Article
Genetics & Heredity
Marcela Hernandez, Shamik Roy, C. William Keevil, Marc G. Dumont
Summary: Using DNA stable isotope probing (SIP) combined with high throughput sequencing, bacteria capable of growing in the presence of multiple antibiotics including meropenem were identified in a British agricultural soil. The results showed that Acidobacteriota and Pseudomonadota were prominent bacteria in response to antibiotics. A metagenome-assembled genome (MAG-1) related to the genus Stenotrophomonas was retrieved, and antimicrobial resistance genes (ARGs) were identified from both heavy and light fractions. The study reveals the presence of non-pathogenic soil bacteria and potential clinical pathogens in the agricultural soil, as well as the existence of ARGs, but the occurrence of horizontal gene transfer between these groups remains unclear.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Engineering, Environmental
Haonan Fan, Shanghua Wu, Wenxu Dong, Xianglong Li, Yuzhu Dong, Shijie Wang, Yong-Guan Zhu, Xuliang Zhuang
Summary: This study identified antibiotic-resistant bacteria in soil-plant systems using stable isotope probing and highlighted the rhizosphere as a hotspot for antibiotic resistance gene transfer.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
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
Soil Science
Yong Zheng, Zhengkun Hu, Xu Pan, Xiaoyun Chen, Delphine Derrien, Feng Hu, Manqiang Liu, Stephan Hattenschwiler
Summary: The study reveals that a significant amount of carbon and nitrogen can be input into the soil from decomposing litters, with slowly decomposing litter favoring carbon and nitrogen storage in the soil.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Geosciences, Multidisciplinary
Renshan Li, Qingpeng Yang, Xin Guan, Longchi Chen, Qingkui Wang, Silong Wang, Weidong Zhang
Summary: The influence of litter quality and soil mesofauna on litter decomposition was studied in a subtropical forest ecosystem. It was found that higher quality litter decomposed faster in the early stage and had a larger fraction of stable residue remaining in the late stage. Soil mesofauna exclusion had no effect on the early decomposition rate but significantly increased the stable residue remaining.
Article
Agronomy
Javier Palomino, Pablo Garcia-Palacios, Gerlinde B. B. De Deyn, Laura Beatriz Martinez-Garcia, Sara Sanchez-Moreno, Ruben Milla
Summary: Plant domestication has led to changes in leaf litter quality, affecting decomposition and soil decomposer communities. Domesticated litters decompose faster and have different impacts on soil bacteria, fungi, and nematodes.
Article
Engineering, Environmental
Flavien Garcia, Aline Reis de Carvalho, Louna Riem-Galliano, Loic Tudesque, Magali Albignac, Alexandra ter Halle, Julien Cucherousset
Summary: A study in the Garonne river found that the abundance of ingested microplastics differed between macroinvertebrates and fish, and was not significantly related to microplastic pollution. The characteristics of microplastics also varied between abiotic and biotic compartments.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
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
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
Ecology
Sara Fareed Mohamed Wahdan, Li Ji, Martin Schadler, Yu-Ting Wu, Chakriya Sansupa, Benjawan Tanunchai, Francois Buscot, Witoon Purahong
Summary: This study investigates the decomposition of wheat straw under future climate conditions and reveals that future climate will accelerate the decay rate of straw only in the early phases of decomposition. It also shows that the projected climate change will increase the abundance of saprotrophic fungi in decomposing wheat straw, and that the impact of future climate on microbial community assembly and interaction networks will depend on the decomposition phase. The study concludes that the impact of future climate on straw decay and microbial traits is limited to the early phases of decomposition.
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
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
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.