Article
Environmental Sciences
Oumayma Kahla, Sondes Melliti Ben Garali, Fatma Karray, Manel Ben Abdallah, Najwa Kallel, Najla Mhiri, Hatem Zaghden, Badreddine Barhoumi, Olivier Pringault, Marianne Quemeneur, Marc Tedetti, Sami Sayadi, Asma Sakka Hlaili
Summary: The efficiency of a benthic diatom-associated bacteria in removing BaP and Flt was investigated in this study. Results showed a co-metabolic synergy between microalgae and associated bacteria in biodegrading PAHs, suggesting their potential application in the bioremediation of contaminated sites.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Engineering, Environmental
Beibei Wang, Ying Teng, Huaiying Yao, Peter Christie
Summary: In this study, DNA-SIP technology was used to detect active BaP-degraders, finding that the diversity of degrading microorganisms was highest in paddy soil. The active BaP-degraders in the mixed microbiome were found to be both identical and unique compared to those in paddy soil, with functional genes of PAH-ring hydroxylating dioxygenases positively related to BaP removal. Gram-positive and Gram-negative bacteria were both found to be active BaP degrading bacteria in the study.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Engineering, Environmental
Tingyu Zheng, Rui Liu, Jianjun Chen, Xuejun Gu, Jian Wang, Lingmei Li, Liqun Hou, Na Li, Yajie Wang
Summary: This study investigated the mechanisms of plant mediated microbial degradation of pyrene in soils contaminated with different levels of the pollutant. It found that pyrene degradation occurred through both double-oxygen and single-oxygen pathways in the rhizosphere of Fire Phoenix, with important microbial genes such as RHD alpha-GP, nidA, and nidB playing a key role in the degradation process. Furthermore, the expression of these genes was significantly correlated with the residual amount of pyrene and total PAH metabolites in the soil, suggesting their importance in the biodegradation of pyrene in the rhizosphere.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Peng Guo, Longguo Jin, Weitong Cui, Yan Yang, Yanjun Cheng, Daoping Wang, Yinghong Pan, Jinghua Jin
Summary: This research investigated the mechanism of pyrene degradation in Mycobacterium sp. 16 F using proteomic analysis. The results showed that there were significant changes in the expression of differential proteins after pyrene exposure, with most of them being dioxygenases and dehydrogenases. Furthermore, the metabolites generated from the pentose phosphate and glycolytic pathways contributed to the production of amino acids and nucleotide precursors, which then entered the shikimate pathway in conjunction with the pyrene degradation pathway.
ENVIRONMENTAL POLLUTANTS AND BIOAVAILABILITY
(2022)
Review
Biotechnology & Applied Microbiology
Mohammad Qutob, Mohd Rafatullah, Syahidah Akmal Muhammad, Abeer M. Alosaimi, Hajer S. Alorfi, Mahmoud A. Hussein
Summary: Polycyclic aromatic hydrocarbons, including pyrene, are priority pollutants due to their environmental effects. Bacterial strains, especially Mycobacterium and Rhodococcus, have been identified as efficient pyrene degraders. This review collected scattered data on degradation efficiency, metabolite formation, bio-toxicity, and proposed degradation pathways. Most Mycobacterium strains showed efficient degradation of pyrene, with 4,5-dihydroxy pyrene, phenanthrene-4,5-dicarboxylate, phthalic acid, and pyrene-4,5-dihydrodiol as the main metabolites. Some metabolites exhibited positive results in mutagenicity tests. This study contributes to the understanding and enhancement of pyrene bioremediation.
FERMENTATION-BASEL
(2022)
Article
Engineering, Environmental
Mukhtiar Ali, Xin Song, Qing Wang, Zhuanxia Zhang, Meng Zhang, Xing Chen, Zhiwen Tang, Xin Liu
Summary: In this study, it was found that the biodegradation rates of benzene and BaP co-contamination were significantly enhanced at elevated temperatures, with increased bioavailability and generation of ROS. The study also revealed that gram-positive bacteria exhibited higher enzymatic activities and PAH-RHD alpha gene expression, indicating their preference for long-term elevated temperatures. ROS species (O(2)(center dot-)and center dot OH) were detected and cleared by increased antioxidant enzyme activities. Soil properties were affected by temperature treatments, indicating metal-organic-associated reactions during TEB. Overall, the results highlight the importance of temperature in enhancing biodegradation under thermally enhanced biodegradation conditions.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Environmental Sciences
Xiaoning Li, Hailong Liu, Weiben Yang, Hongjie Sheng, Fang Wang, Jean Damascene Harindintwali, H. M. S. K. Herath, Yinping Zhang
Summary: The study found that the addition of humic acid (HA) can significantly enhance the biodegradation efficiency of Mycobacterium sp. NJS-1 on pyrene and induce a new degradation pathway. Furthermore, HA also alters the ultrastructure of bacterial cells, promoting their growth and reducing the space between cells, thereby further improving the biodegradation of pyrene.
Article
Multidisciplinary Sciences
Salina Alias, Megawati Omar, Noor Hana Hussain, Nor Amani Filzah Mohd-Kamil, Suhaimi Abdul-Talib
Summary: This study focused on the biodegradation of benzo(a)pyrene by Sphingobacterium spiritovorum in contaminated soil, and established a corresponding biokinetic model. The results showed that enzyme substrate inhibition is the critical factor affecting the degradation of benzo(a)pyrene by S. spiritovorum.
Review
Environmental Sciences
Sumathi K. Rameshpathy Manian
Summary: Soil is a significant environmental matrix that supports the life of all creatures. However, human activities and population growth have caused soil pollution, releasing foreign substances and persistent contaminants. One common toxic substance is polycyclic aromatic hydrocarbons (PAHs), which can change soil characteristics, impact microbial biodiversity, and destroy items. The restoration and cleanup of PAH-polluted areas pose serious technological and environmental challenges due to the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons. This review discusses how PAHs affect soil characteristics and highlights the production of secondary metabolites and carbon dioxide during microbial breakdown processes. Additionally, the advantages of bioremediation strategies are assessed, emphasizing the importance of both legislative and scientific research.
ENVIRONMENTAL MONITORING AND ASSESSMENT
(2023)
Article
Engineering, Environmental
Jiangqiao Bao, Jibing Li, Longfei Jiang, Weiping Mei, Mengke Song, Deyin Huang, Chunling Luo, Gan Zhang
Summary: In this study, DNA-stable isotope probing and high-throughput sequencing were used to investigate the influence of biochar on phenanthrene (PHE) degradation, the active PHE-degrading microbial community, and PAH-degradation genes. The results showed that the addition of biochar significantly decreased PHE biodegradation and bioavailable concentrations, and altered the composition and abundance of the PHE-degrading microbial community. Furthermore, new microbial strains and genes involved in PHE degradation were identified.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Louella Concepta Goveas, Raja Selvaraj, Ramesh Vinayagam, Shyama Prasad Sajankila, Arivalagan Pugazhendhi
Summary: In this study, biodegradation of benzo(a)pyrene was conducted using two strains of Pseudomonas, i.e WDE11 and WD23, isolated from refinery effluent. The maximum tolerances for benzo(a)pyrene were 250 mg/L and 225 mg/L for Pseudomonas sp. WD23 and Pseudomonas sp. WDE11 respectively. The degradation rate constants ranged from 0.0468 to 0.0513/day at 50 mg/L and 0.006 to 0.007 L/mg·day at 100 mg/L. The major degradation metabolites were identified as dihydroxy-pyrene, naphthalene-1,2-dicarboxylic acid, salicylic acid, and oxalic acid. The catechol 2,3 dioxygenase enzyme exhibited significant activity during the benzo(a)pyrene metabolism.
Article
Engineering, Environmental
Zuotao Zhang, Jiao Sun, Xiaoqiang Gong, Chongyang Wang, Hui Wang
Summary: A new sulfate-reducing bacterium, Desulforamulus aquiferis strain DSA, was found to degrade high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) pyrene and benzo[a]pyrene, while reducing sulfate to sulfide. The metabolic processes for anaerobic pyrene and benzo[a]pyrene degradation were proposed based on detecting intermediates and analyzing the genome. This study provides new guidance for anaerobic HMW-PAHs degradation under sulfate-reducing conditions.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Chemistry, Analytical
Cameron P. Oden, Charles J. Werth, Luiza Notini, Lynn E. Katz
Summary: The study found that redox active minerals play a significant role in transforming contaminants like pyrene during thermal treatment, with transformation pathways depending on experimental conditions. Understanding dominant reaction pathways and products is crucial for the design of efficient and safe thermally enhanced treatment systems.
ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS
(2022)
Article
Environmental Sciences
Giovanna Pagnozzi, Sean Carroll, Danny D. Reible, Kayleigh Millerick
Summary: This study demonstrates that PAC amendment enhances naphthalene biodegradation under sulfate-reducing conditions, while naphthalene decay in sand and media-free systems is not linked to biodegradation activity.
ENVIRONMENTAL POLLUTION
(2021)
Article
Environmental Sciences
Guilherme Pinto Cauduro, Ana Lusia Leal, Marcela Marmitt, Leticia Gomes de Avila, Gabriela Kern, Patricia Doerr Quadros, Eshwar Mahenthiralingam, Victor Hugo Valiati
Summary: The study isolated bacteria resistant to polyaromatic hydrocarbons from activated sludge in a Petrochemical Wastewater Treatment Plant, demonstrating the biotechnological potential of Burkholderia cepacia complex strains for use in wastewater treatment and bioremediation.
ENVIRONMENTAL MONITORING AND ASSESSMENT
(2021)
Article
Hematology
Naser Ansari-Pour, Mehmet Samur, Erin Flynt, Sarah Gooding, Fadi Towfic, Nicholas Stong, Maria Ortiz Estevez, Konstantinos Mavrommatis, Brian Walker, Gareth Morgan, Nikhil Munshi, Herve Avet-Loiseau, Anjan Thakurta
Summary: Large-scale analysis of relapsed/refractory multiple myeloma (rrMM) shows significant genomic variation compared to newly diagnosed multiple myeloma (ndMM). This variation may be associated with therapeutic exposures and clonal structure. Genomic aberrations associated with resistance to immunomodulatory agent (IMiD) therapy are identified and their role in therapy evasion should be further evaluated.
Article
Biochemistry & Molecular Biology
Supratim Mukherjee, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Jon Bertsch, Jagadish Chandrabose Sundaramurthi, Mahathi Kandimalla, Paul A. Nicolopoulos, Alessandro Favognano, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The Genomes OnLine Database (GOLD) continues to serve as a flagship genomic metadata repository, providing freely available projects and metadata for large-scale comparative genomics analysis. New features and components have been added in the latest GOLD v.9 version.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin
Summary: We developed a computational pipeline to identify viroid-like cccRNAs and found a 5-fold increase in the number of identified elements compared to previous studies. The presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems suggests that their host range is broader than currently known.
Article
Ecology
Antonio P. Camargo, Rafael S. C. de Souza, Juliana Jose, Isabel R. Gerhardt, Ricardo A. Dante, Supratim Mukherjee, Marcel Huntemann, Nikos C. Kyrpides, Marcelo F. Carazzolle, Paulo Arruda
Summary: The grassland ecosystem of Brazilian campos rupestres has low concentrations of phosphorus and nitrogen, yet supports a high plant diversity. This study explores the taxonomic profile and functional potential of microbial communities associated with two plant species of the campos rupestres. The results show that the soil and rock communities associated with these plants share a core group of efficient colonizers enriched in certain bacterial families. The microbial populations associated with plant roots have a genetic repertoire for organic compound intake, phosphorus and nitrogen turnover, highlighting their role in nutrient availability.
Article
Biotechnology & Applied Microbiology
Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin, Julien Jarroux, Alla L. Lapidus, Hagen U. Tilgner
Summary: IsoQuant is a computational tool that uses intron graphs to accurately reconstruct transcripts with or without reference genome annotation. It reduces the false-positive rate by fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively, for novel transcript discovery. IsoQuant also improves performance for Pacific Biosciences data.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan J. Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Simon Roux
Summary: Viruses play critical roles in all microbiomes and their genomic diversity and impacts on biological processes are extensively explored through metagenomics. IMG/VR is a platform providing access to a large collection of viral sequences along with functional annotation and metadata. The latest version, IMG/VR v4, contains over 15 million virus genomes and genome fragments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan J. Ritter, Cody Webb, Dongying Wu, Neha J. Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The Integrated Microbial Genomes & Microbiomes system (IMG/M) at the Department of Energy Joint Genome Institute (JGI) provides support for comparative analysis of various genomes, metagenomes, and metatranscriptomes. It includes datasets from JGI, as well as imported datasets from public sources and user-submitted datasets. In recent years, efforts have been made to improve annotation pipeline, upgrade reference database versions, and add new analysis functionalities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Stamatia A. Katarachia, Sophia P. Markaki, Athanassios D. Velentzas, Dimitrios J. Stravopodis
Summary: mTORC1 regulates mammalian cell metabolism and growth in response to environmental stimuli. Nutrient signals control the localization of mTORC1 onto lysosomes, and SAMTOR prevents the inhibitory actions of SAM on mTORC1, activating its kinase activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Irene Dervisi, Chrysanthi Valassakis, Aikaterini Koletti, Vassilis N. Kouvelis, Emmanouil Flemetakis, Christos A. Ouzounis, Andreas Roussis
Summary: Selenium-binding proteins (SBPs) are a widely distributed protein family, with SBP1 recently identified as a new stress response regulator in plants. Although SBP1 has been characterized as a methanethiol oxidase, its exact role is still unclear. In mammals, SBP1 is involved in anti-carcinogenic growth regulation, redox modulation, and detoxification. This study investigates the functional potential of specific motifs of SBPs in an evolutionary context. Phylogenetic analysis reveals the absence of SBP in fungi and most non-eukaryotic organisms. The phylogenetic tree also highlights the differentiation and evolution of characteristic SBP motifs, with modifications found in Acidobacteria, Fungi, and Archaea for the CSSC motif and a conserved CC motif in Plants modified to CxxC in Animals. These results suggest that SBPs likely emerged from bacteria as methanethiol oxidases.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Microbiology
Stamatia Asimakoula, Orfeas Marinakos, Epameinondas Tsagogiannis, Anna-Irini Koukkou
Summary: This study aimed to investigate phenol degradation by Pseudarthrobacter phenanthrenivorans Sphe3 cells and the metabolic pathway used by the bacterium. Alginate-immobilized Sphe3 cells were also studied for their efficiency in phenol degradation compared to free cells. Sphe3 was found to be capable of growing using phenol as the sole carbon and energy source up to 1500 mg/L. Both ortho- and meta-cleavage pathways of catechol were active according to qPCR findings, but the ortho-metabolic pathway was predominant for phenol degradation based on enzymatic assays and intermediate product identification. Alginate-entrapped Sphe3 cells completely degraded 1000 mg/L phenol after 192 h, with slower initial degradation compared to free cells. Immobilized Sphe3 cells retained phenol-degrading capacity even after 30 days of storage and could be reused for at least five cycles with over 75% of the original phenol-catabolizing capacity retained.
Article
Geosciences, Multidisciplinary
Evgeny Abakumov, Timur Nizamutdinov, Alla Lapidus, Georgy Istigechev, Sergey Loiko
Summary: The Chernevaya taiga soils are characterized by a strong presence of stone-based matrix, organomineral aggregates, and high biological activity, indicating active material transformation and bioturbation in the region.
Article
Genetics & Heredity
Andreas N. Ioannides, Katerina R. Katsani, Christos A. Ouzounis, Vasilis J. Promponas
Summary: The nuclear pore complex exhibits different manifestations across eukaryotes, with certain components being restricted to specific clades. Using extensive data collection, we create a robust library of nucleoporin protein sequences and their respective family-specific position-specific scoring matrices that can be used to detect nucleoporins in proteomes with high sensitivity and specificity compared to existing methods.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Mathematical & Computational Biology
Supratim Mukherjee, Galina Ovchinnikova, Dimitri Stamatis, Cindy Tianqing Li, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The power of next-generation sequencing has led to a massive increase in projects aiming to understand the diversity of complex microbial environments. However, the lack of standardized reporting standards for microbiome data and samples poses a challenge for follow-up studies. The Genomes OnLine Database (GOLD) has developed a standardized naming system for microbiome samples to address this issue and has continued to enrich the research community with well-curated and understandable names for metagenomes and metatranscriptomes. This naming system should be adopted as a best practice to improve the interoperability and reusability of microbiome data.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Biochemical Research Methods
Dimitrios Vasileiou, Christos Karapiperis, Ismini Baltsavia, Anastasia Chasapi, Dag Ahren, Paul J. Janssen, Ioannis Iliopoulos, Vasilis J. Promponas, Anton J. Enright, Christos A. Ouzounis
Summary: Public-domain availability of bioinformatics software resources is crucial for ensuring long-term sustainability and reproducibility of research and development in the life sciences. This study relaunches a range of established software components for computational genomics, version 1.0.1, suitable for sequence matching, masking, searching, clustering, and visualization in protein family discovery, annotation, and functional characterization at a genome scale. These applications are made available as open source online and are supported by centrally administered bioinformatics infrastructure funding.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Cell Biology
Rekha Seshadri, Simon Roux, Katharina J. Huber, Dongying Wu, Sora Yu, Dan Udwary, Lee Call, Stephen Nayfach, Richard L. Hahnke, Rudiger Pukall, James R. White, Neha J. Varghese, Cody Webb, Krishnaveni Palaniappan, Lorenz C. Reimer, Joaquim Sarda, Jonathon Bertsch, Supratim Mukherjee, T. B. K. Reddy, Patrick P. Hajek, Marcel Huntemann, I-Min A. Chen, Alex Spunde, Alicia Clum, Nicole Shapiro, Zong-Yen Wu, Zhiying Zhao, Yuguang Zhou, Lyudmila Evtushenko, Sofie Thijs, Vincent Stevens, Emiley A. Eloe-Fadrosh, Nigel J. Mouncey, Yasuo Yoshikuni, William B. Whitman, Hans-Peter Klenk, Tanja Woyke, Markus Goeker, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The study presents a comprehensive analysis of actinobacterial diversity, showing that only a small portion of this diversity is represented by sequenced genomes. The comparison of gene functions reveals novel determinants of host-microbe interaction and environment-specific adaptations. The analysis of biosynthetic gene clusters highlights the role of horizontal gene transfer and gene loss in shaping secondary metabolite repertoire.
