Supplementary Table I
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Methanospirillum Hungatei GP1 As an S Layer MAX FIRTEL,1 GORDON SOUTHAM,1 GEORGE HARAUZ,2 and TERRY J
JOURNAL OF BACTERIOLOGY, Dec. 1993, p. 7550-7560 Vol. 175, No. 23 0021-9193/93/237550-11$02.00/0 Copyright © 1993, American Society for Microbiology Characterization of the Cell Wall of the Sheathed Methanogen Methanospirillum hungatei GP1 as an S Layer MAX FIRTEL,1 GORDON SOUTHAM,1 GEORGE HARAUZ,2 AND TERRY J. BEVERIDGE'* Department ofMicrobiology' and Department ofMolecular Biology and Genetics, 2 College of Biological Sciences, University of Guelph, Guelph, Ontario, Canada N1G 2W1 Received 16 June 1993/Accepted 27 September 1993 The cell wall of MethanospiriUum hungatei GP1 is a labile structure that has been difficult to isolate and Downloaded from characterize because the cells which it encases are contained within a sheath. Cell-sized fragments, 560 nm wide by several micrometers long, of cell wall were extracted by a novel method involving the gradual drying of the filaments in 2% (wtlvol) sodium dodecyl sulfate and 10%0 (wt/vol) sucrose in 50 mM N-2-hydroxyeth- ylpiperazine-N'-2-ethanesulfonic acid (HEPES) buffer containing 10 mM EDTA. The surface was a hexagonal array (a = b = 15.1 nm) possessing a helical superstructure with a ca. 2.50 pitch angle. In shadowed relief, the smooth outer face was punctuated with deep pits, whereas the inner face was relatively featureless. Computer-based two-dimensional reconstructed views of the negatively stained layer demonstrated 4.0- and 2.0-nm-wide electron-dense regions on opposite sides of the layer likely corresponding to the openings of funnel-shaped channels. The face featuring the larger openings best corresponds to the outer face of the layer. -
Validation of the Asaim Framework and Its Workflows on HMP Mock Community Samples
Validation of the ASaiM framework and its workflows on HMP mock community samples The ASaiM framework and its workflows have been tested and validated on two mock metagenomic data of an artificial community (with 22 known microbial strains). The datasets are available on EBI metagenomics database (project accession number: SRP004311). First we checked that the targeted abundances (based on number of PCR product) from both mock datasets were similar to the effective abundance (by mapping reads on reference genomes). Second, taxonomic and functional results produced by the ASaiM framework have been extensively analyzed and compared to expectations and to results obtained with the EBI metagenomics pipeline (S. Hunter et al. 2014). For these datasets, the ASaiM framework produces accurate and precise taxonomic assignations, different functional results (gene families, pathways, GO slim terms) and results combining taxonomic and functional information. Despite almost 1.4 million of raw metagenomic sequences, these analyses were executed in less than 6h on a commodity computer. Hence, the ASaiM framework and its workflows are proven to be relevant for the analysis of microbiota datasets. 1Data On EBI metagenomics database, two mock community samples for Human Microbiome Project (HMP) are available. Both samples contain a genomic mixture of 22 known microbial strains. Relative abundance of each strain has been targeted using the number of PCR product of their respective 16S sequences (Table 1). In first sample (SRR072232), the targeted 16S copies of the strains vary by up to four orders of magnitude between the strains (Table 1), whereas in second sample (SRR072233) the same 16S copy number is targeted for each strain (Table 1). -
Genomic Insight Into the Host–Endosymbiont Relationship of Endozoicomonas Montiporae CL-33T with Its Coral Host
ORIGINAL RESEARCH published: 08 March 2016 doi: 10.3389/fmicb.2016.00251 Genomic Insight into the Host–Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host Jiun-Yan Ding 1, Jia-Ho Shiu 1, Wen-Ming Chen 2, Yin-Ru Chiang 1 and Sen-Lin Tang 1* 1 Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, 2 Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University, Kaohsiung, Taiwan The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33T. Its genome had potential sign of ongoing genome erosion and gene exchange with its Edited by: Rekha Seshadri, host. Testosterone degradation and type III secretion system are commonly present in Department of Energy Joint Genome Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Institute, USA Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, Reviewed by: this bacterium could move into coral cells via endocytosis after binding to coral’s Eph Kathleen M. Morrow, University of New Hampshire, USA receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase Jean-Baptiste Raina, are possible type III secretion effectors that might help coral to prevent mitochondrial University of Technology Sydney, Australia dysfunction and promote gluconeogenesis, especially under stress conditions. -
Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts
ORIGINAL RESEARCH published: 12 July 2016 doi: 10.3389/fmicb.2016.01042 Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts Lars Schreiber 1*, Kasper U. Kjeldsen 1, Peter Funch 2, Jeppe Jensen 1, Matthias Obst 3, Susanna López-Legentil 4 and Andreas Schramm 1 1 Department of Bioscience, Center for Geomicrobiology and Section for Microbiology, Aarhus University, Aarhus, Denmark, 2 Section of Genetics, Ecology and Evolution, Department of Bioscience, Aarhus University, Aarhus, Denmark, 3 Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden, 4 Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington NC, USA Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) clade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25–100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence Edited by: in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains Joerg Graf, of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and University of Connecticut, USA characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a Reviewed by: Silvia Bulgheresi, mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. -
Acidification Increases Abundances of Vibrionales And
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Sapientia Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency Tania Aires1,*, Alexandra Serebryakova1,2,*, Frédérique Viard2,3, Ester A. Serrão1 and Aschwin H. Engelen1 1 Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal 2 Sorbonne Université, CNRS, Lab Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU), Station Biologique de Roscoff, Roscoff, France 3 CNRS, UMR 7144, Divco Team, Station Biologique de Roscoff, Roscoff, France * These authors contributed equally to this work. ABSTRACT Ocean acidification significantly affects marine organisms in several ways, with complex interactions. Seaweeds might benefit from rising CO2 through increased photosynthesis and carbon acquisition, with subsequent higher growth rates. However, changes in seaweed chemistry due to increased CO2 may change the nutritional quality of tissue for grazers. In addition, organisms live in close association with a diverse microbiota, which can also be influenced by environmental changes, with feedback effects. As gut microbiomes are often linked to diet, changes in seaweed characteristics and associated microbiome can affect the gut microbiome of the grazer, with possible fitness consequences. In this study, we experimentally investigated the effects of acidification on the microbiome of the invasive brown seaweed Sargassum muticum and a native isopod consumer Synisoma nadejda. Both were exposed to ambient CO2 conditions Submitted 13 September 2017 (380 ppm, pH 8.16) and an acidification treatment (1,000 ppm, pH 7.86) for three Accepted 26 January 2018 weeks. -
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. -
Interplay of Microbial Communities with Mineral Environments in Coralline Algae
Science of the Total Environment 757 (2021) 143877 Contents lists available at ScienceDirect Science of the Total Environment journal homepage: www.elsevier.com/locate/scitotenv Interplay of microbial communities with mineral environments in coralline algae Patricia M. Valdespino-Castillo a,1, Andrea Bautista-García b,1, Fabio Favoretto b,c, Martín Merino-Ibarra d, Rocío J. Alcántara-Hernández e, Teresa Pi-Puig e,f, F. Sergio Castillo d, Silvia Espinosa-Matías g, Hoi-Ying Holman a, Anidia Blanco-Jarvio b,⁎ a Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States b Laboratorio de Bioingeniería y Ciencias Ambientales (BICA), Departamento Académico de Ingeniería en Pesquerías, Universidad Autónoma de Baja California Sur, La Paz, BCS, Mexico c Gulf of California Marine Program, Scripps Institution of Oceanography, University of California San Diego, CA, United States d Unidad Académica de Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico e Instituto de Geología, Universidad Nacional Autónoma de México, Mexico City, Mexico f Laboratorio Nacional de Geoquímica y Mineralogía (LANGEM), Universidad Nacional Autónoma de México, Mexico City, Mexico g Laboratorio de Microscopía Electrónica de Barrido, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico HIGHLIGHTS GRAPHICAL ABSTRACT • The interplay of microorganisms and algal mineral bioconstructions remains poorly understood. • Carbonates rich in Fe and Mg found make CA relevant targets to study coastal resilience. • Halophiles and evaporite minerals con- currently suggest halophilic microenvi- ronments in the thallus. • Bacterial microbiota correlated signifi- cantly with temperature and nutrients. • Key bacteria might play relevant roles in adaptive responses of coralline algae. -
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 -
Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes Versicolor)
animals Article Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes versicolor) Lin Zhang 1,2,*,† , Fang Yang 3,†, Ning Li 4 and Buddhi Dayananda 5 1 School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China 2 State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China 3 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China; [email protected] 4 College of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, China; [email protected] 5 School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; [email protected] * Correspondence: [email protected] † These authors contributed equally to this work. Simple Summary: The different gut sections potentially provide different habitats for gut microbiota. We found that Bacteroidetes, Firmicutes, and Proteobacteria were the three primary phyla in gut micro- biota of C. versicolor. The relative abundance of dominant phyla Bacteroidetes and Firmicutes exhibited an increasing trend from the small intestine to the large intestine, and there was a higher abun- dance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the hindgut, and some metabolic pathways were higher in the hindgut. Our results reveal the variations of gut microbiota composition and metabolic pathways in Citation: Zhang, L.; Yang, F.; Li, N.; different parts of the lizards’ intestine. Dayananda, B. Environment- Dependent Variation in Gut Abstract: Vertebrates maintain complex symbiotic relationships with microbiota living within their Microbiota of an Oviparous Lizard gastrointestinal tracts which reflects the ecological and evolutionary relationship between hosts and (Calotes versicolor). -
D 3111 Suppl
The following supplement accompanies the article Fine-scale transition to lower bacterial diversity and altered community composition precedes shell disease in laboratory-reared juvenile American lobster Sarah G. Feinman, Andrea Unzueta Martínez, Jennifer L. Bowen, Michael F. Tlusty* *Corresponding author: [email protected] Diseases of Aquatic Organisms 124: 41–54 (2017) Figure S1. Principal coordinates analysis of bacterial communities on lobster shell samples taken on different days. Principal coordinates analysis of the weighted UniFrac metric comparing bacterial community composition of diseased lobster shell on different days of sampling. Diseased lobster shell includes samples collected from the site of disease (square), as well as 0.5 cm (circle), 1 cm (triangle), and 1.5 cm (diamond) away from the site of the disease, while colors depict different days of sampling. Note that by day four, two of the lobsters had molted, hence there are fewer red symbols 1 Figure S2. Rank relative abundance curve for the 200+ most abundant OTUs for each shell condition. The number of OTUs, their abundance, and their order varies for each bar graph based on the relative abundance of each OTU in that shell condition. Please note the difference in scale along the y-axis for each bar graph. Bars appear in color if the OTU is a part of the core microbiome of that shell condition or appear in black if the OTU is not a part of the core microbiome of that shell condition. Dotted lines indicate OTUs that are part of the “abundant microbiome,” i.e. those whose cumulative total is ~50%, as well as OTUs that are a part of the “rare microbiome,” i.e. -
Supplemental Material S1.Pdf
Phylogeny of Selenophosphate synthetases (SPS) Supplementary Material S1 ! SelD in prokaryotes! ! ! SelD gene finding in sequenced prokaryotes! We downloaded a total of 8263 prokaryotic genomes from NCBI (see Supplementary Material S7). We scanned them with the program selenoprofiles (Mariotti 2010, http:// big.crg.cat/services/selenoprofiles) using two SPS-family profiles, one prokaryotic (seld) and one mixed eukaryotic-prokaryotic (SPS). Selenoprofiles removes overlapping predictions from different profiles, keeping only the prediction from the profile that seems closer to the candidate sequence. As expected, the great majority of output predictions in prokaryotic genomes were from the seld profile. We will refer to the prokaryotic SPS/SelD !genes as SelD, following the most common nomenclature in literature.! To be able to inspect results by hand, and also to focus on good-quality genomes, we considered a reduced set of species. We took the prok_reference_genomes.txt list from ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/, which NCBI claims to be a "small curated subset of really good and scientifically important prokaryotic genomes". We named this the prokaryotic reference set (223 species - see Supplementary Material S8). We manually curated most of the analysis in this set, while we kept automatized the !analysis on the full set.! We detected SelD proteins in 58 genomes (26.0%) in the prokaryotic reference set (figure 1 in main paper), which become 2805 (33.9%) when considering the prokaryotic full set (figure SM1.1). The difference in proportion between the two sets is due largely to the presence of genomes of very close strains in the full set, which we consider redundant. -
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,