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Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea Across Earth’S Biomes
ARTICLES https://doi.org/10.1038/s41564-019-0510-x Corrected: Author Correction Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Simon Roux 1*, Mart Krupovic 2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz 1, Allison Sharrar5, Paula B. Matheus Carnevali 5, Jan-Fang Cheng1, Natalia N. Ivanova 1, Joseph Bondy-Denomy4,6, Kelly C. Wrighton3, Tanja Woyke 1, Axel Visel 1, Nikos C. Kyrpides1 and Emiley A. Eloe-Fadrosh 1* Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach lever- aging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. -
Toluene Biodegradation in an Algal-Bacterial Airlift Photobioreactor: Influence of the Biomass Concentration and the Presence Of
*Manuscript Click here to view linked References 1 Toluene biodegradation in an algal-bacterial airlift 1 2 2 photobioreactor: influence of the biomass concentration and 3 4 3 the presence of an organic phase 5 4 6 7 8 5 Raquel Lebrero*, Roxana Ángeles, Rebeca Pérez, Raúl Muñoz 9 10 11 12 6 Department of Chemical Engineering and Environmental Technology, University of 13 14 7 Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain. Tel. +34 983186424, Fax: 15 8 +34983423013. 16 17 9 18 19 20 10 *Corresponding author: [email protected] 21 22 11 Keywords: Airlift bioreactor, algal-bacterial photobioreactor, toluene biodegradation, 23 24 12 two-phase partitioning bioreactor 25 26 27 13 28 29 14 Abstract 30 31 32 15 The potential of algal-bacterial symbiosis for off-gas abatement was investigated for the first 33 16 time by comparatively evaluating the performance of a bacterial (CB) and an algal-bacterial 34 35 17 (PB) airlift bioreactors during the treatment of a 6 g m-3 toluene laden air emission. The 36 37 18 influence of biomass concentration and of the addition of a non-aqueous phase was also 38 19 investigated. A poor and fluctuating performance was recorded during the initial stages of the 39 40 20 experiment, which was attributed to the low biomass concentration present in both reactors and 41 42 21 to the accumulation of toxic metabolites. In this sense, an increase in the dilution rate from 0.23 43 22 to 0.45 d-1 and in biomass concentration from ~1 to ~5 g L-1 resulted in elimination capacities 44 45 23 (ECs) of 300 g m-3 h-1 (corresponding to removal efficiencies ~ 90 %). -
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. -
Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment
antibiotics Article Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment Alicia Sorgen 1, James Johnson 2, Kevin Lambirth 2, Sandra M. Clinton 3 , Molly Redmond 1 , Anthony Fodor 2 and Cynthia Gibas 2,* 1 Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (A.S.); [email protected] (M.R.) 2 Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (J.J.); [email protected] (K.L.); [email protected] (A.F.) 3 Department of Geography & Earth Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-704-687-8378 Abstract: Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify Citation: Sorgen, A.; Johnson, J.; phenotypically resistant cultivable portions of these bacterial communities and characterized the Lambirth, K.; Clinton, -
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). -
A New Symbiotic Lineage Related to Neisseria and Snodgrassella Arises from the Dynamic and Diverse Microbiomes in Sucking Lice
bioRxiv preprint doi: https://doi.org/10.1101/867275; this version posted December 6, 2019. 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. A new symbiotic lineage related to Neisseria and Snodgrassella arises from the dynamic and diverse microbiomes in sucking lice Jana Říhová1, Giampiero Batani1, Sonia M. Rodríguez-Ruano1, Jana Martinů1,2, Eva Nováková1,2 and Václav Hypša1,2 1 Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic 2 Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czech Republic Author for correspondence: Václav Hypša, Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic, +42 387 776 276, [email protected] Abstract Phylogenetic diversity of symbiotic bacteria in sucking lice suggests that lice have experienced a complex history of symbiont acquisition, loss, and replacement during their evolution. By combining metagenomics and amplicon screening across several populations of two louse genera (Polyplax and Hoplopleura) we describe a novel louse symbiont lineage related to Neisseria and Snodgrassella, and show its' independent origin within dynamic lice microbiomes. While the genomes of these symbionts are highly similar in both lice genera, their respective distributions and status within lice microbiomes indicate that they have different functions and history. In Hoplopleura acanthopus, the Neisseria-related bacterium is a dominant obligate symbiont universally present across several host’s populations, and seems to be replacing a presumably older and more degenerated obligate symbiont. -
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. -
(Ictalurus Punctatus) Fillets Using the Grovac Process. Milton Ruben Ramos Louisiana State University and Agricultural & Mechanical College
Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 1999 Reduction of Endogenous Bacteria Associated With Catfish (Ictalurus Punctatus) Fillets Using the Grovac Process. Milton Ruben Ramos Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Ramos, Milton Ruben, "Reduction of Endogenous Bacteria Associated With Catfish (Ictalurus Punctatus) Fillets Using the Grovac Process." (1999). LSU Historical Dissertations and Theses. 7122. https://digitalcommons.lsu.edu/gradschool_disstheses/7122 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reprDduced from the microfilm master. UMI films the text directly from the original or copy sutmitted. 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. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substarxtard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript arxl there are missing pages, these will be noted. Also, if unauthorized copyright material had to t>e removed, a rwte 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. -
Bacterial Diversity and Functional Analysis of Severe Early Childhood
www.nature.com/scientificreports OPEN Bacterial diversity and functional analysis of severe early childhood caries and recurrence in India Balakrishnan Kalpana1,3, Puniethaa Prabhu3, Ashaq Hussain Bhat3, Arunsaikiran Senthilkumar3, Raj Pranap Arun1, Sharath Asokan4, Sachin S. Gunthe2 & Rama S. Verma1,5* Dental caries is the most prevalent oral disease afecting nearly 70% of children in India and elsewhere. Micro-ecological niche based acidifcation due to dysbiosis in oral microbiome are crucial for caries onset and progression. Here we report the tooth bacteriome diversity compared in Indian children with caries free (CF), severe early childhood caries (SC) and recurrent caries (RC). High quality V3–V4 amplicon sequencing revealed that SC exhibited high bacterial diversity with unique combination and interrelationship. Gracillibacteria_GN02 and TM7 were unique in CF and SC respectively, while Bacteroidetes, Fusobacteria were signifcantly high in RC. Interestingly, we found Streptococcus oralis subsp. tigurinus clade 071 in all groups with signifcant abundance in SC and RC. Positive correlation between low and high abundant bacteria as well as with TCS, PTS and ABC transporters were seen from co-occurrence network analysis. This could lead to persistence of SC niche resulting in RC. Comparative in vitro assessment of bioflm formation showed that the standard culture of S. oralis and its phylogenetically similar clinical isolates showed profound bioflm formation and augmented the growth and enhanced bioflm formation in S. mutans in both dual and multispecies cultures. Interaction among more than 700 species of microbiota under diferent micro-ecological niches of the human oral cavity1,2 acts as a primary defense against various pathogens. Tis has been observed to play a signifcant role in child’s oral and general health. -
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. -
Altitudinal Patterns of Diversity and Functional Traits of Metabolically Active Microorganisms in Stream Biofilms
The ISME Journal (2015) 9, 2454–2464 © 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej ORIGINAL ARTICLE Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms Linda Wilhelm1, Katharina Besemer2, Lena Fragner3, Hannes Peter4, Wolfram Weckwerth3 and Tom J Battin1,5 1Department of Limnology and Oceanography, Faculty of Life Sciences, University of Vienna, Vienna, Austria; 2School of Engineering, University of Glasgow, Glasgow, UK; 3Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria; 4Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Innsbruck, Austria and 5Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity,