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Spatio-Temporal Study of Microbiology in the Stratified Oxic-Hypoxic-Euxinic, Freshwater- To-Hypersaline Ursu Lake
Spatio-temporal insights into microbiology of the freshwater-to- hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake Baricz, A., Chiriac, C. M., Andrei, A-., Bulzu, P-A., Levei, E. A., Cadar, O., Battes, K. P., Cîmpean, M., enila, M., Cristea, A., Muntean, V., Alexe, M., Coman, C., Szekeres, E. K., Sicora, C. I., Ionescu, A., Blain, D., O’Neill, W. K., Edwards, J., ... Banciu, H. L. (2020). Spatio-temporal insights into microbiology of the freshwater-to- hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake. Environmental Microbiology. https://doi.org/10.1111/1462-2920.14909, https://doi.org/10.1111/1462-2920.14909 Published in: Environmental Microbiology Document Version: Peer reviewed version Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2019 Wiley. This work is made available online in accordance with the publisher’s policies. Please refer to any applicable terms of use of the publisher. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. -
A Noval Investigation of Microbiome from Vermicomposting Liquid Produced by Thai Earthworm, Perionyx Sp
International Journal of Agricultural Technology 2021Vol. 17(4):1363-1372 Available online http://www.ijat-aatsea.com ISSN 2630-0192 (Online) A novel investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1 Kraisittipanit, R.1,2, Tancho, A.2,3, Aumtong, S.3 and Charerntantanakul, W.1* 1Program of Biotechnology, Faculty of Science, Maejo University, Chiang Mai, Thailand; 2Natural Farming Research and Development Center, Maejo University, Chiang Mai, Thailand; 3Faculty of Agricultural Production, Maejo University, Thailand. Kraisittipanit, R., Tancho, A., Aumtong, S. and Charerntantanakul, W. (2021). A noval investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1. International Journal of Agricultural Technology 17(4):1363-1372. Abstract The whole microbiota structure in vermicomposting liquid derived from Thai earthworm, Perionyx sp. 1 was estimated. It showed high richness microbial species and belongs to 127 species, separated in 3 fungal phyla (Ascomycota, Basidiomycota, Mucoromycota), 1 Actinomycetes and 16 bacterial phyla (Acidobacteria, Armatimonadetes, Bacteroidetes, Balneolaeota, Candidatus, Chloroflexi, Deinococcus, Fibrobacteres, Firmicutes, Gemmatimonadates, Ignavibacteriae, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia). The OTUs data analysis revealed the highest taxonomic abundant ratio in bacteria and fungi belong to Proteobacteria (70.20 %) and Ascomycota (5.96 %). The result confirmed that Perionyx sp. 1 -
B6038927fab52adf363dba598a6
Hindawi Archaea Volume 2018, Article ID 9319345, 12 pages https://doi.org/10.1155/2018/9319345 Research Article Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment Xiu-lu Lang, Xiang Chen , Ai-ling Xu, Zhi-wen Song , Xin Wang, and He-bing Wang School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266033, China Correspondence should be addressed to Zhi-wen Song; [email protected] Received 4 May 2018; Accepted 22 July 2018; Published 16 October 2018 Academic Editor: Jin Li Copyright © 2018 Xiu-lu Lang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. -
Biogeochemistry of a Saline, Alkaline, Terminal Lake Ecosystem In
UNLV Theses, Dissertations, Professional Papers, and Capstones 8-1-2016 Biogeochemistry of a Saline, Alkaline, Terminal Lake Ecosystem in Transition; Walker Lake, Nevada Katherine Lynn Willever University of Nevada, Las Vegas, [email protected] Follow this and additional works at: https://digitalscholarship.unlv.edu/thesesdissertations Part of the Fresh Water Studies Commons, and the Microbiology Commons Repository Citation Willever, Katherine Lynn, "Biogeochemistry of a Saline, Alkaline, Terminal Lake Ecosystem in Transition; Walker Lake, Nevada" (2016). UNLV Theses, Dissertations, Professional Papers, and Capstones. 2817. https://digitalscholarship.unlv.edu/thesesdissertations/2817 This Thesis is brought to you for free and open access by Digital Scholarship@UNLV. It has been accepted for inclusion in UNLV Theses, Dissertations, Professional Papers, and Capstones by an authorized administrator of Digital Scholarship@UNLV. For more information, please contact [email protected]. BIOGEOCHEMISTRY OF A SALINE, ALKALINE, TERMINAL LAKE ECOSYSTEM IN TRANSITION; WALKER LAKE, NEVADA, USA By Katherine Lynn Willever Bachelor of Science — Biological Sciences York College of Pennsylvania 2012 A thesis submitted in partial fulfillment of the requirements for the Master of Science — Biological Sciences School of Life Sciences College of Sciences The Graduate College University of Nevada, Las Vegas August 2016 Copyright 2016 by Katherine L. Willever All Rights Reserved Thesis Approval The Graduate College The University of Nevada, Las Vegas July 14, 2016 This thesis prepared by Katherine Lynn Willever entitled Biogeochemistry of a Saline, Alkaline, Terminal Lake Ecosystem in Transition; Walker Lake, Nevada, USA is approved in partial fulfillment of the requirements for the degree of Master of Science – Biological Sciences School of Life Sciences Brian P. -
Egibacter Rhizosphaerae Gen. Nov., Sp. Nov., an Obligately Halophilic, Facultatively Alkaliphilic Actinobacterium and Proposal of Egibaceraceae Fam
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 283–289 DOI 10.1099/ijsem.0.000713 Egibacter rhizosphaerae gen. nov., sp. nov., an obligately halophilic, facultatively alkaliphilic actinobacterium and proposal of Egibaceraceae fam. nov. and Egibacterales ord. nov. Yong-Guang Zhang,1 Hong-Fei Wang,1,2 Ling-Ling Yang,3 Xing-Kui Zhou,4 Xiao-Yang Zhi,3 Yan-Qing Duan,4 Min Xiao,5 Yuan-Ming Zhang1 and Wen-Jun Li1,3,5 Correspondence 1Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Wen-Jun Li Geography, Chinese Academy of Sciences, U¨ ru´mqi 830011, PR China [email protected] or 2College of Life Science, Liaoning Normal University, Dalian, 116029, PR China [email protected] 3Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China 4China Tobacco Yunnan Industrial Co., Ltd, Kunming 650231, PR China 5State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China A novel obligately halophilic, facultatively alkaliphilic actinobacterium, designated EGI 80759T,was isolated from the rhizosphere of Tamarix hispida Willd, Karamay, Xinjiang province, north-west China. Cells of strain EGI 80759T were Gram-stain-positive, non-motile and non-endospore-forming rods. Strain EGI 80759T showed obligately halophilic growth with a tolerance to 8–25 % (w/v) NaCl (optimum growth at 10–12 %, w/v) and facultatively alkaliphilic growth within the pH range 7.0–11.0 (optimum growth at pH 9.0–10.0). Cell-wall hydrolysates of the isolate contained meso- diaminopimelic acid (peptidoglycan type A1c), with glucose, glucosamine, ribose and mannose as the major sugars. -
And Allochthonous-Like Dissolved Organic Matter
fmicb-10-02579 November 5, 2019 Time: 17:10 # 1 ORIGINAL RESEARCH published: 07 November 2019 doi: 10.3389/fmicb.2019.02579 Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter Elias Broman1,2*, Eero Asmala3, Jacob Carstensen4, Jarone Pinhassi1 and Mark Dopson1 1 Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden, 2 Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden, 3 Tvärminne Zoological Station, University of Helsinki, Hanko, Finland, 4 Department of Bioscience, Aarhus University, Roskilde, Denmark Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water Edited by: temperatures, DOM from both allochthonous and autochthonous sources is projected Eva Ortega-Retuerta, to increase. As these transformations are largely regulated by bacteria, we analyzed Laboratoire d’Océanographie microbial community structure data in relation to a 6-month long time-series dataset of Microbienne (LOMIC), France DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results Reviewed by: Craig E. Nelson, showed that the microbial community composition in the outer estuary (closer to the University of Hawai‘i at Manoa,¯ sea) was largely associated with salinity and nutrients, while the inner estuary formed United States Scott Michael Gifford, two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM University of North Carolina at Chapel characteristics. In contrast, the microbial community composition in the streams was Hill, United States found to be mainly associated with allochthonous DOM characteristics. -
Thermophilic and Alkaliphilic Actinobacteria: Biology and Potential Applications
REVIEW published: 25 September 2015 doi: 10.3389/fmicb.2015.01014 Thermophilic and alkaliphilic Actinobacteria: biology and potential applications L. Shivlata and Tulasi Satyanarayana * Department of Microbiology, University of Delhi, New Delhi, India Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive Edited by: compounds, which find multifarious applications. Wen-Jun Li, Sun Yat-Sen University, China Keywords: Actinobacteria, thermophiles, alkaliphiles, polyextremophiles, bioactive compounds, enzymes Reviewed by: Erika Kothe, Friedrich Schiller University Jena, Introduction Germany Hongchen Jiang, The phylum Actinobacteria is one of the most dominant phyla in the bacteria domain (Ventura Miami University, USA et al., 2007), that comprises a heterogeneous Gram-positive and Gram-variable genera. The Qiuyuan Huang, phylum also includes a few Gram-negative species such as Thermoleophilum sp. (Zarilla and Miami University, USA Perry, 1986), Gardenerella vaginalis (Gardner and Dukes, 1955), Saccharomonospora -
UNIVERSITY of CALIFORNIA SANTA CRUZ Ecology and Molecular Genetics of Anoxygenic Photosynthetic Arsenite Oxidation by Arxa A
UNIVERSITY OF CALIFORNIA SANTA CRUZ Ecology and molecular genetics of anoxygenic photosynthetic arsenite oxidation by arxA A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in MICROBIOLOGY AND ENVIRONMENTAL TOXICOLOGY by Jaime Hernandez-Maldonado June 2017 Dissertation of Jaime Hernandez-Maldonado is approved: ____________________________________ Professor Chad W. Saltikov ____________________________________ Professor. Ronald S. Oremland ____________________________________ Professor Jonathan P. Zehr ____________________________________ Professor Karen M. Ottemann ____________________________________ Tyrus Miller Vie Provost and Dean of Graduate Studies Copyright @ by Jaime Hernandez-Maldonado 2017 Table of contents List of figures .……………………..….………………….…...……..…………...… iv Abstract .……...…….……...……….….………………….……...……..………...... vi Dedication …...…....………………….….………………………...………...…..… viii Acknowledgements ...……………….….………………………..….…..………...... ix Chapter 1: Thesis overview ………...……….……….…………..……..…………... 1 Chapter 1: References ...…..…...…….….………………………..…….......……….. 7 Chapter 2: Microbial arsenic review ………………………………………………... 9 Chapter 2: References …………………….……………………….……..………... 30 Chapter 3: Microbial mediated light dependent arsenic cycle .…………….…….... 40 Chapter 3: References …………………….……………………….……..………... 77 Chapter 4: The genetic basis of anoxygenic photosynthetic arsenite oxidation …... 82 Chapter 4: References …………………….……………………….……..………... 91 Chapter 5: Comparative genomics -
Characterizing the Fecal Microbiota and Resistome of Corvus Brachyrhynchos (American Crow) in Fresno and Davis, California
ABSTRACT CHARACTERIZING THE FECAL MICROBIOTA AND RESISTOME OF CORVUS BRACHYRHYNCHOS (AMERICAN CROW) IN FRESNO AND DAVIS, CALIFORNIA American Crows are common across the United States, well adapted to human habitats, and congregate in large winter roosts. We aimed to characterize the bacterial community (microbiota) of the crows’ feces, with an emphasis on human pathogens. The antibiotic resistance (AR) of the bacteria was analyzed to gain insight into the role crows may play in the spread of AR genes. Through 16S rRNA gene and metagenomic sequencing, the microbiota and antibiotic resistance genes (resistome) were determined. The core microbiota (taxa found in all crows) contained Lactobacillales (22.2% relative abundance), Enterobacteriales (21.9%) and Pseudomonadales (13.2%). Among the microbiota were human pathogens including Legionella, Camplycobacter, Staphylococcus, Streptococcus, and Treponema, among others. The Fresno, California crows displayed antibiotic resistance genes for multiple drug efflux pumps, macrolide-lincosamide- streptogramin (MLS), and more. Ubiquitous, urban wildlife like the American Crow may play a role in the spread of AR pathogens to the environment and human populations. Rachel Lee Nelson August 2018 CHARACTERIZING THE FECAL MICROBIOTA AND RESISTOME OF CORVUS BRACHYRHYNCHOS (AMERICAN CROW) IN FRESNO AND DAVIS, CALIFORNIA by Rachel Lee Nelson A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Biology in the College of Science and Mathematics California State University, Fresno August 2018 APPROVED For the Department of Biology: We, the undersigned, certify that the thesis of the following student meets the required standards of scholarship, format, and style of the university and the student's graduate degree program for the awarding of the master's degree. -
And Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments
Originally published as: Genderjahn, S., Alawi, M., Mangelsdorf, K., Horn, F., Wagner, D. (2018): Desiccation- and Saline- Tolerant Bacteria and Archaea in Kalahari Pan Sediments. - Frontiers in Microbiology, 9. DOI: http://doi.org/10.3389/fmicb.2018.02082 fmicb-09-02082 September 19, 2018 Time: 14:22 # 1 ORIGINAL RESEARCH published: 20 September 2018 doi: 10.3389/fmicb.2018.02082 Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments Steffi Genderjahn1,2*, Mashal Alawi1, Kai Mangelsdorf2, Fabian Horn1 and Dirk Wagner1,3 1 GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany, 2 GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, Potsdam, Germany, 3 Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany More than 41% of the Earth’s land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea Edited by: Jesse G. Dillon, in semi-arid, saline, and low-carbon environments. Many of the observed taxa are California State University, Long halophilic and adapted to water-limiting conditions. -
A Metagenomics Roadmap to the Uncultured Genome Diversity in Hypersaline Soda Lake Sediments Charlotte D
Vavourakis et al. Microbiome (2018) 6:168 https://doi.org/10.1186/s40168-018-0548-7 RESEARCH Open Access A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments Charlotte D. Vavourakis1 , Adrian-Stefan Andrei2†, Maliheh Mehrshad2†, Rohit Ghai2, Dimitry Y. Sorokin3,4 and Gerard Muyzer1* Abstract Background: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages. Results: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L−1. The recovered 16S rRNA gene sequences were mostly from Bacteria,evenin the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria. -
Insight Into the Function and Evolution of the Wood–Ljungdahl Pathway in Actinobacteria
The ISME Journal https://doi.org/10.1038/s41396-021-00935-9 ARTICLE Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria 1 2 3 1 1 2 1 Jian-Yu Jiao ● Li Fu ● Zheng-Shuang Hua ● Lan Liu ● Nimaichand Salam ● Peng-Fei Liu ● Ai-Ping Lv ● 4 1 5 1 1,6 7 Geng Wu ● Wen-Dong Xian ● Qiyun Zhu ● En-Min Zhou ● Bao-Zhu Fang ● Aharon Oren ● 8,9 4 5,10,11 2 1,6 Brian P. Hedlund ● Hong-Chen Jiang ● Rob Knight ● Lei Cheng ● Wen-Jun Li Received: 21 September 2020 / Revised: 7 February 2021 / Accepted: 10 February 2021 © The Author(s), under exclusive licence to International Society for Microbial Ecology 2021 Abstract Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood–Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes – 1234567890();,: 1234567890();,: contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b 3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically.