A Study of Microalgal Symbiotic Communities with the Aim to Increase Biomass and Biodiesel Production
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Deep Microbial Community Profiling Along the Fermentation Process of Pulque, a Major Biocultural Resource of Mexico
bioRxiv preprint doi: https://doi.org/10.1101/718999; this version posted July 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico. 1 1 2 Carolina Rocha-Arriaga , Annie Espinal-Centeno , Shamayim Martinez-Sanchez , Juan 1 2 1,3 Caballero-Pérez , Luis D. Alcaraz * & Alfredo Cruz-Ramirez *. 1 Molecular & Developmental Complexity Group, Unit of Advanced Genomics, LANGEBIO-CINVESTAV, Irapuato, México. 2 Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Cd. Universitaria, 04510 Coyoacán, Mexico City, Mexico. 3 Escuela de Agronomía, Universidad de La Salle Bajío, León, Gto, Mexico. *Corresponding authors: [email protected], [email protected] ● Our approach allowed the identification of a broader microbial diversity in Pulque ● We increased 4.4 times bacteria genera and 40 times fungal species detected in mead. ● Newly reported bacteria genera and fungal species associated to Pulque fermentation Abstract Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey. This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as crops, but also part of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli. -
Actinotalea Ferrariae Sp. Nov., Isolated from an Iron Mine, and Emended Description of the Genus Actinotalea
%paper no. ije048512 charlesworth ref: ije048512& New Taxa - Actinobacteria International Journal of Systematic and Evolutionary Microbiology (2013), 63, 000–000 DOI 10.1099/ijs.0.048512-0 Actinotalea ferrariae sp. nov., isolated from an iron mine, and emended description of the genus Actinotalea Yanzhi Li, Fang Chen, Kun Dong and Gejiao Wang Correspondence State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Gejiao Wang Huazhong Agricultural University, Wuhan, Hubei 430070, PR China [email protected] or [email protected] ; A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, designated strain CF5-4T, was isolated from iron mining powder. 16S rRNA gene sequence analysis grouped strain CF5-4T in a single cluster with Actinotalea fermentans DSM 3133T (97.6 % similarity). The major fatty acids T (.5 %) of strain CF5-4 were anteiso-C15 : 0, anteiso-C15 : 1 A, C16 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The predominant respiratory quinone was MK-10(H4) and the genomic DNA G+C content was 74.7 mol%. The major polar lipids were diphosphatidylglycerol and one unidentified phosphoglycolipid. The peptidoglycan type of strain CF5-4T was A4b, containing L-Orn–D-Ser–D-Asp. The cell-wall sugars were rhamnose, fucose, mannose and galactose. The results of DNA–DNA hybridization in combination with the comparison of phenotypic and phylogenetic characteristics among strain CF5-4T and related micro-organisms revealed that the isolate represents a novel species of the genus Actinotalea, for which the name Actinotalea ferrariae sp. nov. is proposed. The type strain is CF5-4T (5KCTC 29134T5CCTCC AB2012198T). -
Proposed Minimal Standards for Describing New Genera and Species of the Suborder Micrococcineae
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1823–1849 DOI 10.1099/ijs.0.012971-0 Proposed minimal standards for describing new genera and species of the suborder Micrococcineae Peter Schumann,1 Peter Ka¨mpfer,2 Hans-Ju¨rgen Busse 3 and Lyudmila I. Evtushenko4 for the Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes Correspondence 1DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, P. Schumann 38124 Braunschweig, Germany [email protected] 2Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t, 35392 Giessen, Germany 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, Austria 4All-Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Pushchino, Moscow Region 142290, Russia The Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes has agreed on minimal standards for describing new genera and species of the suborder Micrococcineae. The minimal standards are intended to provide bacteriologists involved in the taxonomy of members of the suborder Micrococcineae with a set of essential requirements for the description of new taxa. In addition to sequence data comparisons of 16S rRNA genes or other appropriate conservative genes, phenotypic and genotypic criteria are compiled which are considered essential for the comprehensive characterization of new members of the suborder Micrococcineae. Additional features are recommended for the characterization and differentiation of genera and species with validly published names. INTRODUCTION Aureobacterium and Rothia/Stomatococcus) and one pair of homotypic synonyms (Pseudoclavibacter/Zimmer- The suborder Micrococcineae was established by mannella) (Table 1 and http://www.the-icsp.org/taxa/ Stackebrandt et al. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
The Gastric Caeca of Pentatomids As a House for Actinomycetes Tiago D Zucchi1,2*, Simone S Prado2,3 and Fernando L Cônsoli2*
Zucchi et al. BMC Microbiology 2012, 12:101 http://www.biomedcentral.com/1471-2180/12/101 RESEARCH ARTICLE Open Access The gastric caeca of pentatomids as a house for actinomycetes Tiago D Zucchi1,2*, Simone S Prado2,3 and Fernando L Cônsoli2* Abstract Background: Microbes are extensively associated with insects, playing key roles in insect defense, nutrition and reproduction. Most of the associations reported involve Proteobacteria. Despite the fact that Actinobacteria associated with insects were shown to produce antibiotic barriers against pathogens to the hosts or to their food and nutrients, there are few studies focusing on their association with insects. Thus, we surveyed the Actinobacteria diversity on a specific region of the midgut of seven species of stinkbugs (Hemiptera: Pentatomidae) known to carry a diversity of symbiotically-associated Proteobacteria. Results: A total of 34 phylotypes were placed in 11 different Actinobacteria families. Dichelops melacanthus held the highest diversity with six actinobacteria families represented by nine phylotypes. Thyanta perditor (n =7),Edessa meditabunda (n =5),Loxa deducta (n =4)andPellaea stictica (n = 3) were all associated with three families. Piezodorus guildini (n =3)andNezara viridula (n = 3) had the lowest diversity, being associated with two (Propionibacteriaceae and Mycobacteriaceae) and one (Streptomyceataceae) families, respectively. Corynebacteriaceae and Mycobacteriaceae were the most common families with phylotypes from three different insect species each one. Conclusions: Many phylotypes shared a low 16S rRNA gene similarity with their closest type strains and formed new phyletic lines on the periphery of several genera. This is a strong indicative that stinkbug caeca can harbor new species of actinobacteria, which might be derived from specific associations with the species of stinkbugs studied. -
Antibiotic Resistance in Aquaculture Production DISSERTATION
Antibiotic Resistance in Aquaculture Production DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Ying Huang M.S. Graduate Program in Food Science and Technology The Ohio State University 2014 Dissertation Committee: Dr. Hua H. Wang, Advisor Dr. John H. Litchfield Dr. Gireesh Rajashekara Dr. Zhongtang Yu Copyrighted by Ying Huang 2014 Abstract The rapid emergence of antibiotic resistance (AR) has become a major public health concern. Recent findings provided solid evidences suggesting that multiple risk factors contributed to AR development, enrichment, dissemination and persistence, and a comprehensive understanding of AR ecology is essential for targeted mitigation. Following the investigation of AR in aquaculture products from China, a study on AR in fish and aquaculture production-related samples from a U.S. fish farm with controlled practices and no history of antibiotic applications was further conducted to better understand the potential impact of aquaculture production practice on the prevalence of antibiotic resistant (ART) bacteria in the aquaculture ecosystem. Phenotypic resistant populations against sulfamethoxazole with trimethoprim (Sul/Tri), tetracycline (Tet), erythromycin (Erm) or cefotaxime (Ctx) were screened by conventional plating with the corresponding antibiotics, followed by population assessments with denaturing gradient gel electrophoresis (DGGE) and 16S rDNA next generation sequencing (NGS). Despite the absence of antibiotic application in the farm, our results showed that antibiotic resistant (ART) bacteria were abundant in all samples examined, including fish intestine, surface rinsing water, feed, pond water and mud samples. By NGS, a total of 569 genera were identified in Tetr and Ctxr bacteria from five types of samples. -
Investigation of Oral Microbiome in Donkeys and the Effect of Dental
animals Communication Investigation of Oral Microbiome in Donkeys and the Effect of Dental Care on Oral Microbial Composition Yiping Zhu 1, Wuyan Jiang 1, Reed Holyoak 2, Bo Liu 1 and Jing Li 1,* 1 Equine Clinical Diagnostic Center, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; [email protected] (Y.Z.); [email protected] (W.J.); [email protected] (B.L.) 2 College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA; [email protected] * Correspondence: [email protected]; Tel.: +86-135-52228206 Received: 13 November 2020; Accepted: 25 November 2020; Published: 30 November 2020 Simple Summary: Dental health in donkeys has long been neglected, even though it is quite common for them to have dental problems. Therefore, dental care, as basic as dental floating, can be a good start to improve their dental condition. Oral microbiome sequencing is a reliable way to reflect the oral health of animals. However, little is known on the effect of dental care on the oral microbiome of donkeys. Hence, a research project was undertaken to investigate the relationship between dental floating and oral microbial changes using a current sequencing technique. We found that the changes of the oral microbiome were not significant, probably due to the necessity of more specific and consistent treatment. However, the study provided an insight of the oral microbial composition and helped increase awareness of dental care in donkeys. Abstract: The objective of this study was to investigate the oral microbial composition of the donkey and whether basic dental treatment, such as dental floating, would make a difference to the oral microbial environment in donkeys with dental diseases using high-throughput bacterial 16S rRNA gene sequencing. -
Gulosibacter Molinativorax Gen. Nov., Sp
Gulosibacter molinativorax gen. nov., sp. nov., a molinate-degrading bacterium, and classification of ‘Brevibacterium helvolum’ DSM 20419 as Pseudoclavibacter helvolus gen. nov., sp. nov. Ce´lia M. Manaia,1 Balbina Nogales,2,33 Norbert Weiss4 and Olga C. Nunes5 1Escola Superior de Biotecnologia, Universidade Cato´lica Portuguesa, 4200-072 Porto, Portugal 2Division of Microbiology, GBF – German Research Centre for Biotechnology, Braunschweig, Germany 3Area de Microbiologia, Universitat de les Illes Balears, Palma de Mallorca, Spain 4DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D-38124 Braunschweig, Germany 5LEPAE – Departamento de Engenharia Quı´mica, Faculdade de Engenharia, Universidade do Porto, R. Dr Roberto Frias, 4200-465 Porto, Portugal A Gram-positive, molinate-degrading bacterium, strain ON4T (=DSM 13485T=LMG 21909T), was isolated from a mixed bacterial culture able to mineralize the herbicide molinate. The strain was strictly aerobic, oxidase- and catalase-positive and non-acid-fast, with a growth temperature of 10–41 6C. It contained the major menaquinone MK-9 and a cell-wall peptidoglycan based on D-ornithine. 16S rDNA sequence analysis revealed that the strain formed a distinct line of descent in the family Microbacteriaceae, showing the highest 16S rDNA similarity (~95 %) to members of the genus Curtobacterium and ‘Brevibacterium helvolum’ DSM 20419 (=ATCC 13715). The latter was reported to have the cell-wall peptidoglycan type B2c and the major menaquinone MK-9, which are typical of Clavibacter, but it is clearly separated from this genus at the phylogenetic level. Based on low values of 16S rDNA sequence similarity to previously described genera and their distinctive phenotypic characteristics, it is proposed that strains ON4T and ‘B. -
Genome-Based Taxonomic Classification of the Phylum
ORIGINAL RESEARCH published: 22 August 2018 doi: 10.3389/fmicb.2018.02007 Genome-Based Taxonomic Classification of the Phylum Actinobacteria Imen Nouioui 1†, Lorena Carro 1†, Marina García-López 2†, Jan P. Meier-Kolthoff 2, Tanja Woyke 3, Nikos C. Kyrpides 3, Rüdiger Pukall 2, Hans-Peter Klenk 1, Michael Goodfellow 1 and Markus Göker 2* 1 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, 2 Department Edited by: of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Martin G. Klotz, Germany, 3 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Washington State University Tri-Cities, United States The application of phylogenetic taxonomic procedures led to improvements in the Reviewed by: Nicola Segata, classification of bacteria assigned to the phylum Actinobacteria but even so there remains University of Trento, Italy a need to further clarify relationships within a taxon that encompasses organisms of Antonio Ventosa, agricultural, biotechnological, clinical, and ecological importance. Classification of the Universidad de Sevilla, Spain David Moreira, morphologically diverse bacteria belonging to this large phylum based on a limited Centre National de la Recherche number of features has proved to be difficult, not least when taxonomic decisions Scientifique (CNRS), France rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft *Correspondence: Markus Göker genome sequences -
Seed-Associated Bacterial Endophytes from Turf Grasses
SEED-ASSOCIATED BACTERIAL ENDOPHYTES FROM TURF GRASSES PROMOTE SEEDLING GROWTH AND DEFEND PLANTS FROM DISEASE By QIANG CHEN A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Plant Biology Written under the direction of James F. White, Jr. And approved by ___________________________________ ___________________________________ ___________________________________ ___________________________________ New Brunswick, New Jersey May 2020 ABSTRACT OF THE DISSERTATION Seed-Associated Bacterial Endophytes from Turf Grasses Promote Seedling Growth and Defend Plants from Disease by QIANG CHEN Dissertation Director: James F. White, Jr. Animals and plants harbor microbiomes providing benefits to hosts. In plants, both prokaryotic and eukaryotic microbiomes have been universally found and shown to promote plant growth, enhance disease resistance and abiotic stress tolerance. Fungal endophytes from grasses have been well characterized, but bacterial endophytes were rarely studied. This dissertation will present research that was conducted to test the hypothesis that cool-season turfgrass seeds bear bacterial endophytes providing beneficial effects on host, such as seed germination, growth promotion, and antifungal effects. Bacteria were isolated from seeds of different turfgrass species. Among them, Bacillus amyloliquefaciens, Bacillus pumilus, and Pantoea agglomerans were demonstrated to promote seed germination and seedling growth, and alter root architecture on host. B. amyloliquefaciens strains were shown to produce antifungal lipopeptides that suppress the growth of several fungal pathogens. Metagenomic analysis on the bacterial community associated with turfgrass seeds from low and high moisture climate revealed that moisture level influenced the community structure of the bacteria on/in turf seeds. -
Antibiotic Resistance Genes in the Actinobacteria Phylum
European Journal of Clinical Microbiology & Infectious Diseases (2019) 38:1599–1624 https://doi.org/10.1007/s10096-019-03580-5 REVIEW Antibiotic resistance genes in the Actinobacteria phylum Mehdi Fatahi-Bafghi1 Received: 4 March 2019 /Accepted: 1 May 2019 /Published online: 27 June 2019 # Springer-Verlag GmbH Germany, part of Springer Nature 2019 Abstract The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum. Keywords Actinobacteria . Antibiotics . Antibiotics resistance . Antibiotic resistance genes . Phylum Brief introduction about the taxonomy chemical taxonomy: in this method, analysis of cell wall and of Actinobacteria whole cell compositions such as various sugars, amino acids, lipids, menaquinones, proteins, and etc., are studied [5]. (ii) One of the oldest phyla in the bacteria domain that have a Phenotypic classification: there are various phenotypic tests significant role in medicine and biotechnology is the phylum such as the use of conventional and specific staining such as Actinobacteria [1, 2]. In this phylum, DNA contains G + C Gram stain, partially acid-fast, acid-fast (Ziehl-Neelsen stain rich about 50–70%, non-motile (Actinosynnema pretiosum or Kinyoun stain), and methenamine silver staining; morphol- subsp. -
High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits
antibiotics Article High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits Marta Maciejewska 1, Magdalena Całusi ´nska 2 ID , Luc Cornet 3, Delphine Adam 1, Igor S. Pessi 1, Sandrine Malchair 4, Philippe Delfosse 2, Denis Baurain 3, Hazel A. Barton 5, Monique Carnol 4 and Sébastien Rigali 1,* ID 1 InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liège, Belgium; [email protected] (M.M.); [email protected] (D.A.); [email protected] (I.S.P.) 2 Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg; [email protected] (M.C.); [email protected] (P.D.) 3 InBioS—PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium; [email protected] (L.C.); [email protected] (D.B.) 4 InBioS—Plant and Microbial Ecology, Botany B22, University of Liège, B-4000 Liège, Belgium; [email protected] (S.M.); [email protected] (M.C.) 5 Department of Biology, University of Akron, Akron, OH 44325, USA; [email protected] * Correspondence: [email protected]; Tel.: +32-4-366-9830 Received: 12 February 2018; Accepted: 16 March 2018; Published: 21 March 2018 Abstract: Moonmilk are cave carbonate deposits that host a rich microbiome, including antibiotic-producing Actinobacteria, making these speleothems appealing for bioprospecting. Here, we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave “Grotte des Collemboles” via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9% to 23% of the total bacterial population.