Architecture, Component, and Microbiome of Biofilm Involved In
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Community Analysis of Microbial Sharing and Specialization in A
Downloaded from http://rspb.royalsocietypublishing.org/ on March 15, 2017 Community analysis of microbial sharing rspb.royalsocietypublishing.org and specialization in a Costa Rican ant–plant–hemipteran symbiosis Elizabeth G. Pringle1,2 and Corrie S. Moreau3 Research 1Department of Biology, Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Cite this article: Pringle EG, Moreau CS. 2017 Reno, NV 89557, USA 2Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109, USA Community analysis of microbial sharing and 3Department of Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, specialization in a Costa Rican ant–plant– Chicago, IL 60605, USA hemipteran symbiosis. Proc. R. Soc. B 284: EGP, 0000-0002-4398-9272 20162770. http://dx.doi.org/10.1098/rspb.2016.2770 Ants have long been renowned for their intimate mutualisms with tropho- bionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of Received: 14 December 2016 microbes between interacting macroorganisms, affects the composition and Accepted: 17 January 2017 function of symbiotic microbial communities. Here we approached this ques- tion by investigating symbiosis within symbiosis. Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent close contact among the macroorganism partners, which then have substantial opportunity to exchange symbiotic microbes. We used metabarcoding and Subject Category: quantitative PCR to examine community structure of both bacteria and Ecology fungi in a Neotropical ant–plant–scale-insect symbiosis. Both phloem-feed- ing scale insects and honeydew-feeding ants make use of microbial Subject Areas: symbionts to subsist on phloem-derived diets of suboptimal nutritional qual- ecology, evolution, microbiology ity. -
Prokaryotic Community Successions and Interactions in Marine Biofilms
Prokaryotic community successions and interactions in marine biofilms: the key role of Flavobacteriia Thomas Pollet, Lyria Berdjeb, Cédric Garnier, Gaël Durrieu, Christophe Le Poupon, Benjamin Misson, Jean-François Briand To cite this version: Thomas Pollet, Lyria Berdjeb, Cédric Garnier, Gaël Durrieu, Christophe Le Poupon, et al.. Prokary- otic community successions and interactions in marine biofilms: the key role of Flavobacteriia. FEMS Microbiology Ecology, Wiley-Blackwell, 2018, 94 (6), 10.1093/femsec/fiy083. hal-02024255 HAL Id: hal-02024255 https://hal-amu.archives-ouvertes.fr/hal-02024255 Submitted on 2 Mar 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Prokaryotic community successions and interactions in marine biofilms: the key role of Flavobacteriia Thomas Pollet, Lyria Berdjeb, Cédric Garnier, Gaël Durrieu, Christophe Le Poupon, Benjamin Misson, Jean-François Briand To cite this version: Thomas Pollet, Lyria Berdjeb, Cédric Garnier, Gaël Durrieu, Christophe -
Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
How to Build a Biofilm
RESEARCH HIGHLIGHTS MICROBIOME IN brIEF Let the gut do the guiding SYMBIOSIS Growing evidence suggests that the the Gram-negative bacterium Finding the difference microbiome of animals not only Providencia, particularly Providencia The microbial gut communities of social bees comprise only affects host health but also their alcalifaciens strain JUb39, a few bacterial groups and are an emerging model system to study host-associated microbial communities. In this study, behaviour. However, the mechan- decreased avoidance of the volatile Engel and colleagues used comparative metagenomics to isms involved in the gut–brain repellent odorant octanol, an analyse the gut microbiota of two closely related honey bee axis are not well understood. effect that they refer to as octanol species, Apis mellifera and Apis cerana. Although they are In a recent study, O’Donnell, modulation. Moreover, JUb39 is colonized mostly by the same 16S rRNA phylotypes, the authors Sengupta and colleagues report that ingested by C. elegans, colonizes found that at genomic resolution, each host species harbours a gut-coloniz ing commensal bacteria the posterior intestine of the highly distinct bacterial community. Compared with A. cerana, A. mellifera displayed a much higher diversity of strains and produce a neuro trans mitter that worms and, interestingly, the extent functional gene content in the microbiota, encoding more modulates the sensory behaviour of colonization diverse enzymes for polysaccharide degradation, which may of their host. correlated with provide more metabolic flexibility. Studies are now needed The authors used chemotaxis the level to understand the mechanisms and functional consequences assays to test the influence of various of strain-level diversity among related host-associated non-pathogenic communities. -
Leadbetterella Byssophila Type Strain (4M15)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Leadbetterella byssophila type strain (4M15). Permalink https://escholarship.org/uc/item/907989cw Journal Standards in genomic sciences, 4(1) ISSN 1944-3277 Authors Abt, Birte Teshima, Hazuki Lucas, Susan et al. Publication Date 2011-03-04 DOI 10.4056/sigs.1413518 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 4:2-12 DOI:10.4056/sigs.1413518 Complete genome sequence of Leadbetterella byssophila type strain (4M15T) Birte Abt1, Hazuki Teshima2,3, Susan Lucas2, Alla Lapidus2, Tijana Glavina Del Rio2, Matt Nolan2, Hope Tice2, Jan-Fang Cheng2, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Konstantinos Mavromatis2, Amrita Pati2, Roxane Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Manfred Rohde6, Markus Göker1, Brian J. Tindall1, John C. Detter2,3, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Hans-Peter Klenk1, and Nikos C. Kyrpides2* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Lawrence Livermore National Laboratory, Livermore, California, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Nikos C. -
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. -
Supporting Information
Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs. -
Acholeplasma Florum, a New Species Isolated from Plants? R
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1984, p. 11-15 Vol. 34, No. 1 0020-7713/84/010011-05$02.OO/O Copyright 0 1984, International Union of Microbiological Societies Acholeplasma florum, a New Species Isolated from Plants? R. E. McCOY,l* H. G. BASHAM,' J. G. TULLY,* D. L. ROSE,2 P. CARLE,3 AND J. M. BOVE3 University of Florida Agricultural Research and Education Center, Fort Lauderdale, Florida 33314'; Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Frederick, Maryland 21 70i2;and lnstitut National de la Recherche Agronomique, Pont de la Maye 33140, France3 Three acholeplasmas isolated from floral surfaces of healthy plants in Florida were found to be similar in their biochemical and serological properties. These organisms did not require serum or cholesterol for growth, although addition of some supplementary fatty acids (as represented by Tween 80) was necessary for growth to occur in serum-free medium. The three strains possessed biochemical properties typical of the Acholeplasmataceae and were distinguished from the nine previously recognized Acholeplasma species by serological and deoxyribopucleic acid-deoxyribonucleic acid hybridization techniques. The genome molec- ular weight of the three Acholeplasma strains was lo9, and the guanine-plus-cytosine content of the deoxyribonucleic acid was 27 to 28 mol%. On the basis of these results and other morphological, biological, and serological properties, we propose that these organisms represent a new species, Acholeplasmaflorurn. Strain L1 (= ATCC 33453) is the type strain. Plant surfaces, particularly flowers, have recently been Media and cultivation procedures. Isolates were routinely proven to be fertile sites for isolation of members of the grown in MC broth or in the serum fraction medium de- Mycoplasrnatales (5, 11-13, 26). -
Multilevel Social Structure and Diet Shape the Gut Microbiota of the Gelada Monkey, the Only Grazing Primate Pål Trosvik 1*, Eric J
Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate Pål Trosvik 1*, Eric J. de Muinck 1, Eli K. Rueness 1, Peter J. Fashing 2, Evan C. Beierschmitt 3, Kadie R. Callingham 4, Jacob B. Kraus 5, Thomas H. Trew 6, Amera Moges 7, Addisu Mekonnen 1,8 , Vivek V. Venkataraman 9, Nga Nguyen 2 Supplementary information: Supplementary Figures 1-17, Supplementary Tables 1-10. Figure S1. Relative abundances of the eight most prevalent phyla in the gelada samples. Data are shown for all samples combined, as well as split into samples collected during the dry or wet season. The category “Other” includes OTUs that could not be classified to the phylum level with a probability higher than 0.5. Figure S2. Between-sample weighted (a) and unweighted (b) UniFrac distances in gelada samples collected during the dry (n=142) or the wet (n=174) season. Each box represents the interquartile range, with the horizontal lines representing the medians and the whiskers representing 1.5 times the interquartile range. Points outside the whiskers represent outliers. For both comparisons the difference in mean distance was highly significant (t<<0.001 for both comparisons, unpaired t-tests). Figure S3. Non-metric multidimensional scaling of all primate samples based on weighted (a) and unweighted (b) UniFrac distances. The plot shows the two main dimensions of variation, with plotted characters color coded according to sample type. Clustering according to samples type was highly significant, explaining 46.2% and 63.1% of between-sample variation, respectively (p<<0.001 for both tests, PERMANOVA). -
SCREENING of BACTERIAL SYMBIONTS of SEAGRASS Enhalus Sp
Journal of Coastal Development ISSN : 1410-5217 Volume 13, Number 2, February 2010 : 126-132 Accredited : 83/Dikti/Kep/2009 Original Paper SCREENING OF BACTERIAL SYMBIONTS OF SEAGRASS Enhalus sp. AGAINST BIOFILM-FORMING BACTERIA Bintang Marhaeni1*, Ocky Karna Radjasa 2, Dietriech G. Bengen1 dan Richardus.F.Kaswadji1 1 Graduate School of Marine Science, Bogor Agricultural University, Bogor, Indonesia 2 Department of Marine Science, Diponegoro University, Semarang 50275, Central Java, Indonesia Received : January, 3 th 2010 Accepted : January, 29th 2010 ABSTRACT Seagrasses have been known to produce secondary metabolites that have important ecological roles, including preventing from pathogen infections and fouling organisms. A research aimed at screening the potential of bacterial symbionts of seagrass Enhalus sp. was performed. Bacterial symbionts including endophytes and epiphytes were isolated from the seagrass, and marine biofilm-forming bacteria were isolated from the fiber and wooden panels from the surrounding colonies. A total of 17 epiphyte and 6 endophyte isolates were obtained, however more biological activity was found among endophytes (100%) compared to epiphytes (47%) against biofilm-forming bacteria. In addition, bacterial endophytes inhibited more biofilm-forming bacteria than epiphytes. Interestingly more isolates were obtained from rough surfaces both from fiber and wooden panels than smoothe surfaces. Bacterial symbionts of seagrass Enhalus sp., in particular its endophytes show potential source as natural marine antifoulants. Key words: bacterial symbionts, epiphytes, endophytes, Enhalus sp. Correspondence: Phone: +62-251-622961-; Fax: +231-251-622986 ; E-mail: [email protected] INTRODUCTION Biofouling is defined as the attachment and attachement and metamorphosis of some metabolism of microorganisms (microbial marine invertebrate larvae (Maki and Mitchell, fouling) and macroorganims (macrofouling) to 1988). -
Taxonomy JN869023
Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075 -
Metabarcoding for Bacterial Diversity Assessment: Looking Inside Didymosphenia Geminata Mats in Patagonian Aquatic Ecosystems
Aquatic Invasions (2021) Volume 16, Issue 1: 43–61 Special Issue: Proceedings of the 21st International Conference on Aquatic Invasive Species Guest editors: Sarah Bailey, Bonnie Holmes and Oscar Casas-Monroy CORRECTED PROOF Research Article Metabarcoding for bacterial diversity assessment: looking inside Didymosphenia geminata mats in Patagonian aquatic ecosystems Ana Victoria Suescún1,*, Karla Martinez-Cruz2, Maialen Barret3 and Leyla Cárdenas1,4 1Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile 2Environmental Biogeochemistry in Extreme Ecosystems Laboratory, Universidad de Magallanes, Punta Arenas, Chile 3Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France 4Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Chile Author e-mails: [email protected] (AVS), [email protected] (KM), [email protected] (MB), [email protected] (LC) *Corresponding author Co-Editors’ Note: This study was contributed in relation to the 21st International Conference Abstract on Aquatic Invasive Species held in Montreal, Canada, October 27–31, 2019 (http://www.icais. The number of organisms that spread and invade new habitats has increased in recent org/html/previous21.html). This conference has decades as a result of drastic environmental changes such as climate change and provided a venue for the exchange of anthropogenic activities. Microbial species invasions occur worldwide in terrestrial information on various aspects of aquatic and aquatic systems and represent an emerging challenge to our understanding of invasive species since its inception in 1990. The conference continues to provide an the interplay between biodiversity and ecosystem functioning. Due to the difficulty opportunity for dialog between academia, of detecting and evaluating non-indigenous microorganisms, little is known about industry and environmental regulators.