Article
Environmental Sciences
Kevin J. Lyons, Jenni Ikonen, Anna-Maria Hokajarvi, Teemu Rasanen, Tarja Pitkanen, Ari Kauppinen, Katharina Kujala, Pekka M. Rossi, Ilkka T. Miettinen
Summary: Groundwater quality monitoring often relies on sporadic and slow manual sampling and laboratory analyses, which may result in undetected water quality deficiencies. In Finland, enhanced monitoring of untreated groundwater quality using real-time online monitoring, isotopic analysis, and microbial community analysis revealed indications of surface water intrusion and faecal contamination. The findings demonstrated the usefulness of supplementary methods and suggested their wider implementation to enhance groundwater quality monitoring.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Qiaomei Zhou, Jingang Huang, Kangyin Guo, Yucheng Lou, Haibo Wang, Rongbing Zhou, Junhong Tang, Pingzhi Hou
Summary: Centralized water supply in rural areas is crucial for implementing the Rural Revitalization Strategy Plan in China. This study found that opportunistic pathogens were widely present in rural drinking water regardless of the water supply mode, and their abundance was higher than in urban tap water. The insufficient residual chlorine and higher turbidity in warm seasons triggered microbial proliferation and seasonal variation in opportunistic pathogens. The small-central water supply mode in rural areas had a higher relative abundance of pathogenic genes and infectious risks. This study provides important scientific insights into the microbial safety of rural drinking water and highlights the need to address opportunistic pathogens risks in small-central water supply mode.
ENVIRONMENTAL RESEARCH
(2023)
Review
Food Science & Technology
Jianming Ye, Jiaqing Guo, Tairan Li, Jiaxin Tian, Mengxi Yu, Xiaochen Wang, Usman Majeed, Wei Song, Jianbo Xiao, Yane Luo, Tianli Yue
Summary: This article reviews the application of phage-based luminescent detection technologies in food safety. These technologies can rapidly and sensitively detect trace pathogens and toxins by the specific recognition and adherence ability of phages, and differentiate between viable and dead microbes, as well as qualitatively and quantitatively detect toxins.
COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY
(2022)
Article
Engineering, Environmental
Baoyan Chi, Ying Huang, Zhenfeng Xiong, Jiali Tan, Weidong Zhou, Zhuo Yang, Kemei Zhou, Xinxin Duan, Ao Chen, Rong Zha, Keting Gui
Summary: In this study, a new sludge reduction technology called LTBC-AAO process was proposed, which combines sludge lysis based on thermophilic bacterial community and the anaerobic-anoxic-oxic process. The LTBC-AAO process showed promising results in reducing sludge and improving COD and TN removal efficiency.
JOURNAL OF WATER PROCESS ENGINEERING
(2023)
Article
Engineering, Environmental
Adriana Gonzalez-Fernandez, Erin M. Symonds, Javier F. Gallard-Gongora, Bonnie Mull, Jerzy O. Lukasik, Pablo Rivera Navarro, Andrei Badilla Aguilar, Jayme Peraud, Megan L. Brown, Darner Mora Alvarado, Mya Breitbart, Maryann R. Cairns, Valerie J. Harwood
Summary: The study revealed that microbial concentrations in tropical coastal waters vary by season and tidal stage, with a close relationship between rainfall and pathogen prevalence, which may impact the health risks of beach users.
Article
Environmental Sciences
Jane R. de Lambert, James F. Walsh, Deanna P. Scher, Aaron D. Firnstahl, Mark A. Borchardt
Summary: Urban stormwater can contain a variety of pollutants, including viruses, pathogens, and emerging contaminants like pharmaceuticals. The study found that microbial and chemical contaminants were lower in the water table than in the vadose zone, with human-specific Bacteroides being the most frequently detected. Factors such as precipitation and chloride-bromide ratio were significantly associated with microbial load, and geologically sensitive aquifers with a protective cap of fine-grained sediments are less vulnerable to contamination from urban stormwater.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Soil Science
Ihsan Muhammad, Jun Wang, Upendra M. Sainju, Shaohong Zhang, Fazhu Zhao, Ahmad Khan
Summary: Cover crops enhance soil microbial community biomass and affect community structure compared to no cover crops, with responses varying depending on soil type, climatic conditions, and cover crop types. Incorporating cover crop residue into the soil can increase certain microbial parameters but decrease others.
Article
Ecology
Francesco Delogu, Benoit J. Kunath, Pedro M. Queiros, Rashi Halder, Laura A. Lebrun, Phillip B. Pope, Patrick May, Stefanie Widder, Emilie E. L. Muller, Paul Wilmes
Summary: The study summarizes 14 months of data from a biological wastewater treatment plant (BWWTPs) and predicts future signals accuracy for six signals. The research demonstrates the ability to forecast the dynamics of open microbial ecosystems using interactions between community cycles and environmental parameters.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Engineering, Environmental
Chengsong Ye, Yuming Chen, Lin Feng, Kun Wan, Jianguo Li, Mingbao Feng, Xin Yu
Summary: This study investigated the occurrence of pathogens, antibiotic resistance genes (ARGs), and bacterial communities in UV/chlorine-treated reclaimed water samples. The results showed that UV/chlorine treatment effectively reduced the numbers of pathogens and changed the bacterial community structure. Additionally, the treatment decreased the abundance of ARGs and mobile genetic elements (MGEs). However, certain ARGs and MGEs were consistently detected across different seasons, indicating the need for attention.
FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING
(2022)
Article
Engineering, Environmental
Jie Zhang, Yilin Dong, Qiuwen Wang, Dongyu Xu, Longyi Lv, Wenfang Gao, Li Sun, Guangming Zhang, Zhijun Ren
Summary: Ultrasonic irradiation was used for in-situ sludge reduction, with different frequencies of ultrasonic lysis tested. The optimal ultrasonic lysis frequency was found to be 1/d, resulting in a sludge reduction of 47.90%. The use of ultrasound did not have a significant impact on the removal of COD, TN, and NH3-N, but it decreased the removal rate of TP, reaching the lowest rate of 37.58% at an ultrasonic lysis frequency of 2/d. Introduction of ultrasound also affected the particle size, surface roughness, and chemical composition of the sludge.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Environmental Sciences
Jia-Cheng Zhou, Yi-Fei Wang, Dong Zhu, Yong-Guan Zhu
Summary: The reliance of modern society on indoor environments has increased, making them important sites for human exposure to microbes. This study examined the distribution of microbes at different locations within a single home and identified potential pathogens and microbial functions using PacBio Sequel full-length amplicon sequencing. The results showed significant differences in microbial communities among indoor sampling sites, with potential pathogens significantly enriched on door handles. The study also highlighted the role of microbial interactions in the development of a healthy immune system.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Pamela B. Vilela, Rondon P. Mendonca Neto, Maria Clara V. M. Starling, Alessandra da S. Martins, Giovanna F. F. Pires, Felipe A. R. Souza, Camila C. Amorim
Summary: Advanced technologies, such as solar photo-Fenton, have been effective in eliminating antibiotic resistant bacteria and resistance genes from wastewater. High throughput metagenomic analysis revealed significant removal of main phyla and reduction of ARGs using solar-enhanced photo-Fenton.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biology
Kai Kang, Hui Chong, Kang Ning
Summary: This study presents Meta-Prism 2.0, a method for analyzing microbial community samples that achieves ultra-fast, memory-efficient, flexible, and accurate search among millions of samples. Results demonstrate that Meta-Prism 2.0 is one of the most efficient sample analysis methods, with comparable or better accuracy compared to contemporary methods.
Review
Microbiology
Yan Wang, Rory N. Pruitt, Thorsten Nuernberger, Yuanchao Wang
Summary: Plant pathogens utilize various strategies to evade plant immunity, hindering the effective use of host genetic resistance for disease control. This Review discusses current knowledge on how microbial pathogens successfully infect plants by evading their immune responses and explores the potential for engineering crop resistance based on this knowledge.
NATURE REVIEWS MICROBIOLOGY
(2022)
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
Ecology
Abdoirazagh Hashemi Shahraki, Subba Rao Chaganti, Daniel D. Heath
Summary: The study revealed significant short-term temporal variation in freshwater bacterial communities, especially during nighttime. Multiple sampling can provide a more accurate assessment of freshwater safety and human health risks.
Article
Multidisciplinary Sciences
Nathaniel T. Marshall, Henry A. Vanderploeg, Subba Rao Chaganti
Summary: Environmental DNA (eDNA) analysis is essential for conservation biology and biodiversity management, but accurate estimation of age and origin is complicated by various factors. Investigating degradation relationships in genomic material from non-indigenous Dreissena mussels revealed a significant decrease in eRNA:eDNA ratio throughout degradation, potentially providing an estimate for genomic material age. The quantification of eRNA can enhance detection capabilities and improve interpretation of positive detections.
SCIENTIFIC REPORTS
(2021)
Review
Microbiology
Abdolrazagh Hashemi Shahraki, Mehdi Mirsaeidi
Summary: Members of Mycobacterium abscessus complex are highly resistant organisms causing severe infections. Successful phage therapy has been reported against drug-resistant superbugs, but there are limitations such as the absence of lytic phages with broad host-range. Advanced genomic technologies have enabled the development of engineered phages for therapeutic purposes.
Article
Microbiology
Abdolrazagh Hashemi Shahraki, Subba Rao Chaganti, Daniel Heath
Summary: Spatial variation of BCC was observed between lakes Erie and St. Clair, as well as among sampling locations. Five distinct temporal clusters were identified, corresponding to seasonal variation over the 15-month sampling period. Significant differences in taxonomic composition were found between summer months of 2016 and 2017.
Letter
Medicine, General & Internal
Abdolrazagh Hashemi Shahraki, Majid Vahed, Mehdi Mirsaeidi
EUROPEAN JOURNAL OF INTERNAL MEDICINE
(2021)
Article
Engineering, Environmental
Subba Rao Chaganti, Claire Plouff, Mohammad Madani, Abdolrazagh Hashemi Shahraki, Adrian A. Vasquez, Rajesh Seth, Daniel D. Heath, Jeffrey L. Ram
Summary: Understanding the diversity of bacteria and E.coli levels at beaches is crucial for managing health risks. This study compared the temporal changes of bacterial communities at two beaches near the origin of the Detroit River. The findings showed different bacterial communities in different months and at different beaches. Bird contamination was dominant at both beaches, while only a small percentage of samples showed evidence of human-associated bacteria.
Article
Environmental Sciences
Nathaniel T. Marshall, Henry A. Vanderploeg, Subba Rao Chaganti
Summary: The recent genetic revolution in analyzing aquatic environmental DNA (eDNA) has provided a powerful tool for detecting rare and invasive species. In this study, new eDNA assays were designed to target the extended repeat sections of the genomes of zebra and quagga mussels. These assays greatly improved the sensitivity of detecting genomic DNA for both species and showed longer durations of detection during decay experiments and greater sensitivity for detecting eDNA from water samples. This work demonstrates the importance of understanding the complete genomic structure of an organism in improving eDNA analysis.
Article
Environmental Sciences
Bingyuan Tan, Pengfei Hu, Xiaoxu Niu, Xing Zhang, Jiakun Liu, Thijs Frenken, Paul B. Hamilton, G. Douglas Haffner, S. Rao Chaganti, Amechi S. Nwankwegu, Lei Zhang
Summary: The microbial food-loop is critical for energy flow in aquatic food webs. This study tracked the response of the microbial community during a 7-day algal bloom event in the Three Gorges Reservoir in May 2018 and found that both the algal bloom and a storm event significantly modified the composition and relative abundance of species in the microbial community.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Paul A. Den A. Uyl, Luke R. Thompson, Reagan M. Errera, James M. Birch, Christina M. Preston, Colleen Yancey, William E. Ussler III, Subba Rao Chaganti, Steven A. Ruberg, Gregory J. Doucette, Gregory J. Dick, Christopher A. Scholin, Kelly D. Goodwin
Summary: This study demonstrated the importance of using a third-generation Environmental Sample Processor (3G ESP) integrated with a long-range autonomous underwater vehicle (LRAUV) for autonomous sampling during cyanobacterial harmful algal blooms (cyanoHABs) in western Lake Erie. Results showed equivalency between autonomous and manual methods, as well as additional sampling capacity and revealed differences between field seasons.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Immunology
Mohammad Hashemzadeh, Aram Asareh Zadegan Dezfuli, Azar Dokht Khosravi, Nazanin Ahmad Khosravi, Abdorazagh Hashemi Shahraki
Summary: This study aimed to identify the drug susceptibility and mutations related to clarithromycin and linezolid resistance in clinical isolates of Mycobacterium fortuitum in Iran. The results showed that 64% of M. fortuitum isolates were resistant to clarithromycin and 18% were resistant to linezolid. DNA sequencing revealed multiple mutations in the erm(39) gene and rrl gene. These findings indicate a high level of antibiotic resistance in M. fortuitum isolates.
ACTA MICROBIOLOGICA ET IMMUNOLOGICA HUNGARICA
(2023)
Article
Microbiology
Abdolrazagh Hashemi Shahraki, Majid Vahed, Roshan Dinparastisaleh, Mehdi Mirsaeidi
Summary: In this study, we introduce UF_RH5, a novel lytic phage that targets clinically isolated Pseudomonas aeruginosa. It belongs to the Siphovirus morphology family, Septimatrevirus genus, with a 42,566-bp genome and a GC content of 53.60%, encoding 58 proteins. Under electron microscopy, UF_RH5 is observed to have a length of 121 nm and a capsid size of 45 nm.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Abdolrazagh Hashemi Shahraki, Majid Vahed, Mehdi Mirsaeidi
Summary: Here, the genome sequence of a new Pseudomonas aeruginosa bacteriophage, UF_RH1, is presented. This lytic phage has a genome size of 42,567 bp and belongs to the Siphoviridae family and Septimatrevirus genus. UF_RH1 shows genetic similarities with Stenotrophomonas phage vB_SmaS-DLP_2.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Abdolrazagh Hashemi Shahraki, Majid Vahed, Shahla Masood, Mehdi Mirsaeidi
Summary: We present the genome sequence of a lytic phage, UF_RH6, that infects Pseudomonas aeruginosa. This phage was isolated from a respiratory secretion sample obtained from a patient with pulmonary P. aeruginosa. UF_RH6 belongs to the Caudoviricetes family and the Samunavirus genus. The genome of UF_RH6 is 94,715 bp long and encodes 130 proteins.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Environmental Sciences
Javad Sadeghi, Abdolrazagh Hashemi Shahraki, Subba Rao Chaganti, Daniel Heath
Summary: This study used metatranscriptomics to investigate the gene transcription variation of freshwater bacterial communities across three seasons in Ontario, Canada. The results showed high transcriptional activity in summer and fall, and surprisingly, a significant portion of genes associated with physiological and ecological activity remained active in freezing temperatures during winter. The study provides a baseline for further research on freshwater bacterial communities, health-related microbial activity/dormancy, and the factors driving their functional variation.
ENVIRONMENTAL RESEARCH
(2023)
