa Mamadou Sitor Ndour, Adnane Bargaz, Zineb Rchiad, Mark Pawlett, Ian M. Clark, Tim H. Mauchline, Jim Harris, Karim Lyamlouli
Summary: Microbial catabolic activity (MCA) is commonly used to assess soil microbial function potential, and methods such as multi-substrate-induced respiration (MSIR) are available to measure MCA and estimate functional diversity. This review compares different techniques for measuring soil MCA and discusses the effectiveness of MSIR-based approaches as indicators of microbial function. It also explores the relationship between MSIR measurements and agricultural practices, soil enzyme activities, and soil chemical properties. Additionally, the potential of using molecular tools and stable isotope probing in MCA measurement is proposed.
Article
Biochemistry & Molecular Biology
Clement Gain, Benedicte Rhone, Philippe Cubry, Israfel Salazar, Florence Forbes, Yves Vigouroux, Flora Jay, Olivier Francois
Summary: Genomic offset statistics can predict population maladaptation to rapid habitat alteration, but they have limitations. We proposed a geometric measure to predict fitness after rapid change in the local environment and verified our theory with computer simulations and empirical data. This research provides a theoretical foundation for the potential application of genomic offset statistics in conservation management.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Soil Science
M. Oscar Kisaka, Chris Shisanya, Laurent Cournac, J. Raphael Manlay, Harun Gitari, Jonathan Muriuki
Summary: Conservation agriculture with trees (CAWT) is a beneficial strategy for improving soil quality in smallholder farming. This study identified key soil quality indicators under CAWT and assessed the effects of different components on soil quality. The results have important implications for maize production.
SOIL & TILLAGE RESEARCH
(2023)
Article
Genetics & Heredity
Marine Salson, Julie Orjuela, Cedric Mariac, Leila Zekraoui, Marie Couderc, Sandrine Arribat, Nathalie Rodde, Adama Faye, Ndjido A. Kane, Christine Tranchant-Dubreuil, Yves Vigouroux, Cecile Berthouly-Salazar
Summary: An improved quality assembly of the pearl millet genome was obtained using long-read sequencing and optical maps, resulting in a more complete and higher quality assembly. This will greatly benefit research on structural variants, genomics studies, and pearl millet breeding.
G3-GENES GENOMES GENETICS
(2023)
Article
Genetics & Heredity
Donald Tchouomo Dondjou, Abdala Gamby Diedhiou, Daouda Mbodj, Marie-Therese Mofini, Sarah Pignoly, Cheikh Ndiaye, Issa Diedhiou, Komi Assigbetse, Baboucarr Manneh, Laurent Laplaze, Aboubacry Kane
Summary: This study investigates the impact of long-term fertilizer usage on the rhizosphere microbial communities in rice paddy fields. The results show that the effect varies with the rice developmental stage and the type of microorganisms. The microbial communities at the panicle initiation stage are more sensitive to long-term fertilizer usage. Additionally, the study reveals the co-occurrence patterns of bacteria and archaea in the rice rhizosphere and their pivotal roles in microbial interactions across developmental stages.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Biochemistry & Molecular Biology
Florian Turbant, Jehan Waeytens, Anais Blache, Emeline Esnouf, Vincent Raussens, Grzegorz Wegrzyn, Wafa Achouak, Frank Wien, Veronique Arluison
Summary: The carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. This study shows that the protein Hfq, which is needed for the function of these sRNAs, can be translocated into the periplasm and exported in OMVs, where it may bind to sRNAs. Furthermore, Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Tranchant-Dubreuil Christine, Chenal Clothilde, Blaison Mathieu, Albar Laurence, Klein Valentin, Mariac Cedric, A. Wing Rod, Vigouroux Yves, Sabot Francois
Summary: FrangiPANe is a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. The pipeline allows for the anchoring of new contigs within the reference genome and annotation of new genes. It simplifies the construction of a panreference and can be used for pangenome studies and selection detection.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Soil Science
Kenji Fujisaki, Tiphaine Chevallier, Antonio Bispo, Jean-Baptiste Laurent, Francois Thevenin, Lydie Chapuis-Lardy, Remi Cardinael, Christine Le Bas, Vincent Freycon, Fabrice Benedet, Vincent Blanfort, Michel Brossard, Marie Tella, Julien Demenois
Summary: Identifying the drivers of soil organic carbon (SOC) stock changes is crucial for addressing global challenges related to climate change, land degradation, biodiversity loss, and food security. However, evaluating the impacts of land use and management practices on SOC remains challenging. This paper presents a comprehensive thesaurus (DATA4C+) that categorizes and defines 224 terms related to management practices in agriculture and forestry, specifically focusing on SOC storage. The DATA4C+ thesaurus aims to promote uniformity in describing practices influencing SOC and is accessible through Agroportal to enhance its usability and accessibility for scientists, laboratories, and land managers.
Article
Environmental Sciences
Issiakou Allade Houssoukpevi, Herve Nonwegnon Sayimi Aholoukpe, Demayi Jores Mauryo Fassinou, Murielle Nancy Rakotondrazafy, Guillaume Lucien Amadji, Lydie Chapuis-Lardy, Tiphaine Chevallier
Summary: The inventory of carbon pools in Africa's ecosystems is crucial for climate mitigation policies, but currently lacking. This study quantified the carbon stocks in different land uses in southeast Benin and found that forests have the highest carbon stocks compared to other land uses, while differences in soil carbon stocks between land uses are low.
