Article
Environmental Sciences
Wenshan He, Jingkai Fan, Tao Ya, Minglu Zhang, Tingting Zhang, Xiaohui Wang
Summary: Chlortetracycline (CTC) has irreversible effects on bacterial communities and microbial interactions in activated sludge systems, with high concentrations causing system deterioration and water quality deterioration, while low concentrations enhance system complexity and stability.
ENVIRONMENTAL POLLUTION
(2022)
Article
Engineering, Environmental
Chunli Chen, Zhihao Gan, Ronghua Xu, Fangang Meng
Summary: The presence of influent cellulose did not significantly impact the performance of a membrane bioreactor (MBR). However, it did affect the microbial diversity and community structure, leading to differences in dominant phyla and keystone microbes between scenarios with and without cellulose. Cellulose plays an important role in shaping the microbial community structure in MBR systems.
JOURNAL OF WATER PROCESS ENGINEERING
(2021)
Article
Environmental Sciences
Huimi Lin, Yichen Zheng, Yuankai Yang, Fengyi Liu, Kuo Yang, Bing Zhang, Xianghua Wen
Summary: In this study, a molecular ecological network approach was used to construct co-occurrence networks of core microorganisms (CoreN), whole activated sludge community (WholeN), and microbial communities without core microorganisms (OtherN) in wastewater treatment plants in China. The results showed that WholeN had more complex and tighter connections compared to OtherN. The core microorganisms promoted cooperation between AS microorganisms. Moreover, WholeN exhibited higher robustness and lower vulnerability compared to OtherN. These results demonstrate the importance of the core community in enhancing the stability of the ecological network in activated sludge.
ENVIRONMENTAL RESEARCH
(2023)
Article
Engineering, Environmental
Junyu Liu, Tao Ya, Minglu Zhang, Minghan Zhu, Tingting Zhang, Xiaohui Wang
Summary: This study investigated the long-term effects of different concentrations of polyvinyl chloride microplastics (PVC MPs) on the microbial interaction in anammox process. The results showed that high concentration of PVC MPs caused performance fluctuation in nitrogen removal, while low concentration increased the network size and complexity of microbial community. PVC MPs also significantly reduced microbial diversity and altered the overall microbial community structure.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Yan Huang, Junqi Zhang, Junyu Liu, Xiaoping Gao, Xiaohui Wang
Summary: The main focus of this study was to evaluate the operational stability and changes in microbial interactions of aerobic granular sludge (AGS) systems at reduced C/N. The results showed that the reduction of C/N decreased the removal efficiency of total nitrogen and total phosphorus, as well as the granule settling performance and stability. Molecular ecological network analysis revealed that the decreased C/N ratio made the overall network and subnetworks more complex and tightly connected. Increased competition among microbes in these networks and subnetworks may have contributed to the deterioration in pollutant removal performance.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2024)
Review
Multidisciplinary Sciences
Sho M. Kodera, Promi Das, Jack A. Gilbert, Holly L. Lutz
Summary: Understanding the interactions within microbial communities is crucial in microbial ecology, but it is challenging due to their complexity, dynamics, and numerous unique interactions. Microbial ecologists have to employ various approaches to simplify and conceptualize the study system, in order to gain practical insights into microbial interactions in both simplified and complex systems.
Article
Environmental Sciences
Minghan Zhu, Minglu Zhang, Yibo Yuan, Peilin Zhang, Shuai Du, Tao Ya, Daying Chen, Xiaohui Wang, Tingting Zhang
Summary: The study demonstrated that the BER-S/IAD system showed efficient denitrification and phosphorus removal, as well as good ibuprofen removal under ibuprofen exposure. Additionally, ibuprofen significantly reduced microbial community diversity and changed their structure, impacting bacteria related to denitrification and phosphorus removal.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Review
Microbiology
Gunjan Gupta, Amadou Ndiaye, Marie Filteau
Summary: Microorganisms play a crucial role in ecosystems, and their interactions and networks have significant impacts on ecosystem stability and function. Experimental capture of microbial interactions involves a combination of methods, and the complex nature of microbial interactions leads to diverse outcomes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Breanna J. Putman, Riley Williams, Enjie Li, Gregory B. Pauly
Summary: Studying animals in urban areas poses challenges due to limited accessibility and the difficulty in collecting data on secretive or rare species. However, this study demonstrates that community science can be a powerful tool to overcome these challenges, as shown in the assessment of predation and parasitism in Southern Alligator Lizards. Urbanization was found to be associated with increased predation risk and decreased parasitism in the lizard population.
SCIENTIFIC REPORTS
(2021)
Article
Engineering, Chemical
Anh Q. Nguyen, Luong N. Nguyen, Zhicheng Xu, Wenhai Luo, Long D. Nghiem
Summary: This study investigated fouling-associated microbial communities in a laboratory-scale MBR at different fouling stages, revealing differences in microbial structure between mixed liquor and biofilm, with specific taxa like Victivallales and Blastocatellia 11-24 playing key roles in fouling propensity. Despite their low abundances, these key players positively correlated with fouling indicators, contributing to the development of new fouling control strategies. The biofilm community showed a more complex structure and higher inter-species interaction compared to the mixed liquor community, indicating greater stability and synergy among microbial taxa in the biofilm.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Environmental Sciences
Kenta Suzuki, Masato S. Abe, Daiki Kumakura, Shinji Nakaoka, Fuki Fujiwara, Hirokuni Miyamoto, Teruno Nakaguma, Mashiro Okada, Kengo Sakurai, Shohei Shimizu, Hiroyoshi Iwata, Hiroshi Masuya, Naoto Nihei, Yasunori Ichihashi
Summary: Network-based assessments are crucial for understanding complex microbial and microbial-host interactions, and are essential for microbial engineering. Chemical-mediated interactions play a significant role in the coexistence of microbial species. However, the effectiveness of existing methods in detecting chemical-mediated interactions remains uncertain.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Engineering, Environmental
Depeng Wang, Qi Luo, Kailong Huang, Xu-Xiang Zhang
Summary: This study investigated the assembly processes and interactions of functional bacteria in anammox and denitrification coupling systems using lab-scale up-flow bioreactors. The results showed that the community composition of functional bacteria differed between the systems, and the community assembly was mainly governed by stochastic processes and homogeneous selection. Moreover, the network structures of anammox and denitrifying bacteria varied between the systems.
CHEMICAL ENGINEERING JOURNAL
(2023)
Editorial Material
Microbiology
Kenneth Wasmund
Summary: Sulfate-reducing microorganisms (SRM) play a crucial role in global sulfur and carbon cycles, especially in anoxic marine sediments. They consume fermentation products and hydrogen, affecting microbial communities, particularly members of the Marinilabiliales. This study provides new insights into the ecological networks and community assembly in marine sediment microbes, highlighting the importance of SRM activity in ecosystem functions.
Article
Engineering, Environmental
Jingye She, Juan Liu, Hongping He, Qiong Zhang, Yuyang Lin, Jin Wang, Meiling Yin, Lulu Wang, Xudong Wei, Yeliang Huang, Changzhi Chen, Wenli Lin, Nan Chen, Tangfu Xiao
Summary: This study investigated the co-occurrence patterns of bacterial communities in two different soil profiles near a typical Tl-bearing pyrite mine using 16S rRNA sequencing and network analysis. Results indicated that geochemical parameters were key in shaping microbial community distribution and that microbial modules were significantly associated with variations in Tl geochemical fractionation. The findings may aid in the development of bioremediation strategies for Tl-contaminated soils utilizing indigenous microbes.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Ecology
Lucas A. Camacho, Cecilia Siliansky de Andreazzi, Lucas P. Medeiros, Irina Birskis-Barros, Carine Emer, Carolina Reigada, Paulo R. R. Guimaraes Jr
Summary: A fundamental fact about mutualisms is that there are cheaters that benefit from the use of resources and services without providing any positive feedback to other species. The role of cheaters in the evolutionary dynamics of mutualisms has long been recognized, yet their broader impacts at the community level, beyond species they directly interact with, is still poorly understood. Because mutualisms form networks often involving dozens of species, indirect effects generated by cheaters may cascade through the whole community, reshaping trait evolution.
Article
Ecology
Bin Ma, Kankan Zhao, Xiaofei Lv, Weiqin Su, Zhongmin Dai, Jack A. Gilbert, Philip C. Brookes, Karoline Faust, Jianming Xu
Article
Multidisciplinary Sciences
Bin Ma, Erinne Stirling, Yuanhui Liu, Kankan Zhao, Jizhong Zhou, Brajesh K. Singh, Caixian Tang, Randy A. Dahlgren, Jianming Xu
Summary: This study identified key microbial taxa regulating soil biogeochemical processes using metagenomic data from forest soils in eastern China, highlighting the sensitivity of soil pH as an indicator for functional gene composition and diversity. A bipartite network inferred from metagenomic contigs revealed microbial taxa regulating coupled biogeochemical cycles between carbon and phosphorus, nitrogen and sulfur, and nitrogen and iron, providing novel evidence for the coupling of soil biogeochemical cycles and demonstrating the efficacy of a new approach to investigate soil ecosystem functions.
Article
Ecology
Kankan Zhao, Bin Ma, Yan Xu, Erinne Stirling, Jianming Xu
Summary: Microbial community circadian rhythms in rice rhizosphere soil are influenced by light-dark and constant dark conditions, with different taxa displaying circadian rhythms under the two regimes. Light exposure affects microbial circadian clocks and leads to fewer ecological niches in light communities compared to dark.
Article
Engineering, Environmental
Xuejun Wang, Hao Wu, Xiaoyu Wang, Haixia Wang, Kankan Zhao, Bin Ma, Zhenmei Lu
Summary: DBP contamination decreases microbial community diversity and weakens potential interactions between microorganisms. DBP shifts the interactions between strain ZM05 and other microbes, and nondegrading bacterium Pseudomonas aeruginosa ZM03 has a positive interaction with strain ZM05 during DBP degradation under pH stress.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Soil Science
Ran Xue, Kankan Zhao, Xiuling Yu, Erinne Stirling, Shan Liu, Shudi Ye, Bin Ma, Jianming Xu
Summary: The study revealed the composition differences of microbial communities under different sampling schemes, demonstrating the spatial distribution and ecological process changes of microorganisms at different sampling scales. Increasing sample size leads the bacterial community assembly process to change from variable selection to homogenous selection.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Environmental Sciences
Yike Shen, Hannah E. Laue, Martha J. Shrubsole, Haotian Wu, Tessa R. Bloomquist, Annie Larouche, Kankan Zhao, Feng Gao, Amelie Boivin, Diddier Prada, Darel J. Hunting, Virginie Gillet, Larissa Takser, Andrea A. Baccarelli
Summary: This study assessed the associations between childhood and perinatal blood metal levels and childhood gut microbiome diversity, structure, species, gene family-inferred species, and potential pathway alterations. The results showed significant associations between blood metal levels and the gut microbiome, with stronger associations observed with more recent exposure. These findings may have important implications for further understanding the mechanisms underlying the impact of metal exposure on children's health.
ENVIRONMENTAL HEALTH PERSPECTIVES
(2022)
Article
Microbiology
Yuanhui Liu, Bin Ma, Wenfeng Chen, Klaus Schlaeppi, Matthias Erb, Erinne Stirling, Lingfei Hu, Entao Wang, Yunzeng Zhang, Kankan Zhao, Zhijiang Lu, Shudi Ye, Jianming Xu
Summary: Root-microbiome interactions play a crucial role in plant performance and yield, particularly in legumes which engage in symbiosis with N-2-fixing rhizobia. The rhizobial symbiotic capacity was found to significantly alter root-associated microbiomes by impacting diversity, co-occurrence interactions, and microbial depletion in the rhizosphere and rhizoplane. Root exudates and soil physiochemical properties were closely correlated with microbial community shifts in response to different rhizobial treatments.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Chuhan Dai, Hao Wu, Xuejun Wang, Kankan Zhao, Zhenmei Lu
Summary: This study used metagenomic, metatranscriptomic, and co-occurrence network analyses to investigate the microbial cooperation in the biodegradation of 1,4-dioxane. The results revealed that Ancylobacter polymorphus ZM13 played a key role in the degradation process and cooperated with other bacterial genera. The presence of 1,4-dioxane also facilitated the shift in biodiversity and function of the microbial consortium, with the cooperators providing nutrients and relieving environmental stresses. These findings contribute to our understanding of microbial interactions during 1,4-dioxane degradation and have implications for constructing efficient synthetic consortia for remediation.
Article
Soil Science
Kankan Zhao, Haodan Yu, Ran Xue, Erinne Stirling, Yiling Wang, Jianming Xu, Bin Ma
Summary: This study fills the gap in the evidence of endogenous circadian rhythms regulated by microbial molecular oscillations in soil microbial communities. The study found significant differences in the structure of potentially active microbial communities between the 'day' and 'night' of the surface soil, even under constantly dark, flooded paddy soil conditions. Seven taxa were identified as circadian indicators, which contribute to endogenous circadian rhythms by regulating community diversity, species interactions, and community assembly.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Environmental Sciences
Ran Xue, Shan Liu, Erinne Stirling, Yiling Wang, Kankan Zhao, Haruna Matsumoto, Mengcen Wang, Jianming Xu, Bin Ma
Summary: This study collected 287 phyllosphere bacterial communities from seven ecosystems in east-China and found a similar regional core community that comprised 44.9% of the total bacterial abundance. The regional core community was less affected by environmental variables and less connected in the co-occurrence network compared with other non-core OTUs. This suggests the existence of a robust regional core phyllosphere community regardless of ecosystem or spatial and environmental heterogeneity.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
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
Multidisciplinary Sciences
Bin Ma, Caiyu Lu, Yiling Wang, Jingwen Yu, Kankan Zhao, Ran Xue, Hao Ren, Xiaofei Lv, Ronghui Pan, Jiabao Zhang, Yongguan Zhu, Jianming Xu
Summary: This study conducts a large-scale excavation of soil microbial dark matter by reconstructing metagenome-assembled genomes, uncovering unknown species-level genome bins and previously unexplored viral-host associations.
NATURE COMMUNICATIONS
(2023)
Article
Agriculture, Multidisciplinary
Chenxiao Ding, Yaowei Liu, Marc G. Dumont, Hong Pan, Kankan Zhao, Yuanheng Li, Qichun Zhang, Yu Luo, Shuo Jiao, Hongjie Di, Jianming Xu, Yong Li
Summary: This study explores the linkage between high-affinity methanotroph community assembly processes and CH4 oxidation potential in grasslands. The results show that grassland type and environmental factors, especially mean annual precipitation, play important roles in shaping high-affinity methanotroph community diversity, composition, and activity.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2024)
Article
Genetics & Heredity
Xinwei Song, Yiqun Li, Erinne Stirling, Kankan Zhao, Binhao Wang, Yongguan Zhu, Yongming Luo, Jianming Xu, Bin Ma
Summary: Arsenic is a widely distributed toxic metalloid in nature. Microbe-mediated arsenic metabolism plays a crucial role in global arsenic biogeochemical cycles. However, accurate metagenomic profiling of arsenic metabolism in microbial communities is challenging. In this study, we developed a manually curated As metabolism gene database (AsgeneDB) and applied it for functional and taxonomic profiling of arsenic metabolism in metagenomes from various environments. Our results demonstrated that AsgeneDB significantly improved the mapping ratio and provided more accurate and comprehensive analysis of arsenic metabolic genes compared to other databases.
NAR GENOMICS AND BIOINFORMATICS
(2022)
