Article
Environmental Sciences
Andre C. Pereira, Ana Tenreiro, Monica Cunha
Summary: The combination of FISH and FLOW techniques allows for high-throughput evaluation and sorting of single cells within microbial communities in environmental microbiology, providing a key tool for studying their heterogeneity.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Pathology
Marie-France Gagnon, Sally M. Midthun, James A. Fangel, Cynthia M. Schuh, Ivy M. Luoma, Kathryn E. Pearce, Reid G. Meyer, Sikander Ailawadhi, Mariano J. Arribas, Esteban Braggio, Rafael Fonseca, S. Vincent Rajkumar, Cinthya Zepeda-Mendoza, Xinjie Xu, Patricia T. Greipp, Michael M. Timm, Gregory E. Otteson, Min Shi, Dragan Jevremovic, Horatiu Olteanu, Jess F. Peterson, Rhett P. Ketterling, Shaji Kumar, Linda B. Baughn
Summary: This study compared the efficacy of cytoplasmic immunoglobulin FISH (cIg-FISH) and fluorescence-activated cell sorting FISH (FACS-FISH) in a clinical laboratory setting. The results showed that FACS-FISH increased the detection rate of abnormalities and decreased the number of cells required for FISH analysis, as well as reducing workload and operating costs.
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Multidisciplinary Sciences
Tom O. Delmont
Summary: This study reveals the presence of non-diazotrophic species within the Trichodesmium genus, expanding the biogeography of this prominent marine genus with a previously overlooked functional lifestyle. The findings help refine our understanding of marine nitrogen balance and serve as a reminder that established links between taxonomic lineages and functional traits do not always hold true.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Alison Gallet, Sebastien Halary, Charlotte Duval, Helene Huet, Sebastien Duperron, Benjamin Marie
Summary: This study demonstrates that cyanobacterial blooms affect the composition and functions of fish microbiomes, as well as the metabolome of holobionts. The gut bacterial community of fish exhibits significant changes in response to blooms, while the holobiont's gut metabolome displays major changes. These findings highlight the importance of bloom events to fish health and fitness through microbiome-related effects.
Review
Biotechnology & Applied Microbiology
Wanglin Duan, Xiangbing Bian, Yazhong Bu
Summary: Bioadhesives have shown superiority in clinical applications as tissue adhesives, hemostats, and tissue sealants. This review summarizes the applications of bioadhesives, including wound closure, sealing leakage, and immobilization, both in current clinical use and those showing great potential for future use.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Food Science & Technology
Silvina Perez, Georgina Corti-Monzon, Maria Yeannes, Noemi E. Zaritzky, Marcela Villegas-Plazas, Howard Junca, Silvia E. Murialdo
Summary: This study focused on assembling mixed cultures from halophilic prokaryotes isolated during the salting-ripening anchovy process in order to determine their histamine-degrading capacity.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Review
Food Science & Technology
Prarthi Sagar, Ajmal Aseem, Santosh Kumar Banjara, Shobi Veleri
Summary: The global spread of antimicrobial resistance (AMR) is depleting the supply of antibiotics while the development of new antibiotics remains stagnant. Millions of people are killed annually due to AMR, prompting urgent action from scientific and civil bodies. This review focuses on the various sources of AMR, particularly within the food chain, which serves as a conduit for transmitting AMR pathogens. The indiscriminate use of antibiotics in livestock and agriculture, as well as nosocomial settings, contributes to the emergence of AMR pathogens. A comprehensive approach, utilizing technologies such as new generation sequencing, metagenomics, and bioinformatics, is necessary to monitor and understand the emergence and transmission of AMR.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Environmental Sciences
Xiangqun Chi, Zhiyi Zhao, Qiuxia Han, Huaxiao Yan, Bei Ji, Yating Chai, Shengying Li, Kun Liu
Summary: Seagrass beds contribute up to 10% of ocean carbon storage and greatly affect global carbon cycle. In this study, seagrass bed sediment samples were collected from three sites in Weihai, China, and the carbon fixation strategies were investigated. Five pathways were found, with Calvin and WL being the most dominant. The community structure of microorganisms containing key genes of these pathways was analyzed, and microorganisms with carbon fixing potential were identified. Phosphorus showed a significant negative correlation with these microorganisms. This study provides insights into carbon fixation strategies in seagrass bed sediments.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Marine & Freshwater Biology
Zeyu Jia, Yijing Dong, Heng Xu, Fengping Wang
Summary: The study optimized the HCR-FISH protocol to address the issues of low signal intensity and false-positive signals, successfully identifying HCR initiator/amplifier pairs with high efficiency and specificity. Through the optimization of sample pretreatment methods, HCR-FISH protocol combinations, and image processing, false positive signals were reduced.
MARINE LIFE SCIENCE & TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
P. Bernhard, T. Feilen, M. Rogg, K. Froehlich, M. Cosenza-Contreras, F. Hause, C. Schell, O. Schilling
Summary: Clonal isolation is a crucial step in genome editing and cell engineering, impacting the cellular proteome in a cell line specific manner. The effects of clonal isolation on different biological processes vary and depend on the isolation method. Understanding the impact of clonal isolation is important when interpreting experimental data in these fields.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Plant Sciences
Ying-Li Liu, Ying-Hua Guo, Xue-Qin Song, Meng-Xuan Hu, Shu-Tang Zhao
Summary: Programmed cell death (PCD) is a genetically regulated process in plants, but there is a lack of efficient methods to study PCD in woody plants. This study demonstrates the use of flow cytometry with fluorescence staining to distinguish different stages of PCD in poplar xylem cells. The method allows for quantitative analysis and correlates with gene expression and cell morphology, providing a valuable tool to study PCD in woody plants.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Fisheries
Pablo Martinez-Lara, Marcel Martinez-Porchas, Teresa Gollas-Galvan, Jorge Hernandez-Lopez, Glen R. Robles-Porchas
Summary: Bacterial infections pose a significant threat to fish culture, especially those causing granulomatous processes. Early detection of granulomatous infections is challenging due to the lack of distinct clinical signs and the similarity of symptoms to those caused by other pathogens. There is a lack of evidence for granulomatous co-infections in aquaculture environments, which could complicate the diagnosis of such diseases.
REVIEWS IN AQUACULTURE
(2021)
Article
Chemistry, Physical
Maxime Blatter, Louis Delabays, Clement Furrer, Gerald Huguenin, Christian Pierre Cachelin, Fabian Fischer
Summary: The construction and long-term reliability of large microbial fuel cells (MFCs) are current challenges. Research has shown that MFCs can effectively remove pollutants such as COD, ammonia, and phosphorus from wastewater under specific conditions, while also achieving energy self-sufficiency.
JOURNAL OF POWER SOURCES
(2021)
Article
Microbiology
Zufan Zhang, Shiqing Nie, Yimeng Sang, Shuming Mo, Jinhui Li, Muhammad Kashif, Guijiao Su, Bing Yan, Chengjian Jiang
Summary: This study revealed the efficient nutrient cycling mechanism of mangroves and showed that the invasion of Spartina alterniflora enhanced the coupling effects of NF and PS processes, positively impacting sediment quality and turnover of nutrients. The research provides insights into the effects of S. alterniflora invasion on subtropical mangrove ecosystems and offers theoretical guidance for mangrove protection, restoration, and soil management, as well as potential development of marine biological fertilizers.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Yun Fang, Jun Liu, Jian Yang, Geng Wu, Zhengshuang Hua, Hailiang Dong, Brian P. Hedlund, Brett J. Baker, Hongchen Jiang
Summary: The study investigated the composition and metabolic pathways of autotrophic microorganisms in lacustrine sediments along a salinity gradient using metagenomic analysis. The results showed that salinity had a significant impact on the abundance and community composition of autotrophs, as well as their carbon fixation and glycolysis pathways. The dominant lineage and carbon fixation pathway shifted with decreasing salinity. These findings provide insights into the physiological efficiency and metabolic versatility of autotrophic microorganisms in saline environments and their response to salinity.
Article
Ecology
Nina Bartlau, Antje Wichels, Georg Krohne, Evelien M. Adriaenssens, Anneke Heins, Bernhard M. Fuchs, Rudolf Amann, Cristina Moraru
Summary: This study suggests that phages may modulate the succession of heterotrophic bacteria following phytoplankton blooms in spring. The diverse flavophages identified have the potential to affect their respective host populations in the North Sea microbial community, as stable components.
Article
Ecology
Luis H. Orellana, T. Ben Francis, Marcela Ferraro, Jan-Hendrik Hehemann, Bernhard M. Fuchs, Rudolf Amann
Summary: The study found that small, coccoid, free-living Verrucomicrobiota specialize in consuming fucose and rhamnose during spring algal blooms in the North Sea. These Verrucomicrobiota populations accounted for up to 8% of the bacterioplankton and actively expressed proteins critical for the consumption of fucosylated and sulfated polysaccharides during consecutive spring bloom events. Specialized metabolic pathways of Verrucomicrobiota could determine the fate of complex polysaccharides consumed during algae blooms, particularly those containing methyl pentose sugars.
Article
Ecology
Taylor Priest, Anneke Heins, Jens Harder, Rudolf Amann, Bernhard M. Fuchs
Summary: In this study, we investigate the species-level niche partitioning within the NS5 Marine Group by combining spatiotemporal dynamics and predicted substrate utilization. We identify depth as a key influencing factor in the distribution dynamics of NS5 species, and observe successional dynamics in relation to specialized substrate adaptations. Additionally, we provide a complete genome sequence and morphological insights for Arcticimaribacter forsetii AHE01FL, a candidate species within the NS5 group.
Article
Ecology
Luke J. McKay, Heidi J. Smith, Elliott P. Barnhart, Hannah D. Schweitzer, Rex R. Malmstrom, Danielle Goudeau, Matthew W. Fields
Summary: The study identified translationally active microbial populations involved in methane generation from coal-derived aromatic hydrocarbons in a subsurface coal seam. Metagenome-assembled genomes (MAGs) were recovered for acetoclastic methanogens and Chlorobi members with potential acetate-generating pathways. Environmental parameters indicated redox fluctuations promote facultative energy metabolisms in the coal seam.
Article
Ecology
Robert M. Bowers, Stephen Nayfach, Frederik Schulz, Sean P. Jungbluth, Ilona A. Ruhl, Andriy Sheremet, Janey Lee, Danielle Goudeau, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Rex R. Malmstrom, Nikos C. Kyrpides, Peter F. Dunfield, Tanja Woyke
Summary: Advancements in single-cell genomics have enabled rapid and affordable sequencing of microbial communities, providing a comprehensive snapshot of community composition and function. This approach also allows for the direct linkage of mobile elements to hosts and analysis of population heterogeneity among dominant community members.
Article
Biochemistry & Molecular Biology
Grayson L. Chadwick, Connor T. Skennerton, Rafael Laso-Perez, Andy O. Leu, Daan R. Speth, Hang Yu, Connor Morgan-Lang, Roland Hatzenpichler, Danielle Goudeau, Rex Malmstrom, William J. Brazelton, Tanja Woyke, Steven J. Hallam, Gene W. Tyson, Gunter Wegener, Antje Boetius, Victoria J. Orphan
Summary: The anaerobic oxidation of methane coupled to sulfate reduction is a microbial process that involves a partnership between anaerobic methanotrophic archaea and sulfate-reducing bacteria. This study reconstructed and analyzed 28 ANME genomes, enabling a comparative analysis of all marine ANME clades. The findings suggest that methane production may have evolved from a methanotrophic ancestor.
Article
Biotechnology & Applied Microbiology
Hannah D. Schweitzer, Heidi J. Smith, Elliott P. Barnhart, Luke J. McKay, Robin Gerlach, Alfred B. Cunningham, Rex R. Malmstrom, Danielle Goudeau, Matthew W. Fields
Summary: This study investigates the potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams from the Powder River Basin using environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes. The results reveal the presence of biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways in the active populations across the sampled coal seams.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Biotechnology & Applied Microbiology
Hang Yu, Daan R. Speth, Stephanie A. Connon, Danielle Goudeau, Rex R. Malmstrom, Tanja Woyke, Victoria J. Orphan
Summary: This study successfully enriched ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California, without sediment. By utilizing selective cultivation approaches based on physical characteristics, new opportunities for detailed genomic, physiological, biochemical, and ecological analyses were introduced.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jean-Marie Volland, Silvina Gonzalez-Rizzo, Olivier Gros, Tomas Tyml, Natalia Ivanova, Frederik Schulz, Danielle Goudeau, Nathalie H. Elisabeth, Nandita Nath, Daniel Udwary, Rex R. Malmstrom, Chantal Guidi-Rontani, Susanne Bolte-Kluge, Karen M. Davies, Maitena R. Jean, Jean-Louis Mansot, Nigel J. Mouncey, Esther R. Angert, Tanja Woyke, Shailesh Date
Summary: Through various cellular and genomic techniques, we investigated the bacterium Candidatus (Ca.) Thiomargarita magnifica and found that it has extremely long cell length and unique features that challenge traditional concepts of bacterial cells, indicating evolutionary complexity in the Thiomargarita lineage.
Article
Microbiology
Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone, Jennifer Pett-Ridge
Summary: The study introduced a semi-automated, high-throughput SIP pipeline to support well-replicated experiments in soil microhabitats, showcasing how this approach can improve operational efficiency and reproducibility in studying actively growing microbes within AMF hyphosphere. This method generated a series of metagenome-assembled genomes (MAGs) from C-13-labeled AMF hyphosphere DNA, revealing insights into key processes involved in nutrient cycling within the hyphosphere.
Article
Multidisciplinary Sciences
Julia Anstett, Alvaro M. Plominsky, Edward F. DeLong, Alyse Kiesser, Klaus Juergens, Connor Morgan-Lang, Ramunas Stepanauskas, Frank J. Stewart, Osvaldo Ulloa, Tanja Woyke, Rex Malmstrom, Steven J. Hallam
Summary: Oxygen-deficient marine waters known as OMZs or AMZs are common oceanographic features that host microorganisms adapted to low oxygen conditions. The metabolic interactions of these microorganisms drive biogeochemical cycles and impact nitrogen loss and trace gas production and consumption. With the expansion and intensification of oxygen-deficient waters due to global warming, studying microbial communities in these areas is important for understanding the effects of climate change on marine ecosystem functions and services.
News Item
Microbiology
Rex R. Malmstrom
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ranjani Murali, Hang Yu, Daan R. Speth, Fabai Wu, Kyle S. Metcalfe, Antoine Cremiere, Rafael Laso-Perez, Rex R. Malmstrom, Danielle Goudeau, Tanja Woyke, Roland Hatzenpichler, Grayson L. Chadwick, Stephanie A. Connon, Victoria J. Orphan
Summary: This study investigated the metabolic adaptation of sulfate-reducing bacteria (SRB) in the syntrophic partnership with anaerobic methanotrophic archaea (ANME) using comparative metagenomics and phylogenetics. The results showed that the protein complexes involved in direct interspecies electron transfer (DIET) were conserved between syntrophic lineages, while the proteins involved in electron transfer within the SRB inner membrane differed. Unique adaptations were also found within syntrophic SRB clades, which varied depending on the archaeal partner.
Article
Microbiology
Ryan V. Trexler, Marc W. Van Goethem, Danielle Goudeau, Nandita Nath, Rex R. Malmstrom, Trent R. Northen, Estelle Couradeau
Summary: Determining the active microorganisms in soil communities is key in microbial ecology research. This study applied the BONCAT-FACS-Seq method to profile the diversity and potential functions of active and inactive microorganisms in a biocrust community after rain. The results showed that BONCAT-FACS-Seq can discern the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active fraction of the biocrust community is characterized by taxa commonly observed in other biocrust communities.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Dariia Vyshenska, Pranav Sampara, Kanwar Singh, Andy Tomatsu, W. Berkeley Kauffman, Erin E. Nuccio, Steven J. Blazewicz, Jennifer Pett-Ridge, Katherine B. Louie, Neha Varghese, Matthew Kellom, Alicia Clum, Robert Riley, Simon Roux, Emiley A. Eloe-Fadrosh, Ryan M. Ziels, Rex R. Malmstrom
Summary: Answering the questions, who is eating what? and who is active? within complex microbial communities is essential for modeling, predicting, and modifying microbiomes for improved human and planetary health. Stable isotope probing can be used to track the incorporation of labeled compounds into cellular DNA during microbial growth to address these questions. However, traditional stable isotope methods face challenges in establishing links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. This study presents an experimental and analytical workflow that improves the detection of metabolically active microorganisms and provides better quantitative estimates of genome-resolved isotope incorporation, thus refining ecosystem-scale models for carbon and nutrient fluxes within microbiomes.