Article
Engineering, Environmental
Nan Zhou, Haijiao Guo, Qingxin Liu, Zuotao Zhang, Jiao Sun, Hui Wang
Summary: This study isolated a strain of anaerobic Bacillus firmus named PheN7 from contaminated soil and sludge samples, and successfully applied it in the remediation of PAH-contaminated soil under anaerobic conditions. The results showed that the synergy between PheN7 and indigenous degrading bacteria significantly improved the remediation efficiency of the soil.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Filippo Dell'Anno, Leonardo Joaquim van Zyl, Marla Trindade, Emanuela Buschi, Antonio Cannavacciuolo, Milva Pepi, Clementina Sansone, Christophe Brunet, Adrianna Ianora, Donatella de Pascale, Peter N. Golyshin, Antonio Dell'Anno, Eugenio Rastelli
Summary: Petroleum hydrocarbons and heavy metals are widespread contaminants in marine ecosystems, and microbial-based bioremediation shows promise as an effective and sustainable solution. In this study, we enriched the microbiome of heavily polluted sediments and isolated two novel bacterial strains that exhibited high degradation of PAHs and removal of HMs, with the best results observed for naphthalene, pyrene, and lead. The genetic repertoire of these strains may be further utilized for bioremediation of marine environments contaminated with PAHs and HMs.
ENVIRONMENTAL POLLUTION
(2023)
Review
Biotechnology & Applied Microbiology
Abiram Karanam Rathankumar, Kongkona Saikia, Ponnusamy Senthil Kumar, Sunita Varjani, Shravani Kalita, Nikhil Bharadwaj, Jenet George, Vinoth Kumar Vaidyanathan
Summary: Soil contaminated with hydrophobic organic hydrocarbons, such as polycyclic aromatic hydrocarbons (PAHs), can pose a serious threat to the ecosystem and human health. The use of surfactants to mobilize and remediate PAHs from contaminated soil has garnered increasing attention as an effective method for soil remediation.
JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY
(2022)
Article
Environmental Sciences
Emilio Ritore, Bruno Coquelet, Carmen Arnaiz, Jose Morillo, Jose Usero
Summary: This study determined the most effective surfactants for remediating gasoline and diesel-contaminated soil by integrating soil texture and organic matter information. Anionic surfactants showed better removal rates for hydrocarbons compared to non-ionic surfactants, with results suggesting preferential desorption on different hydrocarbon ranges.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Engineering, Environmental
Panpan Wang, Yunzhe Cao, Huilong Luo, Ting Li, Bin Yang, Huiying Li, Tian Liang, Jingjing Yu, Lina Wang, Fujun Ma, Qingbao Gu, Aizhong Ding, Fasheng Li
Summary: This study examines the direct-fired thermal desorption technology commonly used to treat contaminated soil, with a focus on a site contaminated by polycyclic aromatic hydrocarbons (PAHs). The analysis considers the entire thermal desorption process and evaluates the concentration levels and occurrence characteristics of heavy metals in dust generated during the process. The study also explores possible secondary pollution and environmental impacts. The findings reveal that the dust samples generated during the ex situ direct-fired thermal desorption process have higher amounts of heavy metal accumulation and altered speciation compared to the thermal desorption soil. The study further analyzes the enrichment characteristics and origins of the heavy metals using various microscopic research methods. The results of this study provide a scientific basis for the proper disposal and risk management of dust collected after direct-fired thermal desorption treatment of contaminated soil.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Review
Environmental Sciences
Mahmoud Mazarji, Tatiana Minkina, Svetlana Sushkova, Saglara Mandzhieva, Gholamreza Nabi Bidhendi, Anatoly Barakhov, Amit Bhatnagar
Summary: This article discusses the application of nanomaterials in the remediation of toxic polycyclic aromatic hydrocarbons in soil, highlighting the contributions of different NM characteristics to process enhancement and summarizing the best operating conditions. Additionally, attention is given to the influence of soil type and pollutant type on process performance, as well as the potential implications of NMs and PAHs on soil properties.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Article
Environmental Sciences
Thiloka Kariyawasam, Gregory S. Doran, Julia A. Howitt, Paul D. Prenzler
Summary: PAHs are harmful pollutants in the environment. Extraction and quantification are important steps to understand contamination and implement remediation. Traditional extraction methods have limitations and newer, more environmentally friendly methods are being explored.
Article
Microbiology
Abdulkhaleg M. Alfaify, Mushtaq Ahmad Mir, Sulaiman A. Alrumman
Summary: In this study, a strain of Klebsiella oxytoca with efficient pyrene degradation ability was isolated from petroleum-contaminated soil. Through various experiments and analysis, the mechanism and pathway of pyrene degradation by K. oxytoca were elucidated, demonstrating its potential for soil aromatic hydrocarbon removal.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Environmental Sciences
Wenjie Chen, Yilin Zuo, Zhuonan Hou, Bo Wang, Shangao Xiong, Xiaoyan Ding, Bihui Peng, Kaiyun Zhou, Ji Li, Rui Liu, Guochun Ding, Yuquan Wei, Ting Xu
Summary: This study compared the effects of Rhodococcus bioaugmentation and biostimulation on the degradation of DBT and bacterial community interaction in petroleum-contaminated soils. The results showed that Rhodococcus bioaugmentation had the highest DBT degradation efficiency, with the majority of degradation occurring within the first 30 days. The composition of bacteria differed significantly among the different treatments, and Bacillus and Paenibacillus were identified as the dominant genera involved in DBT degradation.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Engineering, Environmental
Wenjie Ren, Haoran Liu, Tingyu Mao, Ying Teng, Rui Zhao, Yongming Luo
Summary: This study investigated the use of graphene oxide-immobilized bacterial pellets for the removal of polycyclic aromatic hydrocarbons (PAHs) from contaminated soil. The results showed that these immobilized bacterial pellets significantly improved the removal rate of PAHs and enhanced the abundance of degrading bacteria in the soil. They also enriched potential indigenous degrading bacteria and functional genes involved in PAHs degradation. Overall, this nanocomposite bacterial pellets provide a novel microbial immobilization option for remediating organic pollutants in harsh soil environments.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Leiyu Feng, Xiupeng Jiang, Yanning Huang, Dongdong Wen, Tianyu Fu, Rongbing Fu
Summary: The use of indigenous bacterial consortium combined with biosurfactant can enhance the bioremediation efficiency of petroleum hydrocarbon-contaminated soil, reducing the half-life of TPH and improving its bioavailability. Biosurfactant stimulates microbial activities, accelerates the biodegradation process, and serves as an effective auxiliary method for the remediation of petroleum hydrocarbon-contaminated soil.
ENVIRONMENTAL POLLUTION
(2021)
Article
Environmental Sciences
Li Ma, Lei Yao, Yuhong Li
Summary: Bioremediation experiments using ryegrass to degrade polycyclic aromatic hydrocarbons (PAHs) in urban soil showed that ryegrass can enhance PAH degradation while microbes play a dominant role in this process. Planting ryegrass increased the removal efficiency of PAHs from soil, providing insights for mitigating urban soil pollution safely and effectively.
JOURNAL OF SOILS AND SEDIMENTS
(2022)
Article
Environmental Sciences
Carlotta Carlini, Sampriti Chaudhuri, Oliver Mann, Daniel Tomsik, Thorsten Hueffer, Nicolas Greggio, Diego Marazza, Thilo Hofmann, Gabriel Sigmund
Summary: Biochar has been proven to immobilize polycyclic aromatic hydrocarbons (PAH) and hetero-PAH in residually contaminated soils, and performs better than commercial activated carbon (AC). Steam-activated biochar (SABC) showed higher efficacy than AC, while pristine biochar (BC) had slightly lower performance but was still acceptable. Therefore, BC and SABC can be valid substitutes for AC in stabilizing residually contaminated soils.
ENVIRONMENTAL POLLUTION
(2023)
Article
Environmental Sciences
Haren B. Gosai, Haresh Z. Panseriya, Payal G. Patel, Ajay C. Patel, Sunita Varjani, Alka Shankar, Bharti P. Dave
Summary: This study evaluated the effectiveness of PAHs degrading bacteria, including Stenotrophomonas maltophilia, mixed culture, and enriched native microflora at the mesocosm level. The results showed that the mixed culture had the highest degradation rate, followed by Stenotrophomonas maltophilia and enriched native microflora. MiSeq sequencing revealed the dominant bacterial communities and families and genera that play a key role in PAHs degradation. This study provides important insights for future bioremediation studies and policy-making.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Zhijun Luo, Yanghong Min, Lingling Qu, Youye Song, Yongxiang Hong
Summary: The photochemical process of ferrous oxalate effectively degrades phenanthrene in contaminated soil under visible light irradiation by generating hydroxyl radicals. Ferrous oxalate possesses excellent visible light absorption ability, which is crucial for enhancing the degradation efficiency of phenanthrene.
Article
Ecology
Aurelie Labarre, David Lopez-Escard, Francisco Latorre, Guy Leonard, Francois Bucchini, Aleix Obiol, Corinne Cruaud, Michael E. Sieracki, Olivier Jaillon, Patrick Wincker, Klaas Vandepoele, Ramiro Logares, Ramon Massana
Summary: The study utilized single-cell genomics to analyze the genomes of 15 MAST species from marine surface plankton, revealing their potential for phagocytosis and ability to thrive in the photic ocean with the presence of rhodopsin genes. The complexity of phagocytosis machinery in microbial eukaryotes was highlighted, contrasting with the well-defined set of genes for photosynthesis, providing essential insights into the ecophysiology of uncultured species and the function of rhodopsins in stramenopiles.
Correction
Multidisciplinary Sciences
Quentin Carradec, Julie Poulain, Emilie Boissin, Benjamin C. C. Hume, Christian R. Voolstra, Maren Ziegler, Stefan Engelen, Corinne Cruaud, Serge Planes, Patrick Wincker
Summary: The paper has been amended and the revised version can be accessed through a link at the top of the paper.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Lauric Reynes, Thierry Thibaut, Stephane Mauger, Aurelie Blanfune, Florian Holon, Corinne Cruaud, Arnaud Couloux, Myriam Valero, Didier Aurelle
Summary: The study identified genomic signatures of partial clonality in the deep water kelp species Laminaria rodriguezii and compared them with a closely related species Laminaria digitata. The findings showed distinct genetic distributions and different impacts of clonality and genetic drift on population diversity. These results provide insights into the genetic study of asexuality in natural populations and highlight potential applications of RAD-sequencing in investigating partial clonality in various non-model species.
Article
Biology
Elise J. Gay, Jessica L. Soyer, Nicolas Lapalu, Juliette Linglin, Isabelle Fudal, Corinne Da Silva, Patrick Wincker, Jean-Marc Aury, Corinne Cruaud, Anne Levrel, Jocelyne Lemoine, Regine Delourme, Thierry Rouxel, Marie-Helene Balesdent
Summary: This study analyzed the gene expression at different stages of the interaction between Leptosphaeria maculans and Brassica napus, revealing that about 9% of the fungus genes are highly expressed during interactions with the host plant. These highly expressed genes are distributed into eight clusters, enriched in effector genes, with one cluster specific to the saprophytic lifestyle. The study suggests that genes involved in niche adaptation may be located in heterochromatic regions of the genome, providing a plasticity of expression that could be targeted for plant disease control.
Correction
Ecology
Tom O. Delmont, Juan Jose Pierella Karlusich, Iva Veseli, Jessika Fuessel, A. Murat Eren, Rachel A. Foster, Chris Bowler, Patrick Wincker, Eric Pelletier
Article
Ecology
Tom O. Delmont, Juan Jose Pierella Karlusich, Iva Veseli, Jessika Fuessel, A. Murat Eren, Rachel A. Foster, Chris Bowler, Patrick Wincker, Eric Pelletier
Summary: The study utilized metagenomic data from various oceans to identify new marine diazotrophs, expanding the known diversity of nitrogen fixers in the ocean. These diazotrophs include cyanobacterial and heterotrophic bacterial populations, highlighting their importance in the marine nitrogen balance.
Article
Biochemistry & Molecular Biology
Juan Jose Pierella Karlusich, Eric Pelletier, Lucie Zinger, Fabien Lombard, Adriana Zingone, Sebastien Colin, Josep M. Gasol, Richard G. Dorrell, Nicolas Henry, Eleonora Scalco, Silvia G. Acinas, Patrick Wincker, Colomban de Vargas, Chris Bowler
Summary: Phytoplankton, accounting for over 45% of global primary production, play a significant role in aquatic food webs and the Earth System. However, current genetic surveys using PCR amplification of rRNA genes have limitations. This study introduces a PCR-free method targeting the photosynthetic gene psbO, showing improved correlations with flow cytometry and microscopy and providing new insights into the ecology of phytoplankton communities.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Ahmed A. Zayed, James M. Wainaina, Guillermo Dominguez-Huerta, Eric Pelletier, Jiarong Guo, Mohamed Mohssen, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Olivier Zablocki, Dylan Cronin, Lindsey Solden, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Hans-Joachim Ruscheweyh, Guillem Salazar, Elan Shatoff, Ralf Bundschuh, Kurt Fredrick, Laura S. Kubatko, Samuel Chaffron, Alexander Culley, Shinichi Sunagawa, Jens H. Kuhn, Patrick Wincker, Matthew B. Sullivan
Summary: This study expands Earth's RNA virus catalogs and their taxonomy, investigates their evolutionary origins and marine biogeography, and reveals the need for substantive revisions of taxonomy for RNA viruses. The efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
Article
Microbiology
Ophelie Da Silva, Sakina-Dorothee Ayata, Enrico Ser-Giacomi, Jade Leconte, Eric Pelletier, Cecile Fauvelot, Mohammed-Amin Madoui, Lionel Guidi, Fabien Lombard, Lucie Bittner
Summary: High-throughput sequencing has revolutionized the study of marine planktonic communities, revealing the diversity of protists in these ecosystems. In this study, the researchers developed a pipeline to analyze the genomic differentiation of three protist species in the Mediterranean Sea. They found that the differentiation is influenced by both environmental and geographic factors. Despite the challenges in using metagenomics for accurate estimation of protist genomic differentiation, this study provides valuable insights into the ecological and evolutionary processes in marine populations.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Caroline Vernette, Julien Lecubin, Pablo Sanchez, Shinichi Sunagawa, Tom O. Delmont, Silvia G. Acinas, Eric Pelletier, Pascal Hingamp, Magali Lescot
Summary: Testing hypothesis about the biogeography of genes requires significant hardware resources and programming skills. The new release of 'Ocean Gene Atlas' (OGA2) is a freely available online service to mine large and complex marine environmental genomic databases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Guillermo Dominguez-Huerta, Ahmed A. Zayed, James M. Wainaina, Jiarong Guo, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Mohamed Mohssen, Olivier Zablocki, Eric Pelletier, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Tara Oceans Coordinators, Chris Bowler, Damien Eveillard, Lionel Guidi, Eric Karsenti, Jens H. Kuhn, Hiroyuki Ogata, Patrick Wincker, Alexander Culley, Samuel Chaffron, Matthew B. Sullivan
Summary: This study reveals patterns and predictors of marine RNA virus diversity and identifies their ecological impacts on marine ecosystems. The research also highlights unexpectedly high polar ecological interactions.
Article
Biology
Daniel J. Richter, Romain Watteaux, Thomas Vannier, Jade Leconte, Paul Fremont, Gabriel Reygondeau, Nicolas Maillet, Nicolas Henry, Gaetan Benoit, Ophelie Da Silva, Tom O. Delmont, Antonio Fernandez-Guerra, Samir Suweis, Romain Narci, Cedric Berney, Damien Eveillard, Frederick Gavory, Lionel Guidi, Karine Labadie, Eric Mahieu, Julie Poulain, Sarah Romac, Simon Roux, Celine Dimier, Stefanie Kandels, Marc Picheral, Sarah Searson, Tara Oceans Coordinators, Stephane Pesant, Jean-Marc Aury, Jennifer R. Brum, Claire Lemaitre, Eric Pelletier, Peer Bork, Shinichi Sunagawa, Fabien Lombard, Lee Karp-Boss, Chris Bowler, Matthew B. Sullivan, Eric Karsenti, Mahendra Mariadassou, Ian Probert, Pierre Peterlongo, Patrick Wincker, Colomban de Vargas, Maurizio Ribera D'Alcala, Daniele Iudicone, Olivier Jaillon
Summary: This study assesses the global structure of plankton geography by analyzing metagenomes of plankton communities sampled from oceans worldwide. The findings demonstrate the influence of ocean currents on plankton biogeography and reveal characteristic timescales of community dynamics.
Article
Biology
Nina Guerin, Marta Ciccarella, Elisa Flamant, Paul Fremont, Sophie Mangenot, Benjamin Istace, Benjamin Noel, Caroline Belser, Laurie Bertrand, Karine Labadie, Corinne Cruaud, Sarah Romac, Charles Bachy, Martin Gachenot, Eric Pelletier, Adriana Alberti, Olivier Jaillon, Patrick Wincker, Jean-Marc Aury, Quentin Carradec
Summary: The smallest phytoplankton species play a crucial role in ocean biogeochemical cycling and are affected by global environmental changes. This study analyzed the abundance, ecological niche, and potential for adaptation of Pelagomonas calceolata in all oceans based on its complete assembled genome sequence. The results showed that P. calceolata is one of the most abundant eukaryotic species in the oceans, with its abundance favored by high temperature, low-light, and iron-poor conditions. Climate change projections suggest that the habitat of P. calceolata may extend towards the poles by the end of this century. The study also identified specific gene repertoire and expression level variations that may contribute to its ecological success in low-iron and low-nitrate environments.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Charlotte Nef, Mohammed-Amin Madoui, Eric Pelletier, Chris Bowler
Summary: This study explores the genetic diversity and adaptation of Chaetoceros, a diatom genus. The results show that Chaetoceros is prevalent in the Arctic Ocean, with lower distribution in the Pacific, Southern Oceans, and the Mediterranean Sea. The genetic structure of Chaetoceros populations is influenced by abiotic factors rather than geographic distance. Genes involved in nutrient availability responses, particularly for iron, silicate, and phosphate, show positive selection in Chaetoceros. These findings highlight the importance of environmental selection in shaping diatom diversity patterns.
Article
Biology
Richard G. Dorrell, Alan Kuo, Zoltan Fussy, Elisabeth H. Richardson, Asaf Salamov, Nikola Zarevski, Nastasia J. Freyria, Federico M. Ibarbalz, Jerry Jenkins, Juan Jose Pierella Karlusich, Andrei Stecca Steindorff, Robyn E. Edgar, Lori Handley, Kathleen Lail, Anna Lipzen, Vincent Lombard, John McFarlane, Charlotte Nef, Anna M. G. Novak Vanclova, Yi Peng, Chris Plott, Marianne Potvin, Fabio Rocha Jimenez Vieira, Kerrie Barry, Colomban de Vargas, Bernard Henrissat, Eric Pelletier, Jeremy Schmutz, Patrick Wincker, Joel B. Dacks, Chris Bowler, Igor Grigoriev, Connie Lovejoy
Summary: Microbial communities in the world ocean are influenced by oceanic circulation, resulting in distinct marine biomes. This study sequenced microalgae lineages isolated from Arctic waters and sea ice to investigate their evolution and adaptive mechanisms. The findings suggest that Arctic microalgae may have evolved separately from algae in the global ocean, and horizontal gene transfer played a role in their adaptation to the Arctic environment.
LIFE SCIENCE ALLIANCE
(2022)