Article
Environmental Sciences
Ashutosh Kabiraj, Urmi Halder, Annapurna Chitikineni, Rajeev K. Varshney, Rajib Bandopadhyay
Summary: Contamination of arsenic in drinking water and foods is a threat to human beings. Researchers have been studying the bioremediation of arsenic using potent bacteria to reduce its availability. In this study, a strain of Micrococcus luteus was isolated from arsenic-contaminated water in West Bengal, India. This strain showed tolerance to high concentrations of arsenic and other metals, as well as the ability to adsorb arsenic and promote plant growth. These findings suggest its potential application in arsenic bioremediation.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Microbiology
Marco Antonio Lopez Marin, Michal Strejcek, Petra Junkova, Jachym Suman, Jiri Santrucek, Ondrej Uhlik
Summary: The study shows that using a Micrococcus luteus culture supernatant containing resuscitation-promoting factor (SRpf) can increase the number and diversity of cultured bacterial taxa from a nutrient-rich compost soil. After SRpf treatment, potentially novel bacterial species were isolated, demonstrating the effectiveness of SRpf in enhancing the growth of soil bacterial species.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Stephan Schmeing, Mark D. Robinson
Summary: In high-throughput sequencing data, performance comparisons between computational tools are crucial, and ReSeq improves the authenticity of synthetic data by including systematic errors, a fragment-based coverage model, and sampling-matrix estimates based on two-dimensional margins, leading to more accurate performance evaluations.
Article
Microbiology
Hiu-Yin Lao, Timothy Ting-Leung Ng, Ryan Yik-Lam Wong, Celia Sze-Ting Wong, Lam-Kwong Lee, Denise Sze-Hang Wong, Chloe Toi-Mei Chan, Stephanie Hoi-Ching Jim, Jake Siu-Lun Leung, Hazel Wing-Hei Lo, Ivan Tak-Fai Wong, Miranda Chong-Yee Yau, Jimmy Yiu-Wing Lam, Alan Ka-Lun Wu, Gilman Kit-Hang Siu
Summary: In this study, two 16S rRNA gene sequencing tests based on the Illumina and Nanopore sequencing technologies were compared to identify clinical isolates that cannot be identified by MALDI-TOF MS. The results showed that the Nanopore workflow had a higher taxonomic resolution at the species level.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Nasserdine Papa Mze, Idir Kacel, Mamadou Beye, Raphael Tola, Mariema Sarr, Leonardo Basco, Herve Bogreau, Philippe Colson, Pierre-Edouard Fournier
Summary: A rapid and cost-effective sequencing protocol is proposed to validate its reliability by comparing the SARS-CoV-2 genome sequences obtained using the modified Illumina COVIDSeq protocol with the standard protocol. The modified protocol saves time and costs, providing high-quality results comparable to the standard protocol.
Article
Agricultural Engineering
Susan N. James, Arya Vijayanandan
Summary: An anoxic-aerobic-anoxic process was established in a sequencing batch reactor to simultaneously remove organic carbon and nitrogen from wastewater. The study found that the optimum conditions for the process were achieved with a dissolved oxygen level of 1.5 mg/L and 1 hour pre-anoxic and post-anoxic periods. Under these conditions, the removal efficiencies of TOC, NH4+-N, and TN were 98.76%, 98.52%, and 88.23% respectively. Breakpoints in the pH, DO, and ORP curves provided insights into the biochemical reactions occurring in the reactor. Inhibition studies revealed that nitrogen removal pathways such as heterotrophic nitrification or direct conversion contributed to the removal of 27.69% of NH4+-N, while aerobic denitrification accounted for the removal of 20.55% of TN. Microbial community analysis confirmed the presence of heterotrophic nitrifiers and aerobic denitrifiers. The study emphasized the benefits of the varied redox conditions provided by limited aeration for nitrogen removal, leading to reduced energy usage and operating costs.
BIORESOURCE TECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Rose Chinly Mae H. Ortega, Sharon Rose M. Tabugo, Joey Genevieve T. Martinez, Chinee S. Padasas, Jose L. Balcazar
Summary: This study assessed the bacterial community structure in the skin of Barbour's seahorses, with a focus on the Aeromonadaceae family. The presence of Aeromonas genus in the seahorses' skin and its relationship with the surrounding sediment were analyzed. The findings provide baseline information for future research on the role of Aeromonas species in seahorse microbiota and health. Importance rating: 7 out of 10.
Article
Environmental Sciences
Man Jae Kwon, Yunho Hwang, Juyeon Lee, Baknoon Ham, Arifur Rahman, Hossain Azam, Jung-Seok Yang
Summary: Hydroponic cultivation is transforming global agricultural crop production with its minimal environmental impact, but the waste nutrient solutions generated from hydroponic systems may contain high concentrations of nitrogen and phosphorus. This study monitored the concentrations of nutrients in waste nutrient solutions from 10 hydroponic farms and tested a potential treatment technology to address the issue.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Article
Microbiology
Marika Pellegrini, Daniela M. Spera, Claudia Ercole, Maddalena Del Gallo
Summary: The study demonstrated that inoculating a consortium of four bacterial strains onto onion seeds led to improved plant growth parameters, increased yields, and enhanced soil fertility and microbial community diversity. The bacterial treatment positively influenced plant growth, soil health, and soil biodiversity, showcasing the potential of using plant growth-promoting bacteria as a sustainable fertilization strategy to enhance productivity in agricultural landscapes.
Article
Agricultural Engineering
Qiusheng Wu, Wenjie Wan
Summary: Understanding the ecological roles of phosphate-solubilizing bacteria (PSB) is crucial for optimizing composting systems. A study using sequencing, gene quantitation, and statistical analyses found that the inoculation of PSB significantly increased phosphorus availability and altered bacterial community composition in compost. Different factors, such as phosphorus fractions, PSB abundance, phosphorus-cycling gene abundance, and bacterial community composition, contributed to phosphorus availability in different ways.
BIORESOURCE TECHNOLOGY
(2023)
Article
Food Science & Technology
Xiaoyu Xu, Yuanyuan Miao, Huan Wang, Juan Du, Chenqiang Wang, Xuewei Shi, Bin Wang
Summary: This study utilized high-throughput sequencing and high-performance liquid chromatography to investigate the diversity of epiphytic microbial communities and physicochemical indicators in different wine grape varieties. The results showed that the grape variety significantly influences the structure of surface microbial communities.
Article
Soil Science
Manyun Zhang, Patrick J. O'Connor, Jinyu Zhang, Xiaoxin Ye
Summary: Vegetation covers in riparian zones play a crucial role in nutrient cycling, with plant species and biomass influencing soil microbial properties. Soil bacterial and fungal communities respond differently to plant species richness and biomass.
Article
Fisheries
Yufeng Si, Jinxuan Wen, Yao Xu, Patarida Roengjit, Hao Wang
Summary: The 16S rRNA high throughput sequencing technology is increasingly used to discover pathogenic bacteria, with Edwardsiella identified as the main causative pathogen in the diseased turbot outbreak in China. This cost-effective and rapid technology helps in accurate pathogen identification and disease research.
AQUACULTURE REPORTS
(2021)
Article
Genetics & Heredity
Daniela Gaio, Kay Anantanawat, Joyce To, Michael Liu, Leigh Monahan, Aaron E. Darling
Summary: We developed a low-cost method called Hackflex for generating Illumina-compatible sequencing libraries, which can produce up to 14 times more libraries for the same cost compared to the standard Nextera Flex protocol. The libraries generated using Hackflex showed high-quality and uniform coverage. We also introduced new sample barcodes that can be multiplexed with standard Illumina barcodes. This method allows researchers to construct more libraries within a given budget, enabling more data and facilitating research programs that require sequencing of large numbers of libraries.
MICROBIAL GENOMICS
(2022)
Article
Fisheries
Brunno da Silva Cerozi, Josue Wenceslau de Oliveira Neto, Roger Abraao Ribeiro Cardeal Dias Leonel, Angelica Priscila do Carmo Alves
Summary: Aquaponics practitioners have noticed that feeding and growing fish produces nutrient-rich water for plants. However, there is a lack of scientific basis to describe the relationships between inputs and outputs in aquaponic systems. This study proposes a high-throughput assay to predict nutrient inputs and release rates in aquaponics.
AQUACULTURE INTERNATIONAL
(2022)
Article
Environmental Sciences
Jiafang Cai, Aodong Pan, Yilin Li, Yeyuan Xiao, Yan Zhou, Chongjun Chen, Faqian Sun, Xiaomei Su
Summary: The study explored a novel method of using resuscitation-promoting factors (Rpfs) to enhance the degradation efficiency of the dye RB19 in anaerobic processes. Results showed that Rpfs efficiently promoted RB19 decolorization, increasing decolorization efficiency by over 20%. Additionally, Rpfs appeared to stimulate and enrich dye-degrading species of the family Peptostreptococcaceae, leading to higher RB19 decolorization efficiency.
Article
Environmental Sciences
Xiaomei Su, Si Li, Mengqi Xie, Linqin Tao, Yan Zhou, Yeyuan Xiao, Hongjun Lin, Jianrong Chen, Faqian Sun
Summary: Using Rpf from Micrococcus luteus can enhance the biodegradation of PCBs in contaminated environments by resuscitating and stimulating functional bacterial populations. It was found that Rpf significantly altered the composition and abundance of bacterial populations in the phylum Proteobacteria, with Sphingomonas and Pseudomonas identified as key PCB-degraders. These results suggest that Rpf has the potential to improve the efficiency of bioremediation processes in PCB-contaminated environments.
Article
Biotechnology & Applied Microbiology
Mengqi Xie, Luning Xu, Rong Zhang, Yan Zhou, Yeyuan Xiao, Xiaomei Su, Chaofeng Shen, Faqian Sun, Muhammad Zaffar Hashmi, Hongjun Lin, Jianrong Chen
Summary: The study revealed that a yeast strain capable of degrading phenol entered the viable but nonculturable (VBNC) state under high concentrations of contaminants, and the resuscitation of VBNC cells restored their degradation performance. Compared to normal cells, significant morphological, surface, and physiological changes were observed in the VBNC cells.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Review
Environmental Sciences
Muhammad Zaffar Hashmi, Muhammad Kalim, Umar Farooq, Xiaomei Su, Paromita Chakraborty, Shams Ur Rehman
Summary: This review paper discusses the recent development in photocatalytic and chemical techniques for the remediation of PCBs in contaminated soils. Advanced oxidation is found to be an efficient remediation technique with high removal efficiency of PCBs. Persulfate oxidation is identified as a suitable technique that can work under normal environmental conditions. Factors such as pH, temperature, and the use of surfactants and organic solvents affect the effectiveness of these techniques.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Environmental Sciences
Siying Sun, Jiabao Ren, Jiale Liu, Liang Rong, Hangli Wang, Yeyuan Xiao, Faqian Sun, Rongwei Mei, Chongjun Chen, Xiaomei Su
Summary: The study found that pyrite-activated persulfate oxidation efficiently removed organic matter from the effluent of a biological landfill leachate treatment system, and subsequent denitrification was also successful. With the optimal parameters, a COD removal efficiency of about 45% and a nitrate removal rate of around 108 mg L-1 d(-1) were achieved.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Environmental Sciences
Yilin Li, Wenjia Zhang, Yun Dai, Xiaomei Su, Yeyuan Xiao, Dan Wu, Faqian Sun, Rongwu Mei, Jianrong Chen, Hongjun Lin
Summary: This study investigated the start-up, influencing factors, and stable operation of partial denitrification for treating biological effluent from landfill leachate. The research found a suitable ratio of nitrate/ammonium for downstream Anammox process, and highlighted the importance of carbon sources, COD/NO3--N ratio, and salinity in partial denitrification.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Qihua Lin, Xinru Zhou, Shusheng Zhang, Junliang Gao, Mengqi Xie, Linqin Tao, Faqian Sun, Chaofeng Shen, Muhammad Zaffar Hashmi, Xiaomei Su
Summary: Functional microorganisms in a viable but non-culturable state limit the study of PCB-degrading strains. This study found that the resuscitated strain SPC0 from genus Streptococcus has the potential to degrade PCBs through the biphenyl pathway, highlighting the powerful capability of resuscitated strains for bioremediation of PCB-contaminated sites.
ENVIRONMENTAL RESEARCH
(2022)
Review
Biotechnology & Applied Microbiology
Mayada Jamal, Annoor Awadasseid, Xiaomei Su
Summary: Anthraquinone dyes, widely used in textile manufacturing, pose a significant pollution threat due to their complex and stable structures. Microbiological treatment of wastewater has emerged as an economically viable solution, with promising advances in the biodegradation of anthraquinone dyes.
BIOTECHNOLOGY LETTERS
(2022)
Article
Biotechnology & Applied Microbiology
Xiaomei Su, Mengqi Xie, Zhen Han, Yeyuan Xiao, Rui Wang, Chaofeng Shen, Muhammad Zaffar Hashmi, Faqian Sun
Summary: This study discovered the enhancement of Rpf on the anaerobic microbial dechlorination of PCE/PCBs and uncovered the underlying Rpf-responsive populations. It reveals the possibility of rapidly enriching active dechlorinating cultures through Rpf amendment, providing a new approach for massively enriching PCB dechlorinators in short periods of time.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Zhen Han, Qihua Lin, Shusheng Zhang, Xinru Zhou, Si Li, Faqian Sun, Chaofeng Shen, Xiaomei Su
Summary: The study found that the resuscitated strain LS1 has the potential to degrade polychlorinated biphenyls (PCBs), with better performance in degrading PCB 18 and 52. LS1 exhibited lower efficiency in degrading PCB 77. Additionally, LS1 can survive and remain culturable in PCB-contaminated soil for up to 70 days.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Engineering, Environmental
Xinru Zhou, Shusheng Zhang, Rui Wang, Zijing An, Faqian Sun, Chaofeng Shen, Hongjun Lin, Xiaomei Su
Summary: The study found that Rpf of Micrococcus luteus can resuscitate and stimulate the growth of PCB-degrading bacterial populations, thereby improving the bioremediation efficiency of PCBs. Soil microcosms amended with Rpf and LS1 degraded PCBs 1.1-3.2 times faster than control microcosms. The degradation process mainly occurred through the HOPDA-benzoate-catechol/protocatechuate pathways. These results suggest that Rpf and resuscitated strains serve as effective additives and bio-inoculants for enhanced bioremediation, providing new approaches for large-scale applications of in situ bioremediation.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Environmental Sciences
Qihua Lin, Jiayan Ding, Yingying Yang, Faqian Sun, Chaofeng Shen, Hongjun Lin, Xiaomei Su
Summary: The feasibility of utilizing an immobilization approach to enhance the PCBs degradation performance of a resuscitated strain Streptococcus sp. SPC0 was evaluated in this study. The results showed that the mixed matrix of polyvinyl alcohol (PVA) and sodium alginate (SA) provided a porous microstructure for SPC0 colonization and proliferation, leading to enhanced removal of PCBs through simultaneous adsorption and biodegradation. Immobilized SPC0 demonstrated 1.0-7.1 times higher PCB removal than free cells, with higher concentrations achieving more effective removal. Moreover, the immobilized SPC0 showed excellent stability and reusability after four cycles of reuse.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Green & Sustainable Science & Technology
Rong Zhang, Min Zhang, Huaqian Mou, Zijing An, Hailu Fu, Xiaomei Su, Chongjun Chen, Jianrong Chen, Hongjun Lin, Faqian Sun
Summary: Kitchen waste biochar showed better performance in thermophilic co-digestion, reducing the digestion time and increasing methane production. It also improved the microbial community structure and enhanced the acetoclastic methanogenesis in thermophilic co-digestion.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Environmental Sciences
Rui Wang, Zijing An, Lu Fan, Yan Zhou, Xiaomei Su, Junjie Zhu, Qian Zhang, Chongjun Chen, Hongjun Lin, Faqian Sun
Summary: Quorum quenching (QQ) is a novel technique for controlling biofouling in membrane bioreactors (MBRs) by disrupting quorum sensing (QS) and inhibiting biofilm formation. This study evaluated the effectiveness of the QQ strain Brucella sp. ZJ1, encapsulated in alginate beads, in mitigating biofouling. The results showed that MBR with QQ beads extended operation time by 2-3 times without affecting pollutant degradation, and these beads maintained approximately 50% QQ activity even after 50 days of operation.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Environmental Sciences
Junliang Gao, Rui Wang, Yilin Li, Huimin Huang, Xiaomei Su, Zijing An, Wenjun Yin, Lizhen Yang, Liang Rong, Faqian Sun
Summary: The effect of two aeration modes in the aerobic phase on nitrogen removal and N2O emission in treating landfill leachate was compared. Increasing dissolved oxygen showed positive effects on nitrogen removal and minimized N2O emission. However, high dissolved oxygen concentration reduced nitrogen removal and led to high N2O emission.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)