Article
Genetics & Heredity
Artem Nedoluzhko, Svetlana Yu Orlova, Denis S. Kurnosov, Alexei M. Orlov, Jorge Galindo-Villegas, Sergey M. Rastorguev
Summary: Genomic signatures of freshwater adaptivity were found in the lake ecological form of Pacific herring, indicating the influence of directional selection and genetic differentiation. Some of the discriminating loci are associated with osmoregulation, suggesting the role of physiological adaptation in freshwater environments for this species.
Article
Environmental Sciences
Ting Wang, Jialin Li, Hongmei Jing, Song Qin
Summary: Marine Synechococcus, a main group of picocyanobacteria, exhibits high phylogenetical and phenotypical diversity, and understanding its genetic variation, niche division, and potential functions is crucial for gaining a comprehensive understanding of marine ecosystems.
MARINE ENVIRONMENTAL RESEARCH
(2022)
Article
Ecology
F. M. Windsor
Summary: Research in freshwater ecosystems has historically focused on trophic interactions and food webs, but there is a need to investigate a wider range of non-trophic interactions and the ecological networks they form. Understanding all potential interactions, from mutualistic to antagonistic, is crucial for understanding ecosystem assembly, structure, and function. To advance our understanding, we can learn from research in marine and terrestrial ecosystems and utilize emerging technologies to merge ecological interactions in freshwater ecosystems into networks.
JOURNAL OF ANIMAL ECOLOGY
(2023)
Article
Biodiversity Conservation
Andrew S. Watson, Michael J. H. Hickford, David R. Schiel
Summary: Freshwater reserves are undervalued in fisheries conservation, despite being essential for the protection of threatened freshwater ecosystems. The study shows that closed streams have notable reserve effects in increasing fish numbers, although at the cost of smaller individuals. Partially closed streams also offer some fisheries benefits compared to fully open streams.
JOURNAL OF APPLIED ECOLOGY
(2021)
Article
Microbiology
Xiuping Liu, Lu Lyu, Jiaqian Li, Biswarup Sen, Mohan Bai, Jason E. Stajich, Jackie L. Collier, Guangyi Wang
Summary: This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains and investigates their ecological functions from the perspective of organic matter degradation using comparative genomics and biochemical assays. The results show that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems and can actively participate in marine biochemical cycles as decomposers. The study also emphasizes the dual roles of endoglucanase in the process of cellulose degradation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Jian Zeng, Angli Xue, Longda Jiang, Luke R. Lloyd-Jones, Yang Wu, Huanwei Wang, Zhili Zheng, Loic Yengo, Kathryn E. Kemper, Michael E. Goddard, Naomi R. Wray, Peter M. Visscher, Jian Yang
Summary: The study reveals that approximately 1% of the human genome is mutational targets with a mean selection coefficient of 0.001. Common diseases tend to have fewer mutational targets and have undergone stronger selection pressure compared to other traits. The analyses show that selection signatures vary across genomic regions, with coding regions having the strongest selection signature.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Giovanna Capovilla, Rogier Braakman, Gregory P. Fournier, Thomas Hackl, Julia Schwartzman, Xinda Lu, Alexis Yelton, Krista Longnecker, Melissa C. Kido Soule, Elaina Thomas, Gretchen Swarr, Alessandro Mongera, Jack G. Payette, Kurt G. Castro, Jacob R. Waldbauer, Elizabeth B. Kujawinski, Otto X. Cordero, Sallie W. Chisholm
Summary: The widespread occurrence of genes for chitin degradation in marine picocyanobacteria indicates their ability to degrade chitin and enhance growth by attaching to chitin particles. The development of chitin degradation pathway allowed cyanobacteria to adapt and expand in the water column, leading to the rise of modern marine ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Justin C. Podowski, Sara F. Paver, Ryan J. Newton, Maureen L. Coleman
Summary: Microorganisms play critical roles in Earth's nitrogen cycle. However, little is known about freshwater nitrifiers. In this study, genomes of freshwater nitrifiers in the Laurentian Great Lakes were reconstructed, revealing their unique biodiversity and filling important knowledge gaps.
Article
Microbiology
Lena A. Schallenberg, John K. Pearman, Carolyn W. Burns, Susanna A. Wood
Summary: This study used epifluorescence microscopy and 16S rRNA metabarcoding to assess the horizontal-spatial abundance and community structure of freshwater picocyanobacteria (Pcy) in two contrasting lakes in New Zealand. Significant differences in Pcy abundance and community composition were found between and within oligotrophic and hypertrophic lakes, with spatial variability particularly pronounced in the oligotrophic Lake Wanaka. The study suggests that single spot-samples are insufficient to understand Pcy dynamics and phytoplankton dynamics in lakes.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Microbiology
Ebuka Canisius Nwosu, Patricia Roeser, Sizhong Yang, Sylvia Pinkerneil, Lars Ganzert, Elke Dittmann, Achim Brauer, Dirk Wagner, Susanne Liebner
Summary: This study investigated the seasonal and spatial dynamics of cyanobacteria in Lake Tiefer See, NE Germany, using high-throughput DNA sequencing. The results showed significant seasonal variations in cyanobacterial community composition, with different species dominating in different seasons. The study also revealed potential niche specialization and coexistence among cyanobacteria taxa driven by light and nutrient dynamics, as well as considerable spatiotemporal changes in the community of cyanobacteria on the species level.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kenneth K. Askelson, Garth M. Spellman, Darren Irwin
Summary: Analysis of genomic variation reveals high differentiation among white-breasted nuthatch populations, suggesting the existence of at least three species. It also shows evidence of introgression between a ghost lineage and a current population, contributing to differentiation.
Article
Engineering, Environmental
Zhao-Feng Guo, Wiebke J. Boeing, Yao-Yang Xu, Edoardo Borgomeo, Dong Liu, Yong-Guan Zhu
Summary: The geographical distribution, influencing factors and pollution hotspots of ARGs in freshwater reservoirs were discovered through a data-driven framework. The distribution pattern and pollution hotspots of ARGs varied in reservoir waters and sediments based on different internal and external factors. Integrated research and improved understanding of ARG contamination mechanisms are needed, along with the development of targeted monitoring and evaluation systems to maintain ecosystem services in freshwater reservoirs and safeguard human health.
Article
Clinical Neurology
Helena Martins Custodio, Lisa M. Clayton, Ravishankara Bellampalli, Susanna Pagni, Katri Silvennoinen, Richard Caswell, John C. Ambrose, Andreas Brunklaus, Renzo Guerrini, Bobby P. C. Koeleman, Johannes R. Lemke, Rikke S. Moler, Ingrid E. Scheffer, Sarah Weckhuysen, Federico Zara, Sameer Zuberi, Karoline Kuchenbaecker, Simona Balestrini, James D. Mills, Sanjay M. Sisodiya
Summary: Dravet syndrome, a rare severe epilepsy caused by SCN1A variants, shows phenotypic heterogeneity that cannot be fully explained by the causal variant or clinical factors. In this study, additional genomic variation and rare variants in epilepsy-related genes were found to contribute to the phenotypic diversity of adults with SCN1A-related Dravet syndrome. The study also revealed differences in polygenic risk scores for intelligence and longevity between Dravet syndrome and epilepsy controls, suggesting that genetic background plays a role in the syndrome's phenotype and mortality risk.
Article
Biology
Shoichi Kato, Osami Misumi, Shinichiro Maruyama, Hisayoshi Nozaki, Yayoi Tsujimoto-Inui, Mari Takusagawa, Shigekatsu Suzuki, Keiko Kuwata, Saki Noda, Nanami Ito, Yoji Okabe, Takuya Sakamoto, Fumi Yagisawa, Tomoko M. M. Matsunaga, Yoshikatsu Matsubayashi, Haruyo Yamaguchi, Masanobu Kawachi, Haruko Kuroiwa, Tsuneyoshi Kuroiwa, Sachihiro Matsunaga
Summary: Multi-omic and evolutionary analyses of the ultrasmall green alga, Medakomo hakoo, suggest it belongs to a new genus within the class Trebouxiophyceae and provide insight into essential genes for microalgae. With a genome size of 15.8 Mbp and 7629 genes, it is among the smallest genomes in the Viridiplantae. Comparative analyses reveal shared gene sets among 15 ultrasmall algae, enabling identification of essential genes for metabolism and cellular functions.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Karolina Bacela-Spychalska, Remi Wattier, Maria Teixeira, Richard Cordaux, Adrien Quiles, Michal Grabowski, Piotr Wroblewski, Mykola Ovcharenko, Daniel Grabner, Dieter Weber, Alexander M. Weigand, Thierry Rigaud, Adler R. Dillman
Summary: This study characterized Nosema spp. infections in different amphipod species from various European localities using the SSU marker and performed a phylogenetic reconstruction based on RPB1 gene sequences to assess the phylogenetic diversity, host specificity, and evolutionary history of gammarid-infecting Nosema lineages. The results showed that Nosema spp. are abundant, widespread, and diverse in European gammarids, and the use of RPB1 marker revealed more host-parasite relationships compared to the SSU marker.
Article
Environmental Sciences
David M. Costello, Scott D. Tiegs, Luz Boyero, Cristina Canhoto, Krista A. Capps, Michael Danger, Paul C. Frost, Mark O. Gessner, Natalie A. Griffiths, Halvor M. Halvorson, Kevin A. Kuehn, Amy M. Marcarelli, Todd Royer, Devan M. Mathie, Ricardo J. Albarino, Clay P. Arango, Jukka Aroviita, Colden Baxter, Brent J. Bellinger, Andreas Bruder, Francis J. Burdon, Marcos Callisto, Antonio Camacho, Fanny Colas, Julien Cornut, Veronica Crespo-Perez, Wyatt F. Cross, Alison M. Derry, Michael M. Douglas, Arturo Elosegi, Elvira Eyto, Veronica Ferreira, Carmen Ferriol, Tadeusz Fleituch, Jennifer J. Follstad Shah, Andre Frainer, Erica A. Garcia, Liliana Garcia, Pavel E. Garcia, Darren P. Giling, R. Karina Gonzales-Pomar, Manuel A. S. Graca, Hans-Peter Grossart, Francois Guerold, Luiz U. Hepp, Scott N. Higgins, Takuo Hishi, Carlos Iniguez-Armijos, Tomoya Iwata, Andrea E. Kirkwood, Aaron A. Koning, Sarian Kosten, Hjalmar Laudon, Peter R. Leavitt, Aurea L. Lemes da Silva, Shawn J. Leroux, Carri J. LeRoy, Peter J. Lisi, Frank O. Masese, Peter B. McIntyre, Brendan G. McKie, Adriana O. Medeiros, Marko Milisa, Yo Miyake, Robert J. Mooney, Timo Muotka, Jorge Nimptsch, Riku Paavola, Isabel Pardo, Ivan Y. Parnikoza, Christopher J. Patrick, Edwin T. H. M. Peeters, Jesus Pozo, Brian Reid, John S. Richardson, Jose Rincon, Geta Risnoveanu, Christopher T. Robinson, Anna C. Santamans, Gelas M. Simiyu, Agnija Skuja, Jerzy Smykla, Ryan A. Sponseller, Franco Teixeira-de Mello, Sirje Vilbaste, Veronica D. Villanueva, Jackson R. Webster, Stefan Woelfl, Marguerite A. Xenopoulos, Adam G. Yates, Catherine M. Yule, Yixin Zhang, Jacob A. Zwart
Summary: Microbes play a critical role in plant litter decomposition and the fate of carbon in rivers and riparian zones. The process of nutrient immobilization, whereby microbes acquire nitrogen and phosphorus from the environment during the decomposition of low-nutrient plant litter, is influenced by nutrient loading and changing climate. However, environmental controls on immobilization are poorly understood due to the complex interplay between environmental factors and plant litter chemistry.
GLOBAL BIOGEOCHEMICAL CYCLES
(2022)
Article
Environmental Sciences
Antonio Camacho, Cesar Mora, Antonio Picazo, Carlos Rochera, Alba Camacho-Santamans, Daniel Morant, Luis Roca-Perez, Jose Joaquin Ramos-Miras, Jose A. Rodriguez-Martin, Rafael Boluda
Summary: This study examines the relationship between microbial diversity patterns and soil quality in a Mediterranean context, and finds that human activities such as agriculture and deforestation lead to changes in soil properties, which in turn affect microbial diversity and biomass.
Article
Agronomy
Maria Belenguer-Manzanedo, Carles Alcaraz, Antonio Camacho, Carles Ibanez, Mar Catala-Forner, Maite Martinez-Eixarch
Summary: This study aims to evaluate the effects of different combinations of flooding and straw incorporation timing in the post-harvest of paddy agrosystem on greenhouse gas emissions and net ecosystem carbon balance. The results show that non-winter flooding and late straw incorporation strategies are more effective in reducing CH4 and CO2 emissions.
Article
Ecology
Angel Galvez, Pedro R. Peres-Neto, Andreu Castillo-Escriva, Fabian Bonilla, Antonio Camacho, Eduardo M. Garcia-Roger, Sanda Iepure, Javier Miralles-Lorenzo, Juan S. Monros, Carla Olmo, Antonio Picazo, Carmen Rojo, Juan Rueda, Maria Sahuquillo, Mahmood Sasa, Mati Segura, Xavier Armengol, Francesc Mesquita-Joanes
Summary: By studying pond ecosystems in two different geographical regions of the world, it was found that temperate ponds are more influenced by environmental and spatial factors, while tropical ponds are more influenced by climatic variability and dispersal processes. The relative importance of space and environment varies greatly among different taxonomic groups, with active dispersers being more influenced by the environment and passive dispersers being more influenced by spatial factors. These results support the classic view of stronger abiotic niche constraints in temperate areas compared to the tropics.
Article
Microbiology
Asier Zaragoza-Solas, Jose M. Haro-Moreno, Francisco Rodriguez-Valera, Mario Lopez-Perez
Summary: In this study, the recovery of viral diversity from marine samples using long-read sequencing was explored. The results showed that a significant portion of marine viral diversity was directly recovered by PacBio circular consensus sequencing (CCS) reads, with some sequences not being detected in the short- and long-read assembly. Additionally, the hybrid assembly of long and short reads improved the length and host assignment of the viral sequences.
Article
Environmental Sciences
Mirco Bundschuh, Francesc Mesquita-Joanes, Andreu Rico, Antonio Camacho
Summary: Recovery, recolonization, and adaptation are processes that regenerate local populations and communities after chemical stress. Recolonization involves the dispersal of organisms from other areas to fill empty niches, while adaptation refers to phenotypic and genetic changes that allow the persistence of existing taxa. Understanding the relative importance of these processes is crucial for the regeneration of biological communities after chemical exposure. This study provides case studies and recommendations to assess and compare the importance of these processes for risk assessment and ecosystem management.
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY
(2023)
Article
Limnology
Andreu Castillo-Escriva, Angel Baltanas, Antonio Camacho, David J. Horne, Joan Lluis Pretus, Francesc Mesquita-Joanes
Summary: The study establishes a non-marine ostracod database for the Iberian Peninsula, the Balearic Islands, and Macaronesia, providing information on species distribution and biogeography. The updated database is crucial for understanding the biodiversity and biogeographic patterns of these organisms in this hotspot, as well as analyzing their species-environment relationships in the context of global changes.
JOURNAL OF LIMNOLOGY
(2023)
Article
Environmental Sciences
Felipe A. S. Barbosa, Leonardo A. S. Brait, Felipe Hernandes Coutinho, Camilo M. Ferreira, Eduardo Freitas Moreira, Lucas de Queiroz Salles, Pedro Milet Meirelles
Summary: Aquifers are of great importance for society, economy, and ecology as they provide a significant portion of the world's freshwater supply. Analyzing microbial communities in different aquifers can help detect and predict environmental impacts. It was found that aquifer categories and low-abundant candidate taxa are strong predictors of microbial community structure.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Jose M. Haro-Moreno, Mario Lopez-Perez, Alexey Alekseev, Elizaveta Podoliak, Kirill Kovalev, Valentin Gordeliy, Ramunas Stepanauskas, Francisco Rodriguez-Valera
Summary: Microbial rhodopsins can be found multiple times in a single genome with different functions. A new type of rhodopsin, called flotillin-associated rhodopsin (FArhodopsin), was discovered in marine and freshwater microbes. FArhodopsins are associated with dim light conditions and potentially play a role in membrane microstructure formation. The physiological role of FArhodopsins is different from the well-known proteorhodopsin proton pumps.
Article
Limnology
Pedro J. Cabello-Yeves, Antonio Picazo, Juan J. Roda-Garcia, Francisco Rodriguez-Valera, Antonio Camacho
Summary: The microbial ecology of a meromictic lake in Spain was studied using metagenomics. The study found diverse microbial communities in different water layers, with their metabolic capabilities influenced by the physical-chemical environment. Additionally, the study identified microbial communities in high-salinity waters that have potential for biotechnological applications in fermentation and biosynthesis.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Limnology
Angel Galvez, Andreu Castillo-Escriva, Anne Magurran, Ivan Alambiaga, Fabian Bonilla, Antonio Camacho, Eduardo M. Garcia-Roger, Sanda Iepure, Javier Miralles-Lorenzo, Juan S. Monros, Carla Olmo, Antonio Picazo, Carmen Rojo, Juan Rueda, Mahmood Sasa, Mati Segura, Xavier Armengol, Francesc Mesquita-Joanes
Summary: This study compares the diversity of multiple taxa inhabiting tropical and Mediterranean temporary ponds using a spatial and temporal approach. The results show higher gamma and alpha diversity in tropical ponds, but phytoplankton and microinvertebrates from the Mediterranean region matched or exceeded tropical alpha diversity on some occasions. Spatial beta diversity did not differ between regions, and temporal beta diversity showed similar patterns. However, macroinvertebrates and amphibians exhibited differential effects on community variation observable only in animals with longer life-spans.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Microbiology
Izabela Mujakic, Pedro J. Cabello-Yeves, Cristian Villena-Alemany, Kasia Piwosz, Francisco Rodriguez-Valera, Antonio Picazo, Antonio Camacho, Michal Koblizek
Summary: Gemmatimonadota is a bacterial phylum commonly found in various environments, and their adaptation to different environments is reflected in their genomic characteristics and metabolic potential.
MICROBIOLOGY SPECTRUM
(2023)
