Article
Microbiology
William D. Orsi, Tobias Magritsch, Sergio Vargas, Oemer K. Coskun, Aurele Vuillemin, Sebastian Hoehna, Gert Woerheide, Steven D'Hondt, Jesse Shapiro, Paul Carini
Summary: This study reveals the genomic evolution of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments, showing evolution in clonal populations by point mutation with elevated numbers of pseudogenes and numerous insertion-deletion events in a flagellar operon. Compared to type strains, subseafloor bacterial genomes have a significantly lower number of singleton genes.
Article
Biology
Nils-Kare Birkeland, Boyke Bunk, Cathrin Sproeer, Hans-Peter Klenk, Peter Schoenheit
Summary: Hyperthermophiles are microorganisms that thrive in high temperature environments. A new strain of starch-degrading archaeon, Thermococcus bergensis, was isolated and characterized in this study.
Article
Geosciences, Multidisciplinary
Jasmine S. Berg, Mathilde Lepine, Emile Laymand, Xingguo Han, Hendrik Vogel, Marina A. Morlock, Niroshan Gajendra, Adrian Gilli, Stefano M. Bernasconi, Carsten J. Schubert, Guangyi Su, Mark A. Lever
Summary: This study comprehensively investigates the deep lacustrine biosphere in Lake Cadagno and its impact on sediment geochemistry and vice versa. The findings reveal distinct redox gradients, microbial activities, and organic carbon remineralization processes in the deep sediment layers compared to the water column.
FRONTIERS IN EARTH SCIENCE
(2022)
Article
Multidisciplinary Sciences
Henrik Drake, Peter W. Reiners
Summary: The deep biosphere of Earth hosts ancient chemolithotrophic lineages, and understanding the habitability history in this environment is key to unraveling the origin and evolution of life. By applying a thermochronological perspective, this study reveals the evolution of habitability in Precambrian cratons, providing insights into where and when microbial communities may have flourished and identifying potential areas for the oldest records of chemolithotrophic microbes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Pious Thomas, Pramod Kumar Sahu
Summary: Seed transmission of endophytic microorganisms is a growing research area. Studies on watermelon seeds showed abundant bacteria in different tissues, with higher diversity in seedling compared to embryos. Investigations revealed diverse endophytic bacteria in different cultivars with significant implications for plant biology.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Ecology
Indra Banas, Sarah P. Esser, Victoria Turzynski, Andre Soares, Polina Novikova, Patrick May, Cristina Moraru, Mike Hasenberg, Janina Rahlff, Paul Wilmes, Andreas Klingl, Alexander J. Probst
Summary: By using a novel correlative microscopic approach, we linked the morphologies of virocells to their phylogenetic signals and indigenous virus infections in uncultivated archaea. We observed complete cellular segregation of viral DNA from chromosomal DNA in virocells, suggesting replication of these uncultivated viruses occurs alongside host ribosomes. Additionally, we found virus-like particles attached to heavily infected cells, matching virus structures observed via transmission electron microscopy.
Article
Microbiology
Indira J. Quintero, Anakena M. Castillo, Luis C. Mejia
Summary: This study compared the bacterial communities in soil of two mangrove forest sites in the Panama Bay and found that the community was more diverse in the rural mangrove forest. The dominant phyla of bacteria shared between the two sites were Proteobacteria, Desulfobacterota, and Chloroflexi. The relative abundance of certain bacterial genera increased in the transition from dry to rainy season in the urban mangrove forest.
Article
Microbiology
Cristina Casto-Rebollo, Maria Jose Argente, Maria Luz Garcia, Ramona Natacha Pena, Agustin Blasco, Noelia Ibanez-Escriche
Summary: This study reveals that selection for environmental variance (V-E) of litter size can alter the gut microbiome composition of rabbits, impacting immune regulation and resilience. The low V-E population showed suppressed abundance of Megasphaera sp., Acetatifactor muris, Bacteroidetes rodentium, and increased abundance of Alistipes shahii, Alistipes putredinis, Odoribacter splanchnicus, among others. These results highlight the connection between gut immune modulation and resilience.
Article
Biochemistry & Molecular Biology
Jana Rihova, Giampiero Batani, Sonia Maria Rodriguez-Ruano, Jana Martinu, Frantisek Vacha, Eva Novakova, Vaclav Hypsa
Summary: The phylogenetic diversity of symbiotic bacteria in sucking lice plays a crucial role, with different obligate symbionts established in different louse groups. Research reveals that lice have a unique capacity to acquire symbionts from diverse groups of bacteria during their evolution.
Article
Biochemistry & Molecular Biology
Paul A. P. Atkins, Maria Elena S. Gamo, Daniel F. Voytas
Summary: Researchers overcame the limitations posed by donor molecules in gene targeting events by utilizing ONAS technology and developing the PANGEA bioinformatic pipeline, allowing them to collect a large number of plant somatic GT events and conversion tracts in a short period of time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Geochemistry & Geophysics
Malin Bomberg, Hanna Miettinen, Paivi Kinnunen
Summary: Blasting and fracking in mines can cause leaching of metals and acidification of water systems. This study investigated the dissolution of copper and the changes in microbial communities in a microcosm experiment simulating different water conditions. The results showed that copper dissolution was not solely caused by bacteria, but also involved abiotic reactions.
Article
Ecology
Julio Cesar Garcia-Sanchez, Jose Arredondo-Centeno, Maria Guadalupe Segovia-Ramirez, Ariadna Marcela Tenorio Olvera, Gabriela Parra-Olea, Vance T. Vredenburg, Sean M. Rovito
Summary: Factors such as host phylogeny and climate influence the composition of microbial communities on amphibian skin. The composition of bacterial communities is correlated with host phylogeny, while fungal communities are associated with temperature seasonality and precipitation. Co-occurrence networks of bacteria and fungi show differences in connectivity and negative associations. Including fungi in future studies can provide insights into functional interactions within the microbiome.
Article
Biochemistry & Molecular Biology
Emily LaVerriere, Philipp Schwabl, Manuela Carrasquilla, Aimee R. Taylor, Zachary M. Johnson, Meg Shieh, Ruchit Panchal, Timothy J. Straub, Rebecca Kuzma, Sean Watson, Caroline O. Buckee, Carolina M. Andrade, Silvia Portugal, Peter D. Crompton, Boubacar Traore, Julian C. Rayner, Vladimir Corredor, Kashana James, Horace Cox, Angela M. Early, Bronwyn L. MacInnis, Daniel E. Neafsey
Summary: Multiplexed PCR amplicon sequencing (AmpSeq) is a valuable tool for monitoring threatened species and managing wildlife populations, as well as for understanding the genomic epidemiology of infectious diseases. The study describes the design and evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites, and provides guidance on panel design and implementation for infectious disease research.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Ecology
Huahua Jian, Yi Yi, Jiahua Wang, Yali Hao, Mujie Zhang, Siyuan Wang, Canxing Meng, Yue Zhang, Hongmei Jing, Yinzhao Wang, Xiang Xiao
Summary: By analyzing 19 microbial metagenomes from different oceanic trenches, this study established the oceanic trench viral genome dataset (OTVGD) and found that the trench viral communities exhibited high novelty and potential infection to ecologically important microbial clades. Inter-trench and intra-trench exchange of viral communities was proposed, along with niche-dependent distribution patterns and genomic properties in different habitats and ocean zones. Notably, viruses in the hadal zone seemed to prefer lysogenic lifestyles and had specific auxiliary metabolic genes, suggesting their impact on the hadal ecosystem.
Article
Microbiology
Xiaofei Shi, Dong Liu, Xinhua He, Wei Liu, Fuqiang Yu
Summary: This study identifies the pathogenic fungi causing diseases in true morels and reveals that Diploospora longispora is the main culprit. Other low-abundance fungi appear to be saprophytic fungi infecting after D. longispora.
Article
Biochemical Research Methods
Maryam Baniasad, Yongseok Kim, Michael Shaffer, Anice Sabag-Daigle, Ikaia Leleiwi, Rebecca A. Daly, Brian M. M. Ahmer, Kelly C. Wrighton, Vicki H. Wysocki
Summary: Bottom-up proteomics is a powerful method for characterizing mouse gut microbiota. In this study, we systematically evaluated different protein extraction protocols and contaminant removal strategies. Our results recommend using a combination of SDS and urea in Tris-HCl as the protein extraction method and coupling it with the S-Trap method for the most reproducible and highest number of protein identifications. The optimized workflow is straightforward, fast, and requires minimal sample handling.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Rebecca L. Rubinstein, Mikayla A. Borton, Haiyan Zhou, Michael Shaffer, David W. Hoyt, James Stegen, Christopher S. Henry, Kelly C. Wrighton, Roelof Versteeg
Summary: The behavior of nutrients and contaminants in the subsurface is influenced by various coupled hydrobiogeochemical processes occurring at different scales. Microbial processes play a crucial role in affecting macroscopic system behavior through mediating precipitation, dissolution, and altering aqueous geochemistry. The proposed workflow ('Omics to Reactive Transport-ORT) combines metagenomic and environmental data with open-source software packages to improve ecosystem models, demonstrating how microbiological processes can be integrated into reactive transport models for accurate predictions.
Article
Microbiology
Kaela K. Amundson, Mikayla A. Borton, Rebecca A. Daly, David W. Hoyt, Allison Wong, Elizabeth Eder, Joseph Moore, Kenneth Wunch, Kelly C. Wrighton, Michael J. Wilkins
Summary: The colonization and persistence of microorganisms in subsurface shales after hydraulic fracturing are influenced by resource utilization, resistance to viral predation, and physicochemical conditions. Understanding the diversity and dynamics of microbial communities in these engineered deep ecosystems is essential for management and treatment of microbial biomass in hydraulically fractured wells.
Correction
Microbiology
Kaela K. Amundson, Mikayla A. Borton, Rebecca A. Daly, David W. Hoyt, Allison Wong, Elizabeth Eder, Joseph Moore, Kenneth Wunch, Kelly C. Wrighton, Michael J. Wilkins
Article
Biotechnology & Applied Microbiology
Valerie A. Seitz, Bridget B. McGivern, Rebecca A. Daly, Jacqueline M. Chaparro, Mikayla A. Borton, Amy M. Sheflin, Stephen Kresovich, Lindsay Shields, Meagan E. Schipanski, Kelly C. Wrighton, Jessica E. Prenni
Summary: Root exudation plays a crucial role in mediating interactions between plant roots, microorganisms, and the soil matrix. This study investigated the chemical heterogeneity of root exudates and its effects on soil microbial membership and metabolism. The findings highlight the potential of high-resolution multiomics tools to study soil microbiomes and provide valuable information for the development of effective microbiota management strategies in agriculture.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Environmental Sciences
Timothy H. Morin, William J. Riley, Robert F. Grant, Zelalem Mekonnen, Kay C. Stefanik, A. Camilo Rey Sanchez, Molly A. Mulhare, Jorge Villa, Kelly Wrighton, Gil Bohrer
Summary: Wetland water depth influences microbial and plant communities, which in turn affect the carbon cycling of wetlands. This study used a mechanistic model to simulate different water depth scenarios and analyzed the predicted fluxes of carbon dioxide and methane. The results showed that water depth affects greenhouse gas fluxes and wetland vegetation distribution.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Josue A. Rodriguez-Ramos, Mikayla A. Borton, Bridget B. McGivern, Garrett J. Smith, Lindsey M. Solden, Michael Shaffer, Rebecca A. Daly, Samuel O. Purvine, Carrie D. Nicora, Elizabeth K. Eder, Mary Lipton, David W. Hoyt, James C. Stegen, Kelly C. Wrighton
Summary: Rivers play a significant role in global carbon and nitrogen cycles, but research on microbial and viral communities in sediment environments is still in its early stages. By integrating various "omics" data, researchers have created a conceptual model that uncovers new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, and more. They also provide insights into viral modulation of river sediment carbon and nitrogen cycling.
Article
Microbiology
Arsen Yerlan, Rebecca A. Daly, Reza Keshavarz Afshar, Michael Shaffer, Kelly C. Wrighton, Bridget B. McGivern
Summary: This study reports a new species of archaeal nitrifier recovered from agricultural soils, expanding the understanding of nitrogen loss from farmlands.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Rui Zhao, Ibrahim. F. F. Farag, Steffen. L. L. Jorgensen, Jennifer. F. F. Biddle
Summary: This study investigated the abundance, diversity, and metabolic capacities of CPR bacteria in marine sediments, finding a wide distribution and rich diversity of these bacteria compared to existing marker gene surveys. Through metagenome sequencing, the importance of these bacteria in sediments and their potential role in the early diagenesis of organic matter were revealed.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Soil Science
Jorge A. Villa, Gil Bohrer, Yang Ju, Kelly Wrighton, Nicholas Johnson, Lauren Kinsman-Costello
Summary: Wetlands are important for removing nutrients from runoff and storing them in the soil. The study found that carbon sequestration and nitrogen and phosphorus accumulation varied at different microtopographic levels and locations within the wetland. Nitrate load was the most important factor influencing the sequestration and accumulation of carbon, nitrogen, and phosphorus. The findings suggest that incorporating microtopographic relief features and managing upstream nitrate are key to enhancing the capacity of wetlands to sequester carbon and accumulate nutrients.
Article
Microbiology
Paul O'Toole, Rebecca A. Daly, Reza Keshavarz Afshar, Michael Shaffer, Kelly C. Wrighton, Bridget B. McGivern
Summary: The metagenome-assembled genome sequence of a novel salt-tolerant soil microorganism from untilled, surface agricultural soils in western Colorado is reported.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Chemistry, Analytical
Ishi Keenum, Robert Player, Jason Kralj, Stephanie Servetas, Michael D. Sussman, Joseph A. Russell, Jennifer Stone, Sailaja Chandrapati, Shanmuga Sozhamannan
Summary: This study presents the minimum information requirements for AS in biodetection applications, which were developed under the auspices of the AOAC INTERNATIONAL Stakeholder Program. The guidelines aim to improve data quality, track workflow performance, and enhance the trustworthiness of AS results for decision makers.
JOURNAL OF AOAC INTERNATIONAL
(2023)
Article
Microbiology
Daniel A. Schwartz, Josue A. Rodriguez-Ramos, Michael Shaffer, Rory M. Flynn, Rebecca A. Daly, Kelly C. Wrighton, Jay T. Lennon
Summary: Spore-forming bacteria are common in mammalian guts and affect host health and nutrition. Dormant spore production plays a crucial role in the colonization, persistence, and transmission of these bacteria. Recent studies have shown that phages can counteract dormancy-mediated defense mechanisms and alter the transitions between active and inactive states through the expression of phage-carried sporulation genes during infection. Identification of sporulation genes preferentially carried by phages that infect spore-forming bacteria can help in understanding the complex genetic network responsible for spore development.
Article
Microbiology
J. E. Hudson, D. F. Levia, K. M. Yoshimura, N. R. Gottel, S. A. Hudson, J. F. Biddle
Summary: Bacteria inhabiting bark surfaces are not well understood compared to those inhabiting leaves. Based on a preliminary pilot study, it has been suggested that microbial populations vary across tree bark surfaces and may be influenced by surrounding land use. Preliminary findings also indicate that water flow along the bark surface (stemflow) actively transports bacterial communities across a tree. These initial results underscore the need for further research to determine if there are connections between the biodiversity of microbial populations inhabiting bark surfaces, land use, and hydrology.
MICROBIOLOGY SPECTRUM
(2023)
Article
Engineering, Environmental
Michael A. P. Vega, Rachel C. Scholes, Adam R. Brady, Rebecca A. Daly, Adrienne B. Narrowe, Lily B. Bosworth, Kelly C. Wrighton, David L. Sedlak, Jonathan O. Sharp
Summary: This study combines field-scale biomat and laboratory inhibition microcosms to investigate microbial processes contributing to pharmaceutical transformation in shallow open-water wetlands, revealing diverse activities including photosynthesis, nitrification, denitrification, and diatom dominance. The findings highlight the importance of different microbial clades and their environmental requirements for biotransformation.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)