Article
Environmental Sciences
F. H. Coutinho, F. A. B. von Meijenfeldt, J. M. Walter, J. M. Haro-Moreno, M. Lopez-Perez, M. C. van Verk, C. C. Thompson, C. A. N. Cosenza, L. Appolinario, R. Paranhos, A. Cabral, B. E. Dutilh, F. L. Thompson
Summary: The microbiome of the South Atlantic Ocean has unique taxonomic and functional composition at different depths, driven by physical and chemical parameters. Genomes obtained from various depth zones include poorly characterized taxa of Bacteria and Archaea. The viral communities in the water column vary in response to shifts in microbial counterparts, targeting different hosts.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Yunxi Liu, R. A. Leo Elworth, Michael D. Jochum, Kjersti M. Aagaard, Todd J. Treangen
Summary: Contaminant sequences in metagenomic samples can impact interpretation of microbiome studies, especially in low biomass environments. The authors propose a computational approach called Squeegee, which can detect microbial contamination and identify contaminants in publicly available datasets lacking negative controls.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Anwesha Ghosh, Ratul Saha, Punyasloke Bhadury
Summary: This study sampled surface water from the Thakuran and Matla estuaries in Sundarbans mangrove and used metagenomic analysis to characterize the resident microbial communities. The results showed that Proteobacteria were dominant across all stations, with site-specific trends observed for other phyla. Functional annotation revealed widespread metabolic activities and the presence of antibiotic resistance genes and metal resistance genes. These findings suggest the presence of pollutants and a deteriorating ecosystem health status in Sundarbans mangrove.
Article
Environmental Sciences
Maria A. Cavaco, Maya P. Bhatia, Alyse K. Hawley, Monica Torres-Beltran, Winifred M. Johnson, Krista Longnecker, Kishori Konwar, Elizabeth B. Kujawinski, Steven J. Hallam
Summary: Microbial communities in the ocean play crucial roles in nutrient and energy transformations. This study investigates the distribution and expression patterns of metabolic pathways in these communities along a transect in the western South Atlantic Ocean, revealing functional redundancy and vertical stratification.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Maria Pinto, Zihao Zhao, Katja Klun, Eugen Libowitzky, Gerhard J. Herndl
Summary: This study analyzed biofilm communities on low-density polyethylene (LDPE) in the ocean for 2 years, and found that certain taxa of microorganisms can degrade and utilize LDPE as a carbon source. These microorganisms carried genes related to alkane degradation, and experiments showed changes in the LDPE surface over time.
Article
Biotechnology & Applied Microbiology
Ana Carolina Bercini Gusmao, Francielli Vilela Peres, Fabiana S. Paula, Vivian Helena Pellizari, Hedda Elisabeth Kolm, Camila Negrao Signori
Summary: This study examined the diversity and composition of microbial communities in marine sediments in the Sao Paulo Plateau, Brazil. The results showed significant differences in microbial composition among different sampling stations, as well as predicted metabolic pathways related to nitrogen, carbon, and sulfur cycles. This research contributes to a better understanding of microbial communities in an economically important yet underexplored region.
INTERNATIONAL MICROBIOLOGY
(2023)
Article
Marine & Freshwater Biology
Laura Rodrigues da Conceicao, Lilian Elisa Demoner, Juliano Bicalho Pereira, Fernanda Perassoli, Renato David Ghisolfi, Alex Cardoso Bastos, Camilo Dias Junior, Georgette Cristina Salvador Lazaro, Kassia do Nascimento Lemos, Luiz Fernando Loureiro Fernandes
Summary: This study investigated the potential effects of iron ore tailings on the copepod community in the marine area adjacent to the Doce River mouth, with a focus on suspended particulate matter (SPM). The results showed a negative correlation between community composition and higher SPM concentrations, with specific indicator species identified. Water masses were found to be the main factor influencing community structure, with specific species dominating under certain conditions.
ESTUARINE COASTAL AND SHELF SCIENCE
(2021)
Article
Environmental Sciences
Clara Jegousse, Pauline Vannier, Rene Groben, Kristinn Guomundsson, Viggo Thor Marteinsson
Summary: This study investigated the taxonomic and metabolic diversity of marine microorganisms in Icelandic waters using molecular techniques. The results showed correlations between microbial community profiles and water masses, as well as differences in microbial diversity related to seawater temperature. Additionally, three photosynthetic microorganisms were identified as valuable indicators for future monitoring and ecosystem modeling.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Oceanography
Kimberley L. Drouin, M. Susan Lozier, William E. Johns
Summary: Previous studies have suggested that the South Atlantic subtropical gyre has been expanding, shifting poleward, and intensifying. Investigating from an observational standpoint, analyzing seasonal and interannual variability, and long-term trends. The gyre strength follows seasonal heating and cooling, largely influenced by sea surface height gyre maximum, while ocean mass variability is driven by wind stress curl and out of phase with the steric signal. Interannual changes to the southern boundary and gyre strength are related to wind stress curl.
JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
(2021)
Article
Multidisciplinary Sciences
Evan Kiefl, Ozcan C. Esen, Samuel E. Miller, Kourtney L. Kroll, Amy D. Willis, Michael S. Rappe, Tao Pan, A. Murat Eren
Summary: Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. Analyzing genetic variation in the context of predicted protein structures reveals a tight association between genetic variation and protein structure. This approach provides insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.
Review
Oceanography
Claude Estournel, Patrick Marsaleix, Caroline Ulses
Summary: The study compared a simulation of the Mediterranean circulation between 2011 and 2020 at a resolution of 3-4 km in the Eastern basin with vertical profiles and horizontal distributions of temperature and salinity from Argo profilers. The results showed high temporal and spatial correlations, low biases, and strong similarities with satellite imagery for numerous structures at various spatial scales. The simulation revealed differences in surface and intermediate waters circulation between winter and summer seasons, with cyclonic circulation in winter and the presence of anticyclonic circulation in the southeast basin during summer.
PROGRESS IN OCEANOGRAPHY
(2021)
Article
Nutrition & Dietetics
Mayank Kaashyap, Marc Cohen, Nitin Mantri
Summary: Kombucha, a fermented tea, has potential health benefits due to its microbial communities beneficial for the human gut. The study identified previously undescribed microbial species in kombucha, with Acetobacter, Komagataeibacter and Starmerella having potential roles in preventing conditions like diabetes and obesity. Additionally, kombucha has high protein and phenolic content, low sugar content, making it a powerful probiotic with commercial value and immense health benefits.
Review
Oceanography
Markel Gomez-Letona, Javier Aristegui, Nauzet Hernandez-Hernandez, Xose Anton Alvarez-Salgado, Marta Alvarez, Erick Delgadillo, Maria Perez-Lorenzo, Eva Teira, Santiago Hernandez-Leon
Summary: Organic matter influences the composition and metabolism of marine prokaryotes. This study investigates the relationship between fluorescent dissolved organic matter and prokaryotic community composition in the deep ocean. The results show that water mass mixing, oxygen utilization, and productivity proxies are important factors explaining the distribution of different fluorescence components. The diversity and taxonomic composition of prokaryotic communities are found to vary between water masses, suggesting a link between community composition, oxygen utilization, and fluorescent dissolved organic matter.
PROGRESS IN OCEANOGRAPHY
(2022)
Review
Food Science & Technology
Nguyen Nhat Nam, Hoang Dang Khoa Do, Kieu The Loan Trinh, Nae Yoon Lee
Summary: In the era of omics, various fields have been identified, including genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Metagenomics, among them, has significantly contributed to discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide valuable information on microbial diversity and functions on Earth. Therefore, metagenomics has led to new microbe-based applications in human health, agriculture, and the food industry. This review summarizes recent advances in bioinformatic tools and explores the current applications of metagenomics in various fields. Furthermore, it discusses the future perspectives of metagenomics as a powerful tool for studying the microbial world.
Article
Environmental Sciences
Daniel Ford, Gavin H. Tilstone, Jamie D. Shutler, Vassilis Kitidis, Polina Lobanova, Jill Schwarz, Alex J. Poulton, Pablo Serret, Tarron Lamont, Mateus Chuqui, Ray Barlow, Jose Lozano, Milton Kampel, Frederico Brandini
Summary: This study evaluated the performance of MODIS-A algorithms for chlorophyll a, net primary production, and net community production in the South Atlantic Ocean using in situ and satellite data, and generated a 16-year time series to investigate the impacts of climate and environmental drivers on net community production.
REMOTE SENSING OF ENVIRONMENT
(2021)
Article
Virology
Dann Turner, Andrey N. Shkoporov, Cedric Lood, Andrew D. Millard, Bas E. Dutilh, Poliane Alfenas-Zerbini, Leonardo J. van Zyl, Ramy K. Aziz, Hanna M. Oksanen, Minna M. Poranen, Andrew M. Kropinski, Jakub Barylski, J. Rodney Brister, Nina Chanisvili, Rob A. Edwards, Francois Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtboke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata Lobocka, Cristina Moraru, Andrea Moreno Switt, Vera Morozova, Jesca Nakavuma, Alejandro Reyes Munoz, Janis Rumnieks, B. L. Sarkar, Matthew B. Sullivan, Jumpei Uchiyama, Johannes Wittmann, Tong Yigang, Evelien M. Adriaenssens
Summary: This article summarizes the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses from March 2021 to March 2022. It provides an overview of the new classifications proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. The taxonomy of bacterial viruses underwent significant changes, including the abolition of the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae, as well as the order Caudovirales, and the establishment of a binomial nomenclature system for species. Additionally, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
ARCHIVES OF VIROLOGY
(2023)
Review
Chemistry, Medicinal
Anderson de Souza Cabral, Mariana Verdan, Rogerio Presciliano, Felipe Silveira, Tarcisio Correa, Fernanda Abreu
Summary: Magnetotactic bacteria are microorganisms that can synthesize magnetic nanoparticles within their cells, allowing them to align passively along the lines of the geomagnetic field. Recent advances in their cultivation and the isolation of these nanoparticles have greatly expanded their biotechnological potential, with applications ranging from nanotechnology to biomedicine.
Article
Environmental Sciences
Maria Papale, Gabriella Caruso, Giovanna Maimone, Rosabruna La Ferla, Angelina Lo Giudice, Alessandro Ciro Rappazzo, Alessandro Cosenza, Filippo Azzaro, Roberta Ferretti, Rodolfo Paranhos, Anderson Souza Cabral, Massimo Caccia, Angelo Odetti, Giuseppe Zappala, Gabriele Bruzzone, Maurizio Azzaro
Summary: Cold-adapted microorganisms in polar marine environments have significant impacts on water biogeochemistry and ecosystem functions. However, remote regions near glaciers, which are difficult to access, have been neglected and lack microbiological data. To address this gap, a survey of microbial communities in an Arctic region near the Blomstrandbreen glacier was conducted using an Unmanned Autonomous Vehicle equipped with an automatic water sampler. The analysis revealed different sub-regions affected by haline gradient or terrigenous inputs, indicating that ice melting and Atlantic water inflow have varying effects on microbial growth.
Article
Virology
Francisco Murilo Zerbini, Stuart G. Siddell, Elliot J. Lefkowitz, Arcady R. Mushegian, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Donald M. Dempsey, Bas E. Dutilh, Maria Laura Garcia, R. Curtis Hendrickson, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani
Summary: This article reports on changes to virus taxonomy and nomenclature approved by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. All ICTV members were invited to vote on 174 taxonomic proposals and a revision of the ICTV Statutes that had been approved by the ICTV Executive Committee in July 2022. Majority approval was obtained for all proposals and the revised ICTV Statutes. A significant change was the renaming of existing species according to the binomial format and the classification of gene transfer agents (GTAs) as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.
ARCHIVES OF VIROLOGY
(2023)
Article
Ecology
Jose L. Lopez, Arista Fourie, Sanne W. M. Poppeliers, Nikolaos Pappas, Juan J. Sanchez-Gil, Ronnie de Jonge, Bas E. Dutilh
Summary: The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions.
Article
Gastroenterology & Hepatology
Carlijn E. Bruggeling, Maarten te Groen, Daniel R. Garza, Famke van Heeckeren Tot Overlaer, Joyce P. M. Krekels, Basma-Chick Sulaiman, Davy Karel, Athreyu Rulof, Anne R. Schaaphok, Daniel L. A. H. Hornikx, Iris D. Nagtegaal, Bas E. Dutilh, Frank Hoentjen, Annemarie Boleij
Summary: This prospective cohort study found that colonic bacterial biofilms are common in ulcerative colitis (UC) and may increase the risk of dysplasia through oncogenic traits. Moreover, the study also found that bacterial composition is associated with biofilms and dysplasia risk. The presence of biofilms is not significantly associated with dysplasia in UC, while ClbB is independently associated with dysplasia and FadA and Fusobacteriales are associated with a decreased risk of dysplasia in UC.
JOURNAL OF CROHNS & COLITIS
(2023)
Review
Biotechnology & Applied Microbiology
Stuart G. Siddell, Donald B. Smith, Evelien Adriaenssens, Poliane Alfenas-Zerbini, Bas E. Dutilh, Maria Laura Garcia, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Malgorzata Lobocka, Arcady R. Mushegian, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani, F. Murilo Zerbini
Summary: The International Committee on Taxonomy of Viruses (ICTV) is responsible for the development and oversight of virus taxonomy. It approves and ratifies taxonomic proposals and maintains a list of approved virus names. The ICTV has a democratic decision-making process with approximately 180 members who vote on proposals. Taxon-specific Study Groups, comprised of over 600 scientists, provide expertise and contribute to taxonomic proposals.
JOURNAL OF GENERAL VIROLOGY
(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
Virology
Liliane S. S. Oliveira, Alejandro Reyes, Bas E. E. Dutilh, Arthur Gruber
Summary: The study developed protocols for the rational design of profile HMMs, which can automatically identify informative sequence motifs and construct profile HMMs. These methods were applied to detect and classify different viral groups and related transposable elements.
Article
Biochemistry & Molecular Biology
Simon E. Roux, Antonio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, Stephen Nayfach, Andrew Tritt
Summary: The extraordinary diversity of viruses infecting bacteria and archaea can be studied through metagenomics. However, metagenome-derived viral sequences lack key information about host association. We introduce iPHoP, a framework that integrates multiple methods to predict host taxonomy for a range of uncultivated viruses, while maintaining a low false discovery rate. Using a large dataset from the IMG/VR database, iPHoP shows promise in providing extensive host prediction for uncultivated viruses.
Article
Ecology
F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, Bas E. Dutilh
Summary: Defining the niche of a microorganism is challenging because it depends on an objective definition of the environment. In this study, researchers used the community a microorganism resides in as the environment and developed a quantitative measure called social niche breadth. They found that social generalists have a more diverse and open genome compared to social specialists, and observed two distinct evolutionary strategies for specialists in different habitats.
NATURE ECOLOGY & EVOLUTION
(2023)
Correction
Virology
Francisco Murilo Zerbini, Stuart G. Siddell, Elliot J. Lefkowitz, Arcady R. Mushegian, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Donald M. Dempsey, Bas E. Dutilh, Maria Laura Garcia, R. Curtis Hendrickson, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani
ARCHIVES OF VIROLOGY
(2023)
Article
Ecology
R. S. A. Chielle, R. V. Marins, F. J. S. Dias, K. K. Borges, C. E. Rezende
Summary: In this study, the authors conducted sampling and analysis in the main channel and secondary channels of the Parnaiba Delta to investigate the dynamics of CO2. They found that different channels have distinct drivers of CO2 dynamics, with organic matter decomposition and primary production in the main channel and mangroves, and carbonate equilibrium in the river mouth. The study also revealed the significant influence of river discharge on the carbon dynamics of the estuary, with a majority of CO2 emissions estimated to be from riverine sources. The estuary was found to be a strong source of CO2.
REGIONAL STUDIES IN MARINE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Cynara Pedrosa Fragoso, Pedro Vianna Gatts, Ana Paula Madeira Di Beneditto, Luiz Antonio Martinelli, Luiz Drude de Lacerda, Carlos Eduardo de Rezende
Summary: The structure of food webs is important for understanding trophic interactions and nutrient transfer in ecosystems. Stable isotopes and mercury are commonly used tools in aquatic food web research, and their combination can provide better results. Using multiple tracers can help overcome limitations and expand our knowledge of food webs.
Article
Ecology
Daniel R. Garza, F. A. Bastiaan von Meijenfeldt, Bram van Dijk, Annemarie Boleij, Martijn A. Huynen, Bas E. Dutilh
Summary: We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics.
BMC ECOLOGY AND EVOLUTION
(2022)