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Mining Saltmarsh Sediment Microbes for Enzymes to Degrade Recalcitrant Biomass
Mining saltmarsh sediment microbes for enzymes to degrade recalcitrant biomass Juliana Sanchez Alponti PhD University of York Biology September 2019 Abstract Abstract The recalcitrance of biomass represents a major bottleneck for the efficient production of fermentable sugars from biomass. Cellulase cocktails are often only able to release 75-80% of the potential sugars from biomass and this adds to the overall costs of lignocellulosic processing. The high amounts of fresh water used in biomass processing also adds to the overall costs and environmental footprint of this process. A more sustainable approach could be the use of seawater during the process, saving the valuable fresh water for human consumption and agriculture. For such replacement to be viable, there is a need to identify salt tolerant lignocellulose-degrading enzymes. We have been prospecting for enzymes from the marine environment that attack the more recalcitrant components of lignocellulosic biomass. To achieve these ends, we have carried out selective culture enrichments using highly degraded biomass and inoculum taken from a saltmarsh. Saltmarshes are highly productive ecosystems, where most of the biomass is provided by land plants and is therefore rich in lignocellulose. Lignocellulose forms the major source of biomass to feed the large communities of heterotrophic organisms living in saltmarshes, which are likely to contain a range of microbial species specialised for the degradation of lignocellulosic biomass. We took biomass from the saltmarsh grass Spartina anglica that had been previously degraded by microbes over a 10-week period, losing 70% of its content in the process. This recalcitrant biomass was then used as the sole carbon source in a shake-flask culture inoculated with saltmarsh sediment. -
The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Multilayered Horizontal Operon Transfers from Bacteria Reconstruct a Thiamine Salvage Pathway in Yeasts
Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts Carla Gonçalvesa and Paula Gonçalvesa,1 aApplied Molecular Biosciences Unit-UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved September 22, 2019 (received for review June 14, 2019) Horizontal acquisition of bacterial genes is presently recognized as nisms presumed to have facilitated a transition from bacterial an important contribution to the adaptation and evolution of operon transcription to eukaryotic-style gene expression were eukaryotic genomes. However, the mechanisms underlying ex- proposed, such as gene fusion giving rise to multifunctional pro- pression and consequent selection and fixation of the prokaryotic teins (6, 23, 24), increase in intergenic distances between genes to genes in the new eukaryotic setting are largely unknown. Here we generate room for eukaryotic promoters, and independent tran- show that genes composing the pathway for the synthesis of the scription producing mRNAs with poly(A) tails have been dem- essential vitamin B1 (thiamine) were lost in an ancestor of a yeast onstrated (22). In the best documented study, which concerns a lineage, the Wickerhamiella/Starmerella (W/S) clade, known to bacterial siderophore biosynthesis operon acquired by yeasts be- harbor an unusually large number of genes of alien origin. The longing to the Wickerhamiella/Starmerella (W/S) clade, the bacte- thiamine pathway was subsequently reassembled, at least twice, rial genes acquired as an operon were shown to be functional (22). by multiple HGT events from different bacterial donors involving Thiamine, commonly known as vitamin B1, is essential for all both single genes and entire operons. -
Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified; -
Updating the Taxonomic Toolbox: Classification of Alteromonas Spp
1 Updating the taxonomic toolbox: classification of Alteromonas spp. 2 using Multilocus Phylogenetic Analysis and MALDI-TOF Mass 3 Spectrometry a a a 4 Hooi Jun Ng , Hayden K. Webb , Russell J. Crawford , François a b b c 5 Malherbe , Henry Butt , Rachel Knight , Valery V. Mikhailov and a, 6 Elena P. Ivanova * 7 aFaculty of Life and Social Sciences, Swinburne University of Technology, 8 PO Box 218, Hawthorn, Vic 3122, Australia 9 bBioscreen, Bio21 Institute, The University of Melbourne, Vic 3010, Australia 10 cG.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian 11 Academy of Sciences, Vladivostok 690022, Russian Federation 12 13 *Corresponding author: Tel: +61-3-9214-5137. Fax: +61-3-9214-5050. 14 E-mail: [email protected] 15 16 Abstract 17 Bacteria of the genus Alteromonas are Gram-negative, strictly aerobic, motile, 18 heterotrophic marine bacteria, known for their versatile metabolic activities. 19 Identification and classification of novel species belonging to the genus Alteromonas 20 generally involves DNA-DNA hybridization (DDH) as distinct species often fail to be 1 21 resolved at the 97% threshold value of the 16S rRNA gene sequence similarity. In this 22 study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix- 23 Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF 24 MS) for the differentiation of Alteromonas species has been evaluated. Phylogenetic 25 analysis incorporating five house-keeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) 26 revealed a threshold value of 98.9% that could be considered as the species cut-off 27 value for the delineation of Alteromonas spp. -
Prokaryotes Exposed to Elevated Hydrostatic Pressure - Daniel Prieur
EXTREMOPHILES – Vol. III - Piezophily: Prokaryotes Exposed to Elevated Hydrostatic Pressure - Daniel Prieur PIEZOPHILY: PROKARYOTES EXPOSED TO ELEVATED HYDROSTATIC PRESSURE Daniel Prieur Université de Bretagne occidentale, Plouzané, France. Keywords: archea, bacteria, deep biosphere, deep sea, Europa, exobiology, hydrothermal vents, hydrostatic pressure, hyperthermophile, Mars, oil reservoirs, prokaryote. Contents 1. Introduction 2. Deep-Sea Microbiology 2.1. A Brief History 2.2. Deep-Sea Psychrophiles 2.2.1. General Features 2.2.2. Adaptations to Elevated Hydrostatic Pressure 2.3. Deep-Sea Hydrothermal Vents 2.3.1. Deep-Sea Hyperthermophiles 2.3.2. Responses to Hydrostatic Pressure 3. Other Natural Environments Exposed to Hydrostatic Pressure 3.1. Deep Marine Sediments 3.2. Deep Oil Reservoirs 3.3. Deep Rocks and Aquifers 3.4. Sub-Antarctic Lakes 4. Other Worlds 4.1. Mars 4.2. Europa 5. Conclusions Acknowledgements Glossary Bibliography Biographical Sketch SummaryUNESCO – EOLSS All living organisms, and particularly prokaryotes, which colonize the most extreme environments, SAMPLEhave their physiology cont rolledCHAPTERS by a variety of physicochemical parameters whose different values contribute to the definition of biotopes. Hydrostatic pressure is one of the major parameters influencing life, but its importance is limited to only some environments, especially the deep sea. If the deep sea is defined as water layers below one kilometer depth, this amount of water, which is exposed to pressures up to 100 MPa, represents 62% of the volume of the total Earth biosphere. A rather small numbers of investigators have studied the prokaryotes that, alongside invertebrates and vertebrates, inhabit this extreme environment. Deep-sea prokaryotes show different levels of adaptation to elevated hydrostatic pressure, from the barosensitive organisms to the obligate piezophiles. -
Acinetobacter Baumannii – a Neglected Pathogen in Veterinary and Environmental Health in Germany
Veterinary Research Communications (2019) 43:1–6 https://doi.org/10.1007/s11259-018-9742-0 REVIEW ARTICLE Acinetobacter baumannii – a neglected pathogen in veterinary and environmental health in Germany Gamal Wareth1 & Heinrich Neubauer1 & Lisa D. Sprague1 Received: 25 October 2018 /Accepted: 6 December 2018 /Published online: 27 December 2018 # The Author(s) 2018 Abstract The emergence and global spread of drug resistant Acinetobacter (A.) baumannii is a cause of great concern. The current knowledge on antibiotic resistance in A. baumannii from animal origin is mostly based on few internationally published case reports, investigations of strain collections and several whole genome analyses. This lack of data results in a somewhat sketchy picture on how to assess the possible impact of drug resistant A. baumannii strains on veterinary and public health in Germany. Consequently, there is an urgent need to intensify the surveillance of A. baumannii in pet animals, the farm animal population and wildlife. Keywords Acinetobacter baumannii . Review . Antibiotic resistance . Germany Introduction limited number of widespread clones appear to be responsible for hospital outbreaks in many countries (Diancourt et al. Acinetobacter (A.) baumannii is a gram-negative opportunis- 2010). Eight international clonal lineages have been described tic nosocomial pathogen belonging to the genus Acinetobacter so far and comparative typing of outbreak strains obtained all and a member of the family Moraxellaceae. Acinetobacter over Europe revealed the dominance of three clones, original- spp. are non-motile, non-fastidious Gram-negative, non- ly named European clones I-III (Dijkshoorn et al. 1996; Karah fermenting, catalase positive, oxidase negative, strictly aero- et al. -
Characterization of a Microbial Community Capable of Nitrification At
Bioresource Technology 101 (2010) 491–500 Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Characterization of a microbial community capable of nitrification at cold temperature Thomas F. Ducey *, Matias B. Vanotti, Anthony D. Shriner, Ariel A. Szogi, Aprel Q. Ellison Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, USDA, 2611 West Lucas Street, Florence, SC 29501, United States article info abstract Article history: While the oxidation of ammonia is an integral component of advanced aerobic livestock wastewater Received 5 February 2009 treatment, the rate of nitrification by ammonia-oxidizing bacteria is drastically reduced at colder temper- Received in revised form 30 July 2009 atures. In this study we report an acclimated lagoon nitrifying sludge that is capable of high rates of nitri- Accepted 30 July 2009 fication at temperatures from 5 °C (11.2 mg N/g MLVSS/h) to 20 °C (40.4 mg N/g MLVSS/h). The Available online 5 September 2009 composition of the microbial community present in the nitrifying sludge was investigated by partial 16S rRNA gene sequencing. After DNA extraction and the creation of a plasmid library, 153 partial length Keywords: 16S rRNA gene clones were sequenced and analyzed phylogenetically. Over 80% of these clones were Nitrite affiliated with the Proteobacteria, and grouped with the b- (114 clones), - (7 clones), and -classes (2 Ammonia-oxidizing bacteria c a Nitrosomonas clones). The remaining clones were affiliated with the Acidobacteria (1 clone), Actinobacteria (8 clones), Activated sludge Bacteroidetes (16 clones), and Verrucomicrobia (5 clones). The majority of the clones belonged to the genus 16S rRNA gene Nitrosomonas, while other clones affiliated with microorganisms previously identified as having floc forming or psychrotolerance characteristics. -
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 -
Linking the Resistome and Plasmidome to the Microbiome
The ISME Journal (2019) 13:2437–2446 https://doi.org/10.1038/s41396-019-0446-4 ARTICLE Linking the resistome and plasmidome to the microbiome 1,2 3 3 3 1,2 Thibault Stalder ● Maximilian O. Press ● Shawn Sullivan ● Ivan Liachko ● Eva M. Top Received: 15 February 2019 / Revised: 2 May 2019 / Accepted: 10 May 2019 / Published online: 30 May 2019 © The Author(s) 2019. This article is published with open access Abstract The rapid spread of antibiotic resistance among bacterial pathogens is a serious human health threat. While a range of environments have been identified as reservoirs of antibiotic resistance genes (ARGs), we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to our inability to identify the natural bacterial hosts of ARGs and the mobile genetic elements that mediate this spread, such as plasmids and integrons. Here we demonstrate that the in vivo proximity-ligation method Hi-C can reconstruct a known plasmid-host association from a wastewater community, and identify the in situ host range of ARGs, plasmids, and integrons by physically linking them to their host chromosomes. Hi-C detected both previously known and novel associations between ARGs, mobile genetic elements and host genomes, thus validating this method. We showed that IncQ plasmids and class 1 integrons had the broadest host range in this wastewater, and identified bacteria belonging to Moraxellaceae, Bacteroides,andPrevotella, and 1234567890();,: 1234567890();,: especially Aeromonadaceae as the most likely reservoirs of ARGs in this community. A better identification of the natural carriers of ARGs will aid the development of strategies to limit resistance spread to pathogens. -
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. -
Alishewanella Jeotgali Sp. Nov., Isolated from Traditional Fermented Food, and Emended Description of the Genus Alishewanella
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2313–2316 DOI 10.1099/ijs.0.007260-0 Alishewanella jeotgali sp. nov., isolated from traditional fermented food, and emended description of the genus Alishewanella Min-Soo Kim,1,2 Seong Woon Roh,1,2 Young-Do Nam,1,2 Ho-Won Chang,1 Kyoung-Ho Kim,1 Mi-Ja Jung,1 Jung-Hye Choi,1 Eun-Jin Park1 and Jin-Woo Bae1,2 Correspondence 1Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee Jin-Woo Bae University, Seoul 130-701, Republic of Korea [email protected] 2University of Science and Technology, Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea A novel Gram-negative and facultative anaerobic strain, designated MS1T, was isolated from gajami sikhae, a traditional fermented food in Korea made from flatfish. Strain MS1T was motile, rod-shaped and oxidase- and catalase-positive, and required 1–2 % (w/v) NaCl for growth. Growth occurred at temperatures ranging from 4 to 40 6C and the pH range for optimal growth was pH 6.5–9.0. Strain MS1T was capable of reducing trimethylamine oxide, nitrate and thiosulfate. Phylogenetic analysis placed strain MS1T within the genus Alishewanella. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MS1T was related closely to Alishewanella aestuarii B11T (98.67 % similarity) and Alishewanella fetalis CCUG 30811T (98.04 % similarity). However, DNA–DNA reassociation experiments between strain MS1T and reference strains showed relatedness values ,70 % (42.6 and 14.8 % with A.