Toluene Biodegradation in an Algal-Bacterial Airlift Photobioreactor: Influence of the Biomass Concentration and the Presence Of
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Rubisco POSTER 2016 MACUB
Direct PCR Detection, Cloning, and Characterization of Bacterial RubisCO Genes from New Jersey Soils Stephanie Zapata*, Anna Gonzalez, Margarita Kulko, Ryan Kim, Theranda Jashari, Aidan Holwerda, Tina Choe, and Luis Jimenez Department of Biology and Horticulture, Bergen Community College, Paramus, New Jersey, USA Abstract Materials and Methods Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by PCR detection of bacterial RubisCO genes in soil the abbreviation RubisCO, is an enzyme involved in the first major step of Cloning libraries carbon fixation, a process by which atmospheric carbon dioxide is The DNA fragments from the PCR amplification of RubisCO converted by bacteria to energy-rich molecules such as glucose. genes were cloned using plasmid pCR®4-TOPO (Life Microbial DNA was extracted from temperate soils using the Zymo Technologies, Thermo Fisher Scientific, Grand Island, NY) Microbe DNA MiniPrep protocol. RubisCo gene sequences were according to the manufacturer’s instructions. Transformations amplified by PCR using degenerate primers cbbLG1F and cbbLG1R. were performed using Mix and Go Competent E. coli strains DNA fragments of approximately 800 base pair were detected in all positive soil samples. Clone libraries were constructed with the amplified (Zymo Research, Irvine, CA). White colonies grown on Luria ç800 bp DNA fragments by ligating the detected fragments with vector pCR®4- Bertani (LB) Agar with ampicillin (50 ug/ml) were transferred to LB TOPO. Transformations were performed using competent Mix and Go broth containing ampicillin (50 ug/ml). Samples were incubated Escherichia coli cells. Plasmids were isolated from each clone using the overnight at 37°C. Zyppy Plasmid Miniprep and inserts were screened by PCR using M13 Plasmids were isolated from each clone using the Zyppy Plasmid DNA primers. -
Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas
Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively). -
The Different Dietary Sugars Modulate The
Wang et al. BMC Microbiology (2020) 20:61 https://doi.org/10.1186/s12866-020-01726-6 RESEARCH ARTICLE Open Access The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering Hongfang Wang, Chunlei Liu, Zhenguo Liu, Ying Wang, Lanting Ma and Baohua Xu* Abstract Background: The health of honeybee colonies is critical for bee products and agricultural production, and colony health is closely associated with the bacteria in the guts of honeybees. Although colony loss in winter is now the primary restriction in beekeeping, the effects of different sugars as winter food on the health of honeybee colonies are not well understood. Therefore, in this study, the influence of different sugar diets on honeybee gut bacteria during overwintering was examined. Results: The bacterial communities in honeybee midguts and hindguts before winter and after bees were fed honey, sucrose, and high-fructose syrup as winter-food were determined by targeting the V3-V4 region of 16S rDNA using the Illumina MiSeq platform. The dominant microbiota in honeybee guts were the phyla Proteobacteria (63.17%), Firmicutes (17.61%; Lactobacillus, 15.91%), Actinobacteria (4.06%; Bifidobacterium, 3.34%), and Bacteroidetes (1.72%). The dominant taxa were conserved and not affected by season, type of overwintering sugar, or spatial position in the gut. However, the relative abundance of the dominant taxa was affected by those factors. In the midgut, microbial diversity of the sucrose group was higher than that of the honey and high-fructose syrup groups, but in the hindgut, microbial diversity of the honey and high-fructose groups was higher than that in the sucrose group. -
1 Horizontal Gene Transfer of a Unique Nif Island Drives Convergent Evolution of Free-Living
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.03.429501; this version posted February 3, 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 Horizontal gene transfer of a unique nif island drives convergent evolution of free-living 2 N2-fixing Bradyrhizobium 3 4 Jinjin Tao^, Sishuo Wang^, Tianhua Liao, Haiwei Luo* 5 6 Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of 7 Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 8 9 ^These authors contribute equally to this work. 10 11 *Corresponding author: 12 Haiwei Luo 13 School of Life Sciences, The Chinese University of Hong Kong 14 Shatin, Hong Kong SAR 15 Phone: (+852) 39436121 16 E-mail: [email protected] 17 18 Running Title: Free-living Bradyrhizobium evolution 19 Keywords: free-living Bradyrhizobium, nitrogen fixation, lifestyle, HGT 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.03.429501; this version posted February 3, 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. 20 Summary 21 The alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that 22 nodulate legumes, supported by the nif and nod gene clusters. -
Characterization of Bacterial Communities Associated
www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5. -
Phylogenetic and Functional Characterization of Symbiotic Bacteria in Gutless Marine Worms (Annelida, Oligochaeta)
Phylogenetic and functional characterization of symbiotic bacteria in gutless marine worms (Annelida, Oligochaeta) Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften -Dr. rer. nat.- dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Anna Blazejak Oktober 2005 Die vorliegende Arbeit wurde in der Zeit vom März 2002 bis Oktober 2005 am Max-Planck-Institut für Marine Mikrobiologie in Bremen angefertigt. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: Prof. Dr. Ulrich Fischer Tag des Promotionskolloquiums: 22. November 2005 Contents Summary ………………………………………………………………………………….… 1 Zusammenfassung ………………………………………………………………………… 2 Part I: Combined Presentation of Results A Introduction .…………………………………………………………………… 4 1 Definition and characteristics of symbiosis ...……………………………………. 4 2 Chemoautotrophic symbioses ..…………………………………………………… 6 2.1 Habitats of chemoautotrophic symbioses .………………………………… 8 2.2 Diversity of hosts harboring chemoautotrophic bacteria ………………… 10 2.2.1 Phylogenetic diversity of chemoautotrophic symbionts …………… 11 3 Symbiotic associations in gutless oligochaetes ………………………………… 13 3.1 Biogeography and phylogeny of the hosts …..……………………………. 13 3.2 The environment …..…………………………………………………………. 14 3.3 Structure of the symbiosis ………..…………………………………………. 16 3.4 Transmission of the symbionts ………..……………………………………. 18 3.5 Molecular characterization of the symbionts …..………………………….. 19 3.6 Function of the symbionts in gutless oligochaetes ..…..…………………. 20 4 Goals of this thesis …….………………………………………………………….. -
Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights Into the Origin and Distribution of Nitrogen Fixation Across Bacteria and Archaea
microorganisms Article Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea Amrit Koirala 1 and Volker S. Brözel 1,2,* 1 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA; [email protected] 2 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa * Correspondence: [email protected]; Tel.: +1-605-688-6144 Abstract: The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico predic- tion of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocu- Citation: Koirala, A.; Brözel, V.S. mented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes Phylogeny of Nitrogenase Structural and Assembly Components Reveals are currently supported by biochemical evidence of diazotrophy. -
Monitoring of Bacterial Communities in a Phytoremediation Plant for the Decontamination of Polluted Marine Sediments”
Research Doctorate School in Biological and Molecular Sciences Cycle XXV “Monitoring of bacterial communities in a phytoremediation plant for the decontamination of polluted marine sediments” Candidate: Carolina Chiellini Supervisors: Dott. Giulio Petroni Prof. Ing. Renato Iannelli 2013 BIO/05 INDEX SUMMARY .......................................................................................................................................................... 1 RIASSUNTO ........................................................................................................................................................ 3 1 INTRODUCTION: AN OVERVIEW ON THE TOPIC ........................................................................... 5 1.1 THE NORMATIVE CONCERNING DREDGED SEDIMENTS ........................................................................ 7 1.1.1 The European scenario ......................................................................................................................... 7 1.1.2 The Italian scenario ................................................................................................................................ 9 1.2 THE PROBLEM OF DREDGED SEDIMENTS ................................................................................................ 12 1.2.1 Types and sources of pollutants in marine sediments .............................................................. 12 1.2.2 How to treat polluted sediments ...................................................................................................... -
Research Collection
Research Collection Doctoral Thesis Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil Author(s): Ragot, Sabine A. Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010630685 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO.23284 DEVELOPMENT AND APPLICATION OF MOLECULAR TOOLS TO INVESTIGATE MICROBIAL ALKALINE PHOSPHATASE GENES IN SOIL A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by SABINE ANNE RAGOT Master of Science UZH in Biology born on 25.02.1987 citizen of Fribourg, FR accepted on the recommendation of Prof. Dr. Emmanuel Frossard, examiner PD Dr. Else Katrin Bünemann-König, co-examiner Prof. Dr. Michael Kertesz, co-examiner Dr. Claude Plassard, co-examiner 2016 Sabine Anne Ragot: Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil, c 2016 ⃝ ABSTRACT Phosphatase enzymes play an important role in soil phosphorus cycling by hydrolyzing organic phosphorus to orthophosphate, which can be taken up by plants and microorgan- isms. PhoD and PhoX alkaline phosphatases and AcpA acid phosphatase are produced by microorganisms in response to phosphorus limitation in the environment. In this thesis, the current knowledge of the prevalence of phoD and phoX in the environment and of their taxonomic distribution was assessed, and new molecular tools were developed to target the phoD and phoX alkaline phosphatase genes in soil microorganisms. -
Identification of Culturable Endophytes in 'Champaka' Pineapple Grown In
Vol. 8(26), pp. 3422-3430, 11 July, 2013 DOI: 10.5897/AJAR2012.2308 African Journal of Agricultural ISSN 1991-637X ©2013 Academic Journals Research http://www.academicjournals.org/AJAR Full Length Research Paper Identification of culturable endophytes in ‘Champaka’ pineapple grown in an organic system Olmar Baller Weber1*, Sandy Sampaio Videira2 and Jean Luiz Simões de Araújo2 1Embrapa Tropical Agroindustry, Dra. Sara Mesquita, 2270, Pici, 60511-110, Fortaleza, Ceará, Brazil. 2Embrapa Agrobiology, BR 465, km07, 23890-000, Seropédica, Rio de Janeiro, Brazil. Accepted 26 March, 2013 The objective of the study was to characterize culturable diazotrophic endophytic bacteria from ‘Champaka’ pineapple plants during the fruiting period in an organic system. Micropropagated plants were inoculated with the diazotrophic endophytic bacterium, strain AB 219a, during acclimatization phase. In the field, the plants were fertilized with different dosages and sources of organic compost. After 17 months of field cultivation, roots and stems were collected for the isolation of endophytes, DNA extraction, 16S rDNA amplification and molecular analysis. A total of nine bacterial groups were identified, and species Burkholderia silvatlantica, Azorhizobium caulinodans, Pantoea eucrina, Erwinia sp. and unculturable bacterium occurred in inoculated plants. In contrast, non-inoculated plants were associated endophytes related to Burkholderia cenocepacia, Azospirillum brasilense, Enterobacter oryzae, Erwinia sp. and Sphingobium yanoikuyae. Segments of 360 base pair from nifH gene were amplified from representative endophytes within identified species, except from the Pantoea eucrina strain AB 295. 16S rDNA phylogenetic analysis of endophytes isolated from inoculated plants revealed distinct families: Xanthobacteraceae, Burkholderiaceae and Enterobacteriaceae; and from non- inoculated plants, Rodospirillaceae and Sphingomonadaceae families were also identified. -
A Microbiotic Survey of Lichen-Associated Bacteria Reveals a New Lineage from the Rhizobiales
SYMBIOSIS (2009) 49, 163–180 ©Springer Science+Business Media B.V. 2009 ISSN 0334-5114 A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales Brendan P. Hodkinson* and François Lutzoni Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA, Tel. +1-443-340-0917, Fax. +1-919-660-7293, Email. [email protected] (Received June 10, 2008; Accepted November 5, 2009) Abstract This study uses a set of PCR-based methods to examine the putative microbiota associated with lichen thalli. In initial experiments, generalized oligonucleotide-primers for the 16S rRNA gene resulted in amplicon pools populated almost exclusively with fragments derived from lichen photobionts (i.e., Cyanobacteria or chloroplasts of algae). This effectively masked the presence of other lichen-associated prokaryotes. In order to facilitate the study of the lichen microbiota, 16S ribosomal oligonucleotide-primers were developed to target Bacteria, but exclude sequences derived from chloroplasts and Cyanobacteria. A preliminary microbiotic survey of lichen thalli using these new primers has revealed the identity of several bacterial associates, including representatives of the extremophilic Acidobacteria, bacteria in the families Acetobacteraceae and Brucellaceae, strains belonging to the genus Methylobacterium, and members of an undescribed lineage in the Rhizobiales. This new lineage was investigated and characterized through molecular cloning, and was found to be present in all examined lichens that are associated with green algae. There is evidence to suggest that members of this lineage may both account for a large proportion of the lichen-associated bacterial community and assist in providing the lichen thallus with crucial nutrients such as fixed nitrogen. -
Biofilm Composition and Threshold Concentration for Growth Of
PUBLIC AND ENVIRONMENTAL HEALTH MICROBIOLOGY crossm Biofilm Composition and Threshold Concentration for Growth of Legionella pneumophila on Surfaces Exposed to Flowing Warm Tap Water without Disinfectant Downloaded from Dick van der Kooij,a Geo L. Bakker,b Ronald Italiaander,a Harm R. Veenendaal,a Bart A. Wullingsa KWR Watercycle Research Institute, Nieuwegein, the Netherlandsa; Vitens NV, Zwolle, the Netherlandsb ABSTRACT Legionella pneumophila in potable water installations poses a potential Received 1 October 2016 Accepted 13 health risk, but quantitative information about its replication in biofilms in relation http://aem.asm.org/ to water quality is scarce. Therefore, biofilm formation on the surfaces of glass and December 2016 Accepted manuscript posted online 6 chlorinated polyvinyl chloride (CPVC) in contact with tap water at 34 to 39°C was in- January 2017 vestigated under controlled hydraulic conditions in a model system inoculated with Citation van der Kooij D, Bakker GL, biofilm-grown L. pneumophila. The biofilm on glass (average steady-state concen- Italiaander R, Veenendaal HR, Wullings BA. tration, 23 Ϯ 9 pg ATP cmϪ2) exposed to treated aerobic groundwater (0.3 mg C 2017. Biofilm composition and threshold concentration for growth of Legionella Ϫ1 Ϫ1 liter ;1 g assimilable organic carbon [AOC] liter ) did not support growth of the pneumophila on surfaces exposed to flowing organism, which also disappeared from the biofilm on CPVC (49 Ϯ 9 pg ATP cmϪ2) warm tap water without disinfectant. Appl Ϫ2 Environ Microbiol 83:e02737-16. https:// after initial growth. L. pneumophila attained a level of 4.3 log CFU cm in the bio- on February 16, 2017 by guest doi.org/10.1128/AEM.02737-16.