Characterization of Biocarbon-Source Recovery and Microbial Community Shifts from Waste Activated Sludge by Conditioning with Co
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Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium from the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella Atlantisensis Gen
fmicb-10-01497 July 16, 2019 Time: 16:31 # 1 ORIGINAL RESEARCH published: 16 July 2019 doi: 10.3389/fmicb.2019.01497 Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov. Marianne Quéméneur1, Gaël Erauso1, Eléonore Frouin1, Emna Zeghal1, Céline Vandecasteele2, Bernard Ollivier1, Christian Tamburini1, Marc Garel1, Bénédicte Ménez3 and Anne Postec1* Edited by: 1 Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France, 2 INRA, US 1426, GeT-PlaGe, Isabelle Daniel, Genotoul, Castanet-Tolosan, France, 3 Université de Paris, Institut de Physique du Globe de Paris, CNRS UMR 7154, Paris, Université Claude Bernard Lyon 1, France France Reviewed by: Rock-hosted subseafloor habitats are very challenging for life, and current knowledge Ida Helene Steen, University of Bergen, Norway about microorganisms inhabiting such lithic environments is still limited. This study Lotta Purkamo, explored the cultivable microbial diversity in anaerobic enrichment cultures from cores Geological Survey of Finland, Finland recovered during the International Ocean Discovery Program (IODP) Expedition 357 from *Correspondence: ◦ Anne Postec the Atlantis Massif (Mid-Atlantic Ridge, 30 N). 16S rRNA gene survey of enrichment ◦ [email protected] cultures grown at 10–25 C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed Specialty section: This article was submitted to depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures Extreme Microbiology, (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly a section of the journal anaerobic bacterium designated 70B-AT was isolated from core M0070C-3R1 (1150 Frontiers in Microbiology meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. -
Phylogenomic Analysis of 589 Metagenome-Assembled Genomes Encompassing All Major Prokaryotic Lineages from the Gut of Higher Termites
Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites Vincent Hervé1, Pengfei Liu1, Carsten Dietrich1, David Sillam-Dussès2, Petr Stiblik3, Jan Šobotník3 and Andreas Brune1 1 Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany 2 Laboratory of Experimental and Comparative Ethology EA 4443, Université Paris 13, Villetaneuse, France 3 Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic ABSTRACT “Higher” termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different Submitted 29 August 2019 gut compartments of eight higher termite species that encompass 17 prokaryotic -
Biodegradation Treatment of Petrochemical Wastewaters
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre Dissertação Mestrado em Microbiologia Aplicada Orientadores Doutora Sandra Sanches Professora Doutora Lélia Chambel 2015 Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre 2015 This thesis was fully performed at the Institute of Experimental and Technologic Biology (IBET) of Instituto de Tecnologia Química e Bioquímica (ITQB) under the direct supervision of Drª Sandra Sanches in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Prof. Drª Lélia Chambel was the internal designated supervisor in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Agradecimentos Gostaria de agradecer a todas as pessoas que estiveram directamente ou indirectamente envolvidas na execução da minha tese de mestrado, pois sem eles a sua realização não teria sido possível. Queria começar por agradecer à Doutora Sandra Sanches, que se demonstrou sempre disponível para esclarecer dúvidas quando precisei, e que fez questão de me ensinar de forma rigorosa e exigente. À Doutora Maria Teresa Crespo, que assim que lhe pedi para me orientar me disse que sim imediatamente, fez questão de me treinar em vários contextos e sempre estimulou o meu envolvimento nas rotinas do laboratório. À Professora Doutora Lélia Chambel, que sempre me esclareceu dúvidas sobre processos burocráticos, me deu conselhos quando eu mais precisei e que me apoiou durante toda a minha tese. Queria também agradecer à Doutora Dulce Brito, que sempre se mostrou disponível para ajudar quando a nossa equipa mais precisava dela, e sempre me ajudou a realizar as tarefas mais básicas do meu trabalho até eu ter ganho a minha autonomia no laboratório. -
EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI 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 Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Paludibacter Propionicigenes Type Strain (WB4)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Paludibacter propionicigenes type strain (WB4). Permalink https://escholarship.org/uc/item/4kr5k5w1 Journal Standards in genomic sciences, 4(1) ISSN 1944-3277 Authors Gronow, Sabine Munk, Christine Lapidus, Alla et al. Publication Date 2011 DOI 10.4056/sigs.1503846 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 4:36-44 DOI:10.4056/sigs.1503846 Complete genome sequence of Paludibacter propionicigenes type strain (WB4T) Sabine Gronow1, Christine Munk2,3, Alla Lapidus2, Matt Nolan2, Susan Lucas2, Nancy Hammon2, Shweta Deshpande2, Jan-Fang Cheng2, Roxane Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Natalia Ivanova2, Konstantinos Mavromatis2, Natalia Mikhailova2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Evelyne Brambilla1, Manfred Rohde6, Markus Göker1, John C. Detter2,3, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Nikos C. Kyrpides2, and Hans-Peter Klenk1* 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 Oak Ridge -
Page 1 of 41 RSC Advances
RSC Advances This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. This Accepted Manuscript will be replaced by the edited, formatted and paginated article as soon as this is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/advances Page 1 of 41 RSC Advances 1 Regulation of acidogenic metabolism towards enhanced short chain fatty acids biosynthesis 2 from waste: Metagenomic Profiling 3 4 Omprakash Sarkar, A. Naresh Kumar, Shikha Dahiya, K.Vamshi Krishna, Dileep Kumar 5 Yeruva, S.Venkata Mohan* 6 Bioengineering and Environmental Sciences (BEES), CSIR-Indian Institute of Chemical 7 Technology (CSIR-IICT), Hyderabad 500 007, India 8 *E-mail: [email protected]; Tel: 0091-40-27161765 9 10 Abstract 11 Short chain carboxylic (volatile fatty) acids (VFA) production in mixed microbiomes is majorly 12 limited by the prevalence of the methanogenic bacteria and availability of substrate from waste 13 to the biocatalyst during the fermentation process. -
Determining the Culturability of the Rumen Bacterial Microbiome
bs_bs_banner Determining the culturability of the rumen bacterial microbiome Christopher J. Creevey,1,2 William J. Kelly,3,4* list of cultured rumen isolates that are representative Gemma Henderson3,4 and Sinead C. Leahy3,4 of abundant, novel and core bacterial species in the 1Animal and Bioscience Research Department, Animal rumen. In addition, we have identified taxa, particu- and Grassland Research and Innovation Centre, larly within the phylum Bacteroidetes, where further Teagasc, Grange, Dunsany, Co. Meath, Ireland. cultivation efforts are clearly required. 2Institute of Biological, Environmental and Rural This information is being used to guide the isola- Sciences, Aberystwyth University, Aberystwyth, tion efforts and selection of bacteria from the rumen Ceredigion, UK. microbiota for sequencing through the Hungate1000. 3Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand. Introduction 4New Zealand Agricultural Greenhouse Gas Research Ruminants have evolved a symbiotic relationship with a Centre, Palmerston North, New Zealand. complex microbiome consisting of bacteria, archaea, fungi, protozoa, and viruses located in their fore-stomach Summary (reticulorumen) that allows these animals to utilize the lignocellulose component of plant material as their main The goal of the Hungate1000 project is to generate a energy source. The microbial degradation of lignocellu- reference set of rumen microbial genome sequences. lose, and fermentation of the released soluble sugars, Toward this goal we have carried out a meta-analysis produces short-chain fatty acids that are absorbed across using information from culture collections, scientific the rumen epithelium and utilized by the ruminant for literature, and the NCBI and RDP databases and growth, while the microbial cells pass from the rumen to linked this with a comparative study of several rumen the digestive tract where they become the main source of 16S rRNA gene-based surveys. -
Genomic Characterization of the Uncultured Bacteroidales Family S24-7 Inhabiting the Guts of Homeothermic Animals Kate L
Ormerod et al. Microbiome (2016) 4:36 DOI 10.1186/s40168-016-0181-2 RESEARCH Open Access Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals Kate L. Ormerod1, David L. A. Wood1, Nancy Lachner1, Shaan L. Gellatly2, Joshua N. Daly1, Jeremy D. Parsons3, Cristiana G. O. Dal’Molin4, Robin W. Palfreyman4, Lars K. Nielsen4, Matthew A. Cooper5, Mark Morrison6, Philip M. Hansbro2 and Philip Hugenholtz1* Abstract Background: Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host. Results: Here, we provide the first whole genome exploration of this family, for which we propose the name “Candidatus Homeothermaceae,” using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of “Ca. Homeothermaceae” to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates. Conclusions: “Ca. Homeothermaceae” representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. -
Discovery of Novel Enzymes with Industrial Potential from a Cold and Alkaline Environment by a Combination of Functional Metagenomics and Culturing
Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing Vester, Jan Kjølhede; Glaring, Mikkel Andreas; Stougaard, Peter Published in: Microbial Cell Factories DOI: 10.1186/1475-2859-13-72 Publication date: 2014 Document version Publisher's PDF, also known as Version of record Citation for published version (APA): Vester, J. K., Glaring, M. A., & Stougaard, P. (2014). Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing. Microbial Cell Factories, 13, [72]. https://doi.org/10.1186/1475-2859-13-72 Download date: 08. apr.. 2020 Vester et al. Microbial Cell Factories 2014, 13:72 http://www.microbialcellfactories.com/content/13/1/72 RESEARCH Open Access Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing Jan Kjølhede Vester, Mikkel Andreas Glaring and Peter Stougaard* Abstract Background: The use of cold-active enzymes has many advantages, including reduced energy consumption and easy inactivation. The ikaite columns of SW Greenland are permanently cold (4-6°C) and alkaline (above pH 10), and the microorganisms living there and their enzymes are adapted to these conditions. Since only a small fraction of the total microbial diversity can be cultured in the laboratory, a combined approach involving functional screening of a strain collection and a metagenomic library was undertaken for discovery of novel enzymes from the ikaite columns. Results: A strain collection with 322 cultured isolates was screened for enzymatic activities identifying a large number of enzyme producers, with a high re-discovery rate to previously characterized strains. -
Cultivable, Host-Specific Bacteroidetes Symbionts Exhibit Diverse Polysaccharolytic Strategies
INVERTEBRATE MICROBIOLOGY crossm Cultivable, Host-Specific Bacteroidetes Symbionts Exhibit Diverse Polysaccharolytic Strategies Downloaded from Arturo Vera-Ponce de León,a Benjamin C. Jahnes,a,b Jun Duan,c Lennel A. Camuy-Vélez,b Zakee L. Sabreea aDepartment of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA bDepartment of Microbiology, The Ohio State University, Columbus, Ohio, USA cPathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada ABSTRACT Beneficial gut microbes can facilitate insect growth on diverse diets. The omnivorous American cockroach, Periplaneta americana (Insecta: Blattodea), http://aem.asm.org/ thrives on a diet rich in plant polysaccharides and harbors a species-rich gut micro- biota responsive to host diet. Bacteroidetes are among the most abundant taxa in P. americana and other cockroaches, based on cultivation-independent gut community profiling, and these potentially polysaccharolytic bacteria may contribute to host diet processing. Eleven Bacteroidetes isolates were cultivated from P. americana di- gestive tracts, and phylogenomic analyses suggest that they were new Bacteroides, Dysgonomonas, Paludibacter, and Parabacteroides species distinct from those previ- ously isolated from other insects, humans, and environmental sources. In addition, com- plete genomes were generated for each isolate, and polysaccharide utilization loci (PULs) on May 10, 2021 at Ohio State University and several non-PUL-associated carbohydrate-active enzyme (CAZyme)-coding genes that putatively target starch, pectin, and/or cellulose were annotated in each of the iso- late genomes. Type IX secretion system (T9SS)- and CAZyme-coding genes tagged with the corresponding T9SS recognition and export C-terminal domain were observed in some isolates, suggesting that these CAZymes were deployed via non-PUL outer membrane translocons. -
Impact of Intestinal Microbiota on Growth and Feed Efficiency
microorganisms Review Impact of Intestinal Microbiota on Growth and Feed Efficiency in Pigs: A Review Gillian E. Gardiner 1,* , Barbara U. Metzler-Zebeli 2 and Peadar G. Lawlor 3 1 Department of Science, Waterford Institute of Technology, X91 K0EK Co. Waterford, Ireland 2 Unit Nutritional Physiology, Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; [email protected] 3 Teagasc, Pig Development Department, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, P61 C996 Co. Cork, Ireland; [email protected] * Correspondence: [email protected]; Tel.: +353-51-302-626 Received: 2 October 2020; Accepted: 25 November 2020; Published: 28 November 2020 Abstract: This review summarises the evidence for a link between the porcine intestinal microbiota and growth and feed efficiency (FE), and suggests microbiota-targeted strategies to improve productivity. However, there are challenges in identifying reliable microbial predictors of host phenotype; environmental factors impact the microbe–host interplay, sequential differences along the intestine result in segment-specific FE- and growth-associated taxa/functionality, and it is often difficult to distinguish cause and effect. However, bacterial taxa involved in nutrient processing and energy harvest, and those with anti-inflammatory effects, are consistently linked with improved productivity. In particular, evidence is emerging for an association of Treponema and methanogens such as Methanobrevibacter in the small and large intestines and Lactobacillus in the large intestine with a leaner phenotype and/or improved FE. Bacterial carbohydrate and/or lipid metabolism pathways are also generally enriched in the large intestine of leaner pigs and/or those with better growth/FE. -
Diet Is Not the Primary Driver of Bacterial Community Structure in the Gut of Litter- Feeding Cockroaches Niclas Lampert1, Aram Mikaelyan1,2 and Andreas Brune1*
Lampert et al. BMC Microbiology (2019) 19:238 https://doi.org/10.1186/s12866-019-1601-9 RESEARCH ARTICLE Open Access Diet is not the primary driver of bacterial community structure in the gut of litter- feeding cockroaches Niclas Lampert1, Aram Mikaelyan1,2 and Andreas Brune1* Abstract Background: Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter. Results: The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood- feeding higher termites. Conclusion: Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.