Activities and Prevalence of Proteobacteria Members Colonizing Echinacea Purpurea Fully Account for Macro- Phage Activation Exhibited by Extracts of This Botanical
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Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas Sp
microorganisms Article Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5 Karel Kopejtka 1 , Yonghui Zeng 1,2, David Kaftan 1,3 , Vadim Selyanin 1, Zdenko Gardian 3,4 , Jürgen Tomasch 5,† , Ruben Sommaruga 6 and Michal Koblížek 1,* 1 Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 81 Tˇreboˇn,Czech Republic; [email protected] (K.K.); [email protected] (Y.Z.); [email protected] (D.K.); [email protected] (V.S.) 2 Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark 3 Faculty of Science, University of South Bohemia, 370 05 Ceskˇ é Budˇejovice,Czech Republic; [email protected] 4 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Ceskˇ é Budˇejovice,Czech Republic 5 Research Group Microbial Communication, Technical University of Braunschweig, 38106 Braunschweig, Germany; [email protected] 6 Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria; [email protected] * Correspondence: [email protected] † Present Address: Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, 38106 Braunschweig, Germany. Abstract: An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 Citation: Kopejtka, K.; Zeng, Y.; (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Ty- Kaftan, D.; Selyanin, V.; Gardian, Z.; rolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic Tomasch, J.; Sommaruga, R.; Koblížek, analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas M. Characterization of the Aerobic and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Anoxygenic Phototrophic Bacterium Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). -
Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China
Article Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China Xiaoping Zhang 1, Zheke Zhong 1,*, Xu Gai 1, Jiafu Ying 2, Weifen Li 2, Xuhua Du 1, Fangyuan Bian 1 and Chuanbao Yang 1 1 China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou 310012, China; [email protected] (X.Z.); [email protected] (X.G.); [email protected] (X.D.); [email protected] (F.B.); [email protected] (C.Y.) 2 College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; [email protected] (J.Y.); wfl[email protected] (W.L.) * Correspondence: [email protected]; Tel.: +86-0571-88860734 Received: 25 January 2019; Accepted: 25 February 2019; Published: 1 March 2019 Abstract: Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. In the present study, we compared the leaf-associated bacterial and fungal communities of moso bamboo (Phyllostachys edulis) in a BCF system and an adjacent moso bamboo forest (MBF). The results showed that Cyanobacteria and Ascomycota were the predominant microbial phyla associated with bamboo leaves. Chicken farming under the bamboo forest significantly increased the bacterial and fungal alpha diversity (observed operational taxonomic units (OTUs) and Simpson’s index) associated with bamboo leaves. Principal components analysis (PCoA) further confirmed the shifts in the bacterial and fungal communities caused by chicken farming. -
Bacterial Dissimilation of Citric Acid Carl Robert Brewer Iowa State College
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1939 Bacterial dissimilation of citric acid Carl Robert Brewer Iowa State College Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Microbiology Commons Recommended Citation Brewer, Carl Robert, "Bacterial dissimilation of citric acid " (1939). Retrospective Theses and Dissertations. 13227. https://lib.dr.iastate.edu/rtd/13227 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Brol<en or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. -
Comparative Genomic Analysis of Nine Sphingobium Strains: Insights Into
Verma et al. BMC Genomics 2014, 15:1014 http://www.biomedcentral.com/1471-2164/15/1014 RESEARCH ARTICLE Open Access Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways Helianthous Verma1†, Roshan Kumar1†, Phoebe Oldach1, Naseer Sangwan1, Jitendra P Khurana2, Jack A Gilbert3,4 and Rup Lal1* Abstract Background: Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6). Results: Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. -
Feasibility of Bacterial Probiotics for Mitigating Coral Bleaching
Feasibility of bacterial probiotics for mitigating coral bleaching Ashley M. Dungan ORCID: 0000-0003-0958-2177 Thesis submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy September 2020 School of BioSciences The University of Melbourne Declaration This is to certify that: 1. This thesis comprises only of my original work towards the PhD, except where indicated in the preface. 2. Due acknowledgements have been made in the text to all other material used. 3. The thesis is under 100,000 words, exclusive of tables, bibliographies, and appendices. Signed: Date: 11 September 2020 ii General abstract Given the increasing frequency of climate change driven coral mass bleaching and mass mortality events, intervention strategies aimed at enhancing coral thermal tolerance (assisted evolution) are urgently needed in addition to strong action to reduce carbon emissions. Without such interventions, coral reefs will not survive. The seven chapters in my thesis explore the feasibility of using a host-sourced bacterial probiotic to mitigate bleaching starting with a history of reactive oxygen species (ROS) as a biological explanation for bleaching (Chapter 1). In part because of the difficulty to experimentally manipulate corals post-bleaching, I use Great Barrier Reef (GBR)-sourced Exaiptasia diaphana as a model organism for this system, which I describe in Chapter 2. The comparatively high levels of physiological and genetic variability among GBR anemone genotypes make these animals representatives of global E. diaphana diversity and thus excellent model organisms. The ‘oxidative stress theory for coral bleaching’ provides rationale for the development of a probiotic with a high free radical scavenging ability. -
Unlocking the Genomic Taxonomy of the Prochlorococcus Collective
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.980698; this version posted March 11, 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 4.0 International license. Unlocking the genomic taxonomy of the Prochlorococcus collective Diogo Tschoeke1#, Livia Vidal1#, Mariana Campeão1, Vinícius W. Salazar1, Jean Swings1,2, Fabiano Thompson1*, Cristiane Thompson1* 1Laboratory of Microbiology. SAGE-COPPE and Institute of Biology. Federal University of Rio de Janeiro. Rio de Janeiro. Brazil. Av. Carlos Chagas Fo 373, CEP 21941-902, RJ, Brazil. 2Laboratory of Microbiology, Ghent University, Gent, Belgium. *Corresponding authors: E-mail: [email protected] , [email protected] Phone no.: +5521981041035, +552139386567 #These authors contributed equally. ABSTRACT 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.980698; this version posted March 11, 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 4.0 International license. Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. -
Bacterial Community Structure in High-Arctic Snow and Freshwater As Revealed by Pyrosequencing of 16S Rrna Genes and Cultivation Annette K
RESEARCH/REVIEW ARTICLE Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation Annette K. Møller,1 Ditte A. Søborg,1 Waleed Abu Al-Soud,2 Søren J. Sørensen2 & Niels Kroer1 1 Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark 2 Department of Biology, University of Copenhagen, Sølvgade 83H, DK-1307 K Copenhagen, Denmark Keywords Abstract Taxonomic diversity; microbial assemblages; bacterial density; DOC. The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA Correspondence genes and 16S rRNA gene sequencing of cultivated isolates. Both the Niels Kroer, pyrosequence and cultivation data indicated that the phylogenetic composition Department of Environmental Science, of the microbial assemblages was different within the snow layers and between Aarhus University, snow and freshwater. The highest diversity was seen in snow. In the middle Frederiksborgvej 399, and top snow layers, , and dominated, DK-4000 Roskilde, Denmark. Proteobacteria Bacteroidetes Cyanobacteria E-mail: [email protected] although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacter- oidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Deep Divergence and Rapid Evolutionary Rates in Gut-Associated Acetobacteraceae of Ants Bryan P
Brown and Wernegreen BMC Microbiology (2016) 16:140 DOI 10.1186/s12866-016-0721-8 RESEARCH ARTICLE Open Access Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants Bryan P. Brown1,2 and Jennifer J. Wernegreen1,2* Abstract Background: Symbiotic associations between gut microbiota and their animal hosts shape the evolutionary trajectories of both partners. The genomic consequences of these relationships are significantly influenced by a variety of factors, including niche localization, interaction potential, and symbiont transmission mode. In eusocial insect hosts, socially transmitted gut microbiota may represent an intermediate point between free living or environmentally acquired bacteria and those with strict host association and maternal transmission. Results: We characterized the bacterial communities associated with an abundant ant species, Camponotus chromaiodes. While many bacteria had sporadic distributions, some taxa were abundant and persistent within and across ant colonies. Specially, two Acetobacteraceae operational taxonomic units (OTUs; referred to as AAB1 and AAB2) were abundant and widespread across host samples. Dissection experiments confirmed that AAB1 and AAB2 occur in C. chromaiodes gut tracts. We explored the distribution and evolution of these Acetobacteraceae OTUs in more depth. We found that Camponotus hosts representing different species and geographical regions possess close relatives of the Acetobacteraceae OTUs detected in C. chromaiodes. Phylogenetic analysis revealed that AAB1 and AAB2 join other ant associates in a monophyletic clade. This clade consists of Acetobacteraceae from three ant tribes, including a third, basal lineage associated with Attine ants. This ant-specific AAB clade exhibits a significant acceleration of substitution rates at the 16S rDNA gene and elevated AT content. -
The Coliform Kind: E. Coli and Its “Cousins” the Good, the Bad, and the Deadly
Scholars Crossing Faculty Publications and Presentations Department of Biology and Chemistry 10-3-2018 The Coliform Kind: E. coli and Its “Cousins” The Good, the Bad, and the Deadly Alan L. Gillen Liberty University, [email protected] Matthew Augusta Follow this and additional works at: https://digitalcommons.liberty.edu/bio_chem_fac_pubs Part of the Biology Commons Recommended Citation Gillen, Alan L. and Augusta, Matthew, "The Coliform Kind: E. coli and Its “Cousins” The Good, the Bad, and the Deadly" (2018). Faculty Publications and Presentations. 125. https://digitalcommons.liberty.edu/bio_chem_fac_pubs/125 This Article is brought to you for free and open access by the Department of Biology and Chemistry at Scholars Crossing. It has been accepted for inclusion in Faculty Publications and Presentations by an authorized administrator of Scholars Crossing. For more information, please contact [email protected]. The Coliform Kind: E. coli and Its “Cousins” The Good, the Bad, and the Deadly by Dr. Alan L. Gillen and Matthew Augusta on October 3, 2018 Abstract Even though some intestinal bacteria strains are pathogenic and even deadly, most coliforms strains still show evidence of being one of God’s “very good” creations. In fact, bacteria serve an intrinsic role in the colon of the human body. These bacteria aid in the early development of the immune system and stimulate up to 80% of immune cells in adults. In addition, digestive enzymes, Vitamins K and B12, are produced byEscherichia coli and other coliforms. E. coli is the best-known bacteria that is classified as coliforms. The term “coliform” name was historically attributed due to the “Bacillus coli-like” forms. -
Citrobacter Braakii
& M cal ed ni ic li a l C G f e Trivedi et al., J Clin Med Genom 2015, 3:1 o n l o a m n r DOI: 10.4172/2472-128X.1000129 i u c s o Journal of Clinical & Medical Genomics J ISSN: 2472-128X ResearchResearch Article Article OpenOpen Access Access Phenotyping and 16S rDNA Analysis after Biofield Treatment on Citrobacter braakii: A Urinary Pathogen Mahendra Kumar Trivedi1, Alice Branton1, Dahryn Trivedi1, Gopal Nayak1, Sambhu Charan Mondal2 and Snehasis Jana2* 1Trivedi Global Inc., Eastern Avenue Suite A-969, Henderson, NV, USA 2Trivedi Science Research Laboratory Pvt. Ltd., Chinar Fortune City, Hoshangabad Rd., Madhya Pradesh, India Abstract Citrobacter braakii (C. braakii) is widespread in nature, mainly found in human urinary tract. The current study was attempted to investigate the effect of Mr. Trivedi’s biofield treatment on C. braakii in lyophilized as well as revived state for antimicrobial susceptibility pattern, biochemical characteristics, and biotype number. Lyophilized vial of ATCC strain of C. braakii was divided into two parts, Group (Gr.) I: control and Gr. II: treated. Gr. II was further subdivided into two parts, Gr. IIA and Gr. IIB. Gr. IIA was analysed on day 10 while Gr. IIB was stored and analysed on day 159 (Study I). After retreatment on day 159, the sample (Study II) was divided into three separate tubes. First, second and third tube was analysed on day 5, 10 and 15, respectively. All experimental parameters were studied using automated MicroScan Walk-Away® system. The 16S rDNA sequencing of lyophilized treated sample was carried out to correlate the phylogenetic relationship of C. -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 2 Microalgae
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. 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 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley,