Article
Biodiversity Conservation
Andres Baselga, Carola Gomez-Rodriguez, Miguel B. Araujo, Adrian Castro-Insua, Miguel Arenas, David Posada, Alfried P. Vogler
Summary: This study developed a predictive framework based on approximate Bayesian computation to quantify the role of dispersal and environmental constraints in community turnover. Simulations showed that spatial turnover rates remain invariant across genealogical scales when dispersal limitation determines species ranges, but vary when environmental constraint limits species ranges. Analysis of empirical biological communities revealed a combination of dispersal and environmental constraints influencing spatial turnover at different scales. The study highlights the importance of considering multiple genealogical scales in understanding the relative role of dispersal and environmental constraints in community turnover.
Article
Plant Sciences
Alisson Borges Miranda Santos, Vinicius Andrade Maia, Cleber Rodrigo de Souza, Nathalle Cristine Alencar Fagundes, Fernanda Moreira Gianasi, Aurelio de Jesus Rodrigues Pais, Natalia de Aguiar-Campos, Gabriela Gomes Pires, Diego Teixeira Girardelli, Jean Daniel Morel, Mariana Caroline Moreira Morelli, Felipe de Carvalho Araujo, Rubens Manoel dos Santos
Summary: The study aimed to investigate the effects of spatial distance, environmental dissimilarity, and paleoclimate on tree community turnover. Results show a weak indirect effect of spatial distance via environmental dissimilarity on taxonomic and phylogenetic turnover. Overall, tree community turnover was primarily driven by neutral, niche-based, and historical processes, with paleoclimate promoting the selection of clades and spatial distances limiting dispersal ranges of species.
JOURNAL OF PLANT ECOLOGY
(2021)
Article
Ecology
Jessica Cote, Nicolas Poulet, Laurence Blanc, Gael Grenouillet
Summary: Evaluating the effects of anthropogenic pressures on biodiversity metrics can inform biodiversity loss management and monitoring. Different types of disturbances lead to different responses in different metrics. This study aimed to understand the effects of different anthropogenic disturbances on freshwater fish communities. The results showed significant responses of all diversity indices to both climatic conditions and anthropogenic disturbances, highlighting the importance of disentangling various types of disturbances when assessing human-induced ecological impacts.
ECOLOGICAL APPLICATIONS
(2023)
Article
Plant Sciences
Guang Feng, Jihong Huang, Yue Xu, Junqing Li, Runguo Zang
Summary: Based on a 15-ha plot in central China, this study found that soil nutrients had significant negative effects on tree species richness and positive effects on species abundance distribution, while topographical characteristics had significant positive effects on species richness and negative effects on species abundance distribution, mostly mediated by soil nutrients. Soil nutrients and topographical characteristics together accounted for 9.5-17.1% of variations in diversity patterns, with soil nutrients accounting for a higher percentage (8.9-13.9%) than topographical characteristics (3.3-10.7%).
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Daniela Aros-Mualin, Sarah Noben, Dirk N. Karger, Cesar I. Carvajal-Hernandez, Laura Salazar, Adriana Hernandez-Rojas, Juergen Kluge, Michael A. Sundue, Marcus Lehnert, Dietmar Quandt, Michael Kessler
Summary: Functional traits are crucial in determining species interactions with the environment, while functional diversity describes how species assemblages are adapted to environmental changes. This study found that functional morphological trait diversity in fern assemblages is primarily driven by species richness, with environmental conditions having only a marginal impact. Increasing species richness leads to increased packing of morphological niche space and decreased morphological expansion until saturation is reached.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biodiversity Conservation
Wei Qi, Peng Jia, Shuaiwei Luo, Xiaomei Kang, Guozhen Du
Summary: The study analyzed plant biomass inequality in Qinghai-Tibetan grassland communities and found that the individual-dimension biomass inequality increased with air temperature but decreased with soil water content, while species-dimension inequality increased with higher soil water content. Community factors such as abundance, species richness, and above-ground biomass also influenced plant biomass inequality in different dimensions. This study suggests that both 'environment constraint' and 'resource competition' mechanisms operate simultaneously in driving plant biomass difference in alpine grassland systems.
ECOLOGICAL INDICATORS
(2021)
Article
Ecology
Natalia M. Koch, Daniel Stanton, Sandra C. Mueller, Leandro Duarte, Adriano A. Spielmann, Robert Luecking
Summary: This study proposes a qualitative trait approach based on nuanced traits and phylogenetic perspectives to uncover overlooked patterns. By sampling epiphytic lichens and using a functional approach, the study investigates the effects of environmental filtering and phylogenetic constraints on community assembly in the Atlantic rainforest. The results show changes in taxonomic, functional, and phylogenetic composition, structure, and diversity, with certain functional traits showing strong responses to succession.
Article
Ecology
Soren Faurby, Rasmus Ostergaard Pedersen, Jens-Christian Svenning, Alexandre Antonelli
Summary: The combined effects of human activities on extinction and speciation rates on biodiversity over geological time-scales are uncertain. While human-driven speciation may counterbalance the loss in species numbers, recovery of phylogenetic diversity could take several millions of years. It is crucial to reduce pressures on biodiversity and consider long-term changes.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Article
Physics, Multidisciplinary
Michiel Stock, Laura Hoebeke, Bernard De Baets
Summary: Shannon's entropy measure is used to quantify ecological diversity, with a fundamental trade-off revealed between species abundance, specificity, and redundancy. The decomposition can be extended to analyze networks over time and space, leading to notions of alpha, beta, and gamma diversity. The work aims to provide an accessible introduction to ecologists, with code available in the EcologicalNetworks.jl package.
Article
Environmental Sciences
Xue Yang, Yujuan Xu, Man Jiang, Yukun Wang, Huayu Lu, Yajie Xue, Jinlong Wang, Nianxi Zhao, Yubao Gao
Summary: Biodiversity loss can affect community processes and ecosystem functioning. This study explored the impact of different levels of biodiversity on biomass production in plant communities, finding that dominant genotypic diversity plays an important role in aboveground biomass production. The relationships between community functional diversity and biomass were mostly nonlinear.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Ecology
Gabriela Marques Peixoto, Rafael de Fraga, William Ernest Magnusson, Pedro Henrique Leitao, Igor Luis Kaefer, Albertina Pimentel Lima
Summary: Understanding the ecological and evolutionary processes that shape species assemblages in heterogeneous regions is crucial. This study aimed to investigate the causes of spatial variation in lizard assemblages in the Amazon rainforest, specifically focusing on species interactions, environmental factors, and geographic distance. The results highlight the importance of environmental filtering and forest type in determining the taxonomic and functional composition of lizard assemblages in different areas.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Environmental Sciences
Laura K. Reynolds, Christine B. Rohal, Whitney A. Scheffel, Carrie Reinhardt Adams, Charles W. Martin, Jodi Slater
Summary: This study found consistent differences in plant traits among plants collected from different locations, which persisted when these plants were grown under the same greenhouse conditions. The results suggest that selection of a single high-performing plant source may be difficult due to unpredictable environmental conditions at restoration sites, so incorporating a diverse set of collection locations is recommended to increase the likelihood of obtaining desirable traits.
ENVIRONMENTAL MANAGEMENT
(2021)
Article
Multidisciplinary Sciences
Yiqiang Chen, Yulin Wang, David Paez-Espino, Martin F. Polz, Tong Zhang
Summary: This study presents a catalogue of approximately 50,000 prokaryotic viruses from six WWTPs, significantly increasing the known diversity of AS viruses. Most viral genera are found in multiple AS systems, spanning various archaeal and bacterial phyla, and linked with functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, associated with AS foaming, is connected with 402 viral genera. These findings expand the current AS virus catalogue and provide insights for phage treatment in controlling undesired microorganisms in WWTPs.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Yi-Chun Yeh, Jed A. Fuhrman
Summary: This study used ribosomal RNA sequencing and viral metagenomics to quantify the microbial community composition in the San-Pedro Ocean Time-series over several years. The results showed that physicochemical factors, as well as the viral and phytoplankton communities, are important determinants of the temporal dynamics of prokaryotes. Biotic interactions play a significant role in shaping the prokaryotic community, and the importance of specific interactions varies depending on lifestyles. Additionally, warming influences the prokaryotic community, with cyanobacterial populations shifting in response.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ronny Richter, Helen Ballasus, Rolf A. Engelmann, Christoph Zielhofer, Anvar Sanaei, Christian Wirth
Summary: Tree canopies are important for buffering climate extremes and mitigating climate change effects. However, our understanding of how environmental and tree characteristics modulate microclimate at the canopy level is limited.
SCIENTIFIC REPORTS
(2022)
Review
Clinical Neurology
Sven Kleine Bardenhorst, Emanuele Cereda, Marco Severgnini, Michela Barichella, Gianni Pezzoli, Ali Keshavarzian, Alessandro Desideri, Daniele Pietrucci, Velma T. E. Aho, Filip Scheperjans, Falk Hildebrand, Severin Weis, Markus Egert, Andre Karch, Marius Vital, Nicole Ruebsamen
Summary: The aim of this study is to reduce methodological heterogeneity in Parkinson's disease (PD) research and perform a pooled analysis. The results show that harmonizing workflows minimizes differences between statistical methods and reveals a small set of taxa associated with PD. Increased shares of Akkermansia and Bifidobacterium and decreased shares of Roseburia and Faecalibacterium are characteristic of PD-associated microbiota.
EUROPEAN JOURNAL OF NEUROLOGY
(2023)
Article
Multidisciplinary Sciences
Katherine M. Kennedy, Marcus C. de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Backhed, Peer Bork, Thorsten Braun, Frederic D. Bushman, Joel Dore, Willem M. de Vos, Ashlee M. Earl, Jonathan A. Eisen, Michal A. Elovitz, Stephanie C. Ganal-Vonarburg, Michael G. Ganzle, Wendy S. Garrett, Lindsay J. Hall, Mathias W. Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J. Macpherson, Ruth C. Massey, Alice Carolyn McHardy, Omry Koren, Trevor D. Lawley, Ruth E. Ley, Liam O'Mahony, Paul W. O'Toole, Eric G. Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M. Sloboda, Gordon C. S. Smith, Harry Sokol, Tim D. Spector, Michael G. Surette, Gerald W. Tannock, Alan W. Walker, Moran Yassour, Jens Walter
Summary: The colonization of microbial communities in the human fetus and the prenatal intrauterine environment is still controversial. Recent studies analyzing microbial populations in human fetuses indicate that the detected signals might be due to contamination during sample collection or DNA sequencing processes. The presence of live and replicating microbial populations in healthy fetal tissues contradicts fundamental concepts in immunology and clinical microbiology. This has significant implications for our understanding of human immune development and highlights the challenges in studying microbial communities in low-biomass environments.
Article
Biochemistry & Molecular Biology
Anthony Fullam, Ivica Letunic, Thomas S. B. Schmidt, Quinten R. Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M. Maistrenko, Lukas Malfertheiner, Alessio Milanese, Joao Frederico Matias Rodrigues, Claudia Sanchis-Lopez, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Christian von Mering, Peer Bork, Daniel R. Mende
Summary: The interpretation of 'omics data relies on well-annotated genomes. As the number of available microbial genomes increases, quality control and consistent annotation become crucial. proGenomes3 is a database containing 907,388 high-quality genomes with consistent annotation, including functional and taxonomic information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lazaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan Bridge, Lucy Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun P. Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman
Summary: The InterPro database has been updated with new data content and website features, providing a more user-friendly access to protein sequence classification and functional domain identification. It has also integrated features from the retiring Pfam website and developed a card game to engage the non-scientific community. Furthermore, the database explores the benefits and challenges of using artificial intelligence for protein structure prediction.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Remi Gschwind, Svetlana Ugarcina Perovic, Maja Weiss, Marie Petitjean, Julie Lao, Luis Pedro Coelho, Etienne Ruppe
Summary: Metagenomics can be utilized to monitor the spread of antibiotic resistance genes (ARGs). However, current databases mainly focus on culturable and pathogenic bacteria, resulting in a lack of information on ARGs from non-culturable and non-pathogenic bacteria. The newly developed ResFinderFG v2.0 database, based on functional metagenomics, allows for the detection of ARGs that were not found using other popular databases. This database provides a more comprehensive understanding of resistomes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Eric J. Armstrong, Julie Le-Hoang, Quentin Carradec, Jean-Marc Aury, Benjamin Noel, Benjamin C. C. Hume, Christian R. Voolstra, Julie Poulain, Caroline Belser, David A. Paz-Garcia, Corinne Cruaud, Karine Labadie, Corinne Da Silva, Cle'mentine Moulin, Emilie Boissin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Fabien Lombard, Stephane Pesant, Stephanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier P. Thomas, Romain Trouble, Rebecca Vega Thurber, Didier Zoccola, Serge Planes, Denis Allemand, Patrick Wincker
Summary: Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This study used DNA and RNA analysis to investigate gene expression patterns in Pocillopora corals across a historical thermal gradient, revealing the importance of host-photosymbiont specificity and host transcriptomic plasticity in thermal acclimatization.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Daniel Hoces, Giorgia Greter, Markus Arnoldini, Melanie L. Staubli, Claudia Moresi, Anna Sintsova, Sara Berent, Isabel Kolinko, Florence Bansept, Aurore Woller, Janine Hafliger, Eric Martens, Wolf-Dietrich Hardt, Shinichi Sunagawa, Claude Loverdo, Emma Slack
Summary: This study used genetically barcoded Bacteroides thetaiotaomicron strains to quantify population bottlenecks during colonization of the mouse gut. The results showed an inverse relationship between microbiota complexity and the colonization probability of wildtype B. theta clones. The polysaccharide capsule of B. theta is important for resistance against attacks, and the acapsular strain loses in competitive colonization.
Article
Multidisciplinary Sciences
Fabien Lombard, Guillaume Bourdin, Stephane Pesant, Sylvain Agostini, Alberto Baudena, Emilie Boissin, Nicolas Cassar, Megan Clampitt, Pascal Conan, Ophelie Da Silva, Celine Dimier, Eric Douville, Amanda Elineau, Jonathan Fin, J. Michel Flores, Jean-Francois Ghiglione, Benjamin C. C. Hume, Laetitia Jalabert, Seth G. John, Rachel L. Kelly, Ilan Koren, Yajuan Lin, Dominique Marie, Ryan McMinds, Zoe Meriguet, Nicolas Metzl, David A. Paz-Garcia, Maria Luiza Pedrotti, Julie Poulain, Mireille Pujo-Pay, Josephine Ras, Gilles Reverdin, Sarah Romac, Alice Rouan, Eric Roettinger, Assaf Vardi, Christian R. Voolstra, Clementine Moulin, Guillaume Iwankow, Bernard Banaigs, Chris Bowler, Colomban de Vargas, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Stephanie Reynaud, Shinichi Sunagawa, Matthew B. Sullivan, Olivier P. Thomas, Romain Trouble, Rebecca Vega Thurber, Patrick Wincker, Didier Zoccola, Denis Allemand, Serge Planes, Emmanuel Boss, Gaby Gorsky
Summary: The Tara Pacific expedition conducted a comprehensive study of coral ecosystems in the Pacific Ocean from 2016 to 2018. The expedition collected nearly 58,000 samples from 32 islands, including corals, fish, plankton, and seawater, for advanced analysis. The methodology of the sampling process is described, and the different datasets generated by the expedition are made accessible. The released datasets provide valuable environmental context data and have the potential to address various scientific questions.
Article
Multidisciplinary Sciences
Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne Da Silva, Stefan Engelen, Paul Mielle, Aude Perdereau, Gaelle R. Samson, Shahinaz E. Gas, Christian R. Voolstra, Pierre E. Galand, J. Michel Flores, Benjamin C. C. Hume, Gabriela Perna, Maren Ziegler, Hans-Joachim Ruscheweyh, Emilie Boissin, Sarah Romac, Guillaume A. Bourdin, Guillaume Iwankow, Clementine Moulin, David A. Paz Garcia, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Didier Forcioli, Paola Furla, Eric Gilson, Fabien Lombard, Stephane P. Pesant, Stephanie Reynaud, Shinichi Sunagawa, Olivier Thomas, Romain Trouble, Rebecca Vega Thurber, Didier H. Zoccola, Claude Scarpelli, E' Krame Jacoby, Pedro Oliveira, Jean-Marc Aury, Denis Allemand, Serge Planes, Patrick Wincker
Summary: Coral reef science aims to understand coral health and resilience to combat reef loss caused by environmental stress. The intricate symbiotic interactions within the coral holobiont play a vital role in coral resilience. The Tara Pacific project utilizes advanced sequencing technologies to study the biodiversity and complexity of coral holobionts across the Pacific Ocean, providing valuable insights for future investigations of coral reef dynamics and their future in the Anthropocene.
Article
Biology
Alex J. Veglia, Kalia S. I. Bistolas, Christian R. Voolstra, Benjamin C. C. Hume, Hans-Joachim Ruscheweyh, Serge Planes, Denis Allemand, Emilie Boissin, Patrick Wincker, Julie Poulain, Clementine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Fabien Lombard, Stephane Pesant, Stephanie Reynaud, Shinichi Sunagawa, Olivier P. Thomas, Romain Trouble, Didier Zoccola, Adrienne M. S. Correa, Rebecca L. Vega L. Thurber
Summary: A study on newly sequenced and publicly available metagenomes and genomes revealed the presence of endogenous +ssRNA viral elements within coral symbionts. These findings provide insight into the evolutionary history and hosts of contemporary viruses. This study highlights the importance of +ssRNA viruses in nested symbioses and their implications for host evolution, exaptation, and immunity in the context of reef health and disease.
COMMUNICATIONS BIOLOGY
(2023)
Article
Endocrinology & Metabolism
Karin H. U. Meier, Julian Trouillon, Hai Li, Melanie Lang, Tobias Fuhrer, Nicola Zamboni, Shinichi Sunagawa, Andrew J. Macpherson, Uwe Sauer
Summary: Anatomically resolved maps of small molecules reveal distinct spatial patterns throughout the gut of colonized and germ-free mice, which can be associated with specific microorganisms. The map of the longitudinal metabolome in the gut of healthy mice shows a shift from amino acids to organic acids, vitamins, and nucleotides along the gut. Comparisons between colonized and germ-free mice help identify the origin of metabolites and suggest specific microbial influence on the metabolome.
Article
Biochemical Research Methods
Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho
Summary: This study proposes a new semi-supervised binning method, SemiBin2, which utilizes self-supervised learning to learn feature embeddings from contigs. The results show that self-supervised learning achieves better performance than semi-supervised learning used in SemiBin1, and SemiBin2 outperforms other state-of-the-art binners. The proposed method also shows improved performance in handling long-read data.
Review
Environmental Sciences
Johan Bengtsson-Palme, Anna Abramova, Thomas U. Berendonk, Luis Pedro Coelho, Sofia K. Forslund, Remi Gschwind, Annamari Heikinheimo, Victor Hugo Jarquin-Diaz, Ayaz Ali Khan, Uli Kluemper, Ulrike Loeber, Marmar Nekoro, Adriana D. Osinska, Svetlana Ugarcina Perovic, Tarja Pitkanen, Ernst Kristian Rodland, Etienne Ruppe, Yngvild Wasteson, Astrid Louise Wester, Rabaab Zahra
Summary: Antimicrobial resistance (AMR) poses a global threat to human and animal health, and monitoring resistant bacteria and genes is crucial. However, monitoring of AMR in the environment is lacking, hindering our understanding of how resistant microorganisms are disseminated and the human health risks. This lack of knowledge includes the "normal" background levels of environmental AMR, high-risk environments for transmission, antibiotic concentration effects, and detecting non-circulating resistance genes. We need to address these knowledge gaps before implementing large-scale AMR monitoring in the environment.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Thomas S. B. Schmidt, Anthony Fullam, Pamela Ferretti, Askarbek Orakov, Oleksandr M. Maistrenko, Hans-Joachim Ruscheweyh, Ivica Letunic, Yiqian Duan, Thea Van Rossum, Shinichi Sunagawa, Daniel R. Mende, Robert D. Finn, Michael Kuhn, Luis Pedro Coelho, Peer Bork
Summary: SPIRE is a searchable planetary-scale microbiome resource that integrates various metagenome-derived microbial data modalities. It includes a large number of metagenomic samples and newly constructed high-quality genomes, as well as functional annotation and taxonomic classification information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Chuqing Sun, Jingchao Chen, Menglu Jin, Xueyang Zhao, Yun Li, Yanqi Dong, Na Gao, Zhi Liu, Peer Bork, Xing-Ming Zhao, Wei-Hua Chen
Summary: In this study, DNA methylation patterns in 8848 high-quality phages from 104 fecal samples were analyzed using single-molecule real-time sequencing. The results show that 97.60% of gut phages exhibit methylation, and certain factors correlate with methylation densities. Phages with higher methylation densities have potential viability advantages. More than one-third of the phages possess their own DNA methyltransferases (MTases), and increased MTase copies are associated with higher genome methylation densities and specific methylation motifs. These findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems.