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
Engineering, Environmental
Jinha Kim, Myung Hwangbo, Chih-Hsuan Shih, Kung-Hui Chu
Summary: Stable isotope probing (SIP) is a powerful tool for studying microbial community structure and function. It has provided substantial information to understand complex microbial ecosystems. This review provides an overview of the advances and applications of SIP-based technologies and discusses important factors to be considered in experimental designs and data interpretation.
Article
Environmental Sciences
Wenlong Zhang, Xinzi Wang, Yuanyuan Miao, Yi Li, Huanjun Zhang, Lihua Niu, Longfei Wang
Summary: Research suggests that sertraline negatively impacts key components in the microbial food web, leading to long-term disturbance in nutrient cycling in river sediment ecosystems. Sertraline not only increases nitrogen-transforming microorganisms, but also promotes the participation of more species in the nitrogen transformation process.
ENVIRONMENTAL RESEARCH
(2021)
Article
Engineering, Environmental
Zhifeng Huang, Abdul Qadeer, Saisai Zheng, Fangfang Ge, Kexin Zhang, Daqiang Yin, Binghui Zheng, Xingru Zhao
Summary: This study investigated the concentrations of PCB congeners, stable isotope levels, and FAs composition in ten freshwater species of Dongtinghu Lake, China. The results showed that the concentrations of certain PCB congeners increased with trophic levels, while PCB 155 concentrations remained consistent across trophic levels. Furthermore, there were positive correlations between FAs and PCBs, indicating that FAs can serve as efficient bioindicators of PCB pollution in aquatic food webs.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
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
Samuel E. Barnett, Nicholas D. Youngblut, Chantal N. Koechli, Daniel H. Buckley
Summary: Soil microorganisms play a crucial role in the global carbon cycle by determining the fate of soil organic matter. A study tracking bacterial assimilation of carbon from different sources found low phylogenetic conservation in carbon assimilation dynamics. The bioavailability of carbon sources significantly impacts carbon mineralization dynamics, bacterial guild structures, and biogeographical distribution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Environmental Sciences
Yujiao Sun, Meng Yin, Danyang Zheng, Tiandai Wang, Xiaohui Zhao, Chunling Luo, Jibing Li, Yueqiao Liu, Shangwei Xu, Songqiang Deng, Xinzi Wang, Dayi Zhang
Summary: In this study, active acetonitrile degraders in wastewater activated sludge were successfully identified using stable isotope probing and magnetic nanoparticle mediated isolation. Different active degraders were found between short-term ANAMMOX and SBR, with MMI significantly enriching more degraders for low-assimilation substrates.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Engineering, Environmental
Haohao Sun, Kailong Huang, Xuxiang Zhang, Hongqiang Ren, Lin Ye
Summary: This study investigated the degradation of refractory organic compounds (ROCs) in sewage and found that different ROCs are degraded by different bacterial communities. Only six bacterial genera were common to all 10 ROCs. The study also showed that these bacteria are difficult to isolate using conventional methods and have low abundance in wastewater treatment.
Article
Environmental Sciences
Tingting Teng, Jidong Liang, Jinwei Zhu, Pengkang Jin, Dayi Zhang
Summary: Bioaugmentation aided by biosurfactant is an effective method for removing pyrene from contaminated sites. This process accelerates pyrene degradation and increases the diversity of active pyrene-degrading bacteria.
ENVIRONMENTAL POLLUTION
(2022)
Article
Environmental Sciences
Hyuntae Choi, Bohyung Choi, Yoshito Chikaraishi, Yoshinori Takano, Haryun Kim, Kitack Lee, Dhongil Lim, Kyung-Hoon Shin
Summary: This study used compound-specific isotope analysis to investigate the variation of delta N-15 associated with microbial processes in marine sediment samples. The results showed that the decrease in amino acid concentrations in sediment was accompanied by an increase in delta N-15 values. Phenylalanine displayed a depth-dependent variation in microbial utilization, while glycine showed the highest relative molar contribution and delta N-15 increase in deep sediment. These findings provide an important basis for interpreting the delta N-15 values of amino acids in sediment.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Ecology
Emily R. Arsenault, James H. Thorp, Michael J. Polito, Mario Minder, Walter K. Dodds, Flavia Tromboni, Alain Maasri, Mark Pyron, Bud Mendsaikhan, Amarbat Otgonganbat, Solongo Altangerel, Sudeep Chandra, Robert Shields, Caleb Artz, Hayat Bennadji
Summary: Using compound-specific stable carbon isotope analysis, the study found that aquatic resources played a consistent and important role in supporting fish consumers in streams, while terrestrial carbon did not directly contribute to their diet.
Article
Engineering, Environmental
Weimin Sun, Xiaoxu Sun, Max M. Haggblom, Max Kolton, Ling Lan, Baoqin Li, Yiran Dong, Rui Xu, Fangbai Li
Summary: Microorganisms play an important role in altering the speciation, mobility, and bioavailability of antimony (Sb), particularly in the reduction of Sb(V). By using DNA-stable isotope probing and metagenomics analysis, this study identified Pseudomonas and Geobacter as potential Sb(V)-reducing bacteria in Sb-contaminated sites, with Geobacter potentially playing a key role in Sb(V) reduction based on the presence of specific genes. This work provides valuable insights into the microbial community responsible for Sb(V) reduction.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Geosciences, Multidisciplinary
Wenyue Liang, Tiantian Yu, Liang Dong, Zhongjun Jia, Fengping Wang
Summary: Bathyarchaeota has been found to have the ability to fix carbon, as its abundance increased 15.3 times after long-term cultivation with lignin and sodium bicarbonate. Through DNA separation, it was confirmed that Bathyarchaeota DNA contained C-13, indicating its carbon fixation capacity.
SCIENCE CHINA-EARTH SCIENCES
(2023)
Article
Ecology
Ulrike Hanz, Philip Riekenberg, Anna de Kluijver, Marcel van der Meer, Jack J. Middelburg, Jasper M. de Goeij, Martijn C. Bart, Erik Wurz, Ana Colaco, Gerard C. A. Duineveld, Gert-Jan Reichart, Hans-Tore Rapp, Furu Mienis
Summary: This study reveals how deep-sea sponge grounds survive in a food-limited environment through stable isotope analysis. Sponge with high microbial abundance utilize dissolved resources and efficient recycling pathways to sustain themselves and other organisms. Additionally, sponges provide organic material to support the otherwise food-limited associated fauna, contributing to the thriving deep-sea ecosystems.
FUNCTIONAL ECOLOGY
(2022)
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
Gastroenterology & Hepatology
Laura Krieg, Konrad Didt, Isabel Karkossa, Stephan H. Bernhart, Stephanie Kehr, Narmadha Subramanian, Andreas Lindhorst, Alexander Schaudinn, Shirin Tabei, Maria Keller, Michael Stumvoll, Arne Dietrich, Martin von Bergen, Peter F. Stadler, Jurga Laurencikiene, Martin Krueger, Matthias Blueher, Martin Gericke, Kristin Schubert, Peter Kovacs, Rima Chakaroun, Lucas Massier
Summary: The study compared different fat depots in 70 obese patients undergoing Roux-en-Y gastric bypass surgery, revealing significant differences in metabolism and inflammatory pathways, with epiploic fat tissue showing the highest gene expression levels.
Article
Ecology
Martin Taubert, Will A. Overholt, Beatrix M. Heinze, Georgette Azemtsop Matanfack, Rola Houhou, Nico Jehmlich, Martin von Bergen, Petra Roesch, Juergen Popp, Kirsten Kuesel
Summary: Using Stable Isotope Cluster Analysis, it was found that mixotrophs, rather than strict autotrophs, were the most abundant active organisms in groundwater microcosms. These mixotrophs employ different strategies to satisfy their carbon requirements, providing fitness under nutrient-limited conditions.
Article
Multidisciplinary Sciences
Christian Schoene, Anja Poehlein, Nico Jehmlich, Norman Adlung, Rolf Daniel, Martin von Bergen, Silvan Scheller, Michael Rother
Summary: The study converted a methanogen into an acetogen and showed that Methanosarcina acetivorans can completely abandon methanogenesis for energy conservation. The results revealed that the metabolic flexibility of methanogenic archaea might be much greater than currently known.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Patricia Geesink, Martin Taubert, Nico Jehmlich, Martin von Bergen, Kirsten Kuesel
Summary: This study investigated the effects of adding necromass to the microbial community in fractured bedrock groundwater. The results showed that a few primary degraders rapidly utilized the labeled necromass, followed by a concerted action of groundwater microorganisms, and eukaryotes assimilated necromass-derived carbon either directly or indirectly.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Sarah Riesbeck, Hannes Petruschke, Ulrike Rolle-Kampczyk, Christian Schori, Christian H. Ahrens, Christian Eberlein, Hermann J. Heipieper, Martin von Bergen, Nico Jehmlich
Summary: Bisphenols can disturb the gut microbiome and inhibit the growth of human commensal bacteria, leading to changes in physiological and functional state of cells. These findings help to better understand the impact of bisphenols on host health and disease development.
Article
Biochemistry & Molecular Biology
Sven-Bastiaan Haange, Andreas Till, Per-Olof Bergh, Guenter Fauler, Michael Gigl, Anita Loefgren-Sandblom, Frank G. Schaap, Thomas Clavel, Christian Trautwein, Wiebke Fenske, Karin Kleigrewe, Hanns-Ulrich Marschall, Steven W. M. Olde Damink, Tarek Moustafa, Martin von Bergen, Ulrike Rolle-Kampczyk
Summary: This study compares and harmonizes methodologies for quantification of bile acids, including primary and secondary bile acids, in different samples. The results show that measurement of hydrophobic bile acids is the most challenging, but the quality assessments are generally similar, and data from chosen locations can be used for comparisons between studies.
Article
Biochemistry & Molecular Biology
Lei Zhang, Marina Toplak, Raspudin Saleem-Batcha, Lars Hoeing, Roman Jakob, Nico Jehmlich, Martin von Bergen, Timm Maier, Robin Teufel
Summary: Antimicrobial resistance is a serious threat to human health, and understanding the underlying mechanisms is crucial. This study discovered and characterized oxidoreductases that inactivate the broad-spectrum antibiotic chloramphenicol through dual oxidation of the C3-hydroxyl group. These enzymes also enable the inactivation of related compounds but not the fluorinated derivative. Phylogenetic analyses suggest that distinct isofunctional enzymes evolved independently in Gram-positive and Gram-negative bacteria. Mechanistic and structural studies provide insights into the catalytic mechanisms of these enzymes, which have both negative and positive impacts on antibiotic resistance and chloramphenicol bioremediation.
Article
Ecology
Nelson Khan, Edward Muge, Francis J. Mulaa, Benson Wamalwa, Martin von Bergen, Nico Jehmlich, Lukas Y. Wick
Summary: Fungi play a crucial role in the biodegradation of soil organochlorine pesticides by facilitating bacterial dispersal and nutrient release. Experimental results indicate that the transfer of nutrients from fungi to bacteria can enhance the degradation of organic pollutants, highlighting the importance of fungal-bacterial interactions.
Article
Virology
Johan S. Saenz, Bibiana Rios-Galicia, Bianca Rehkugler, Jana Seifert
Summary: Ensilaging is a common process for preserving feed, using lactic acid bacteria to stabilize feed quality. This study investigated the composition of bacterial and viral communities during grass silage preservation, revealing a correlation between changes in pH, bacterial composition, and viral diversity. The results suggest that viral communities play a role in the establishment of the bacterial community during silage preservation.
Article
Ecology
Markus Krueger, Narendrakumar Chaudhari, Bo Thamdrup, Will A. Overholt, Laura A. Bristow, Martin Taubert, Kirsten Kuesel, Nico Jehmlich, Martin von Bergen, Martina Herrmann
Summary: The study reveals that complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in oligotrophic carbonate rock aquifers, due to their ecophysiological characteristics and wide occurrence in groundwater. However, their specific contribution to nitrification processes has been unclear. The research aimed to unravel the contribution of CMX, AOA, and AOB to nitrification and identify the environmental drivers of their niche differentiation in oligotrophic carbonate rock aquifers.
Article
Agriculture, Dairy & Animal Science
G. Lazzari, A. Munger, L. Eggerschwiler, D. Borda-Molina, J. Seifert, A. Camarinha-Silva, S. Schrade, M. Zahner, K. Zeyer, M. Kreuzer, F. Dohme-Meier
Summary: This study investigated the effects of acacia and sainfoin as condensed tannin-rich sources on ruminal and manure methane emissions. The results showed that neither acacia nor sainfoin reduced the methane yield or emission intensity. Acacia supplementation reduced milk production and dry matter intake, while sainfoin reduced milk protein content and yield. Therefore, a careful evaluation is necessary before implementing tanniferous feeds in farm practice, as it may result in productivity losses.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Ecology
Sarah-Alica Dahl, Jana Seifert, Amelia Camarinha-Silva, Yu-Chieh Cheng, Angelica Hernandez-Arriaga, Martina Hudler, Wilhelm Windisch, Andreas Koenig
Summary: This study aims to investigate the rumen content of Bavarian roe deer and explore the composition of nutrients and microbiota. The results revealed significant differences in nutrient concentrations and microbial composition based on habitat, season, and age class. Additionally, a core bacterial community that plays a crucial role in the roe deer's rumen was identified.
Article
Biochemistry & Molecular Biology
Sergio Serrano-Villar, Camilla Tincati, Sajan C. Raju, Johan S. Saenz, Elena Moreno, Rafael Bargiela, Alfonso Cabello-Ubeda, Elena Sendagorta, Alina Kurz, Jose Perez A. Molina, Amparo de Benito, Johannes R. Hov, Laura Fernandez-Lopez, Alfonso Muriel, Rosa del Campo, Santiago Moreno, Marius Troseid, Jana Seifert, Manuel Ferrer
Summary: Human papillomavirus can lead to HSILs in the anogenital area, and the microbiome may play a role. HIV-MSM individuals have a high risk of anal cancer, but current screening methods for HSILs lack specificity. This study found that elevated levels of microbiome-encoded proteins were associated with HSILs, and measuring these biomarkers improved the current strategy of anal cancer screening.
Article
Microbiology
Nida Amin, Sarah Schwarzkopf, Johanna Troescher-Mussotter, Amelia Camarinha-Silva, Sven Daenicke, Korinna Huber, Jana Frahm, Jana Seifert
Summary: This study examined the faecal microbiome and plasma metabolome of Holstein calves during different developmental stages and weaning times. The results showed that the timing of weaning has significant effects on the calf's microbiota and metabolism, with early weaning leading to changes in microbiome composition and decreased plasma concentrations of certain metabolites.
Article
Microbiology
Bibiana Rios Galicia, Johan Sebastian Saenz, Timur Yergaliyev, Amelia Camarinha-Silva, Jana Seifert
Summary: This study explores the pan-genome of Ligilactobacillus aviarius to describe its functional adaptability to the avian gastrointestinal environment. The species exhibits high prevalence in poultry gut and encodes various gene clusters involved in interactions with host cells and antiviral mechanisms.
CURRENT RESEARCH IN MICROBIAL SCIENCES
(2023)