Spatial Environmental Heterogeneity Determines Young Biofilm
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
Dissertation Implementing Organic Amendments To
DISSERTATION IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE Submitted by Erika J. Foster Graduate Degree Program in Ecology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Summer 2018 Doctoral Committee: Advisor: M. Francesca Cotrufo Louise Comas Charles Rhoades Matthew D. Wallenstein Copyright by Erika J. Foster 2018 All Rights Reserved i ABSTRACT IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE To sustain agricultural production into the future, management should enhance natural biogeochemical cycling within the soil. Strategies to increase yield while reducing chemical fertilizer inputs and irrigation require robust research and development before widespread implementation. Current innovations in crop production use amendments such as manure and biochar charcoal to increase soil organic matter and improve soil structure, water, and nutrient content. Organic amendments also provide substrate and habitat for soil microorganisms that can play a key role cycling nutrients, improving nutrient availability for crops. Additional plant growth promoting bacteria can be incorporated into the soil as inocula to enhance soil nutrient cycling through mechanisms like phosphorus solubilization. Since microbial inoculation is highly effective under drought conditions, this technique pairs well in agricultural systems using limited irrigation to save water, particularly in semi-arid regions where climate change and population growth exacerbate water scarcity. The research in this dissertation examines synergistic techniques to reduce irrigation inputs, while building soil organic matter, and promoting natural microbial function to increase crop available nutrients. The research was conducted on conventional irrigated maize systems at the Agricultural Research Development and Education Center north of Fort Collins, CO. -
Bacterial Biofilms on Microplastics in the Baltic Sea – Composition, Influences, and Interactions with Their Environment
Bacterial biofilms on microplastics in the Baltic Sea – Composition, influences, and interactions with their environment kumulative Dissertation zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Universität Rostock vorgelegt von Katharina Kesy, geb. am 06.11.1985 in Berlin aus Rostock Rostock, 17.09.2019 https://doi.org/10.18453/rosdok_id00002636 Gutachter: Prof. Dr. Matthias Labrenz, Sektion Biologische Meereskunde, Leibniz-Institut für Ostseeforschug Warnemünde Assist. Prof. Dr. Melissa Duhaime, Department of Computational Medicine and Bioinformatics, University of Michigan, USA Jahr der Einreichung: 2019 Jahr der Verteidigung: 2020 Table of contents i Table of contents Summary/Zusammenfassung ............................................................................................. 1 General introduction ........................................................................................................... 6 Biofilms, their formation, and influential factors ............................................................. 6 The ecological importance of biofilms in aquatic systems ............................................... 8 Microplastics in aquatic environments: a newly available habitat for surface associated microorganisms and possible vector for potential pathogens ........................................... 9 Description of research aims ............................................................................................ 15 Summary -
Architecture, Component, and Microbiome of Biofilm Involved In
www.nature.com/npjbiofilms ARTICLE OPEN Architecture, component, and microbiome of biofilm involved in the fouling of membrane bioreactors Tomohiro Inaba1, Tomoyuki Hori1, Hidenobu Aizawa1, Atsushi Ogata1 and Hiroshi Habe1 Biofilm formation on the filtration membrane and the subsequent clogging of membrane pores (called biofouling) is one of the most persistent problems in membrane bioreactors for wastewater treatment and reclamation. Here, we investigated the structure and microbiome of fouling-related biofilms in the membrane bioreactor using non-destructive confocal reflection microscopy and high-throughput Illumina sequencing of 16S rRNA genes. Direct confocal reflection microscopy indicated that the thin biofilms were formed and maintained regardless of the increasing transmembrane pressure, which is a common indicator of membrane fouling, at low organic-loading rates. Their solid components were primarily extracellular polysaccharides and microbial cells. In contrast, high organic-loading rates resulted in a rapid increase in the transmembrane pressure and the development of the thick biofilms mainly composed of extracellular lipids. High-throughput sequencing revealed that the biofilm microbiomes, including major and minor microorganisms, substantially changed in response to the organic-loading rates and biofilm development. These results demonstrated for the first time that the architectures, chemical components, and microbiomes of the biofilms on fouled membranes were tightly associated with one another and differed considerably depending on the organic-loading conditions in the membrane bioreactor, emphasizing the significance of alternative indicators other than the transmembrane pressure for membrane biofouling. npj Biofilms and Microbiomes (2017) 3:5 ; doi:10.1038/s41522-016-0010-1 INTRODUCTION improvement of confocal reflection microscopy (CRM).9, 10 This Membrane bioreactors (MBRs) have been broadly exploited for the unique analytical technique uses a special installed beam splitter treatment of municipal and industrial wastewaters. -
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. -
Metaproteomics Characterization of the Alphaproteobacteria
Avian Pathology ISSN: 0307-9457 (Print) 1465-3338 (Online) Journal homepage: https://www.tandfonline.com/loi/cavp20 Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar To cite this article: José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar (2019) Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssusgallinae (De Geer, 1778), Avian Pathology, 48:sup1, S52-S59, DOI: 10.1080/03079457.2019.1635679 To link to this article: https://doi.org/10.1080/03079457.2019.1635679 © 2019 The Author(s). Published by Informa View supplementary material UK Limited, trading as Taylor & Francis Group Accepted author version posted online: 03 Submit your article to this journal Jul 2019. Published online: 02 Aug 2019. Article views: 694 View related articles View Crossmark data Citing articles: 3 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=cavp20 AVIAN PATHOLOGY 2019, VOL. 48, NO. S1, S52–S59 https://doi.org/10.1080/03079457.2019.1635679 ORIGINAL ARTICLE Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero a,b, Sandra Díaz-Sanchez a, Olivier Sparagano c, Robert D. Finn d, José de la Fuente a,e and Margarita Villar a aSaBio. -
Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. -
Non-Rhizobial Nodulation in Legumes
Biotechnology and Molecular Biology Review Vol. 2 (2), pp. 049-057, June 2007 Available online at http://www.academicjournals.org/BMBR ISSN 1538-2273 © 2007 Academic Journals Mini Review Non-rhizobial nodulation in legumes D. Balachandar*, P. Raja, K. Kumar and SP. Sundaram Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore – 641 003, India Accepted 27 February, 2007 Legume - Rhizobium associations are undoubtedly form the most important N2-fixing symbiosis and play a subtle role in contributing nitrogen and maintaining/improving soil fertility. A great diversity in the rhizobial species nodulating legumes has been recognized, which belongs to α subgroup of proteobacteria covering the genera, Rhizobium, Sinorhizobium (renamed as Ensifer), Mesorhizobium, Bradyrhizobium and Azorhizobium. Recently, several non-rhizobial species, belonging to α and β subgroup of Proteobacteria such as Methylobacterium, Blastobacter, Devosia, Phyllobacterium, Ochro- bactrum, Agrobacterium, Cupriavidus, Herbaspirillum, Burkholderia and some γ-Proteobacteria have been reported to form nodules and fix nitrogen in legume roots. The phylogenetic relationship of these non-rhizobial species with the recognized rhizobial species and the diversity of their hosts are discussed in this review. Key words: Legumes, Nodulation, Proteobacteria, Rhizobium Table of content 1. Introduction 2. Non-rhizobial nodulation 2.1. ∝-Proteobacteria 2.1.1. Methylobacterium 2.1.2. Blastobacter 2.1.3. Devosia 2.1.4. Phyllobacterium 2.1.5. Ochrobactrum 2.1.6. Agrobacterium 2.2. β-Proteobacteria 2.2.1. Cupriavidus 2.2.2. Herbaspirillum 2.2.3. Burkholderia 2.3. γ-Proteobacteria 3. Conclusion 4. References INTRODUCTION Members of the leguminosae form the largest plant family tance since they are responsible for most of the atmos- on earth with around 19,000 species (Polhill et al., 1981). -
Manuscript Revised 30 07 2014
Marine microorganisms as source of stereoselective esterases and ketoreductases: kinetic resolution of a prostaglandin intermediate Valerio De Vitis1, Benedetta Guidi,1 Martina Letizia Contente1, Tiziana Granato1, Paola Conti2, Francesco Molinari1, Elena Crotti1, Francesca Mapelli1, Sara Borin1, Daniele Daffonchio1 and Diego Romano1* 1 Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, via Mangiagalli 25, 20133 Milan, Italy. 2 Department of Pharmaceutical Sciences (DISFARM), University of Milan, via Mangiagalli 25, 20133 Milan, Italy. * Author to whom correspondence should be addressed; e-mail: [email protected]; Tel.: +39 0250319134; Fax +39 0250319191 Abstract A screening among bacterial strains isolated from water-brine interface of the deep hypersaline anoxic basins (DHABs) of the Eastern Mediterranean was carried out for the biocatalytical resolution of racemic propyl ester of anti-2-oxotricyclo[2.2.1.0]heptan-7-carboxylic acid (R,S)-1, a key intermediate for the synthesis of D-cloprostenol. B. hornekiae 15A gave highly stereoselective reduction of (R,S)-1, whereas H. aquamarina 9B enantioselectively hydrolysed (R,S)-1; in both cases, enantiomerically pure unreacted (R)-1 could be easily recovered and purified at molar conversion below 57-58%, showing the potential of DHABs extremophile microbiome and marine-derived enzymes in stereoselective biocatalysis. Keywords: esterase, ketoreductase, deep-sea hypersaline anoxic basins (DHABs), marine enzymes, stereoselective, biocatalysis, prostaglandin 1 1. Introduction The biocatalytic preparation of optically pure chiral building blocks for the fine chemistry as well as pharmaceutical sector is a valid alternative to conventional chemical methods (Patel 2008). In this context, the recruitment of new robust enzymes able to catalyse stereoselective reactions is highly demanded. -
Symbiont Replacement Between Bacteria of Different Classes Reveals Additional Layers of Complexity in the Evolution of Symbiosis
Protist, Vol. 169, 43–52, xx 2018 http://www.elsevier.de/protis Published online date 20 December 2017 ORIGINAL PAPER Symbiont replacement between bacteria of different classes reveals additional layers of complexity in the evolution of symbiosis in the ciliate Euplotes a,b a,c a Vittorio Boscaro , Sergei I. Fokin , Giulio Petroni , a b a,1 Franco Verni , Patrick J. Keeling , and Claudia Vannini a University of Pisa, Department of Biology, Italy b University of British Columbia, Department of Botany, Canada c St.-Petersburg State University, Department of Invertebrate Zoology, Russia Submitted July 5, 2017; Accepted December 12, 2017 Monitoring Editor: Genoveva F. Esteban Symbiosis is a diverse and complex phenomenon requiring diverse model systems. The obligate rela- tionship between a monophyletic group of Euplotes species (“clade B”) and the betaproteobacteria Polynucleobacter and “Candidatus Protistobacter” is among the best-studied in ciliates, and provides a framework to investigate symbiont replacements. Several other Euplotes-bacteria relationships exist but are less understood, such as the co-dependent symbiosis between Euplotes magnicirratus (which belongs to “clade A”) and the alphaproteobacterium “Candidatus Devosia euplotis”. Here we describe a new Devosia inhabiting the cytoplasm of a strain of Euplotes harpa, a clade B species that usually depends on Polynucleobacter for survival. The novel bacterial species, “Candidatus Devosia symbi- otica”, is closely related to the symbiont of E. magnicirratus, casting a different light on the history of bacteria colonizing ciliates of this genus. The two Devosia species may have become symbionts independently or as the result of a symbiont exchange between hosts, in either case replacing a pre- vious essential bacterium in E. -
Choosing Source of Microorganisms and Processing Technology for Next
www.nature.com/scientificreports OPEN Choosing source of microorganisms and processing technology for next generation beet bioinoculant Sonia Szymańska1, Marcin Sikora2, Katarzyna Hrynkiewicz1*, Jarosław Tyburski2,3, Andrzej Tretyn2,3 & Marcin Gołębiewski2,3* The increase of human population and associated increasing demand for agricultural products lead to soil over-exploitation. Biofertilizers based on lyophilized plant material containing living plant growth-promoting microorganisms (PGPM) could be an alternative to conventional fertilizers that fts into sustainable agricultural technologies ideas. We aimed to: (1) assess the diversity of endophytic bacteria in sugar and sea beet roots and (2) determine the infuence of osmoprotectants (trehalose and ectoine) addition during lyophilization on bacterial density, viability and salt tolerance. Microbiome diversity was assessed based on 16S rRNA amplicons sequencing, bacterial density and salt tolerance was evaluated in cultures, while bacterial viability was calculated by using fuorescence microscopy and fow cytometry. Here we show that plant genotype shapes its endophytic microbiome diversity and determines rhizosphere soil properties. Sea beet endophytic microbiome, consisting of genera characteristic for extreme environments, is more diverse and salt resistant than its crop relative. Supplementing osmoprotectants during root tissue lyophilization exerts a positive efect on bacterial community salt stress tolerance, viability and density. Trehalose improves the above-mentioned parameters more efectively than ectoine, moreover its use is economically advantageous, thus it may be used to formulate improved biofertilizers. Conventional agriculture practices negatively afect environment, e.g. by decreasing microbial diversity, soil quality, water supply and plant productivity1,2. Wide adoption of sustainable agricultural technologies, e.g. biofer- tilizers, may signifcantly decrease the use of chemical fertilizers, reducing negative consequences of agriculture on the environment2,3. -
Horizontal Transfer of Symbiosis Genes Within and Between Rhizobial Genera : Occurrence and Importance
This is a repository copy of Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera : Occurrence and Importance. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/132864/ Version: Published Version Article: Andrews, Mitchell, Meyer, Sofie, James, Euan K. et al. (4 more authors) (2018) Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera : Occurrence and Importance. Genes. ISSN 2073-4425 https://doi.org/10.3390/genes9070321 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ G C A T T A C G G C A T genes Review Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance Mitchell Andrews 1,*, Sofie De Meyer 2,3 ID , Euan K. James 4 ID , Tomasz St˛epkowski 5, Simon Hodge 1 ID , Marcelo F. Simon 6 ID and J. Peter W. Young 7 ID 1 Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand; [email protected] 2 Centre for