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
Yongbin Li, Lifang Guo, Rui Yang, Zhaohui Yang, Haihan Zhang, Qiqian Li, Zhiguo Cao, Xin Zhang, Pin Gao, Wenlong Gao, Geng Yan, Duanyi Huang, Weimin Sun
Summary: This study discovered an As(III) oxidation-dependent biological nitrogen fixing (As-dependent BNF) process that is catalyzed by microorganisms harboring nifH and aioA genes. Investigation of As-contaminated soils and sediments revealed that Thiobacillus spp. and Anaeromyxobacter spp. could be potential As-dependent BNF bacteria. These findings demonstrate the occurrence of As-dependent BNF in various As-contaminated habitats, with different types of soil enriched with different As-dependent BNF bacteria based on contrasting geochemical conditions.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Engineering, Environmental
Jinyu Hou, Yun Zhang, Xianghua Wu, Linmeng Liu, Yucheng Wu, Wuxing Liu, Peter Christie
Summary: The study found that zero-valent iron (ZVI) can promote the biomineralization of lindane, but it has a certain inhibitory effect on the growth and functions of soil bacterial community. Metagenomic analysis revealed that the genes involved in the degradation of lindane were upregulated, but the presence of genes responsible for lindane dechlorination was not confirmed. In addition, the benzoate biodegradation pathway linked to the downstream catabolism of lindane was enhanced.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Engineering, Environmental
Geng Yan, Xiaoxu Sun, Yiran Dong, Wenlong Gao, Pin Gao, Baoqin Li, Wangwang Yan, Haihan Zhang, Mohsen Soleimani, Bei Yan, Weimin Sun, Max M. Haggblom
Summary: This study identified microorganisms responsible for vanadate reduction in contaminated river sediments and predicted their metabolic mechanisms using DNA-stable isotope probing and metagenomic-binning analysis.
Article
Environmental Sciences
Yongjing Guan, Xue Xue, Jia Jia, Xuening Li, Haoran Xing, Zaizhao Wang
Summary: This study analyzed the genes in water samples and Hemiculter leucisculus samples to understand the transmission of antibiotic resistance genes (ARGs) and the impact on fish gut microbiomes due to human activities. The results showed that ARG abundance decreased in water microbiomes along the environmental gradient, while it increased in fish gut microbiomes. Plasmids played a role in enhancing the spread of ARGs and the co-transfer potential of ARGs and metal resistance genes (MRGs) under anthropogenic pressures. The study also found that anthropogenic contamination affected fish gut resistome mainly by influencing ARG host bacteria in water microbiomes.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Biochemical Research Methods
Natalie J. Wu-Woods, Jacob T. Barlow, Florian Trigodet, Dustin G. Shaw, Anna E. Romano, Bana Jabri, A. Murat Eren, Rustem F. Ismagilov
Summary: This study introduces a microbial-enrichment method (MEM) that enables the removal of host DNA in human intestinal biopsies and allows for the characterization of low-abundance microbial taxa. The method provides deeper insights into the high-throughput characterization of the gut microbiome and demonstrates the construction of metagenome-assembled genomes from human intestinal biopsies.
Article
Mathematical & Computational Biology
Zhongjun Jiang, Xiaobo Li, Lijun Guo
Summary: This study proposes a new method for metagenomic contig binning, which utilizes unsupervised clustering methods and reference databases to address the challenges faced by current methods. Experimental results demonstrate that this method can improve the binning effect.
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
(2022)
Article
Microbiology
Yongbin Li, Rui Yang, Max M. Haggblom, Mengyan Li, Lifang Guo, Baoqin Li, Max Kolton, Zhiguo Cao, Mohsen Solemani, Zheng Chen, Zhimin Xu, Wenlong Gao, Bei Yan, Weimin Sun
Summary: This study found that diazotrophic endophytes have the potential to promote the growth and colonization of pioneer plant Bidens pilosa in mine tailings, which can contribute to the phytoremediation of mine tailings.
Article
Environmental Sciences
Xiuli Chen, Ji Wang, Chaoyi Pan, Lishi Feng, Qingwei Guo, Sili Chen, Shuguang Xie
Summary: This study explored the microbial communities in river sediments impacted by accidental antimony (Sb) spill, revealing higher relative abundance of Proteobacteria and Actinobacteria in Sb-polluted sites. Under Sb stress, microbial functions related to DNA repair and ion transport were enhanced, along with an increase in heavy metal resistance genes, particularly the arsB gene. Horizontal gene transfer may contribute to the increase in heavy metal resistance genes and antibiotic resistance genes at Sb spill-impacted sites.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Yinping Xiang, Weiping Xiong, Rui Xu, Zhaohui Yang, Yanru Zhang, Meiying Jia, Haihao Peng
Summary: This study investigated the long-term effects of antibiotics on sludge anaerobic digestion and revealed the response mechanism of dominant microbiome to antibiotic stress. The results showed that many functional genes associated with glycolysis, protein hydrolysis, and acidification increased under antibiotic stress, while genes related to acetate and acetyl-coA conversion decreased. Additionally, the major methanogenic metabolic pathways were altered, and the dominant microbial genomes contained abundant functional genes associated with EPS biosynthesis, secondary metabolite biosynthesis, and bacterial chemotaxis.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2023)
Article
Environmental Sciences
Yuyin Yang, Jianfei Chen, Jennifer Pratscher, Shuguang Xie
Summary: Methanotrophs are the main consumers of methane in lake sediments and play a key role in regulating methane flux and carbon cycling. In this study, nucleic acid stable isotope probing was used to investigate the active methanotrophic microbial community in eutrophication-affected shallow lakes. The results showed that gamma-proteobacterial methanotrophs and beta-proteobacterial methanol-utilizers were involved in methane-derived carbon assimilation, with Crenothrix being the key methane consumer. The wide distribution of Crenothrix in lake sediments and its active methane assimilation suggest its importance as a biological sink for methane in shallow lakes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemical Research Methods
Vijini Mallawaarachchi, Yu Lin
Summary: Metagenomics allows recovery of genetic materials from different species, with MetaCoAG being a stand-out binning tool that utilizes assembly graph information for improved binning performance.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Harihara Subrahmaniam Muralidharan, Nidhi Shah, Jacquelyn S. Meisel, Mihai Pop
Summary: High-throughput sequencing has transformed microbiology, but reconstructing complete genomes from metagenomic data is still challenging due to the fragmented nature. Scientists use binning to cluster contigs from the same organism, and this study suggests using assembly graphs to improve binning strategies. The Binnacle tool extracts information from assembly graphs to cluster scaffolds into comprehensive bins, enhancing the quality and contiguity of the resulting bins.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Engineering, Environmental
Maosheng Zheng, Zhichao Tian, Zimin Chai, Anqi Zhang, Ailu Gu, Guangli Mu, Dedong Wu, Jianhua Guo
Summary: The recent discovery of complete ammonia oxidation (comammox) bacteria has challenged the traditional understanding of nitrification. However, their importance in wastewater treatment plants (WWTPs) is still not well understood. This study found that comammox Nitrospira was present in all 25 WWTPs and even outnumbered other ammonia oxidizers. It was also confirmed that comammox Nitrospira actively participated in ammonia oxidation. These findings demonstrate the widespread occurrence and functional dominance of comammox in WWTPs.
Article
Environmental Sciences
Shuang Wang, Jibing Li, Longfei Jiang, Shanquan Wang, Xuan Zhao, Yeliang Dai, Chunling Luo, Gan Zhang
Summary: The study applied stable-isotope probing to investigate the degradation of PCBs mediated by RD-AO, confirming the impact of the anaerobic stage on subsequent AO and its potential mechanism. Additionally, four lineages (Arenimonas, Steroidobacter, Sulfurifustis, and Thermoanaerobacterales) were identified as PCB degraders for the first time, suggesting the recruitment of novel bacteria involved in PCB aerobic degradation in the anaerobic-aerobic two-stage treatment.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Yongbin Li, Lifang Guo, Max M. Haggblom, Rui Yang, Mengyan Li, Xiaoxu Sun, Zheng Chen, Fangbai Li, Xianfa Su, Geng Yan, Enzong Xiao, Haihan Zhang, Weimin Sun
Summary: Serratia spp. bacteria have been found to perform biological nitrogen fixation (BNF) by oxidizing arsenic (As) in addition to using reduced sulfur (S). This discovery suggests that As-dependent BNF may be widespread in As-rich habitats and is a common metabolic trait in Serratia spp.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Ecology
Xiaoxu Sun, Tianle Kong, Fangbai Li, Max M. Haggblom, Max Kolton, Ling Lan, Maggie C. Y. Lau Vetter, Yiran Dong, Peng Gao, Joel E. Kostka, Baoqin Li, Weimin Sun
Summary: This study discovered a novel biogeochemical process, S oxidation coupled to Sb(V) reduction, mediated by Desulfurivibrio bacteria through enzymatic reactions. Desulfurivibrio showed a high relative abundance in Sb mine tailings. The metabolic potential encoded by non-canonical enzymes was found in the Desulfurivibrio genomes retrieved from metal-contaminated sites.
Article
Environmental Sciences
Haihan Zhang, Xiang Liu, Tinglin Huang, Ben Ma, Weimin Sun, Kexin Zhao, Raju Sekar, Yan Xing
Summary: This study assessed the effects of indoor heating and overnight stagnation on bacterial community structure and cell count in the drinking water distribution system. It found that the growth of low nucleic acid (LNA) cells played a crucial role in increasing adenosine triphosphate (ATP). Opportunistic pathogens increased the risk of disease in stagnant water and water temperature, residual chlorine and iron significantly affected the abundance and composition of bacterial community.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Zhimin Xu, Xinyue Wu, Jiexiang Zhang, Ping Cheng, Zhihao Xu, Weimin Sun, Yuming Zhong, Yifan Wang, Guohui Yu, Hui Liu
Summary: This study found that microplastics are widely detected in the gut of black soldier flies (BSFs), causing gut cell damage, inflammation, and fecal hardening, which hinders organic mineralization and antibiotic degradation. Microplastic intake significantly reshapes the microbial community structure and promotes the colonization of pathogenic bacteria carrying antibiotic-resistant genes, leading to the enhancement of antibiotic resistance. Therefore, isolating microplastics in feces before insect transformation is necessary.
ENVIRONMENTAL POLLUTION
(2023)
Article
Engineering, Environmental
Yongbin Li, Lifang Guo, Max Kolton, Rui Yang, Miaomiao Zhang, Fangjie Qi, Mohsen Soleimani, Xiaoxu Sun, Baoqin Li, Wenlong Gao, Geng Yan, Rui Xu, Weimin Sun
Summary: The presence of Sb-dependent BNF was observed in slurries from Sb-contaminated habitats, suggesting its widespread occurrence in the South China Sb belt. Bacteria associated with Rhodocyclaceae and Rhizobiaceae were identified as potential microorganisms responsible for Sb-dependent BNF.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Engineering, Electrical & Electronic
Yue Liu, Jiabin Wang, Wenhuan Chen, Jian Zhou, Jiayu Hao, Xinzhe Zeng, Xingyu Yang, Yunxiang Yan, Weimin Sun, Tao Geng
Summary: A novel tapered two-mode fiber embedded long period fiber grating (TTMF-LPFG) sensor is proposed, which shows high sensitivity with a smaller diameter and low sensitivity to temperature. Traditional taper fiber requires a very thin waist to excite a strong evanescent field (EF) for large RI sensitivity, making the sensor fragile. In contrast, the TTMF-LPFG structure allows for LPFG formation and improved sensitivity through tapering, making it suitable for chemical composition analysis and biomedical applications.
IEEE PHOTONICS TECHNOLOGY LETTERS
(2023)
Article
Allergy
Xueting Liu, Yanmei Wang, Yueling Zeng, De Wang, Yuhuan Wen, Limin Fan, Ying He, Junyan Zhang, Weimin Sun, Yongping Liu, Ailin Tao
Summary: This study discovers the contribution of spinal astrocytes to chronic itch through sensitization of GRPR(+) neurons. It also reveals the interaction between microglia and GRPR(+) neurons in promoting chronic itch.
Article
Environmental Sciences
Zhenyu Chen, Jinchan Yang, Duanyi Huang, Shuni Wang, Kai Jiang, Weimin Sun, Zhihua Chen, Zhiguo Cao, Youhua Ren, Qi Wang, Huaqing Liu, Xin Zhang, Xiaoxu Sun
Summary: Microplastic contamination is widespread in aquatic environments, with increasing plastic production leading to a rise in microplastic pollutants released into the environment. These plastic particles can absorb various chemical pollutants and contribute to toxin accumulation in the food chain. This study investigated the adsorption behavior of aniline, a priority environmental pollutant, on polystyrene microplastics (mPS). The results showed that mPS had a maximum adsorption capacity of 0.060 mg/g, with equilibrium reached after 24 hours. The adsorption kinetics followed a pseudo-second-order model and the Freundlich model described the adsorption isotherms. The adsorption mechanisms may involve 7C-7C interactions and hydrophobic interactions. Factors such as pH, ionic strength, and temperature of the solution played significant roles in the adsorption process.
Review
Ecology
Uttpal Anand, Tarun Pal, Niraj Yadav, Vipin Kumar Singh, Vijay Tripathi, Krishna Kumar Choudhary, Awadhesh Kumar Shukla, Kumari Sunita, Ajay Kumar, Elza Bontempi, Ying Ma, Max Kolton, Amit Kishore Singh
Summary: Globally, substantial research is being conducted on endophytic microbes to increase agricultural and environmental sustainability. Endophytic microbes, such as bacteria, actinomycetes, and fungi, inhabit plant tissues without causing harm and can regulate various host functions. They play a dominant role in nutrient cycling, biodegradation, and bioremediation, and have potential applications in industries. Endophytes can also synthesize bioactive compounds with high competence, making them promising candidates for new drugs. Biotechnological interventions with endophytes have played a pivotal role in crop improvement and could open new avenues in agricultural research and development.
Article
Optics
Wenze Xiong, Shengjia Wang, Shuai Gao, Zhan Gao, Hao Tang, Alexander W. Koch, Sijin Wu, Weimin Sun
Summary: Phase map filtering is a crucial process in speckle interferometric optics measurement. The conventional sine-cosine domain filtering framework consumes a significant amount of calculation resources, limiting the temporal property of measurements. To address this issue, a new filtering domain called complex amplitude domain filtering is proposed. This domain offers a good filtering efficiency, preserves details, and does not generate additional phase shifts during filtering. Preliminary experiments show that the proposed complex amplitude domain filtering accelerates the filtering process by at least 40% without sacrificing filtering quality, especially with the PDE noise reduction method.
OPTICS COMMUNICATIONS
(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
Xiaoxu Sun, Tianle Kong, Duanyi Huang, Zhenyu Chen, Max Kolton, Jinchan Yang, Yuqing Huang, Yue Cao, Peng Gao, Nie Yang, Baoqin Li, Huaqing Liu, Weimin Sun
Summary: This study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. Results showed that microbial As(III) oxidation was the dominant As-biotransformation process in P. vittata roots, and members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Plant Sciences
Timothy J. Waller, Max M. Haggblom, Peter V. Oudemans
Summary: Aqueous extracts from flowers have a stimulating effect on the germination, secondary conidiation, and appressorial formation of fruit rotting fungi. Even raindrops passing over flowers can accumulate sufficient activity to influence the infectivity of these fungi. Nonpolar components of the cuticle were found to have high levels of bioactivity. Specific fatty acids and fatty acid methyl esters were identified as bioactive components, stimulating appressorial formation and secondary conidiation. This study emphasizes the importance of the bloom period for infection and suggests that the presence of specific fatty acids may affect the host susceptibility.
Article
Microbiology
Tianze Song, Yutong Liu, Max Kolton, Rachel M. Wilson, Jason K. Keller, Jose L. Rolando, Jeffrey P. Chanton, Joel E. Kostka
Summary: Northern peatlands contain a significant amount of soil carbon and are vulnerable to increased greenhouse gas production and emission due to climate warming. The decomposition of peat soil organic matter is controlled by porewater dissolved organic matter and temperature, with warming alleviating the inhibitory effect of inhibitory compounds. The response of microbial organic matter decomposition to warming is regulated by interactions between organic compounds in porewater and peat.
FEMS MICROBIOLOGY ECOLOGY
(2023)
