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
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
Samuel E. Barnett, Rob Egan, Brian Foster, Emiley A. Eloe-Fadrosh, Daniel H. Buckley
Summary: Soil microbes play a crucial role in the global carbon cycle, but our understanding of how the carbon cycle operates in soil communities is limited. This is mainly due to the lack of functional genes that define carbon transformations. Through metagenomic stable isotope probing, we linked genomic features of bacteria to their carbon acquisition and growth dynamics in soil. We identified genomic traits that can predict bacterial ecological strategies, providing insights into bacterial interactions with soil carbon.
Article
Chemistry, Analytical
Malama Chisanga, Howbeer Muhamadali, Danielle McDougall, Yun Xu, Nicholas Lockyer, Royston Goodacre
Summary: This study utilized Raman and FT-IR spectroscopy combined with SIP to measure 13C carbon incorporation rates and unravel microbial metabolism and interactions. The findings demonstrated the feasibility of identifying metabolic kinetics and interactions within microbial consortia using these techniques.
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
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
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
Geochemistry & Geophysics
Wenhong Johnson Qiu, Mei-Fu Zhou, Xiaochun Li, Fang Huang, John Malpas
Summary: The study investigates the formation of sediment-hosted stratiform sulfide (SHSS) deposits using Fe, S, and C isotopes. It found that pyrite grains in laminated ores and black shales from the Devonian Dajiangping SHSS-type pyrite deposit in South China exhibit different isotopic compositions, with positive Fe isotopic values in black shales indicating gradual crystallization from sediment-derived iron and negative Fe isotopic values in laminated ores due to kinetic fractionation in hydrothermal plumes.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2021)
Article
Biochemical Research Methods
Pan Deng, Taylor Valentino, Michael D. Flythe, Hunter N. B. Moseley, Jacqueline R. Leachman, Andrew J. Morris, Bernhard Hennig
Summary: By studying metabolites produced by the gut microbiome, differences in the utilization of different dietary fibers for biosynthesis of essential molecules were observed, providing a new method for a deeper understanding of the metabolic function of the gut microbiome.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Willemien de Kock, Meaghan Mackie, Max Ramsoe, Morten E. Allentoft, Annette C. Broderick, Julia C. Haywood, Brendan J. Godley, Robin T. E. Snape, Phil J. Bradshaw, Hermann Genz, Matthew von Tersch, Michael W. Dee, Per J. Palsboll, Michelle Alexander, Alberto J. Taurozzi, Canan Cakirlar
Summary: By combining bioarchaeology with contemporary data, researchers have found that Mediterranean green turtles have been using the same North African seagrass meadows for at least 5,000 years, highlighting the significance of protecting these critical coastal habitats.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Maria Mooshammer, Katharina Kitzinger, Arno Schintlmeister, Soeren Ahmerkamp, Jeppe Lund Nielsen, Per Halkjaer Nielsen, Michael Wagner
Summary: The study introduces a SIP approach that significantly reduces cross-feeding in complex microbial communities by continuously exposing microbial cells to isotopically labeled substrate on a membrane filter. This approach removes metabolites and degradation products constantly, preventing the consumption of secondary substrates, thus allowing for the distinction between primary consumers and other members of microbial food webs.
Article
Environmental Sciences
Huanjun Zhang, Yin Lu, Yi Li, Lei Wang, Wenlong Zhang, Longfei Wang, Lihua Niu, Zhongjun Jia
Summary: This study identified bacteria involved in estrogen metabolism in sediments from different bays of Taihu Lake using DNA-SIP technology, revealing their distinct roles in the biodegradation process of E2. The results showed a significant and positive correlation between the increase in relative abundance of these bacteria and E2 mineralization rate.
ENVIRONMENTAL POLLUTION
(2021)
Article
Environmental Sciences
Weimin Sun, Xiaoxu Sun
Summary: This study found that methane can be produced through anaerobic degradation of toluene over a long-term enrichment experiment. The DNA-SIP technique identified bacteria in the phylum Proteobacteria as the dominant toluene-degrading bacteria under anaerobic conditions.
WATER AIR AND SOIL POLLUTION
(2021)