Article
Environmental Sciences
Shuang Li, Pengqiang Du, Xiaohu Wu, Hairong He, Lin Zhou, Fengshou Dong, Xingang Liu, Yongquan Zheng
Summary: This study investigated the impact of trifluralin on soil microbial communities and functions in a greenhouse setting. The results showed that trifluralin significantly affected the diversity and community structures of bacteria and fungi. It decreased the functions of chemoheterotrophy and sulfur oxidation, but significantly increased the ability of hydrocarbon degradation. Additionally, amino acid metabolism and ABC transporter were significantly reduced, while nitrogen metabolism and ribosome translation were significantly increased.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2022)
Article
Engineering, Multidisciplinary
Rana Hossam Elden, Vidan Fathi Ghonim, Marwa M. A. Hadhoud, Walid Al-Atabany
Summary: This study aimed to demonstrate the feasibility of using the HGSO method for gene selection to predict pediatric sepsis and evaluate survival rate. By analyzing the gene expression profile of peripheral blood cells, 26 informative genes were selected. Cross-validation and experiments showed that these genes had high accuracy in early identification of pediatric sepsis and evaluating survival rate.
ALEXANDRIA ENGINEERING JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Muyan Xiao, Tao Huang, Yazhou Xu, Zhen Peng, Zhanggen Liu, Qianqian Guan, Mingyong Xie, Tao Xiong
Summary: This study comprehensively explored the active microbial community members and key transcripts in the fermentation process of Chinese Sichuan Paocai using metatranscriptomics. Carbon metabolism was the most abundant pathway, with GH and GT being the two most highly expressed carbohydrate-active enzymes.
Article
Engineering, Environmental
Abdelmajeed Adam Lagum, Maria Elektorowicz
Summary: The effect of intermittent direct current on the nitrifying community structure and performance in a membrane electro-bioreactor (MEBR) was investigated. The MEBR achieved substantial nitrification rates and enhanced NH3+ -N removal compared to a conventional membrane bioreactor (MBR). Different nitrifying bacteria species dominance in the MEBR and MBR led to differences in nitrification performance. Developing a fast and robust nitrifying community in MEBR can lead to cost savings in WWTPs.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Biochemical Research Methods
Kristina Lietz, Babak Saremi, Lena Wiese
Summary: This study developed a web application that simplifies the analysis of microarray data and allows for the comparison of results from different technologies and organisms. The application provides a convenient and customizable analysis process and allows users to gain further insights from existing study data.
BMC BIOINFORMATICS
(2023)
Article
Microbiology
Xiayan Liu, Yu Shi, Lingyu Kong, Lihong Tong, Haoxuan Cao, Hu Zhou, Yizhong Lv
Summary: The use of bio-compost significantly influences the diversity, composition, and structure of soil microbial communities. It increases the richness of beneficial microorganisms and decreases the abundance of harmful microorganisms. Factors such as electrical conductivity, soil organic matter, and total phosphorus play key roles in shaping the microbial community composition.
Article
Environmental Sciences
Siyu Liu, Xuchao Zhuang, Chuandong Wang
Summary: The study found that after the addition of PAC in urban river sediments, prokaryotic diversity decreased while eukaryotic diversity increased. The abundance of core microbiota was influenced by physicochemical factors such as salinity, total dissolved solids, and metal contents.
Article
Engineering, Environmental
JunHee Ryu, JaeHyun Jung, KiYoung Park, WonJung Song, ByeongGyu Choi, JiHyang Kweon
Summary: The membrane bioreactor with humic acid substrate (MBR-H) showed effective organic removal and the Proteobacteria phylum played a significant role in humic acid degradation. Various operational parameters in MBRs can be adjusted to facilitate the evolution of microbial consortia for efficient degradation of refractory organic matter.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Engineering, Environmental
Zhi-Ling Li, Rui Cheng, Fan Chen, Xiao-Qiu Lin, Xiao-Jing Yao, Bin Liang, Cong Huang, Kai Sun, Ai-Jie Wang
Summary: The study demonstrated that sulfamethoxazole, chlortetracycline and amoxicillin have inhibitory effects on microbial denitrification performance, resulting in decreased nitrate removal efficiencies and decreased expression of important genes. Higher concentrations of antibiotics lead to stronger inhibitory effects, potentially causing changes in the abundance of denitrifying bacterial genera.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Environmental Sciences
Xiaoling Wang, Tao Sun, Shengjun Yan, Shangyi Chen, Yue Zhang
Summary: Variations in microbial species and functional composition in coastal sediment are often attributed to human activities and nutrient supplements. However, the response of microbiome stability to restocking biological resources is not well understood. This study evaluated the composition, function, and stability of microbes in a coastal area where sea cucumbers were restocked after six months, using metagenomics and microbiome co-occurrence networks. The results showed changes in microbial composition, function, and community stability, suggesting that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
Dongsheng Wang, Haike Ren
Summary: This study aimed to assess the impacts of nitrogen application rate on microbial diversity, community and functionality in rhizosphere of Tartary buckwheat in short-time. The results showed that the microbial diversity was not affected, but the microbial community and functionality were affected by the nitrogen application rate.
Article
Environmental Sciences
Sha Zhou, Jieying Wang, Lan Chen, Jun Wang, Fazhu Zhao
Summary: This study investigated the afforestation effects on soil organic carbon decomposition and the role of microbial communities using metagenomic sequencing and labeling analyses. The results showed that the priming effect initially increased and reached a peak at 20 years of afforestation, driven by changes in microbial community structure and function, particularly the expression of stable C decomposition genes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Green & Sustainable Science & Technology
Boxi Wang, Robert Duran, Thierry Pigot, Cristiana Cravo-Laureau
Summary: Performic acid (PFA), a new generation of disinfectant, has shown remarkable performance for wastewater treatment. However, its effect on wastewater microbial community and the differences compared to commonly used disinfectants is poorly documented. This study provides an overview of the effects of PFA, chlorine, and UV on microbial diversity and structure in wastewater. The results show that PFA is more effective at inactivating pathogen microorganisms and has the potential for safe wastewater reuse.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Biochemical Research Methods
Kristen D. Curry, Qi Wang, Michael G. Nute, Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, Tor Savidge, Sonia Villapol, Alexander Dilthey, Todd J. Treangen
Summary: 16S ribosomal RNA-based analysis is the standard method for studying microbial community composition. Full-length 16S rRNA gene sequences have the potential to provide species-level accuracy. Emu is an approach that can generate taxonomic abundance profiles from full-length 16S rRNA reads, accurately estimating microbial abundance.
Article
Immunology
Li-Juan Lv, Sheng-Hui Li, Ji-Ying Wen, Guang-Yang Wang, Hui Li, Tian-Wen He, Qing-Bo Lv, Man-Chun Xiao, Hong-Li Duan, Min-Chai Chen, Zhou-Ting Yi, Qiu-Long Yan, Ai-Hua Yin
Summary: This study compared the gut microbiome of patients with preeclampsia (PE) and healthy pregnant women. The results showed that the gut microbiota of PE patients had certain enriched species and microbial functions, while the gut microbiome of healthy pregnant women had different enriched species and functions. The diagnostic potential of gut microbial biomarkers for PE was also developed.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biodiversity Conservation
Zhiwei Liang, Ayik Abdillah, Wenwen Fang, Rongliang Qiu, Bixian Mai, Zhili He, Philippe Juneau, Marcelo Pedrosa Gomes, Cindy Rianti Priadi, Shanquan Wang
Summary: Microbial community assembly and assembly-driving processes in organic matter-polluted urban rivers are influenced by both organic matter and geographic conditions. Water and sediment community assembly in organic matter-polluted urban rivers show universality in dynamics, with prokaryotic communities being deterministic and eukaryotic communities being stochastic.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Engineering, Chemical
Jinxi Feng, Tiantian Zhang, Wen Yan, Jingxiang Sun, Shuanghong Tian, Zhili He, Ya Xiong
Summary: A new piezo-catalytic reactor (PCR) was constructed to investigate the piezocatalytic degradation of pollutants and simultaneous response of current. The PCR with SnO2/t-BaTiO3/ITO film anode showed a more favorable piezocatalytic degradation and piezo-current response compared to PCR with only ITO or tBaTiO(3)/ITO film anode. The anodic process involved the piezocatalytic oxidations of H2O to center dot OH and HCOOH to CO2, while the cathodic process was related to the reduction of O-2 to center dot O-2(-) or H2O2 and reduction of H+ ion to H-2. These results deepen the understanding of piezo-current response and extend the application of piezocatalysis to fuel cell.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Soil Science
Ruiwen Hu, Songfeng Liu, Haiming Zhao, Zhigang Wang, Longfei Shu, Jiaxiong Zeng, Quanying Cai, Cehui Mo, Zhili He, Cheng Wang
Summary: This study examines the biodegradation kinetics of DEHP in soil, showing that it can be divided into two phases with different microbial communities involved. Different bacterial genera are responsible for DEHP degradation in each phase, and the interaction between bacteria and fungi may affect the degradation rates. This research provides a fundamental basis for developing efficient strategies for DEHP removal in soil.
BIOLOGY AND FERTILITY OF SOILS
(2023)
Article
Biodiversity Conservation
Mengmeng Wang, Xin Sun, Baichuan Cao, Nona R. Chiariello, Kathryn M. Docherty, Christopher B. Field, Qun Gao, Jessica L. M. Gutknecht, Xue Guo, Genhe He, Bruce A. Hungate, Jiesi Lei, Audrey Niboyet, Xavier Le Roux, Zhou Shi, Wensheng Shu, Mengting Yuan, Jizhong Zhou, Yunfeng Yang
Summary: Global climate models predict an increase in frequency and intensity of precipitation events worldwide. However, the biosphere-climate feedback to elevated precipitation (eP) is not well understood. This study reports on a long-term experiment assessing the effects of eP, alone or in combination with other climate change drivers, on plants and soil. It was found that eP induced soil C loss and decreased plant root production, possibly due to changes in microbial community composition. The study highlights the importance of the biosphere-climate feedback in water-limited ecosystems.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Ecology
Lu Zhang, Xinyu Huang, Jizhong Zhou, Feng Ju
Summary: This study uses stable isotope probing to identify diverse uncultivated predatory bacteria in activated sludge microbiota and finds Myxococcota species to be prevalent and potentially influential in wastewater treatment processes.
Article
Ecology
Tao Xu, Xuanyu Tao, Hongxi He, Megan L. Kempher, Siping Zhang, Xiaochun Liu, Jun Wang, Dongyu Wang, Daliang Ning, Chongle Pan, Honghua Ge, Nannan Zhang, Yong-Xing He, Jizhong Zhou
Summary: Carbohydrate utilization is critical for microbial survival. The phosphotransferase system (PTS) is a well-known microbial system involved in carbohydrate metabolism, but its role in non-model prokaryotes remains underexplored. In this study, the prevalence of incomplete PTSs in prokaryotes was investigated, and lignocellulose-degrading clostridia was found to have lost PTS sugar transporters and carry a substitution in the core PTS component. Functional and structural diversification of PTS components were observed, providing novel insights into the regulatory mechanisms of incomplete PTSs.
Article
Microbiology
Lingyue Zhu, Yan Chen, Ruibo Sun, Jiabao Zhang, Lauren Hale, Kenneth Dumack, Stefan Geisen, Ye Deng, Yinghua Duan, Bo Zhu, Yan Li, Wenzhao Liu, Xiaoyue Wang, Bryan S. Griffiths, Michael Bonkowski, Jizhong Zhou, Bo Sun
Summary: To achieve long-term sustainability of intensive agricultural practices, understanding belowground functional stability is crucial. This study investigated how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability. The results showed that higher resource availability increased potential cross-trophic interactions, while low resource availability made stability more dependent on within trophic interactions and soil biodiversity.
Article
Microbiology
Yulin Zhang, Yulin Wang, Mingxi Tang, Jizhong Zhou, Tong Zhang
Summary: This paper conducted a global meta-analysis of microbial dark matter (MDM) in wastewater treatment plants (WWTPs), revealing the high proportion of MDM in WWTPs. The study also proposed a wanted list for priority targets in further investigations of activated sludge and verified the effectiveness of several genome mining methods. The methodology proposed in this study can be applied to other ecosystems, enhancing our understanding of ecosystem structure across diverse habitats.
Article
Microbiology
Xiaolan Lin, Baoyi Qiao, Ruirui Chang, Yixin Li, Wei Zheng, Zhili He, Yun Tian
Summary: In this study, Sulfurovum and Sulfurimonas were identified as keystone taxa in microbial communities. They played different roles in different experimental models and formed key symbiotic relationships with other microorganisms. Comparative genomics and metagenome-assembled genome (MAG) analysis revealed their metabolic potential in keystone guilds. Experimental verification demonstrated the important role of Sulfurovum in the degradative microbiome against Benzo[a]-pyrene toxicity.
Article
Environmental Sciences
Min Zhou, Xiaotong Guan, Ting Deng, Ruiwen Hu, Lu Qian, Xueqin Yang, Bo Wu, Juan Li, Qiang He, Longfei Shu, Qingyun Yan, Zhili He
Summary: This study found that the phylogenetic diversity of bacterial communities is related to their denitrification rates and temporal stability. By experimentally evolving synthetic denitrifying communities with different phylogenetic distances, it was found that communities with higher phylogenetic diversity exhibited higher function and stability. This has important implications for using synthetic communities to address environmental issues and mitigate greenhouse gas emissions.
ENVIRONMENTAL RESEARCH
(2023)
Article
Engineering, Environmental
Xiaokun Liu, Lian Zhang, Rui Shen, Qihong Lu, Qinglu Zeng, Xiaojun Zhang, Zhili He, Simona Rossetti, Shanquan Wang
Summary: This study identified FeS as a major catalyzing matter for the abiotic dechlorination of chloroethenes (CEs) in soil. Acetylene was found to be an indicator of FeS-mediated abiotic CE dechlorination. Organohalide-respiring bacteria (OHRB)-mediated dechlorination enhanced the conversion of CEs to acetylene, while FeS inhibited OHRB-mediated dechlorination and its inhibition could be alleviated by the addition of soil humic substances. Sulfate-reducing bacteria and fermenting microorganisms affected FeS-mediated abiotic dechlorination by re-generating FeS and providing short chain fatty acids, respectively. These findings provide insights into the interactions between abiotic and biotic dechlorination processes in soil and can guide the sustainable management of CE-contaminated sites.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Ecology
Carolyn R. Cornell, Ya Zhang, Daliang Ning, Naijia Xiao, Pradeep Wagle, Xiangming Xiao, Jizhong Zhou
Summary: This study found that conventional tilled cropland increased the complexity and stability of soil microbial communities, compensating for the loss of biodiversity due to agricultural disturbance. These findings suggest that agricultural practices can impact species interactions, leading to changes in ecosystem function.
Article
Chemistry, Multidisciplinary
Binhao Wang, Jianming Xu, Yiling Wang, Erinne Stirling, Kankan Zhao, Caiyu Lu, Xiangfeng Tan, Dedong Kong, Qingyun Yan, Zhili He, Yunjie Ruan, Bin Ma
Summary: Antibiotic overuse and environmental contamination of residual antibiotics contribute to the global spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. This study investigated the antibiotic resistance of soilborne pathogens at a global scale, identifying 407 ARG-carrying pathogens (APs) in 1443 samples. Agricultural soils exhibited a higher richness of APs compared to non-agricultural ecosystems, with a prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. A global map of soil AP richness was generated, highlighting hot spots in East Asia, South Asia, and the eastern United States, which can guide efforts to control soilborne APs worldwide.
Article
Microbiology
Qiannan Peng, Lu Lin, Qichao Tu, Xiaopeng Wang, Yueyue Zhou, Jiyu Chen, Nianzhi Jiao, Jizhong Zhou
Summary: This study demonstrates the impacts of different lignocellulose substrates and exposure times on long-term bacterial community assembly and identifies comprehensive potential decomposers at the levels of taxa and functional genes. The links between ligninolytic functional traits and taxonomic groups of substrate-specific populations are revealed. It shows that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.
Article
Food Science & Technology
Chaoyang Liu, Meitong Jiang, Mengting Maggie Yuan, Ertao Wang, Yang Bai, Thomas W. Crowther, Jizhong Zhou, Zhiyuan Ma, Li Zhang, Yu Wang, Jixian Ding, Wuxing Liu, Bo Sun, Renfang Shen, Jiabao Zhang, Yuting Liang
Summary: This study identifies aluminium-resistant bacteria and their potential contribution to increased rice yields in acidic soils. The synthetic community composed of highly Al-resistant bacterial strains harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation.
