Article
Genetics & Heredity
Jose M. Haro-Moreno, Pedro J. Cabello-Yeves, M. Pilar Garcillan-Barcia, Alexandra Zakharenko, Tamara I. Zemskaya, Francisco Rodriguez-Valera
Summary: By using long-read metagenomic sequencing, we have analyzed the Candidatus Patescibacteria in the deep waters of Lake Baikal. We have identified a novel and potentially endemic group of Candidatus Patescibacteria with high intraclade diversity. These microbes are similar to other Candidatus Patescibacteria but possess more anabolic pathways.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Biotechnology & Applied Microbiology
Ekaterina Shchapova, Anna Nazarova, Uliana Vasilyeva, Anton Gurkov, Alexander Ostyak, Andrei Mutin, Renat Adelshin, Natalia Belkova, Maxim Timofeyev
Summary: Research shows that the internal environment of crustaceans may not always be sterile, with some species harboring microorganisms even in the absence of visible pathological processes. Genetically modified indigenous hemolymph microorganisms could potentially be used for biotechnological purposes, either as local producers of compounds or sensors to physiological parameters.
MARINE BIOTECHNOLOGY
(2021)
Article
Environmental Sciences
Tiefu Xu, Yu Tao, Lan Song, Haoyu Wang, Binqiao Ren
Summary: Microbial activities in highly polluted waters are promoted, and a unique microbiome was discovered in East Lake with Proteobacteria being the dominant taxonomic group. Functional analysis revealed abundant predicted functional genes for sulfur compound respiration and sulfate respiration. This work provides evidence for future microbiome studies in nutrient-rich, alkalic, and seasonally frozen water habitats.
ENVIRONMENTAL RESEARCH
(2022)
Article
Biodiversity Conservation
Valeria Itskovich, Oxana Kaluzhnaya, Olga Glyzina, Ragothaman Prathiviraj, George Seghal Kiran, Joseph Selvin
Summary: The study of the microbial communities in Baikal sponges revealed significant differences in microbial composition between healthy and diseased sponges, with a decrease in Chlorophyta and an increase in Bacteroidetes and Cyanobacteria in diseased specimens. Additionally, the bacterial composition of diseased sponges underwent nonspecific changes, indicating a general increase in Cyanobacteria. The findings suggest that the bacterial community composition in sponge microbiomes is influenced by sponge type and the degree of disease affecting them.
Article
Geosciences, Multidisciplinary
Hyunho Lee, Gantuya Ganbat, Han-Gyul Jin, Jaemyeong Mango Seo, Sungju Moon, Hyejeong Bok, Jong-Jin Baik
Summary: This study explores the influence of Lake Baikal, the largest and deepest freshwater lake in the world, on local precipitation climate. Satellite observations and reanalysis data indicate that Lake Baikal has less summertime precipitation compared to its surrounding areas. Two simulations, one at a cloud-resolving scale and another with the lake replaced by a forest, confirm that the lake reduces summertime precipitation by 15%. This reduction is attributed to the lake's impact on air temperature, atmospheric stability, latent heat flux, and moisture convergence/divergence.
GEOPHYSICAL RESEARCH LETTERS
(2023)
Article
Remote Sensing
Kai Li, Juanle Wang, Wenjing Cheng, Yi Wang, Yezhi Zhou, Ochir Altansukh
Summary: Studying the water distribution in the Lake Baikal Basin is crucial for understanding its water resources and environment, as well as its impact on climate change and disaster prevention. This study combines local deep learning training and cloud-based big data computing to empower the Google Earth Engine with deep learning capabilities, enabling the rapid deployment of deep learning models. The method successfully extracts water bodies in the basin using various input features and improves classification accuracy.
INTERNATIONAL JOURNAL OF APPLIED EARTH OBSERVATION AND GEOINFORMATION
(2022)
Article
Microbiology
Sergey Potapov, Andrey Krasnopeev, Irina Tikhonova, Galina Podlesnaya, Anna Gorshkova, Olga Belykh
Summary: This study characterized viral fraction metatranscriptomes from the pelagic zone of oligotrophic Lake Baikal in Russia, revealing the dominance of DNA viruses such as bacteriophages and algal viruses. Transcripts similar to Pithovirus sibericum and various RNA viruses were identified. Cluster analysis showed that the transcripts from Lake Baikal grouped together with transcripts from other freshwater lakes, marine, and oceanic waters, without any separation based on trophic state, plankton fraction size, or salinity.
Article
Environmental Sciences
Malgorzata Adamczuk
Summary: This study examines the spatial distribution of 39 species of Chydoridae in Lake Piaseczno in Poland, finding differences in the distribution patterns of species in the littoral and pelagic zones. The results also show high spatial segregation among species based on depth and habitat architecture.
Article
Environmental Sciences
Andrea Gallorini, Jean-Luc Loizeau
Summary: This study investigates MeHg and THg concentrations in lake snow of Lake Geneva and suggests that lake snow can be a micro-niche for Hg methylation similar to marine snow. The study also proposes a conceptual model and mass balance model to explain the behavior of MeHg in lake snow and estimate the time required to reach a steady state in the water column.
Review
Environmental Sciences
Tracey T. Sutton, Rosanna J. Milligan, Kendra Daly, Kevin M. Boswell, April B. Cook, Maelle Cornic, Tamara Frank, Kaitlin Frasier, Daniel Hahn, Frank Hernandez, John Hildebrand, Chuanmin Hu, Matthew W. Johnston, Samantha B. Joye, Heather Judkins, Jon A. Moore, Steven A. Murawski, Nina M. Pruzinsky, John A. Quinlan, Andrew Remsen, Kelly L. Robinson, Isabel C. Romero, Jay R. Rooker, Michael Vecchione, R. J. David Wells
Summary: The Deepwater Horizon disaster had unprecedented impacts on the open-ocean ecosystem, affecting the ecology and animal populations significantly. Many animal populations continue to decline a decade later, highlighting their vulnerability and the extent of damage.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Entomology
Ekaterina Madyarova, Yulia Shirokova, Anton Gurkov, Polina Drozdova, Boris Baduev, Yulia Lubyaga, Zhanna Shatilina, Maria Vishnevskaya, Maxim Timofeyev
Summary: This study compared the metabolic reactions of two deep-water amphipods from Lake Baikal to pressure decreases. Despite some differences in long-term survival, both species are suitable for laboratory studies as freshwater model organisms adapted to large pressure variations.
Article
Microbiology
Daniel G. Dunlap, Libing Yang, Shulin Qin, Kelvin Li, Adam Fitch, Laurence Huang, Bryan J. McVerry, Timothy W. Hand, Barbara A. Methe, Alison Morris
Summary: We applied magnetic-activated cell sorting to identify immunoglobulin G-bound bacteria in the lung and found distinct bacterial communities that differed from raw bronchoalveolar lavage, revealing differences not detected by traditional analyses. We also discovered that immunoglobulin binding of lung bacteria is associated with the production of pulmonary cytokines.
Article
Environmental Sciences
Xiuping Liu, Jiaqian Li, Xueyan Ding, Kalyani Sen, Yaodong He, Mohan Bai, Guangyi Wang
Summary: This study reveals significant annual dynamics in bacterioplankton community in the South China Sea, showing that epipelagic-bathypelagic connective amplicon sequence variants influence both the community structure and carbon cycling functions of deep-sea bacterioplankton.
Article
Biodiversity Conservation
Diana Arva, Attila Mozsar, Barbara Barta, Andras Specziar, Monika Toth, Attila Bohus, Blanka Gal, Denes Schmera
Summary: The recreational use of water bodies poses new challenges to lake ecosystems, as shown by a study on the impact of recreational beaches on the shoreline biodiversity of Lake Balaton in Hungary. The establishment and use of recreational beaches were found to have negative effects on local biodiversity, highlighting the importance of carefully considering both economic and conservation aspects when planning and maintaining recreational beaches.
ECOLOGICAL INDICATORS
(2021)
Article
Biochemistry & Molecular Biology
Carl A. St John, Thaddaeus J. Buser, Victoria E. Kee, Sergei Kirilchik, Bakhtiar Bogdanov, David Neely, Michael Sandel, Andres Aguilar
Summary: This study examined the evolutionary relationships and novel morphological adaptations within the Baikal cottid genus Cottocomephorus using a combination of mitochondrial DNA and restriction site associated DNA sequencing. Three lineages were uncovered within Cottocomephorus, with evidence of recent divergence, admixture, and deep divergence among species. Contrary to other fish radiations, there was no evidence of ancient hybridization among Cottocomephorus species. Digital morphology revealed highly specialized pelagic phenotypes reflecting adaptation to the benthopelagic niche, with ongoing adaptation to the pelagic zone observed among species. This study highlights the importance of speciation along a benthic-pelagic gradient in Cottocomephorus and other adaptive fish radiations.
Article
Microbiology
Ana Duran-Viseras, Adrian-Stefan Andrei, Blanca Vera-Gargallo, Rohit Ghai, Cristina Sanchez-Porro, Antonio Ventosa
Summary: The study isolated two new species of haloarchaea using a culturomics-based approach in hypersaline environments, revealing their unique lifestyles and worldwide distribution. This research is significant for advancing our understanding of microbial diversity and ecological functions.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Correction
Microbiology
Vinicius S. Kavagutti, Adrian-Stefan Andrei, Maliheh Mehrshad, Michaela M. Salcher, Rohit Ghai
Article
Limnology
Cristiana Callieri, Edoardo Mandolini, Roberto Bertoni, Rosaria Lauceri, Antonio Picazo, Antonio Camacho, Pedro J. Cabello-Yeves
Summary: This atlas provides an overview of picocyanobacteria cultures held by the CNR-IRSA collection, mainly monoclonal strains of Synechococcus and Cyanobium genera isolated from lakes around the world. These strains are not available in other collections and researchers can request them for research purposes.
JOURNAL OF LIMNOLOGY
(2021)
Article
Microbiology
Izabela Mujakic, Adrian- Stefan Andrei, Tanja Shabarova, Livia Kolesar Fecskeova, Michaela M. Salcher, Kasia Piwosz, Rohit Ghai, Michal Koblizek
Summary: Gemmatimonadota bacteria are widely distributed in natural environments, including soil and water bodies. Analysis of metagenomes from five freshwater lakes in central Europe revealed diverse Gemmatimonadota populations, some of which are closely associated with phytoplankton and possess unique mitochondrial assembly genes.
Article
Genetics & Heredity
Pedro J. Cabello-Yeves, Cristiana Callieri, Antonio Picazo, Maliheh Mehrshad, Jose M. Haro-Moreno, Juan J. Roda-Garcia, Nina Dzhembekova, Violeta Slabakova, Nataliya Slabakova, Snejana Moncheva, Francisco Rodriguez-Valera
Summary: The Black Sea has unique characteristics in its microbiome, with stability in its microbial community and a diverse range of metabolic types. The microbiome of the Black Sea provides critical information about this important ecosystem.
ENVIRONMENTAL MICROBIOME
(2021)
Article
Ecology
O. N. Pavlova, O. N. Izosimova, S. M. Chernitsyna, V. G. Ivanov, T. Pogodaeva, A. Khabuev, A. G. Gorshkov, T. Zemskaya
Summary: This study presents experimental data on microbial communities from sediments of Gorevoy Utes' natural oil seep degrading petroleum hydrocarbons under anaerobic conditions. It found that under sulfate-reducing conditions, a more diverse bacterial community was formed with a higher loss of n-alkanes compared to methanogenic conditions, indicating a preference for degrading polycyclic aromatic hydrocarbons.
Article
Microbiology
O. V. Shubenkova, A. S. Zakharenko, Yu. P. Galach'yants, G. V. Kalmychkov, V. G. Ivanov, A. V. Khabuev, T. V. Pogodaeva, S. M. Chernitsyna, T. I. Zemskaya
Summary: The diversity of methano- and methylotrophic bacteria in enrichments from oxidized sediment layers at 10 degrees C was studied by high-throughput sequencing of the 16S rRNA gene. Different cultivation conditions with methanol and nitrogen sources were found to impact the diversity and development of bacterial communities.
Article
Microbiology
Subhasish Saha, Paul-Adrian Bulzu, Petra Urajova, Jan Mares, Grzegorz Konert, Joao Camara Manoel, Marketa Macho, Daniela Ewe, Pavel Hrouzek, Jiri Masojidek, Rohit Ghai, Kumar Saurav
Summary: The regulation of cyanopeptide production is crucial for understanding their ecological role, and our study sheds light on the control of microviridin production by epibionts through quorum-sensing mechanisms, suggesting their widespread presence in natural cyanobacterial bloom community regulation.
Article
Microbiology
Paul-Adrian Bulzu, Vinicius Silva Kavagutti, Maria-Cecilia Chiriac, Charlotte D. Vavourakis, Keiichi Inoue, Hideki Kandori, Adrian-Stefan Andrei, Rohit Ghai
Summary: This study reveals that heliorhodopsins are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes, with restricted distribution in monoderms. Researchers suggest that heliorhodopsins likely function as generalized light-dependent switches involved in the regulation of light-induced oxidative stress and metabolic circuitry. Their role as sensory rhodopsins is supported by their photocycle dynamics and their presence/function in monoderms.
Article
Marine & Freshwater Biology
Tatiana Ya Sitnikova, Tatiana Naumova, Irina Mekhanikova, Sergey Kiyashko, Gennady Kalmychkov, Ivana Karanovic, Alexandra S. Zakharenko, Yuri S. Bukin, Andrey Khabuev, Vyacheslav G. Ivanov, Oleg M. Khlystov, Tamara Zemskaya
Summary: The study analysed the relationship between invertebrate abundance and environmental factors in freshwater methane seeps. The results showed significant variations in abundance among different samples and stations, and identified various biotic and abiotic factors influencing the abundance of invertebrates.
Article
Microbiology
Maria-Cecilia Chiriac, Paul-Adrian Bulzu, Adrian-Stefan Andrei, Yusuke Okazaki, Shin-ichi Nakano, Markus Haber, Vinicius Silva Kavagutti, Paul Layoun, Rohit Ghai, Michaela M. Salcher
Summary: The study explored the diversity and abundance of candidate phyla radiation (CPR) bacteria in freshwater lakes. By conducting deep metagenomic sequencing, the researchers recovered a high diversity of CPR genomes, which showed reduced metabolic capacities and potential lifestyles. The findings suggest that CPR bacteria have a wide range of potential strategies for survival and adaptation.
Article
Ecology
Karel Simek, Indranil Mukherjee, Tiberiu Szoke-Nagy, Markus Haber, Michaela M. Salcher, Rohit Ghai
Summary: Morphologically indistinguishable aplastidic cryptophytes were found to be ubiquitous and prominent protistan bacterivores in freshwater ecosystems, playing important roles in carbon flow. These heterotrophic cryptophytes were generally smaller and more abundant than their chloroplast-bearing counterparts, and their diversity has been largely undiscovered.
Article
Microbiology
Paul-Adrian Bulzu, Vinicius S. Kavagutti, Adrian-Stefan Andrei, Rohit Ghai
Summary: Rhodopsins are versatile proteins that convert electromagnetic radiation into physicochemical signals, playing various roles across different domains of life. This study explored the genomic and metagenomic sequencing data to identify new clades and sequence motifs in Type-1 and Type-3 rhodopsins, expanding the optogenetics toolbox. The researchers discovered that a highly conserved arginine residue (Arg82) in the rhodopsin fold was substituted multiple times during evolution by various amino acids, leading to the proposal of Alt-rhodopsins (AltRs) as a new classification. The study also delved into the phylogenetic relationship between AltRs and heliorhodopsins, suggesting a eukaryotic origin for heliorhodopsins before their diversification in prokaryotes.
Article
Multidisciplinary Sciences
David Kamanda Ngugi, Michaela M. Salcher, Adrian-Stefan Andrei, Rohit Ghai, Franziska Klotz, Maria-Cecilia Chiriac, Danny Ionescu, Petra Buesing, Hans-Peter Grossart, Peng Xing, John C. Priscu, Salmor Alymkulov, Michael Pester
Summary: A study has found that the species diversity of ammonia-oxidizing archaea (AOA) in freshwater is lower compared to marine environments. The research also reveals that an uncultured freshwater AOA, Candidatus Nitrosopumilus limneticus, evolved in European lakes 13 million years ago and has remained genetically stable. These findings provide insights into the genetic diversity and adaptive mechanisms of AOA in lakes.
Article
Microbiology
Anna Lomakina, Sergei Bukin, Olga Shubenkova, Tatyana Pogodaeva, Vyacheslav Ivanov, Yuri Bukin, Tamara Zemskaya
Summary: We analyzed the diversity and metabolic potential of microbial communities in sediments from two sites in the northern basin of Lake Baikal using amplicons of the 16S rRNA genes and metagenome-assembled genomes (MAGs). The dominant communities in the surface layers were Organotrophic Chloroflexota, Actionobacteriota, Acidobacteriota, Methylococcales, and Methylomirabilota. The composition of archaeal communities was similar between sites but differed with depth, with Nitrososphaeria predominating in surface sediments and Methanoperedenaceae and Bathyarchaeia increasing in deep sediments. Metagenome sequencing revealed the presence of genes related to carbon fixation, N, S, and CH4 metabolism, Fe and Mn pathways, indicating the coexistence of diverse biogeochemical cycles and microbial communities.
