Article
Multidisciplinary Sciences
Tristan A. Caro, Jamie McFarlin, Sierra Jech, Noah Fierer, Sebastian Kopf
Summary: In this study, the growth rates of soil microorganisms were measured using hydrogen-stable isotope probing of lipids with 2H-enriched water. The results showed that microbial growth rates in soil are slow, with average generation times of 14 to 45 days. Furthermore, there is a decoupling of microbial abundance and growth in soil microbiomes. This study highlights the importance of measuring growth rates to complement standard analyses of soil microbial communities.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Engineering, Environmental
Ernestina Hauptfeld, Jordi Pelkmans, Terry T. Huisman, Armin Anocic, Basten L. Snoek, F. A. Bastiaan von Meijenfeldt, Jan Gerritse, Johan van Leeuwen, Gert Leurink, Arie van Lit, Ruud van Uffelen, Margot C. Koster, Bas E. Dutilh
Summary: This study investigates the microbial communities involved in the biodegradation of poly-contaminants in a groundwater treatment system. The genome-resolved metagenomic analysis revealed significant differences in microbial populations between the plant and the contaminated park groundwater. The findings provide valuable insights into the efficacy of microbial biodegradation in treating complex groundwater contaminants.
Article
Engineering, Environmental
Ernestina Hauptfeld, Jordi Pelkmans, Terry T. Huisman, Armin Anocic, Basten L. Snoek, F. A. Bastiaan von Meijenfeldt, Jan Gerritse, Johan van Leeuwen, Gert Leurink, Arie van Lit, Ruud van Uffelen, Margot C. Koster, Bas E. Dutilh
Summary: Biodegradation is a sustainable and cost-effective solution for groundwater pollution. In this study, the microbial populations involved in the biodegradation of poly-contaminants in a heavily contaminated groundwater pipeline were investigated. The microbial communities were analyzed using genome-resolved metagenomic analysis, revealing the changing microbial communities in a highly effective groundwater treatment system.
Article
Biochemical Research Methods
Jiro Karlo, Ashish Kumar Dhillon, Soumik Siddhanta, Surya Pratap Singh
Summary: Abnormal protein kinetics can cause diseases associated with essential life processes. Understanding protein dynamics and turnover is important for developing diagnostic or therapeutic tools. Raman spectroscopy combined with stable isotope probes has been breakthrough in studying metabolites. In this work, Raman-SIP was used to monitor dynamic changes in the proteome. The incorporation of C-13-labeled glucose in microbial biomass was verified, and shifts in Raman spectral vibrations of biomolecules were observed. The feasibility of protein turnover monitoring was demonstrated by measuring changes in intensity of these bands. Kanamycin was used to assess effects on protein turnover. Successful application of this method can provide a nondestructive tool for monitoring proteome-level changes.
JOURNAL OF BIOPHOTONICS
(2023)
Article
Microbiology
Ella T. Sieradzki, Michael Morando, Jed A. Fuhrman
Summary: The study investigated the diversity and functional potential of a seed community in the chronically polluted Port of Los Angeles (POLA), demonstrating the ability of degraders at POLA to incorporate carbon from naphthalene and shift microbial community composition. The findings suggest that promiscuous dehydrogenases may replace canonical naphthalene degradation enzymes at this site, calling for further research. Additionally, genomic-based recommendations for future optimization of PAH bioremediation at POLA were proposed, targeting specific metabolic pathways to stimulate the activity of oil-degrading bacteria in case of an oil spill.
Article
Biotechnology & Applied Microbiology
Kathryn Wigley, Emmanuel Egbadon, Carlo R. Carere, Louise Weaver, Kim Baronian, Lee Burbery, Pierre Y. Dupont, Sarah J. Bury, Peter A. Gostomski
Summary: This study identified the active micro-organisms involved in aerobic methane oxidation coupled to denitrification (AME-D) using RNA-SIP and high-throughput sequencing techniques. Methanotrophs, methylotrophs, and denitrifiers were found to be actively participating in the AME-D process. It is the first study to utilize RNA-SIP and high-throughput sequencing to determine the active bacteria within an AME-D community.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Environmental Sciences
Kevin J. Lyons, Jenni Ikonen, Anna-Maria Hokajarvi, Teemu Rasanen, Tarja Pitkanen, Ari Kauppinen, Katharina Kujala, Pekka M. Rossi, Ilkka T. Miettinen
Summary: Groundwater quality monitoring often relies on sporadic and slow manual sampling and laboratory analyses, which may result in undetected water quality deficiencies. In Finland, enhanced monitoring of untreated groundwater quality using real-time online monitoring, isotopic analysis, and microbial community analysis revealed indications of surface water intrusion and faecal contamination. The findings demonstrated the usefulness of supplementary methods and suggested their wider implementation to enhance groundwater quality monitoring.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Alex Greenlon, Ella Sieradzki, Olivier Zablocki, Benjamin J. Koch, Megan M. Foley, Jeffrey A. Kimbrel, Bruce A. Hungate, Steven J. Blazewicz, Erin E. Nuccio, Christine L. Sun, Aaron Chew, Cynthia-Jeanette Mancilla, Matthew B. Sullivan, Mary Firestone, Jennifer Pett-Ridge, Jillian F. Banfield
Summary: The growth and physiology of soil microorganisms are influenced by both current and historical soil environmental conditions. By using genome-resolved metagenomics, we found that precipitation levels have a significant impact on the activity and growth rates of soil microorganisms. In addition, the activity of bacteriophages in the soil is correlated with the activity of their hosts. Contrary to expectations, the ability to decompose organic matter and oxidize carbon compounds is broadly distributed among active and inactive bacteria.
Article
Environmental Sciences
Yuncai Miao, Yongxin Lin, Zengming Chen, Huijie Zheng, Yuhui Niu, Yakov Kuzyakov, Deyan Liu, Weixin Ding
Summary: This study investigated fungal succession and co-occurrence trends during cellulose decomposition using C-13 stable isotope probing. The findings suggest that compost amendment can increase the decomposition capacity of dominant fungal taxa and facilitate fungal colonization in smaller aggregates. The study also highlights differences in fungal interactions between microaggregates and macroaggregates.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Ecology
Tengfei Guo, Qian Zhang, Dali Song, Chao Ai, Shuiqing Zhang, Ke Yue, Shaomin Huang, Wei Zhou
Summary: This study investigated the impact of long-term fertilization practices on the decomposition of crop residues by soil microbes. The results showed that different fertilization regimes led to distinct microbial communities involved in straw decomposition. Certain key bacterial and fungal taxa were positively associated with straw decomposition. The study also found that the availability of nutrients influenced the microbial response and community structure.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2022)
Article
Ecology
Andrew G. McLeish, Se Gong, Paul Greenfield, David J. Midgley, Ian T. Paulsen
Summary: The study utilizes 16S rRNA microbial surveys to observe shifts in microbial community composition in the presence of different organic matter, revealing that 135 microbes became enriched when organic matter was added. These surveys allow for detailed analysis of microbial compositions to determine which taxa favor growth in the presence of varying organic matter types. This study also generated a conceptual model mapping putative degradation pathways for subsurface microbial consortia for the first time.
Article
Biochemistry & Molecular Biology
Sander Wuyts, Renato Alves, Maria Zimmermann-Kogadeeva, Suguru Nishijima, Sonja Blasche, Marja Driessen, Philipp E. Geyer, Rajna Hercog, Ece Kartal, Lisa Maier, Johannes B. Mueller, Sarela Garcia Santamarina, Thomas Sebastian B. Schmidt, Daniel C. Sevin, Anja Telzerow, Peter Treit, Tobias Wenzel, Athanasios Typas, Kiran R. Patil, Matthias Mann, Michael Kuhn, Peer Bork
Summary: Multi-omics analyses were used to study the molecular changes in microbial communities under different conditions. Using five omics layers, the study mapped the molecular response of a synthetic community of gut bacteria to three non-antibiotic drugs. The results showed that the omics methods were consistent in estimating relative species abundances and complemented each other in capturing functional changes.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Review
Dentistry, Oral Surgery & Medicine
Purnima S. Kumar, Shareef M. Dabdoub, Sukirth M. Ganesan
Summary: The study of the periodontal microbial community has been influenced by a long history of cultivation-based and microscopic investigations, leading to the recognition of a discrepancy between culturable and uncultured bacteria. The development of DNA sequencing as a tool to study microbial dark matter has revolutionized the field, enabling the discovery of new species and functions and challenging traditional views on the role of the oral microbiome in health and disease.
PERIODONTOLOGY 2000
(2021)
Article
Environmental Sciences
Tingting Teng, Jidong Liang, Zijun Wu, Pengkang Jin, Dayi Zhang
Summary: Bioaugmentation was used to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soils, and biochar immobilization on PHE degraders significantly enhanced degradation efficiency compared to free-cell mediated bioaugmentation. RNA-stable isotope probing identified bacterial lineages responsible for in situ PHE degradation. The findings expanded the understanding of active PHE degraders and suggested biochar-immobilization assisted bioaugmentation as a promising strategy for PAH-contaminated soil bioremediation.
SCIENCE OF THE TOTAL ENVIRONMENT
(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.
Article
Limnology
Winifred M. Johnson, Krista Longnecker, Melissa C. Kido Soule, William A. Arnold, Maya P. Bhatia, Steven J. Hallam, Benjamin A. S. Van Mooy, Elizabeth B. Kujawinski
LIMNOLOGY AND OCEANOGRAPHY
(2020)
Review
Astronomy & Astrophysics
Lauren Seyler, Elizabeth B. Kujawinski, Armando Azua-Bustos, Michael D. Lee, Jeffrey Marlow, Scott M. Perl, Henderson James Cleaves
Article
Ecology
Frank Xavier Ferrer-Gonzalez, Brittany Widner, Nicole R. Holderman, John Glushka, Arthur S. Edison, Elizabeth B. Kujawinski, Mary Ann Moran
Summary: The communities of bacteria around marine microphytoplankton are dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Analysis showed that bacterial uptake molecules in the ocean surface contain a high percentage of nitrogen and organic sulfur compounds, indicating their importance in the link between microbial autotrophs and heterotrophs.
Review
Environmental Sciences
Andrew D. Steen, Stephanie Kusch, Hussain A. Abdulla, Nevenka Cakic, Sarah Coffinet, Thorsten Dittmar, James M. Fulton, Valier Galy, Kai-Uwe Hinrichs, Anitra E. Ingalls, Boris P. Koch, Elizabeth Kujawinski, Zhanfei Liu, Helena Osterholz, Darci Rush, Michael Seidel, Julio Sepulveda, Stuart G. Wakeham
FRONTIERS IN MARINE SCIENCE
(2020)
Article
Environmental Sciences
Laura Weber, Maickel Armenteros, Melissa Kido Soule, Krista Longnecker, Elizabeth B. Kujawinski, Amy Apprill
FRONTIERS IN MARINE SCIENCE
(2020)
Article
Chemistry, Analytical
Brittany Widner, Melissa C. Kido Soule, Frank Xavier Ferrer-Gonzalez, Mary Ann Moran, Elizabeth B. Kujawinski
Summary: Utilizing pre-extraction derivatization and ultrahigh performance liquid chromatography electrospray ionization tandem mass spectrometry, targeted dissolved metabolites in seawater and saline culture media were successfully detected and quantified. This quantitative method has been optimized for 73 common metabolites, with 50 requiring derivatization for quantification due to low extraction efficiencies.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Katelyn S. Foppe, Elizabeth B. Kujawinski, Claire Duvallet, Noriko Endo, Timothy B. Erickson, Peter R. Chai, Mariana Matus
Summary: This paper presents an HPLC-MS/MS method for quantifying glucuronide conjugates and other drug metabolites in wastewater systems. By shifting the sample collection point upstream, unambiguous markers of human exposure can be better captured, demonstrating the potential of expanding WBE to monitoring labile metabolites in upstream wastewater networks.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Article
Environmental Sciences
Maya P. Bhatia, Stephanie Waterman, David O. Burgess, Patrick L. Williams, Randelle M. Bundy, Travis Mellett, Megan Roberts, Erin M. Bertrand
Summary: The Canadian Arctic Archipelago is vulnerable to climate warming, with its glaciers impacting nutrient delivery to surface waters through upwelling and direct discharge. The strength of upwelling and nutrient delivery scales with subglacial meltwater discharge, with potential consequences for local productivity and regional micronutrient cycling. As glaciers retreat, the impacts on marine ecosystems are likely to be amplified initially but eventually muted as the ice masses diminish.
GLOBAL BIOGEOCHEMICAL CYCLES
(2021)
Article
Environmental Sciences
Patrick L. Williams, David O. Burgess, Stephanie Waterman, Megan Roberts, Erin M. Bertrand, Maya P. Bhatia
Summary: A variety of glacial processes impact coastal ecosystems by supplying essential nutrients and labile carbon to the ocean. This study in the Canadian Arctic Archipelago demonstrates that while meltwater from a shallow tidewater glacier may not directly increase downstream carbon and nutrient concentrations, it induces upwelling of deeper nutrient-rich marine water. Understanding the effects of increased meltwater output from retreating Arctic glaciers on marine ecosystems is crucial.
JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES
(2021)
Review
Chemistry, Analytical
Stephen A. Wise, Ryan P. Rodgers, Christopher M. Reddy, Robert K. Nelson, Elizabeth B. Kujawinski, Terry L. Wade, Andres D. Campiglia, Zhanfei Liu
Summary: Analytical techniques for chemical analysis of oil and its transformation products have greatly benefited from research following the Deepwater Horizon oil spill. Advanced gas chromatography and high-resolution mass spectrometry have provided a better understanding of the composition and complexity of oil, while novel separation approaches have increased the information available on spilled oil. The development of these techniques is important for future oil spills and investigations into the fate and effects of petroleum and dispersants.
CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY
(2023)
Article
Microbiology
Shuting Liu, Krista Longnecker, Elizabeth B. Kujawinski, Kevin Vergin, Luis M. Bolanos, Stephen J. Giovannoni, Rachel Parsons, Keri Opalk, Elisa Halewood, Dennis A. Hansell, Rod Johnson, Ruth Curry, Craig A. Carlson
Summary: Deep convective mixing plays an important role in the export and transformation of dissolved organic matter in the ocean. This study conducted in the Sargasso Sea revealed that winter convective mixing resulted in changes in the composition and oxidation of DOM. Specific dissolved metabolites were produced or lost during deep mixing, accompanied by bacterial growth and response of specific bacterial lineages. The findings highlight the role of microbes in altering the quantity and quality of DOM in the ocean.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Mary Ann Moran, Elizabeth B. Kujawinski, William F. Schroer, Shady A. Amin, Nicholas R. Bates, Erin M. Bertrand, Rogier Braakman, C. Titus Brown, Markus W. Covert, Scott C. Doney, Sonya T. Dyhrman, Arthur S. Edison, A. Murat Eren, Naomi M. Levine, Liang Li, Avena C. Ross, Mak A. Saito, Alyson E. Santoro, Daniel Segre, Ashley Shade, Matthew B. Sullivan, Assaf Vardi
Summary: This article reviews the sources, roles, and methods of analysis for microbial metabolites in the surface ocean.
NATURE MICROBIOLOGY
(2022)
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
Limnology
Winifred M. Johnson, Melissa Kido C. Soule, Krista Longnecker, Maya P. Bhatia, Steven J. Hallam, Michael W. Lomas, Elizabeth B. Kujawinski
Summary: Metabolites, the small organic molecules synthesized during cell metabolism, form a complex and dynamic carbon pool in the ocean. Understanding the distribution of metabolites inside microbial cells and dissolved in seawater is crucial for understanding their production and fate, as well as their role in shaping marine microbial food webs.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Ecology
Liam Heffernan, Maria A. Cavaco, Maya P. Bhatia, Cristian Estop-Aragones, Klaus-Holger Knorr, David Olefeldt
Summary: Permafrost thaw in northern peatlands leads to increased methane emissions, and this study investigates the factors responsible and their duration. The researchers found that microbial communities, temperature, and saturated surface conditions enhance methane emissions in young thermokarst bogs. However, these favorable conditions only persist for the initial decades after permafrost thaw.