Partitioning of Hydrophobic Organic Contaminants and Microbial Communities on Microplastics
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ORIGINAL RESEARCH published: 16 May 2017 doi: 10.3389/fmicb.2017.00877 Streptomyces colonosanans sp. nov., A Novel Actinobacterium Isolated from Malaysia Mangrove Soil Exhibiting Antioxidative Activity and Cytotoxic Potential against Human Colon Cancer Cell Lines Jodi Woan-Fei Law 1, Hooi-Leng Ser 1, Acharaporn Duangjai 2, 3, Surasak Saokaew 1, 3, 4, Sarah I. Bukhari 5, Tahir M. Khan 1, 6, Nurul-Syakima Ab Mutalib 7, Kok-Gan Chan 8, Edited by: Bey-Hing Goh 1, 3* and Learn-Han Lee 1, 3* Dongsheng Zhou, Beijing Institute of Microbiology and 1 Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Epidemiology, China Malaysia, 2 Division of Physiology, School of Medical Sciences, University of Phayao, Phayao, Thailand, 3 Center of Health Reviewed by: Outcomes Research and Therapeutic Safety, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand, 4 Andrei A. Zimin, Faculty of Pharmaceutical Sciences, Pharmaceutical Outcomes Research Center, Naresuan University, Phitsanulok, 5 6 Institute of Biochemistry and Thailand, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia, Department of 7 Physiology of Microorganisms (RAS), Pharmacy, Absyn University Peshawar, Peshawar, Pakistan, UKM Medical Molecular Biology Institute, UKM Medical Centre, 8 Russia University Kebangsaan Malaysia, Kuala Lumpur, Malaysia, Division of Genetics and Molecular Biology, Faculty of Science, Antoine Danchin, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia Institut de Cardiométabolisme et Nutrition (ICAN), France Streptomyces colonosanans MUSC 93JT, a novel strain isolated from mangrove forest *Correspondence: Bey-Hing Goh soil located at Sarawak, Malaysia. The bacterium was noted to be Gram-positive and [email protected] to form light yellow aerial and vivid yellow substrate mycelium on ISP 2 agar. -
DAFTAR PUSTAKA Abidin, Z. A. Z., A. J. K. Chowdhury
160 DAFTAR PUSTAKA AKTINOMISETES PENGHASIL ANTIBIOTIK DARI HUTAN BAKAU TOROSIAJE GORONTALO YULIANA RETNOWATI, PROF. DR. A. ENDANG SUTARININGSIH SOETARTO, M.SC; PROF. DR. SUKARTI MOELJOPAWIRO, M.APP.SC; PROF. DR. TJUT SUGANDAWATY DJOHAN, M.SC Universitas Gadjah Mada, 2019 | Diunduh dari http://etd.repository.ugm.ac.id/ Abidin, Z. A. Z., A. J. K. Chowdhury, N. A. Malek, and Z. Zainuddin. 2018. Diversity, antimicrobial capabilities, and biosynthetic potential of mangrove actinomycetes from coastal waters in Pahang, Malaysia. J. Coast. Res., 82:174–179 Adegboye, M. F., and O. O. Babalola. 2012. Taxonomy and ecology of antibiotic producing actinomycetes. Afr. J. Agric. Res., 7(15):2255-2261 Adegboye, M.,F., and O. O. Babalola. 2013. Actinomycetes: a yet inexhausative source of bioactive secondary metabolites. Microbial pathogen and strategies for combating them: science, technology and eductaion, (A.Mendez-Vila, Ed.). Pp. 786 – 795. Adegboye, M. F., and O. O. Babalola. 2015. Evaluation of biosynthesis antibiotic potential of actinomycete isolates to produces antimicrobial agents. Br. Microbiol. Res. J., 7(5):243-254. Accoceberry, I., and T. Noel. 2006. Antifungal cellular target and mechanisms of resistance. Therapie., 61(3): 195-199. Abstract. Alongi, D. M. 2009. The energetics of mangrove forests. Springer, New Delhi. India Alongi, D. M. 2012. Carbon sequestration in mangrove forests. Carbon Management, 3(3):313-322 Amrita, K., J. Nitin, and C. S. Devi. 2012. Novel bioactive compounds from mangrove dirived Actinomycetes. Int. Res. J. Pharm., 3(2):25-29 Ara, I., M. A Bakir, W. N. Hozzein, and T. Kudo. 2013. Population, morphological and chemotaxonomical characterization of diverse rare actinomycetes in the mangrove and medicinal plant rhizozphere. -
Textile Waste and Microplastic Induce Activity and Development of Unique
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.08.939876; this version posted February 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Textile waste and microplastic induce activity and 2 development of unique hydrocarbon-degrading marine 3 bacterial communities 4 5 Elsa B. Girard1, Melanie Kaliwoda2, Wolfgang W. Schmahl1,2,3, Gert Wörheide1,3,4 and 6 William D. Orsi1,3* 7 8 1 Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 9 80333 Munich, Germany 10 2 SNSB - Mineralogische Staatssammlung München, 80333 München, Germany 11 3 GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, 80333 Munich, Germany 12 4 SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, 80333 Munich, Germany 13 *Corresponding author (e-mail: [email protected]) 14 15 16 17 18 KEYWORDS 19 Microplastic, Fiber, Hydrocarbon-degrading bacteria, Microbial community, Pollution 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.08.939876; this version posted February 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 22 ABSTRACT 23 Biofilm-forming microbial communities on plastics and textile fibers are of growing interest since 24 they have potential to contribute to disease outbreaks and material biodegradability in the 25 environment. -
Quantitative Modeling for Microbial Ecology and Clinical Trials Scott
Quantitative modeling for microbial ecology and clinical trials by Scott Wilder Olesen B.A., Williams College (2010) M.A.St., University of Cambridge (2011) M.Phil., University of Cambridge (2012) Submitted to the Department of Biological Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Engineering at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY September 2016 c Massachusetts Institute of Technology 2016. All rights reserved. ○ Author................................................................ Department of Biological Engineering 19 August 2016 Certified by. Eric J. Alm Professor Thesis Supervisor Accepted by . Forest White Chair of Graduate Program, Department of Biological Engineering Quantitative modeling for microbial ecology and clinical trials by Scott Wilder Olesen Submitted to the Department of Biological Engineering on 19 August 2016, in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Engineering Abstract Microbial ecology has benefited from the decreased cost and increased quality of next-generation DNA sequencing. In general, studies that use DNA sequencing are no longer limited by the sequencing itself but instead by the acquisition of the samples and by methods for analyzing and interpreting the resulting sequence data. In this thesis, I describe the results of three projects that address challenges to interpreting or acquiring sequence data. In the first project, I developed a method for analyzing the dynamics of the relative abundance of operational taxonomic units measured by next- generation amplicon sequencing in microbial ecology experiments without replication. In the second project, I and my co-author combined a taxonomic survey of a dimictic lake, an ecosystem-level biogeochemical model of microbial metabolisms in the lake, and the results of a single-cell genetic assay to infer the identity of taxonomically- diverse, putatively-syntrophic microbial consortia. -
Microbial Community Composition of Deep-Sea Corals from the Red Sea
www.nature.com/scientificreports OPEN Microbial community composition of deep-sea corals from the Red Sea provides insight into functional Received: 30 November 2016 Accepted: 13 February 2017 adaption to a unique environment Published: 17 March 2017 Till Röthig*, Lauren K. Yum*, Stephan G. Kremb, Anna Roik & Christian R. Voolstra Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L−1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment. A growing number of studies support the notion that bacteria associated with multicellular hosts provide impor- tant functions related to metabolism, immunity, and environmental adaptation (among others)1. -
The Roles of Streptomyces and Novel Species Discovery
Review Article Progress in Microbes and Molecular Biology A Review on Mangrove Actinobacterial Diversity: The Roles of Streptomyces and Novel Species Discovery Jodi Woan-Fei Law1,2, Priyia Pusparajah1, Nurul-Syakima Ab Mutalib3, Sunny Hei Wong4, Bey-Hing Goh5*, Learn-Han Lee1* 1Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor Darul Ehsan, Malaysia 2Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China 3UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, University Kebangsaan Malaysia, Kuala Lum- pur, Malaysia 4Li Ka Shing Institute of Health Sciences, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong 5Biofunctional Molecule Exploratory Research Group (BMEX), School of Pharmacy, Monash University Malaysia, Selangor Darul Ehsan, Malaysia Abstract : In the class Actinobacteria, the renowned genus Streptomyces comprised of a group of uniquely complex bacteria that capable of synthesizing a great variety of bioactive metabolites. Streptomycetes are noted to possess several special qual- ities such as multicellular life cycle and large linearized chromosomes. The significant contribution of Streptomyces in mi- crobial drug discovery as witnessed through the discovery of many important antibiotic drugs has undeniably encourage the exploration of these bacteria from different environments, especially the mangrove environments. This review emphasizes on the genus Streptomyces and reports on the diversity of actinobacterial population from mangroves at different regions of the world as well as discovery of mangrove-derived novel Streptomyces species. Overall, the research on diversity of Actinobac- teria in the mangrove environments remains limited. -
Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju. -
Fungal Suppressive Activities of Selected Rhizospheric Streptomyces Spp
FUNGAL SUPPRESSIVE ACTIVITIES OF SELECTED RHIZOSPHERIC STREPTOMYCES SPP. ISOLATED FROM HYLOCEREUS POLYRHIZUS KAMALANATHAN RAMACHANDARAN FACULTY OF SCIENCE UNIVERSITY OF MALAYA KUALA LUMPUR 2014 FUNGAL SUPPRESSIVE ACTIVITIES OF SELECTED RHIZOSPHERIC STREPTOMYCES SPP. ISOLATED FROM HYLOCEREUS POLYRHIZUS KAMALANATHAN RAMACHANDARAN DISSERTATION SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE INSTITUTE OF BIOLOGICAL SCIENCES FACULTY OF SCIENCE UNIVERSITY OF MALAYA KUALA LUMPUR 2014 ABSTRACT Actinomycetes, mainly Streptomyces spp., have been extensively studied as potential biocontrol agents against plant pathogenic fungi. This study was aimed at isolating and screening Streptomyces strains from rhizosphere soils of Hylocereus polyrhizus collected in Kuala Pilah for potential in vitro antifungal activity. A total of 162 putative strains of actinomycetes was isolated from moist-heat treated soil plated on starch- casein-nitrate agar, humic-acid-vitamin agar and raffinose-histidine agar. Based on the ability to produce abundant aerial mycelium, 110 strains were categorised as Streptomycete-like. Seven main groups based on aerial mycelium colour observed in this study were grey (41.4%), white (37.7%), brown (8.0%), orange (4.3%), yellow (4.3%), green (2.5%) and black (1.9%). Three pathogenic fungi, namely, Fusarium semitactum, Fusarium decemcellulare and Fusarium oxysporum were isolated from the diseased stem regions of Hylocereus polyrhizus. The actinomycetes were screened for in vitro antagonistic activity against the isolated pathogenic fungi. In the qualitative screening, 23 strains were able to inhibit at least one of the three pathogenic fungi. In the quantitative screening, three strains, C17, C68 and K98, showed the highest antagonistic activity (70-89%) against all the fungal pathogens. -
In Newly Isolated Streptomyces Mangrovisoli Sp. Nov
ORIGINAL RESEARCH published: 20 August 2015 doi: 10.3389/fmicb.2015.00854 Presence of antioxidative agent, Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro- in newly isolated Streptomyces mangrovisoli sp. nov. Hooi-Leng Ser1, Uma D. Palanisamy1, Wai-Fong Yin2, Sri N. Abd Malek3, Kok-Gan Chan2,Bey-HingGoh1* and Learn-Han Lee1* 1 Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia, 2 Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia, 3 Biochemistry Program, Institute of Biological Sciences, Faculty of Science, Edited by: University of Malaya, Kuala Lumpur, Malaysia Wen-Jun Li, Sun Yat-Sen University, China T Reviewed by: AnovelStreptomyces, strain MUSC 149 was isolated from mangrove soil. A polyphasic James A. Coker, approach was used to study the taxonomy of MUSC 149T, which shows a range of University of Maryland University College, USA phylogenetic and chemotaxonomic properties consistent with those of the members Jeremy Dodsworth, of the genus Streptomyces. The diamino acid of the cell wall peptidoglycan was California State University LL-diaminopimelic acid. The predominant menaquinones were identified as MK9(H8) San Bernardino, USA and MK9(H6). Phylogenetic analysis indicated that closely related strains include *Correspondence: T Learn-Han Lee and Streptomyces rhizophilus NBRC 108885 (99.2% sequence similarity), S. gramineus Bey-Hing Goh, NBRC 107863T (98.7%) and S. graminisoli NBRC 108883T (98.5%). The DNA–DNA Biomedical Research Laboratory, T Jeffrey Cheah School of Medicine relatedness values between MUSC 149 and closely related type strains ranged from and Health Sciences, Monash 12.4 ± 3.3% to 27.3 ± 1.9%. -
Niche Partitioning Between Coastal and Offshore Shelf Waters Results in 2 Differential Expression of Alkane and PAH Catabolic Pathways 3 4 5 6 Shawn M
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.16.994715; this version posted July 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Niche Partitioning Between Coastal and Offshore Shelf Waters Results in 2 Differential Expression of Alkane and PAH Catabolic Pathways 3 4 5 6 Shawn M. Doylea#, Genmei Linb, Maya Morales-McDevittc, Terry L. 7 Wadea,d, Antonietta Quigga,e, and Jason B. Sylvana# 8 9 10 11 aDepartment of Oceanography, Texas A&M University, College Station, TX, USA. 12 bSchool of Marine Sciences, Sun Yet-Sen University, Zhuhai, China. 13 cGraduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA. 14 dGeochemical and Environmental Research Group, Texas A&M University, College Station, 15 TX, USA 16 eDepartment of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA. 17 18 19 20 Running title: Niche partitioning of oil degrading bacterial ecotypes 21 22 Abstract word count: 232 for abstract, 120 for importance 23 Main text word count (with Materials and Methods): 6182 24 Main text word count (without Materials and Methods): 4069 25 26 #Corresponding authors: 27 Shawn M. Doyle 28 Jason B, Sylvan 29 Department of Oceanography 30 Texas A&M University 31 Eller O&M Bldg, Rm 716 32 College Station, TX, 77843-3146 33 Tel: 979-845-5105 34 E-mail: [email protected] 35 [email protected] 36 37 38 39 40 41 42 43 44 45 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.16.994715; this version posted July 21, 2020. -
Microbial Community Composition of Deep-Sea Corals from the Red Sea
www.nature.com/scientificreports OPEN Microbial community composition of deep-sea corals from the Red Sea provides insight into functional Received: 30 November 2016 Accepted: 13 February 2017 adaption to a unique environment Published: 17 March 2017 Till Röthig*, Lauren K. Yum*, Stephan G. Kremb, Anna Roik & Christian R. Voolstra Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L−1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment. A growing number of studies support the notion that bacteria associated with multicellular hosts provide impor- tant functions related to metabolism, immunity, and environmental adaptation (among others)1. -
A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.” Edited by Jean-François Humbert
A Novel Analysis Method for Paired- Sample Microbial Ecology Experiments The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Olesen, Scott W., Suhani Vora, Stephen M. Techtmann, Julian L. Fortney, Juan R. Bastidas-Oyanedel, Jorge Rodríguez, Terry C. Hazen, and Eric J. Alm. “A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.” Edited by Jean-François Humbert. PLoS ONE 11, no. 5 (May 6, 2016): e0154804. As Published http://dx.doi.org/10.1371/journal.pone.0154804 Publisher Public Library of Science Version Final published version Citable link http://hdl.handle.net/1721.1/109394 Terms of Use Creative Commons CC0 Detailed Terms https://creativecommons.org/publicdomain/zero/1.0/ RESEARCH ARTICLE A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments Scott W. Olesen1, Suhani Vora1, Stephen M. Techtmann2, Julian L. Fortney2,3, Juan R. Bastidas-Oyanedel4, Jorge Rodríguez4, Terry C. Hazen2,3, Eric J. Alm1* 1 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America, 2 Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States of America, 3 Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America, 4 Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, Abu Dhabi, UAE a11111 * [email protected] Abstract Many microbial ecology experiments use sequencing data to measure a community’s OPEN ACCESS response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the Citation: Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodríguez J, et experimental unit.