DOCSLIB.ORG

The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance fmicb-10-00247 February 11, 2019 Time: 18:14 # 1 Erschienen in: Frontiers in Microbiology ; 10 (2019). - 247 http://dx.doi.org/10.3389/fmicb.2019.00247 ORIGINAL RESEARCH published: 13 February 2019 doi: 10.3389/fmicb.2019.00247 The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance Susanne Wörner1,2 and Michael Pester1,2,3* 1 Department of Biology, University of Konstanz, Konstanz, Germany, 2 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell cultures, Braunschweig, Germany, 3 Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany Active sulfate-reducing microorganisms (SRM) in freshwater sediments are under- examined, despite the well-documented cryptic sulfur cycle occurring in these low- Edited by: sulfate habitats. In Lake Constance sediment, sulfate reduction rates of up to 1,800 nmol Kenneth Wasmund, cm−3 day−1 were previously measured. To characterize its SRM community, we used University of Vienna, Austria a tripartite amplicon sequencing approach based on 16S rRNA genes, 16S rRNA, Reviewed by: Paula Dalcin Martins, and dsrB transcripts (encoding the beta subunit of dissimilatory sulfite reductase). Radboud University Nijmegen, We followed the respective amplicon dynamics in four anoxic microcosm setups Netherlands supplemented either with (i) chitin and sulfate, (ii) sulfate only, (iii) chitin only, or Christina Pavloudi, Hellenic Centre for Marine Research (iv) no amendment. Chitin was used as a general substrate for the whole carbon (HCMR), Greece degradation chain. Sulfate turnover in sulfate-supplemented microcosms ranged from Jesse G. Dillon, −1 −1 California State University, Long 38 to 955 nmol day (g sediment f. wt.) and was paralleled by a decrease of Beach, United States 90–100% in methanogenesis as compared to the respective methanogenic controls. *Correspondence: In the initial sediment, relative abundances of recognized SRM lineages accounted for Michael Pester 3.1 and 4.4% of all bacterial 16S rRNA gene and 16S rRNA sequences, respectively. [email protected] When normalized against the 1.4 × 108 total prokaryotic 16S rRNA gene copies as Specialty section: determined by qPCR and taking multiple rrn operons per genome into account, this This article was submitted to 5 6 −1 Aquatic Microbiology, resulted in approximately 10 –10 SRM cells (g sediment f. wt.) . The three amplicon a section of the journal approaches jointly identified Desulfobacteraceae and Syntrophobacteraceae as the Frontiers in Microbiology numerically dominant and transcriptionally most active SRM in the initial sediment. Received: 09 November 2018 This was corroborated in the time course analyses of sulfate-consuming sediment Accepted: 30 January 2019 Published: 13 February 2019 microcosms irrespective of chitin amendment. Uncultured dsrAB family-level lineages Citation: constituted in sum only 1.9% of all dsrB transcripts, with uncultured lineage 5 and 6 Wörner S and Pester M (2019) being transcriptionally most active. Our study is the first holistic molecular approach to The Active Sulfate-Reducing Microbial Community in Littoral Sediment quantify and characterize active SRM including uncultured dsrAB lineages not only in of Oligotrophic Lake Constance. Lake Constance but for lake sediments in general. Front. Microbiol. 10:247. doi: 10.3389/fmicb.2019.00247 Keywords: lake sediment, next-generation amplicon sequencing, chitin, sulfate reduction, dsrB transcripts Frontiers in Microbiology| www.frontiersin.org 1 February 2019| Volume 10| Article 247 Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-2-dtsrg0xr6hqj6 fmicb-10-00247 February 11, 2019 Time: 18:14 # 2 Wörner and Pester Active Sulfate Reducers in Lake Sediments INTRODUCTION so far not associated with this metabolic trait (Anantharaman et al., 2018; Hausmann et al., 2018; Zecchin et al., 2018). These Lake Constance is a typical pre-alpine lake that has currently included among others the Acidobacteria, Planctomycetes, an oligotrophic status and is oxygenated down to the sediment Verrucomicrobia, and Armatimonadetes. In specific, 8 of these (Güde and Straile, 2016). Within the first millimeters of its 13 newly identified SRM groups are candidate phyla without sediment, oxygen is completely depleted (Gerhardt et al., 2005) isolated representatives (Anantharaman et al., 2018). In parallel, leaving room for anaerobic degradation of organic matter either microbial diversity assays based on the functional marker genes by fermenters that share their degradation products (acetate dsrAB, which encode the dissimilatory sulfite reductase and and H2) with methanogenic archaea (Rothfuss and Conrad, 1993; are commonly used as diagnostic markers in detecting SRM, Thebrath et al., 1993) or by nitrate- (Hauck et al., 2001), Fe (III)- indicate an even larger phylogenetic diversity with at least 13 (Gerhardt et al., 2005), humic acid- (Kappler et al., 2004), and uncultured family-level dsrAB lineages (Pester et al., 2012; Müller sulfate-reducing microorganisms (Bak and Pfennig, 1991a,b). et al., 2015). So far, the latter only partially overlap with the A major component of organic matter entering the sediment metagenome-discovered putative SRM, e.g., uncultured dsrAB is chitin as an abundant biopolymer in aquatic environments lineage 8 is represented by Acidobacteria (Hausmann et al., (Gooday, 1990; Cauchie, 2002). It consists of linked amino-sugar 2018) and uncultured dsrAB lineage 13 is closely related to subunits with ß-1,4-N-acetyl-D-glucosamine as the monomeric mesophilic Nitrospirae (Zecchin et al., 2018). Extending upon structure and serves as structural element in the exoskeleton of the phylogenetic framework for dsrAB genes that was proposed arthropods (e.g., zooplankton) and the cell wall of fungi and by Müller et al.(2015), a recent dsrB amplicon survey of 200 certain algae and protozoa (Gooday, 1990). The estimated annual environmental samples including various freshwater habitats production of 28 × 106 tons by crustaceans and insects in increased the number of known species-level operational freshwater ecosystems and its efficient turnover in freshwater taxonomic units (OTUs) related to potential SRM from ca. 800 sediments (50–75%, Beier and Bertilsson, 2013) indicate chitin as (Müller et al., 2015) to more than 150,000 (Vigneron et al., 2018). an important carbon and nitrogen source for microorganisms in Considering the ca. 240 cultivated sulfate-reducing microbial these habitats (Gooday, 1990; Cauchie, 2002). species (Rabus et al., 2013), this result uncovered that less than In Lake Constance, sulfate concentrations of 50–300 mM can 0.2% of all potential SRM are available in pure culture. The same be measured in the upper layers of the littoral sediments. Here, study revealed that among uncultured SRM those belonging to maximum sulfate reduction rates (SRR) as determined using uncultured dsrAB lineage 5 are quite prevalent in freshwater 35 2− −3 S-SO4 as a radiotracer reached values of 1,800 nmol cm habitats (Vigneron et al., 2018). day−1 at 1–2 cm sediment depth (Bak and Pfennig, 1991a). This Despite the importance of sulfate reduction for the sediment surpasses typical SRR in sulfate-rich marine surface sediments biogeochemistry of Lake Constance as a typical freshwater lake, by one order of magnitude, where sulfate reduction is one of its SRM community is so far very poorly characterized. The the major anaerobic carbon degradation pathways (Jørgensen, only attempt was based on enrichment cultures grown on H2, 1982; Bowles et al., 2014). The high SRR at concomitant low lactate, acetate, propionate or long chain fatty acids, with isolates sulfate concentrations in Lake Constance are explained by a fast being affiliated to the genera Desulfovibrio, Desulfobulbus, and and effective cycling of sulfur species between their oxidized and Desulfotomaculum (Bak and Pfennig, 1991b). Therefore, we reduced states, which is controlled by a cryptic sulfur cycle as attempted to systematically analyze and quantify the littoral is typical for freshwater sediments and wetlands (Pester et al., SRM community of Lake Constance using a tripartite, high 2012). In particular, sulfide as the end product of sulfate reduction throughput amplicon sequencing approach based on 16S rRNA does not accumulate beyond 80 mM in littoral sediments of Lake genes, 16S rRNA, and dsrB transcripts. To delineate active Constance (Gerhardt, 2004), but is likely rapidly re-oxidized back SRM, sediment was incubated in the presence of chitin as to sulfate at oxic-anoxic interfaces or under completely anoxic a general substrate for the complete anaerobic degradation conditions using nitrate, Fe (III), or humic acids as electron network in the presence and absence of externally supplied acceptor (Pester et al., 2012). SRR in Lake Constance sediments pulses of sulfate. This was compared to sediment incubated are saturated at 60 mM sulfate, reaching maximum values of with sulfate pulses only or without any external additions. Our 3,000 nmol cm−3 day−1 in sediment slurries (Bak and Pfennig, results show that SRM constitute about 3% of the total bacterial 1991a). This shows that SRR are not limited by the prevailing sediment community with their major representatives being sulfate concentrations in Lake Constance (Bak and Pfennig, affiliated to the deltaproteobacterial families Desulfobacteraceae 1991a; Güde and Straile, 2016), which is also true for many other and Syntrophobacteraceae. freshwater lakes
Load more

Recommended publications
  • Thermophilic Anaerobic Digestion of Second Cheese Whey: Microbial Community Response to H2 Addition in a Partially Immobilized Anaerobic Hybrid Reactor
    processes Article Thermophilic Anaerobic Digestion of Second Cheese Whey: Microbial Community Response to H2 Addition in a Partially Immobilized Anaerobic Hybrid Reactor Giuseppe Lembo 1,2, Silvia Rosa 1, Valentina Mazzurco Miritana 1,3 , Antonella Marone 4, Giulia Massini 1, Massimiliano Fenice 2 and Antonella Signorini 1,* 1 Department of Energy Technologies and Renewable Source, Casaccia Research Center, ENEA-Italian Agency for New Technologies, Energy and Sustainable Development, Via Anguillarese 301, 00123 Rome, Italy; [email protected] (G.L.); [email protected] (S.R.); [email protected] (V.M.M.); [email protected] (G.M.) 2 Ecological and Biological Sciences Department, University of Tuscia, 01100 Viterbo, Italy; [email protected] 3 Water Research Institute, National Research Council (IRSA-CNR) Via Salaria km 29,300-C.P. 10, Monterotondo Street, 00015 Rome, Italy 4 Department of Energy Efficiency Unit, Casaccia Research Center, ENEA-Italian Agency for New Technologies, Energy and Sustainable Development, Via Anguillarese 301, 00123 Rome, Italy; [email protected] * Correspondence: [email protected] Abstract: In this study, we investigated thermophilic (55 ◦C) anaerobic digestion (AD) performance and microbial community structure, before and after hydrogen addition, in a novel hybrid gas-stirred tank reactor (GSTR) implemented with a partial immobilization of the microbial community and fed with second cheese whey (SCW). The results showed that H2 addition led to a 25% increase in the methane production rate and to a decrease of 13% in the CH4 concentration as compared with the control. The recovery of methane content (56%) was reached by decreasing the H2 flow rate.
    [Show full text]
  • Quasialign: Position Sensitive P-Mer Frequency Clustering with Applications to Genomic Classification and Differentiation
    QuasiAlign: Position Sensitive P-Mer Frequency Clustering with Applications to Genomic Classification and Differentiation Anurag Nagar Michael Hahsler Southern Methodist University Southern Methodist University Abstract Recent advances in Metagenomics and the Human Microbiome provide a complex landscape for dealing with a multitude of genomes all at once. One of the many challenges in this field is classification of the genomes present in a sample. Effective metagenomic classification and diversity analysis require complex representations of taxa. With this package we develop a suite of tools, based on novel quasi-alignment techniques to rapidly classify organisms using our new approach on a laptop computer instead of several multi- processor servers. This approach will facilitate the development of fast and inexpensive devices for microbiome-based health screening in the near future. Keywords:~data mining, clustering, Markov chain. 1. Introduction Metagenomics (Handelsman, Rondon, Brady, Clardy, and Goodman 1998) and the Human Microbiome Turnbaugh, Ley, Hamady, Fraser-Liggett, Knight, and Gordon(2007); Mai, Ukhanova, and Baer(2010) provide a complex landscape for dealing with a multitude of genomes all at once. One of the many challenges in this field is classification of the genomes present in the sample. Effective metagenomic classification and diversity analysis require complex representations of taxa. A common characteristic of most sequence-based classification techniques (e.g., BAlibase (Smith and Waterman 1981), BLAST (Altschul, Gish, Miller, Myers, and Lipman 1990), T-Coffee (Notredame, Higgins, and Heringa 2000), MAFFT (Katoh, Misawa, Kuma, and Miyata 2002), MUSCLE (Edgar 2004b,a), Kalign (Lassmann and Sonnhammer 2006) and ClustalW2 and ClustalX2 (Larkin, Blackshields, Brown, Chenna, McGettigan, McWilliam, Valentin, Wallace, Wilm, Lopez, Thompson, Gibson, and Higgins 2007)) is the use of com- putationally very expensive sequence alignment.
    [Show full text]
  • Petroleum Hydrocarbon Rich Oil Refinery Sludge of North-East India
    Roy et al. BMC Microbiology (2018) 18:151 https://doi.org/10.1186/s12866-018-1275-8 RESEARCHARTICLE Open Access Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations Ajoy Roy1, Pinaki Sar2, Jayeeta Sarkar2, Avishek Dutta2,3, Poulomi Sarkar2, Abhishek Gupta2, Balaram Mohapatra2, Siddhartha Pal1 and Sufia K Kazy1* Abstract Background: Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on- site bioremediation. Results: All sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea
    [Show full text]
  • 4 Metabolic and Taxonomic Diversification in Continental Magmatic Hydrothermal Systems
    Maximiliano J. Amenabar, Matthew R. Urschel, and Eric S. Boyd 4 Metabolic and taxonomic diversification in continental magmatic hydrothermal systems 4.1 Introduction Hydrothermal systems integrate geological processes from the deep crust to the Earth’s surface yielding an extensive array of spring types with an extraordinary diversity of geochemical compositions. Such geochemical diversity selects for unique metabolic properties expressed through novel enzymes and functional characteristics that are tailored to the specific conditions of their local environment. This dynamic interaction between geochemical variation and biology has played out over evolu- tionary time to engender tightly coupled and efficient biogeochemical cycles. The timescales by which these evolutionary events took place, however, are typically in- accessible for direct observation. This inaccessibility impedes experimentation aimed at understanding the causative principles of linked biological and geological change unless alternative approaches are used. A successful approach that is commonly used in geological studies involves comparative analysis of spatial variations to test ideas about temporal changes that occur over inaccessible (i.e. geological) timescales. The same approach can be used to examine the links between biology and environment with the aim of reconstructing the sequence of evolutionary events that resulted in the diversity of organisms that inhabit modern day hydrothermal environments and the mechanisms by which this sequence of events occurred. By combining molecu- lar biological and geochemical analyses with robust phylogenetic frameworks using approaches commonly referred to as phylogenetic ecology [1, 2], it is now possible to take advantage of variation within the present – the distribution of biodiversity and metabolic strategies across geochemical gradients – to recognize the extent of diversity and the reasons that it exists.
    [Show full text]
  • Distribution of Long Linear and Branched Polyamines in the Thermophiles Belonging to the Domain Bacteria
    Journal of Japanese Society for Extremophiles (2008) Vol.7 (1) Journal of Japanese Society for Extremophiles (2008), Vol. 7, 10-20 ORIGINAL PAPER Hamana Ka,b,e, Hosoya Ra, Yokota Ac, Niitsu Md, Hayashi He and Itoh Tb Distribution of long linear and branched polyamines in the thermophiles belonging to the domain Bacteria a Gunma University School of Health Sciences, Maebashi, Gunma 371-8514, Japan. bJapan Collection of Microorganisms, RIKEN, BioResource Center, Wako, Saitama 351-0198, Japan. c Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan. d Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0290, Japan. e Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan. Corresponding author : Koei Hamana, [email protected] Phone : +81-27-220-8916, FAX : +81-27-220-8999 Received: April 3, 2008/ Reviced:May 26, 2008/ Acepted:June 3, 2008 Abstract Cellular polyamines of 44 newly validated have been published in eubacteria 15, 16). However, the eubacterial thermophiles growing at 45-80℃, belonging degree of thermophily is roughly estimated and not to eight orders (six phyla) of the domain Bacteria, were defined exactly. The cellular occurrence of long linear analyzed by HPLC and GC. A quaternary branched and/or branched polyamines in extremely thermophilic penta-amine, N4-bis(aminopropyl)norspermidine, was (or hyperthermophilic) eubacteria suggested that the found in Hydrogenivirga and Sulfurihydrogenibium extreme thermophiles (or hyperthermophiles) may have belonging to the order of Aquificales. Another some novel polyamine synthetic abilities possibly quaternary branched penta-amine, N4-bis(aminopropyl) associated with their thermophily 8-11, 13-15, 18, 23, 24).
    [Show full text]
  • Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
    Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment.
    [Show full text]
  • Journal Club
    A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring Koji Mori, Hongik Kim, Takeshi Kakegawa and Satoshi Handa Extremophiles (2003) &: 283-290 Sulfate Reducing Microorganisms • 6 phylogenetic lineages • 4 Bacterial lineages in two clades (δ-Proteobacteria and Bacillus/Clostridia group) • Bacterial lineages are mesophilic to moderately thermophilic • 2 Archaeal lineages in two genera (Archeaoglobus and Caldivirga) • Archaeal lineages are hyperthermophilic http://mcb.berkeley.edu/labs/kustu/mcb112/nov9. htm The Plan • Isolate and characterize a novel thermophilic sulfate-reducer from Narugo hot spring in Miyagi, Japan • Once isolated analyze 16S, DsrAB (dissimilatory sulfite reductase) and ApsA (alpha subunit of the adenosine-5’-phosphosulfate reductase) • Characterize cellular morphology • Characterize fatty acid content and genomic G+C content Miyagi Prefecture, Japan Growth and Isolation • Isolated sections of the collected microbial mat were inoculated into a reduced anaerobic medium designed to enrich for sulfate reducers • After 4 days of growth at 55°C pronounced H2S production was detected • After several transfers isolated colonies were seen on solid media • Final purification on solid media yielded an isolate Na82T Morphology and Physiology of Na82T • Rod-shaped (0.5x2-4 µm) • Non-motile • Non-spore forming • Gram negative • Strict Anaerobe • Growth coupled to Sulfate reduction • Temperature regieme between
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insight Into The
    www.nature.com/scientificreports Corrected: Author Correction OPEN Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal Received: 17 August 2018 Accepted: 17 January 2019 pools in Kamchatka, Russia Published online: 28 February 2019 Laetitia G. E. Wilkins1,2, Cassandra L. Ettinger 2, Guillaume Jospin2 & Jonathan A. Eisen 2,3,4 Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refned, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka. Terrestrial hydrothermal systems are of great interest to the general public and to scientists alike due to their unique and extreme conditions.
    [Show full text]
  • Supplement of Biogeosciences, 16, 4229–4241, 2019 © Author(S) 2019
    Supplement of Biogeosciences, 16, 4229–4241, 2019 https://doi.org/10.5194/bg-16-4229-2019-supplement © Author(s) 2019. This work is distributed under the Creative Commons Attribution 4.0 License. Supplement of Identifying the core bacterial microbiome of hydrocarbon degradation and a shift of dominant methanogenesis pathways in the oil and aqueous phases of petroleum reservoirs of different temperatures from China Zhichao Zhou et al. Correspondence to: Ji-Dong Gu ([email protected]) and Bo-Zhong Mu ([email protected]) The copyright of individual parts of the supplement might differ from the CC BY 4.0 License. 1 Supplementary Data 1.1 Characterization of geographic properties of sampling reservoirs Petroleum fluids samples were collected from eight sampling sites across China covering oilfields of different geological properties. The reservoir and crude oil properties together with the aqueous phase chemical concentration characteristics were listed in Table 1. P1 represents the sample collected from Zhan3-26 well located in Shengli Oilfield. Zhan3 block region in Shengli Oilfield is located in the coastal area from the Yellow River Estuary to the Bohai Sea. It is a medium-high temperature reservoir of fluvial face, made of a thin layer of crossed sand-mudstones, pebbled sandstones and fine sandstones. P2 represents the sample collected from Ba-51 well, which is located in Bayindulan reservoir layer of Erlian Basin, east Inner Mongolia Autonomous Region. It is a reservoir with highly heterogeneous layers, high crude oil viscosity and low formation fluid temperature. It was dedicated to water-flooding, however, due to low permeability and high viscosity of crude oil, displacement efficiency of water-flooding driving process was slowed down along the increase of water-cut rate.
    [Show full text]
  • Supplementary Information
    K-mer similarity, networks of microbial genomes and taxonomic rank Guillaume Bernard, Paul Greenfield, Mark A. Ragan, Cheong Xin Chan. Supplementary Figures Legends # Supplementary Figure S1: P- network of prokaryote phyla using !" with k=25, based on rRNAs. Edges represent connections between isolates of two phyla. The node size is proportional to the number of isolates in a phylum. Distance threshold = 6. Supplementary Figure S2: PCA analysis performed on the raw data of the COG categories profile for each genus. Each phylum is color-coded. Supplementary Figure S3: PCA analysis performed on the raw data of the COG categories profile for each genus. Each genus is color-coded according to the number of isolates. Supplementary Figure S4: PCA analysis performed on the normalised counts of center-scaled COG categories. Each phylum is color-coded. Supplementary Tables Legends Supplementary Table S1: List of the 2785 isolates used in this analysis. Supplementary Table S2: Network analysis of the I-network for 2705 complete genomes of bacteria and archaea. Supplementary Table S3: Network analysis of the I-network for 2616 genomes of bacteria and archaea, with rRNA genes removed. Supplementary Table S4: Network analysis of the rRNA gene sequences I-network of 2616 bacterial and archaeal isolates. Supplementary Table S5: Network analysis of the plasmid genomes I-network of 921 bacterial and plasmid genomes. Supplementary Table S6: Statistics of core k-mers for 151 genera. Supplementary Table S7: COG category profiles for 16 phyla. 1 Figure S1
    [Show full text]
  • Aquatic Microbial Ecology 79:115–125 (2017)
    The following supplement accompanies the article Unique and highly variable bacterial communities inhabiting the surface microlayer of an oligotrophic lake Mylène Hugoni, Agnès Vellet, Didier Debroas* *Corresponding author: [email protected] Aquatic Microbial Ecology 79:115–125 (2017) Table S1. Phylogenetic affiliation of the surface micro-layer (SML) specific OTUs, the epilimnion (E) specific OTUs and shared to both layers. OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared Acidobacteria;Acidobacteria;Acidobacteriales;Acidobacteriaceae (Subgroup 1);Granulicella; 2 0 0 Acidobacteria;Acidobacteria;Acidobacteriales;Acidobacteriaceae (Subgroup 1);uncultured; 1 0 0 Acidobacteria;Acidobacteria;JG37-AG-116; 24 0 0 Acidobacteria;Acidobacteria;Subgroup 13; 0 1 0 Acidobacteria;Acidobacteria;Subgroup 3;Family Incertae Sedis;Bryobacter; 0 0 1 Acidobacteria;Acidobacteria;Subgroup 3;SJA-149; 0 1 1 Acidobacteria;Acidobacteria;Subgroup 4;RB41; 0 1 0 Acidobacteria;Acidobacteria;Subgroup 6; 0 0 1 Actinobacteria;AcI;AcI-A; 0 4 13 Actinobacteria;AcI;AcI-A;AcI-A3; 0 4 0 Actinobacteria;AcI;AcI-A;AcI-A5; 3 1 1 Actinobacteria;AcI;AcI-A;AcI-A7; 0 1 0 Actinobacteria;AcI;AcI-B;AcI-B1; 0 8 1 Actinobacteria;AcI;AcI-B;AcI-B2; 0 7 0 Actinobacteria;Acidimicrobia;Acidimicrobiales;Acidimicrobiaceae;CL500-29 marine group; 7 34 11 Actinobacteria;Acidimicrobia;Acidimicrobiales;Family Incertae Sedis;Candidatus Microthrix; 0 1 0 Actinobacteria;Acidimicrobia;Acidimicrobiales;uncultured; 0 4 1 Actinobacteria;AcIV; 0 2 0 Actinobacteria;AcIV;Iluma-A2;
    [Show full text]
  • A Validated and Optimized Asaim Workflow for Metatranscriptomics Analysis Within Galaxy Framework [Version 2; Peer Review: 2 Approved]
    F1000Research 2021, 10:103 Last updated: 02 SEP 2021 METHOD ARTICLE ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework [version 2; peer review: 2 approved] Subina Mehta 1, Marie Crane 1, Emma Leith1, Bérénice Batut 2, Saskia Hiltemann3, Magnus Ø Arntzen4, Benoit J. Kunath 4, Phillip B. Pope4, Francesco Delogu4, Ray Sajulga1, Praveen Kumar1, James E. Johnson1, Timothy J. Griffin 1, Pratik D. Jagtap 1 1University of Minnesota, Twin Cities, MN, 55455, USA 2Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany 3Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands 4Norwegian University of Life Sciences, Ås, 1430, Norway v2 First published: 11 Feb 2021, 10:103 Open Peer Review https://doi.org/10.12688/f1000research.28608.1 Latest published: 19 Apr 2021, 10:103 https://doi.org/10.12688/f1000research.28608.2 Reviewer Status Invited Reviewers Abstract The Earth Microbiome Project (EMP) aided in understanding the role 1 2 of microbial communities and the influence of collective genetic material (the ‘microbiome’) and microbial diversity patterns across the version 2 habitats of our planet. With the evolution of new sequencing (revision) report report technologies, researchers can now investigate the microbiome and 19 Apr 2021 map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data version 1 analysis have helped researchers to gain an in-depth knowledge 11 Feb 2021 report about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it 1.
    [Show full text]