Article
Plant Sciences
Hannah V. Baker, Jorge R. Ibarra Caballero, Cynthia Gleason, Courtney E. Jahn, Cedar N. Hesse, Jane E. Stewart, Inga A. Zasada
Summary: In this study, a manually curated database called NemaTaxa was developed for nematode 18S sequence analysis and compared with other databases (PR2 and Silva v132). The results showed that NemaTaxa performed well in classifying nematode communities at the genus, family, and order levels, making it suitable for studying nematode community ecology.
PHYTOBIOMES JOURNAL
(2023)
Article
Environmental Sciences
Blaire M. Padayhag, Michael Angelou L. Nada, Jake Ivan P. Baquiran, Marilou P. Sison-Mangus, Maria Lourdes San Diego-McGlone, Patrick C. Cabaitan, Cecilia Conaco
Summary: This study found that the microbial biofilm communities near mariculture areas can affect the settlement of coral larvae. The biofilm farthest from the mariculture area had a higher effectiveness in inducing the settlement of Acropora tenuis larvae. These biofilms were characterized by a greater proportion of crustose coralline algae and gammaproteobacterial taxa, while biofilms closer to the mariculture zone had a higher proportion of cyanobacteria and no crustose coralline algae. These findings suggest that nutrient enrichment from mariculture activities can alter the composition of biofilm-associated microbiome and indirectly affect coral larval settlement.
MARINE POLLUTION BULLETIN
(2023)
Article
Ecology
Maura Palacios Mejia, Connie A. Rojas, Emily Curd, Mark A. Renshaw, Kiumars Edalati, Beverly Shih, Nitin Vincent, Meixi Lin, Peggy H. Nguyen, Robert Wayne, Kelsey Jessup, Sophie S. Parker
Summary: This study investigates the impact of long-term contamination on the soil microbiome composition and diversity at an urban brownfield in Los Angeles. The findings suggest that the presence of heavy metals and organic pollutants shape the soil microbiome diversity, and certain bacteria and fungi show tolerance to these contaminants. The study recommends incorporating DNA-based multi-marker microbial community profiling in brownfield site assessment and restoration.
Article
Engineering, Environmental
Fabian Fischer, Nancy Merino, Marc Sugnaux, Gerald Huguenin, Kenneth H. Nealson
Summary: Microbial fuel cell stacks often experience voltage reversals, and this study provides new insights into the causes and potential solutions for this issue. The researchers examined the microbiomes of twelve MFC units and tested different methods of biofilm repair. They found that certain repair methods could slowly heal damaged biofilms, and that biofilms in voltage-reversed MFC units were different from healthy ones. By combining electrotechnical and microbial community analyses, the researchers gained a better understanding of problematic MFC units and the potential success of repair methods. Thicker biofilms were generally healthier and stronger, but there was also a trend of stronger anodes becoming even stronger while others weakened.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biology
Kai Kang, Hui Chong, Kang Ning
Summary: This study presents Meta-Prism 2.0, a method for analyzing microbial community samples that achieves ultra-fast, memory-efficient, flexible, and accurate search among millions of samples. Results demonstrate that Meta-Prism 2.0 is one of the most efficient sample analysis methods, with comparable or better accuracy compared to contemporary methods.
Article
Food Science & Technology
Dayun Sun, Junjie Qu, Yu Huang, Jiang Lu, Ling Yin
Summary: Microorganisms in grape skins play important roles in grapevine health, productivity, wine quality, and organoleptic properties. The diversity and composition of microbes in muscadine grape skins were found to be affected by the cultivar, with complex interactions observed among different bacteria and fungi across different cultivars. Predictions of metabolic pathways showed enrichment in carbohydrate, cofactor, amino acid, and other secondary metabolite biosynthesis.
FOOD RESEARCH INTERNATIONAL
(2021)
Article
Plant Sciences
Cintia Caroline Gouveia da Silva, Erika Valente de Medeiros, Giselle Gomes Monteiro Fracetto, Felipe Jose Cury Fracetto, Argemiro Pereira Martins Filho, Jose Romualdo de Sousa Lima, Gustavo Pereira Duda, Diogo Paes da Costa, Claude Hammecker
Summary: The combination of coffee biochar residue with cow manure fertilizer significantly improved the chemical and microbiological attributes of sandy soil cultivated with beans. Different dosages of biochar had distinct effects on the structure of the soil microbial community.
JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION
(2021)
Article
Microbiology
Vishnu Raja Vijayakumar, Karthikeyan Saravanan, Maharaja Somasundaram, Rajkumar Jayaraj, Panneerselvam Annamalai, Thajuddin Nooruddin, Dhanasekaran Dharumadurai
Summary: A lichen is a composite organism formed of algae or cyanobacteria that live in a symbiotic relationship with fungus. This study analyzed the microbial composition of lichen samples from different habitats and found distinct differences in their profiles. The results suggest that the bacterial population associated with corticolous lichen is influenced by geographic locations and growth environments.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Ningning Xu, Wenlei Wang, Kai Xu, Yan Xu, Dehua Ji, Changsheng Chen, Chaotian Xie
Summary: This study investigated the effects of seasons and different seaweed species on microbial communities. The results showed that environmental factors in seaweed cultivation zones significantly influenced the variability of fungal and bacterial communities. Certain microbial groups responded positively to seaweed cultivation, and their enrichment was influenced by the composition of dissolved organic matter (DOM).
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Food Science & Technology
Niki Mougiou, Antiopi Tsoureki, Spyros Didos, Ioanna Bouzouka, Sofia Michailidou, Anagnostis Argiriou
Summary: The analysis of table olives microbiome using next-generation sequencing has provided valuable information about the microbial community composition of this popular fermented food. This study used 16S and 18S rRNA sequencing to evaluate the microbial communities of table olives from five Greek popular cultivars, fermented by Greek or Spanish style. The results showed that different curing and fermentation methods had an impact on the microbial composition and biochemical properties of the olives.
Article
Microbiology
Melanie L. Blanchette, Mark A. Lund
Summary: This research aimed to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The study found that water quality and microbial assemblages in pit lakes varied significantly across space and time, with most taxa being rare. Microbial communities were influenced by environmental variables, however, no single variable was consistently significant spatially or temporally.
Article
Microbiology
Eva Garcia-Lopez, Sandra Serrano, Miguel Angel Calvo, Sonia Pena Perez, Silvia Sanchez-Casanova, Laura Garcia-Descalzo, Cristina Cid
Summary: The study found that the englacial ecosystem in Antarctic glaciers shows a great diversity of bacteria and microeukaryotes, with differences in microbial composition between glaciers. There is a gradient in the abundance and diversity of microbial communities from the volcano, with a trend of increasing from west to east.
Article
Marine & Freshwater Biology
Patricia Gomez-Villegas, Jose Luis Guerrero, Miguel Perez-Rodriguez, Juan Pedro Bolivar, Antonio Morillo, Javier Vigara, Rosa Leon
Summary: This study investigated the microbial community in phosphogypsum (PG) deposits in Huelva, Spain and identified a diverse range of microbial species that can thrive in the extreme acidic and polluted environment. The study also discovered the presence of algae, fungi, and ciliates in the PG stacks. The findings suggest that the microbial community in these PG deposits may play a significant role in the dynamics of contaminating compounds and have potential for biotechnological applications.
AQUATIC TOXICOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Junwon Yang, Jonghyun Park, Yeonjae Jung, Jongsik Chun
Summary: The Animal Microbiome Database (AMDB) is the first to provide taxonomic profiles of gut microbiota in various animal species, facilitating research on the relationship between gut microbiota and animal hosts.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Geosciences, Multidisciplinary
Tiago de Oliveira Santos, Felipe Jose Cury Fracetto, Valdomiro Severino de Souza Junior, Jose Coelho de Araujo Filho, Mario Andrade Lira Junior, Jose Petronio Mendes Junior, Marcos Siqueira Neto, Yure Romero Oliveira da Silva, Felipe Martins do Rego Barros, Giselle Gomes Monteiro Fracetto
Summary: Overexploitation of natural forest resources in the tropical semiarid region of Brazil leads to soil degradation, reduction in microbial and plant biomass, and loss of C and N from soils. This study found that degraded soils had significantly lower C and N stocks, abundance and activity of total bacteria and fungi, and decreased abundance of diazotrophic and phosphorus-mineralizing bacteria compared to preserved or partially degraded soils. However, the abundance of total bacteria and fungi genes and glomalin content remained unchanged. The alkaline phosphatase activity indicated that mineralizing microorganisms can still make phosphorus constantly available in soils without vegetation cover.
Article
Ecology
Nicolas Ferry, Marion Cordonnier, Florence D. Hulot, Farisayi Dakwa, Lovelater Sebele, Stephane Dray, Herve Fritz, Marion Valeix
JOURNAL OF ARID ENVIRONMENTS
(2020)
Article
Plant Sciences
Eliane Schermer, Marie-Claude Bel-Venner, Jean-Michel Gaillard, Stephane Dray, Vincent Boulanger, Iris Le Ronce, Gilles Oliver, Isabelle Chuine, Sylvain Delzon, Samuel Venner
Article
Biochemistry & Molecular Biology
Benjamin Alric, Cajo J. F. ter Braak, Yves Desdevises, Hugo Lebredonchel, Stephane Dray
MOLECULAR ECOLOGY RESOURCES
(2020)
Article
Ecology
Nicolas Ferry, Moreangels M. Mbizah, Andrew J. Loveridge, David W. Macdonald, Stephane Dray, Herve Fritz, Marion Valeix
Article
Evolutionary Biology
Jean Thioulouse, Sabrina Renaud, Anne-Beatrice Dufour, Stephane Dray
Summary: Recent papers have highlighted issues with between-group Principal Component Analysis (bgPCA), such as inflated and artificial differences between groups, which can be circumvented using cross-validation. The ade4 package for R statistical software provides tools and functions for computing bgPCA, testing significant group presence, performing cross-validation, and avoiding spurious groups. Validating this approach with real data and random numbers tables shows its effectiveness in various experimental and numerical conditions, with potential to extend to other multivariate analysis methods.
EVOLUTIONARY BIOLOGY
(2021)
Article
Ecology
Chloe Schmidt, Stephane Dray, Colin J. Garroway
Summary: The formation mechanisms of species richness gradients are not well understood, but research suggests that resource-based limits on species quantity within a region may play a role. This could impact population demography and genetic diversity, and a hypothetical framework based on ecological limits and resource availability has been developed to explain spatial biodiversity patterns. Data analysis on mammal species in North America shows that genetic diversity and species richness share spatial structure, with species richness hotspots having lower levels of genetic variation within species. A structural equation model including eco-evolutionary processes supports these spatial patterns, indicating that broad-scale patterns of species richness and genetic diversity may be influenced by intraspecific demographic and evolutionary processes acting simultaneously.
Article
Plant Sciences
Nicolas Ferry, Stephane Dray, Herve Fritz, Audrey Ipavec, Benjamin J. Wigley, Tristan Charles-Dominique, Mathieu Bourgarel, Lovelater Sebele, Marion Valeix
Summary: The study investigated the long-term effects of high elephant densities on vegetation structure and species composition in the woodland savanna of Hwange National Park, Zimbabwe. While elephants had some impact on vegetation structure, changes in plant community composition and functional traits were minimal.
JOURNAL OF VEGETATION SCIENCE
(2021)
Article
Ecology
Christophe Botella, Stephane Dray, Catherine Matias, Vincent Miele, Wilfried Thuiller
Summary: This study evaluated the ability of seven graph embedding methods to disentangle architectural similarities of interactions networks for supervised and unsupervised posterior analytic tasks. The performance of the methods depended on the targeted ecological properties and the importance of normalizing the embedding for network sizes was highlighted for meaningful posterior unsupervised analyses.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Editorial Material
Ecology
Gilles Guillot, Ali Arab, Janine Baerbel Illian, Stephane Dray
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Chloe Schmidt, Jason Munshi-South, Stephane Dray, Colin J. Garroway
Summary: This study examined the patterns of genetic diversity and species richness in amphibians in North America. The results showed that the spatial patterns of population genetic diversity were opposite to patterns of species richness and genetic differentiation. While resource availability and niche heterogeneity predicted a large proportion of the variation in species richness, they were poor predictors of genetic diversity. The findings suggest that heterogeneity plays a significant role in shaping genetic and species biodiversity patterns in amphibians, but the considerable variation in life history across amphibians makes it difficult to infer general processes producing spatial patterns of amphibian genetic diversity.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Multidisciplinary Sciences
Sandra Diaz, Jens Kattge, Johannes H. C. Cornelissen, Ian J. Wright, Sandra Lavorel, Stephane Dray, Bjoern Reu, Michael Kleyer, Christian Wirth, I. Colin Prentice, Eric Garnier, Gerhard Boenisch, Mark Westoby, Hendrik Poorter, Peter B. Reich, Angela T. Moles, John Dickie, Amy E. Zanne, Jerome Chave, S. Joseph Wright, Serge N. Sheremetiev, Herve Jactel, Christopher Baraloto, Bruno E. L. Cerabolini, Simon Pierce, Bill Shipley, Fernando Casanoves, Julia S. Joswig, Angela Guenther, Valeria Falczuk, Nadja Rueger, Miguel D. Mahecha, Lucas D. Gorne, Bernard Amiaud, Owen K. Atkin, Michael Bahn, Dennis Baldocchi, Michael Beckmann, Benjamin Blonder, William Bond, Ben Bond-Lamberty, Kerry Brown, Sabina Burrascano, Chaeho Byun, Giandiego Campetella, Jeannine Cavender-Bares, F. Stuart Chapin, Brendan Choat, David Anthony Coomes, William K. Cornwell, Joseph Craine, Dylan Craven, Matteo Dainese, Alessandro Carioca de Araujo, Franciska T. de Vries, Tomas Ferreira Domingues, Brian J. Enquist, Jaime Fagundez, Jingyun Fang, Fernando Fernandez-Mendez, Maria T. Fernandez-Piedade, Henry Ford, Estelle Forey, Gregoire T. Freschet, Sophie Gachet, Rachael Gallagher, Walton Green, Greg R. Guerin, Alvaro G. Gutierrez, Sandy P. Harrison, Wesley Neil Hattingh, Tianhua He, Thomas Hickler, Steven I. Higgins, Pedro Higuchi, Jugo Ilic, Robert B. Jackson, Adel Jalili, Steven Jansen, Fumito Koike, Christian Koenig, Nathan Kraft, Koen Kramer, Holger Kreft, Ingolf Kuehn, Hiroko Kurokawa, Eric G. Lamb, Daniel C. Laughlin, Michelle Leishman, Simon Lewis, Frederique Louault, Ana C. M. Malhado, Peter Manning, Patrick Meir, Maurizio Mencuccini, Julie Messier, Regis Miller, Vanessa Minden, Jane Molofsky, Rebecca Montgomery, Gabriel Montserrat-Marti, Marco Moretti, Sandra Mueller, UElo Niinemets, Roma Ogaya, Kinga Oellerer, Vladimir Onipchenko, Yusuke Onoda, Wim A. Ozinga, Juli G. Pausas, Begona Peco, Josep Penuelas, Valerio D. Pillar, Clara Pladevall, Christine Roemermann, Lawren Sack, Norma Salinas, Brody Sandel, Jordi Sardans, Brandon Schamp, Michael Scherer-Lorenzen, Ernst-Detlef Schulze, Fritz Schweingruber, Satomi Shiodera, Enio Sosinski, Nadejda Soudzilovskaia, Marko J. Spasojevic, Emily Swaine, Nathan Swenson, Susanne Tautenhahn, Ken Thompson, Alexia Totte, Rocio Urrutia-Jalabert, Fernando Valladares, Peter van Bodegom, Francois Vasseur, Kris Verheyen, Denis Vile, Cyrille Violle, Betsy von Holle, Patrick Weigelt, Evan Weiher, Michael C. Wiemann, Mathew Williams, Justin Wright, Gerhard Zotz
Summary: The 'Global Spectrum of Plant Form and Function Dataset' provides species mean values for six vascular plant traits on a global scale. Based on a large number of trait records, the dataset is the largest and most accurate compilation of vascular plant species mean traits to date, with comprehensive quality control.
Article
Ecology
Marc Ohlmann, Catherine Matias, Giovanni Poggiato, Stephane Dray, Wilfried Thuiller, Vincent Miele
Summary: Separating the effects of environmental factors and interspecific interactions on species distributions has been a major challenge in community ecology. A new statistical model called ELGRIN has been developed to address this challenge by combining knowledge on interspecific interactions, environmental data, and species occurrences. The model has been successfully tested on simulated and empirical data, and applied to vertebrate trophic networks in the European Alps. It has been found that factors such as altitude, species richness, and connectance significantly influence the overall effect of biotic interactions on species distributions.
ECOLOGICAL MODELLING
(2023)
Article
Biology
Mathieu Douhard, Stephane Dray
Summary: Fisher's principle states that natural selection favors equal numbers of male and female births, but differences in rearing costs and mortality rates can affect sex ratios. A study found that globally, male-biased childhood mortality does influence male birth proportions, but this relationship disappears when accounting for spatial autocorrelation.
Article
Biochemistry & Molecular Biology
Daniel Aguirre de Carcer
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)
Article
Genetics & Heredity
Marcos Parras-Molto, Daniel Aguirre de Carcer
MICROBIAL GENOMICS
(2020)