Evaluation of the H2S Method for Detection of Fecal Contamination of Drinking Water
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The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment. -
Impacts of Desulfobacterales and Chromatiales on Sulfate Reduction in The
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.16.252635; this version posted November 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Impacts of Desulfobacterales and Chromatiales on sulfate reduction in the 2 subtropical mangrove ecosystem as revealed by SMDB analysis 3 Shuming Mo 1, †, Jinhui Li 1, †, Bin Li 2, Ran Yu 1, Shiqing Nie 1, Zufan Zhang 1, Jianping 4 Liao 3, Qiong Jiang 1, Bing Yan 2, *, and Chengjian Jiang 1, 2 * 5 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro- 6 bioresources, Guangxi Research Center for Microbial and Enzyme Engineering 7 Technology, College of Life Science and Technology, Guangxi University, Nanning 8 530004, China. 9 2 Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove 10 Research Center, Guangxi Academy of Sciences, Beihai 536000, China. 11 3 School of Computer and Information Engineering, Nanning Normal University, 12 Nanning 530299, China. 13 † These authors contributed equally to this work. 14 *: Corresponding Author: 15 Tel: +86-771-3270736; Fax: +86-771-3237873 16 Email: [email protected] (CJ); [email protected] (BY) 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.16.252635; this version posted November 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Exploring the Lipidomes of Shallow-Water and Deep-Sea Hydrothermal Systems
Exploring the lipidomes of shallow-water and deep-sea hydrothermal systems Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - Am Fachbereich Geowissenschaften der Universität Bremen vorgelegt von Miriam Sollich Bremen Mai 2018 1. Gutachter: Dr. Solveig I. Bühring 2. Gutachter: Associate Prof. Dr. Eoghan P. Reeves Tag des Promotionskolloquiums:16. Februar 2018 Den Wissenschaftlern geht es wie den Chaoten. Es ist alles da, man muss es nur suchen. - Franz Kern - CONTENTS Abstract Zusammenfassung Acknowledgements List of Abbreviations Chapter I 1 Introduction and Methods Chapter II 37 Scope and Outline Chapter III 43 Heat stress dictates the microbial lipid composition along a thermal gradient in marine sediments Chapter IV 91 Shallow-water hydrothermal systems offer ideal conditions to study archaeal lipid membrane adaptations to environmental extremes Chapter V 113 Transfer of chemosynthetic fixed carbon and its ecological significance revealed by lipid analysis of fluids at diffuse flow deep-sea vents (East Pacific Rise 9°50’N) Chapter VI 143 Concluding Remarks and Future Perspectives ABSTRACT Shallow-water and deep-sea hydrothermal systems are environments where seawater percolates downward through fractures in the oceanic crust, and becomes progressively heated and chemically altered. Finally, the entrained water is expelled into the overlying water column as a hydrothermal fluid. Hydrothermal circulation occurs at all active plate boundaries like mid-ocean ridges, submarine volcanic arcs and backarc basins. They represent one of the most extreme and dynamic ecosystems on the planet with steep physico-chemical gradients. Nevertheless, these environments are characterized by exceptional high biomass representing hotspots of life in the mostly hostile and desolated deep sea. -
High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-Methylalkyl)Succinate Synthase Genes
ORIGINAL RESEARCH published: 07 January 2016 doi: 10.3389/fmicb.2015.01511 High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes Marion H. Stagars1,S.EmilRuff1,2† , Rudolf Amann1 and Katrin Knittel1* 1 Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany, 2 HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen, Germany Edited by: Alkanes comprise a substantial fraction of crude oil and are prevalent at marine seeps. Hans H. Richnow, These environments are typically anoxic and host diverse microbial communities that Helmholtz Centre for Environmental Research, Germany grow on alkanes. The most widely distributed mechanism of anaerobic alkane activation Reviewed by: is the addition of alkanes to fumarate by (1-methylalkyl)succinate synthase (Mas). Here Beth Orcutt, we studied the diversity of MasD, the catalytic subunit of the enzyme, in 12 marine Bigelow Laboratory for Ocean sediments sampled at seven seeps. We aimed to identify cosmopolitan species as well Sciences, USA Zhidan Liu, as to identify factors structuring the alkane-degrading community. Using next generation China Agricultural University, China sequencing we obtained a total of 420 MasD species-level operational taxonomic units *Correspondence: (OTU0.96) at 96% amino acid identity. Diversity analysis shows a high richness and Katrin Knittel [email protected] evenness of alkane-degrading bacteria. Sites with similar hydrocarbon composition harbored similar alkane-degrading communities based on MasD genes; the MasD †Present address: community structure is clearly driven by the hydrocarbon source available at the various S. -
Advance View Proofs
M&E Papers in Press. Published online on March 23, 2012 doi:10.1264/jsme2.ME11357 1 2 Revised ME11357 3 4 Isolation and Characterization of Novel Sulfate-Reducing Bacterium Capable of 5 Anaerobic Degradation of p-Xylene 6 * 7 YURIKO HIGASHIOKA, HISAYA KOJIMA , AND MANABU FUKUI 8 9 The Institute of Low Temperature Science, Hokkaido University, Nishi 8, Kita 19, 10 Kita-ku, Sapporo, Hokkaido 060-0819, Japan 11 Proofs 12 (Received December 21, 2011-Accepted February 2, 2012) 13 View 14 Running headline: p-Xylene-Degrading Sulfate Reducer 15 16 * Corresponding author. E-mail: [email protected]; Tel: 17 +81-11-706-5460;Advance Fax: +81-11-706-5460. 18 19 20 21 1 Copyright 2012 by the Japanese Society of Microbial Ecology / the Japanese Society of Soil Microbiology 22 A novel strain of p-xylene-degrading sulfate reducer was isolated in pure culture. 23 Strain PP31 was obtained from a p-xylene-degrading enrichment culture established 24 from polluted marine sediment. Analyses of the 16S rRNA gene and two functional 25 genes involved in sulfate respiration and anaerobic degradation of aromatic compounds 26 revealed that the isolate was closely related to members of the genus Desulfosarcina. 27 Strain PP31 was capable of growing on p-xylene under sulfate-reducing conditions, and 28 the ratio of generated sulfide and consumed p-xylene suggested complete oxidation by 29 the novel isolate. The strain could not grow on benzene, toluene, ethylbenzene, 30 m-xylene o-xylene, or n-hexane as an electron donor. Strain PP31 is the first isolated 31 bacterium that degrades p-xylene anaerobically, and will be useful to understanding the 32 mechanism of anaerobic degradation of p-xylene. -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Abundance and Diversity of Sulphate-Reducing Bacterioplankton in Lake Suigetsu, a Meromictic Lake in Fukui, Japan
Plankton Benthos Res 1(4): 165–177, 2006 Plankton & Benthos Research © The Plankton Society of Japan Abundance and diversity of sulphate-reducing bacterioplankton in Lake Suigetsu, a meromictic lake in Fukui, Japan RYUJI KONDO*, KYOKO OSAWA, LISA MOCHIZUKI, YUKIYASU FUJIOKA & JUNKI BUTANI Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui 917–0003, Japan Received 10 July 2006; Accepted 14 September 2006 Abstract: The depth distribution of sulphate-reducing bacteria (SRB) in the water column of a meromictic lake, Lake Suigetsu, Fukui, Japan was investigated using quantitative competitive PCR targeting the gene coding for portions of the a-subunit of dissimilatory sulphite reductase (dsrA). The total bacterial cell density (DAPI count) was 5Ϫ13ϫ106 cells mLϪ1 in the water column of the lake with maximum abundance occurring at the oxic-anoxic interface layer. SRB were not detected in oxic surface water using competitive PCR. SRB were found in the anoxic waters below the oxy- cline ranging from 104 to 105 cells mLϪ1, accounting for 0.3–8.9% of the total bacteria. The SRB cell densities were higher than previously estimated using the most-probable-number (MPN) method. Sequencing of the cloned PCR prod- uct of dsrA showed the existence of different SRB groups in the anoxic water. The majority of the dsrA sequences were associated with the Desulfosarcina-Desulfococcus-Desulfonema group and members of the Desulfobulbaceae family. Other dsrA clones belonged to the Desulfomicrobium and Desulfovibrio species as well as to a deeply branched group in the dsrA tree with no representatives from previously isolated SRB groups. These SRB species appear to be impor- tant for the sulphur and carbon cycle in the anoxic waters of Lake Suigetsu. -
Characterization of the Deltaproteobacteria in Contaminated and Uncontaminated Stream Sediments and Identification of Potential Mercury Methylators
Vol. 66: 271–282, 2012 AQUATIC MICROBIAL ECOLOGY Published online July 9 doi: 10.3354/ame01563 Aquat Microb Ecol Characterization of the Deltaproteobacteria in contaminated and uncontaminated stream sediments and identification of potential mercury methylators Jennifer J. Mosher1,3, Tatiana A. Vishnivetskaya1,4, Dwayne A. Elias1, Mircea Podar1, Scott C. Brooks2, Steven D. Brown1, Craig C. Brandt1, Anthony V. Palumbo1,* 1Biosciences Division, and 2Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA 3Present address: Stroud Water Research Center, Avondale, Pennsylvania 19311, USA 4Present address: Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37998, USA ABSTRACT: Microbial communities were examined in surface stream sediments at 5 conta - minated sites and 1 control site near Oak Ridge, TN, USA, to identify bacteria that could be con- tributing to mercury (Hg) methylation. The phylogenetic composition of the sediment bacterial community was examined over 3 quarterly sampling periods (36 samples) using 16S rRNA gene pyro sequencing. Only 3064 sequences (0.85% of the total community) were identified as Delta - proteobacteria, the only group known to methylate Hg, using the Ribosomal Database Project classifier at the 99% confidence threshold. Constrained ordination techniques indicated statisti- cally significant positive linear correlations between Desulfobulbus spp., Desulfonema spp. and Desulfobacca spp. and methyl-Hg concentrations at the Hg-contaminated sites. In contrast, the distribution of organisms related to Byssovorax spp. was significantly correlated to inorganic car- bon, nitrate and uranium concentrations but not to Hg or methyl-Hg. Overall, the abundance and richness of Deltaproteobacteria sequences were higher in uncontaminated sediments, while the majority of the members present at the contaminated sites were either known potential metal- reducers/methylators or metal tolerant species. -
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Vol. 86: 1–19, 2021 AQUATIC MICROBIAL ECOLOGY Published online January 28 https://doi.org/10.3354/ame01954 Aquat Microb Ecol OPEN ACCESS Nitrogen cycling in coastal sediment microbial communities with seasonally variable benthic nutrient fluxes Alexis J. Marshall1,2,5,*, Andrew Longmore3, Lori Phillips2,6, Caixian Tang1, Helen L. Hayden2, Karla B. Heidelberg4, Pauline Mele1,2 1La Trobe University, AgriBio Centre for AgriBiosciences, Melbourne, VIC 3086, Australia 2Agriculture Victoria, Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Melbourne, VIC 3086, Australia 3Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, VIC 3010, Australia 4The University of Southern California, Department of Biology, Los Angeles, CA 90089, USA 5Present address: University of Waikato, Hillcrest, Hamilton 3216, New Zealand 6Present address: Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON N0R1G0, Canada ABSTRACT: Benthic microbial communities contribute to nitrogen (N) cycling in coastal ecosystems through taxon-specific processes such as anammox, nitrification and N-fixation and community attributed pathways such as denitrification. By measuring the total (DNA-based) and active (RNA- based) surface sediment microbial community composition and the abundance and activity profiles of key N-cycling genes in a semi-enclosed embayment — Port Phillip Bay (PPB), Australia — we show that although the total relative abundance of N-cycling taxa is comparatively lower close to estuary inputs (Hobsons Bay [HB]), the capacity for this community to perform diverse N-cycling processes is comparatively higher than in sediments isolated from inputs (Central PPB [CPPB]). In HB, seasonal structuring of the sediment microbial community occurred between spring and sum- mer, co-occurring with decreases in the activity profiles of anammox bacteria and organic carbon content. -
Microscopic Methods for Identification of Sulfate-Reducing Bacteria From
International Journal of Molecular Sciences Review Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats Ivan Kushkevych 1,* , Blanka Hýžová 1, Monika Vítˇezová 1 and Simon K.-M. R. Rittmann 2,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (B.H.); [email protected] (M.V.) 2 Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Wien, Austria * Correspondence: [email protected] (I.K.); [email protected] (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.) Abstract: This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications Citation: Kushkevych, I.; Hýžová, B.; was described. -
Molecular Approaches to Marine Microbial Ecology and the Marine Nitrogen Cycle
18 Mar 2005 11:48 AR AR233-EA33-10.tex XMLPublishSM(2004/02/24) P1: KUV 10.1146/annurev.earth.33.092203.122514 Annu. Rev. Earth Planet. Sci. 2005. 33:301–33 doi: 10.1146/annurev.earth.33.092203.122514 Copyright c 2005 by Annual Reviews. All rights reserved First published online as a Review in Advance on December 15, 2004 MOLECULAR APPROACHES TO MARINE MICROBIAL ECOLOGY AND THE MARINE NITROGEN CYCLE Bess B. Ward Department of Geosciences, Princeton University, Princeton, New Jersey 08544; email: [email protected] KeyWords 16S rRNA, diversity, functional genes, gene expression, genomics ■ Abstract Microbes are recognized as important components of the Earth system, playing key roles in controlling the composition of the atmosphere and surface waters, forming the basis of the marine food web, and the cycling of chemicals in the ocean. A revolution in microbial ecology has occurred in the past 15–20 years with the advent of rapid methods for discovering and sequencing the genes of uncultivated microbes from natural environments. Initially based on sequences from the 16S rRNA gene, this revolution made it possible to identify microorganisms without first cultivating them, to discover and characterize the immense previously unsuspected diversity of the microbial world, and to reconstruct the evolutionary relationships among microbes. Subsequent focus on functional genes, those that encode enzymes that catalyze bio- geochemical transformations, and current work on larger DNA fragments and entire genomes make it possible to link microbial diversity to ecosystem function. These approaches have yielded insights into the regulation of microbial activity and proof of the microbial role in biogeochemical processes previously unknown. -
Ecophysiology of Sulfate-Reducing Bacteria and Syntrophic Communities in Marine Anoxic Sediments” Derya Özüölmez Wageningen, 12 September 2017
Propositions 1. Prolonged incubation is a key strategy toward the enrichment of marine syntrophs. (this thesis) 2. Hydrogen-consuming methanogens can effectively compete with hydrogen- consuming sulfate reducers even at high sulfate concentration. (this thesis) 3. The plastic-eating wax worm, Galleria mellonella, can help cleaning up existing plastic mass (Bombelli et al. 2017, Current Biology 27(8): 292-293), but the real solution to environmental pollution still relies on shifting from disposable plastics to reusable and biodegradable materials. 4. With the discovery of abundant molecular hydrogen in Enceladus’ salty ocean (Waite et al. (2017) Science 356:6334, 155-159) extraterrestrial life in our solar system has become highly probable, and should shift our life-hunting focus from distant stars to our nearby neighbors. 5. With the "Help me to do it myself" motto, the Montessori education leads children to grow into mature, creative and self-confident adults. 6. Nothing is impossible as long as the dream is held close to the heart and patience and persistence are applied for the accomplishment. Propositions belonging to the PhD thesis entitled: “Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments” Derya Özüölmez Wageningen, 12 September 2017 Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments Derya Özüölmez Thesis committee Promotor Prof. Dr Alfons J.M. Stams Personal chair at the Laboratory of Microbiology Wageningen University & Research Co-promotor Dr Caroline M. Plugge Associate professor, Laboratory of Microbiology Wageningen University & Research Other members Prof. Dr Tinka Murk, Wageningen University & Research Prof. Dr Gerard Muyzer, University of Amsterdam, The Netherlands Prof.