Article
Environmental Sciences
Dong Li, Qian Bao, Min Zhao, Fan Xia, Xun Wang
Summary: Soils in the Hailuogou Glacier forefield have the potential to absorb atmospheric CH4, but high soil water content may affect this capacity. The study found that CH4 concentrations and isotopic compositions were influenced by geological factors and microbial activity.
ENVIRONMENTAL RESEARCH
(2022)
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
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
Microbiology
Sara Campana, Kathrin Busch, Ute Hentschel, Gerard Muyzer, Jasper M. de Goeij
Summary: This study used DNA stable isotope probing and 16S rRNA amplicon sequencing to identify metabolically active bacterial taxa involved in dissolved organic matter (DOM) uptake in a sponge holobiont. The results revealed that specific bacterial taxa belonging to PAUC34f, Poribacteria, and Chloroflexi phyla are active consumers of DOM through heterotrophic carbon metabolism, while Nitrospirae may have mixotrophic capabilities. This research provides new insights into the interaction between diverse sponge-associated bacteria and DOM consumption in marine ecosystems.
ENVIRONMENTAL MICROBIOLOGY
(2021)
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
Microbiology
Robert R. Junker, Xie He, Jan-Christoph Otto, Victoria Ruiz-Hernandez, Maximilian Hanusch
Summary: The study indicates that there are differences in community assembly processes between microbes and plants, with microbes being less dispersal limited and plants strongly responding to abiotic factors. Furthermore, the leaf microbiome of plants is species-specific and well buffered from environmental conditions.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Environmental Sciences
Huaqing Liu, Hanzhi Lin, Benru Song, Xiaoxu Sun, Rui Xu, Tianle Kong, Fuqing Xu, Baoqin Li, Weimin Sun
Summary: This study investigated active aniline degraders in different pH environments, revealing that aniline degradation is associated with different bacterial taxa. By comparing three aniline-contaminated cultures, it was found that aniline-degrading bacteria employ diverse survival strategies and exhibit different characteristics in biotic interactions under different pH environments.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Xuan Zhao, Jibing Li, Dayi Zhang, Zilin Huang, Chunling Luo, Longfei Jiang, Deyin Huang, Gan Zhang
Summary: The study found that salicylic acid can enhance the biodegradation of BaP in the rhizosphere by changing the community structure of rhizosphere BaP-degrading bacteria and increasing the abundance of PAH degradation-related genes. This provides new insights into the mechanisms of BaP rhizoremediation in petroleum-contaminated sites.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Huihui Dai, Jingfeng Gao, Dingchang Li, Zhiqi Wang, Wanjun Duan
Summary: This study identified the microbial community involved in triclosan degradation during nitrification, with Sphingobium as the predominant species and glutathione transferase as the main enzyme. It was also found that Sphingobium may degrade triclosan without contributing to the spread of antibiotic resistance genes (ARGs). Thauera and Dechloromonas were identified as key hosts of most ARGs in the wastewater treatment system.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Microbiology
Zijie Yu, Xinhua He, Zhitong Li, Shuang Zhou, Dalu Guo, Hao Pu, Hongyan Luo
Summary: This study investigated the existence, abundance, and diversity of anaerobic ammonium oxidation (anammox) bacteria in purple paddy soils at different temperatures. By using C-13-DNA stable-isotope probe and Illumina MiSeq high-throughput sequencing, the researchers found differences in the abundance and diversity of anammox bacteria in purple paddy soils at different temperatures. These findings contribute to a better understanding of the regulation of soil nitrogen cycling.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Rui Xu, Max Kolton, Wan Tao, Xiaoxu Sun, Pingzhou Su, Duanyi Huang, Miaomiao Zhang, Zhaohui Yang, Zhaohui Guo, Hanbing Gao, Qi Wang, Baoqin Li, Chengyu Chen, Weimin Sun
Summary: This study aimed to identify putative Se(IV)-reducing bacteria (SeIVRB) in anoxic Se-rich sediment and investigate the genetic mechanisms underlying Se(IV) reduction. Results showed that Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter were potential SeIVRB. Metagenome-assembled genomes (MAGs) affiliated with these bacteria were retrieved, and functional gene annotation indicated the presence of putative Se(IV)-reducing genes. Metatranscriptomic analysis revealed the important roles of DMSO reductase, fumarate reductase, and sulfite reductase in Se(IV) reduction. This study expands our knowledge of anaerobic Se(IV) bio-reduction and demonstrates the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Engineering, Environmental
Huihui Dai, Jingfeng Gao, Dingchang Li, Zhiqi Wang, Wanjun Duan
Summary: TCS has an adverse influence on PD performance and microbial community in granule-based PD system, but the system can gradually recover. After domestication, PD granular sludge can achieve a certain efficiency in TCS degradation and adsorption. Microbes may increase their resistance to TCS by increasing the secretion of extracellular polymeric substances.
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
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
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
Ecology
Lettice C. Hicks, Beat Frey, Rasmus Kjoller, Martin Lukac, Mari Moora, James T. Weedon, Johannes Rousk
Summary: The study proposes a function-first framework to predict how microbial communities influence ecosystem functions, linking microbial function to community composition and structure. It describes the dependence of microbial functions on environmental factors and combines functional response curves with current environmental conditions to predict the contribution of the whole community to ecosystem function. Ultimately, indicator taxa may be used as a diagnostic tool to enable predictions of ecosystem function from community composition.
Article
Biodiversity Conservation
Claudia Guidi, Beat Frey, Ivano Brunner, Katrin Meusburger, Michael E. Vogel, Xiaomei Chen, Tobias Stucky, Dariusz J. Gwiazdowicz, Piotr Skubala, Arun K. Bose, Marcus Schaub, Andreas Rigling, Frank Hagedorn
Summary: This study reveals that soil fauna plays a crucial but often overlooked role in the storage of soil organic carbon (SOC) under drought conditions. The activity of soil fauna during drought reduces the incorporation of litter into the mineral soil, leading to a decrease in long-term SOC storage.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Ecology
Mark A. Anthony, Thomas W. Crowther, Sietse van der Linde, Laura M. Suz, Martin Bidartondo, Filipa Cox, Marcus Schaub, Pasi Rautio, Marco Ferretti, Lars Vesterdal, Bruno De Vos, Mike Dettwiler, Nadine Eickenscheidt, Andreas Schmitz, Henning Meesenburg, Henning Andreae, Frank Jacob, Hans-Peter Dietrich, Peter Waldner, Arthur Gessler, Beat Frey, Oliver Schramm, Pim van den Bulk, Arjan Hensen, Colin Averill
Summary: This study investigates the effects of ectomycorrhizal fungi (EMF) on tree growth and finds that the composition of EMF is strongly correlated with tree growth rate. The study also suggests that the proportion of nitrogen acquisition genes and exploration types of EMF communities play a role in determining tree growth.
Article
Environmental Sciences
Carla Perez-Mon, Beat Stierli, Michael Ploetze, Beat Frey
Summary: Global warming in mid-latitude alpine regions is affecting the permafrost microbiome, leading to changes in microbial abundance and composition, potentially impacting soil carbon dynamics.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biodiversity Conservation
Sinikka Robinson, Eoin J. O'Gorman, Beat Frey, Marleena Hagner, Juha Mikola
Summary: The impacts of climate change on high latitude ecosystem structure and functioning are likely to be strong due to biota adaptation to low temperatures and nutrient levels. Long-term soil warming experiments suggest that decomposer organisms are surprisingly resistant to chronic warming, with the exception of fungivorous nematodes. Soil organic matter content drives spatial variation in microorganism abundances and mineral N availability.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Biodiversity Conservation
Monika Carol Resch, Martin Schuetz, Raul Ochoa-Hueso, Nina Buchmann, Beat Frey, Ulrich Graf, Wim H. van der Putten, Stephan Zimmermann, Anita C. Risch
Summary: Evaluation of restoration activities is crucial, and network analyses prove to be powerful in assessing the recovery of ecosystems by examining the response of both biotic and abiotic components.
JOURNAL OF APPLIED ECOLOGY
(2022)
Article
Green & Sustainable Science & Technology
Tong Zhang, Yufei Liu, Xin Sui, Beat Frey, Fuqiang Song
Summary: This study in the Songnen Plain, Northeastern China, investigated the community structures and diversities of soil bacteria and fungi in three typical land-use types. The results showed that land conversion had significant effects on both fungal and bacterial community diversity and abundance, with changes in soil chemical and physical properties driving microbial community composition.
Article
Engineering, Environmental
Joel Ruthi, Basil M. Rast, Weihong Qi, Carla Perez-Mon, Lucrezia Pardi-Comensoli, Ivano Brunner, Beat Frey
Summary: In this study, the impacts of different plastics on the genetic potential of the soil microbiome in alpine soils were investigated using shotgun metagenomics. The results showed that biodegradable plastics, such as Ecovio and BI-OPL, had a greater impact on the soil microbiome compared to polyethylene, with fungi, alpha-, and 8-Proteobacteria dominating on the biodegradable films.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Soil Science
Beat Frey, Barbara Moser, Bjorn Tytgat, Stephan Zimmermann, Juan Alberti, Lori A. Biederman, Elizabeth T. Borer, Arthur A. D. Broadbent, Maria C. Caldeira, Kendi F. Davies, Nico Eisenhauer, Anu Eskelinen, Philip A. Fay, Frank Hagedorn, Yann Hautier, Andrew S. MacDougall, Rebecca L. McCulley, Joslin L. Moore, Maximilian Nepel, Sally A. Powers, Eric W. Seabloom, Eduardo Vazquez, Risto Virtanen, Laura Yahdjian, Anita C. Risch
Summary: This study collected soil samples from grasslands worldwide and analyzed the impact of nitrogen addition on the soil microbiome. The results showed that nitrogen addition had a significant effect on the community structure of soil diazotrophs, but had minimal impact on their diversity and abundance. In contrast, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) responded differently to nitrogen addition. Overall, long-term nitrogen addition had a greater impact on AOB communities compared to soil diazotrophs and AOA.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Ecology
Xin Sui, Mengsha Li, Beat Frey, Mingyu Wang, Xiaohong Weng, Xin Wang, Fuyuan Chen, Xianda Li, Zhong Du, Libin Yang, Mai-He Li
Summary: This study investigated the diversity and structure of soil bacterial communities in a climax forest and four degraded forests in the Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve in northern China. The results revealed distinct differences in bacterial diversity and composition between the climax forest and the degraded forests, and soil physicochemical properties were found to be the main factors shaping the bacterial communities.
ECOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Xin Sui, Beat Frey, Libin Yang, Yingnan Liu, Rongtao Zhang, Hongwei Ni, Mai-He Li
Summary: Acidobacteria are an important component of soil bacteria, and their structure and diversity are influenced by climate changes and human activities. This study investigated the Acidobacterial community and diversity in a typical wetland degradation series in northeastern China. The results showed that the soil physicochemical properties changed significantly along the degradation stages and the composition of Acidobacteria was influenced by different soil environmental factors in wetland and forest stages. These findings highlight the importance of understanding the role of Acidobacteria in wetland ecosystems.
FRONTIERS IN MICROBIOLOGY
(2022)
Correction
Microbiology
X. Sui, B. Frey, L. Yang, Y. Liu, R. Zhang, H. Ni, M. -H. Li
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Xin Sui, Mengsha Li, Beat Frey, Guanhua Dai, Libin Yang, Mai-He Li
Summary: This study evaluated the soil fungal composition and diversity in Deyeuxia angustifolia populations along an elevational gradient in northeastern China. The results showed that soil fungal diversity decreased with increasing elevation. Soil nitrate nitrogen (NO3--N), pH, and moisture were identified as key environmental factors determining soil fungal diversity.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Gilda Varliero, Pedro H. Lebre, Beat Frey, Andrew G. Fountain, Alexandre M. Anesio, Don A. Cowan
Summary: Microbial communities and nutrient dynamics in glaciers and ice sheets are constantly changing due to hydrological conditions. Glaciers and ice sheets act as bioreactors, as microbiomes transform nutrients and impact meltwater chemistry. Global warming affects nutrient and cell export, altering proglacial systems. This review integrates current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics, highlighting their interdependence, variability, and impact on proglacial environments.
Article
Microbiology
Xiaohong Weng, Mingyu Wang, Xin Sui, Beat Frey, Yingnan Liu, Rongtao Zhang, Hongwei Ni, Maihe Li
Summary: The soil microbiome in wetland ecosystems, which plays a vital role in nutrient cycling and climate regulation, is influenced by nitrogen (N) addition. However, the impact of high ammonium nitrogen additions on the diversity and composition of soil bacterial communities in temperate wetland ecosystems is not well understood. This study used high-throughput sequencing to investigate the changes in soil bacterial diversity and community structure with increasing ammonium concentrations in a wetland in China. The results showed that nitrogen addition significantly altered various soil physicochemical parameters, but did not significantly affect the bacterial community structure. Acidobacteriota, Proteobacteria, Chloroflexi, Verrucomicrobiota, and Actinobacteriota were found to be the most dominant bacterial phyla in the soils. Overall, this study provides insights into the response of the soil microbiome in wetland ecosystems to nitrogen deposition.
