DOCSLIB.ORG

Drivers of Bacterial Β-Diversity Depend on Spatial Scale

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Drivers of Bacterial Β-Diversity Depend on Spatial Scale Drivers of bacterial β-diversity depend on spatial scale Jennifer B. H. Martinya,1, Jonathan A. Eisenb, Kevin Pennc, Steven D. Allisona,d, and M. Claire Horner-Devinee aDepartment of Ecology and Evolutionary Biology, and dDepartment of Earth System Science, University of California, Irvine, CA 92697; bDepartment of Evolution and Ecology, University of California Davis Genome Center, Davis, CA 95616; cCenter for Marine Biotechnology and Biomedicine, The Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and eSchool of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195 Edited by Edward F. DeLong, Massachusetts Institute of Technology, Cambridge, MA, and approved March 31, 2011 (received for review November 1, 2010) The factors driving β-diversity (variation in community composi- spatial scale (12). Fifty-years ago, Preston (13) noted that the tion) yield insights into the maintenance of biodiversity on the turnover rate (rate of change) of bird species composition across planet. Here we tested whether the mechanisms that underlie space within a continent is lower than that across continents. He bacterial β-diversity vary over centimeters to continental spatial attributed the high turnover rate across continents to evolu- scales by comparing the composition of ammonia-oxidizing bacte- tionary diversification (i.e., speciation) between faunas as a result ria communities in salt marsh sediments. As observed in studies of dispersal limitation and the lower turnover rates of bird spe- β of macroorganisms, the drivers of salt marsh bacterial -diversity cies within continents as a result of environmental variation. depend on spatial scale. In contrast to macroorganism studies, Here we investigate whether the mechanisms underlying β- fi however, we found no evidence of evolutionary diversi cation diversity in bacteria also vary by spatial scale. We chose to focus of ammonia-oxidizing bacteria taxa at the continental scale, de- on the ammonia-oxidizing bacteria (AOB), which along with the spite an overall relationship between geographic distance and ammonia-oxidizing archaea (14), perform the rate-limiting step of community similarity. Our data are consistent with the idea that nitrification and thus play a key role in nitrogen dynamics. We dispersal limitation at local scales can contribute to β-diversity, compared AOB community composition in 106 sediment samples even though the 16S rRNA genes of the relatively common taxa are globally distributed. These results highlight the importance from 12 salt marshes on three continents. A partially nested of considering multiple spatial scales for understanding microbial sampling design achieved a relatively balanced distribution of biogeography. pairwise distance classes over nine orders of magnitude, from 3 cm to 12,500 km (Fig. 1 and Table S1). We limited our sam- microbial composition | distance-decay | Nitrosomonadales | ecological drift pling to a monophyletic group of bacteria, the AOB within the β-Proteobacteria, and one habitat, salt marshes primarily domi- Spartina iodiversity supports the ecosystem processes upon which so- nated by cordgrass ( spp.). This approach constrained Bciety depends (1). Understanding the mechanisms that gen- the pool of total diversity (richness) and kept the environmental erate and maintain biodiversity is thus key to predicting ecosystem and plant variation relatively constant, increasing our ability to fl responses to future environmental changes. The decrease in identify if dispersal limitation in uences AOB composition. i β — community similarity with geographic distance is a universal We then asked two questions: ( ) Does bacterial -diversity fi — biogeographic pattern observed in communities from all speci cally, the slope of the distance-decay curve vary over domains of life (as in refs. 2–4). Pinpointing the underlying local (within marsh), regional (across marshes within a coast), causes of this “distance-decay” pattern continues to be an area of and continental scales? (ii) Do the underlying factors (environ- intense research (5–9), as such studies of β-diversity (variation in mental variation or dispersal limitation) explaining this diversity community composition) yield insights into the maintenance of vary by spatial scale? Because most bacteria are small, abundant, biodiversity. These studies are still relatively rare for micro- and hardy, we predicted that dispersal limitation would occur organisms, however, and thus our understanding of the mecha- primarily across continents, resulting in genetically divergent nisms underlying microbial diversity—most of the tree of life— microbial “provinces” (15). At the same time, we predicted that remains limited. environmental factors would contribute equally to distance- β-Diversity, and therefore distance-decay patterns, could be decay at all scales, resulting in the steepest slope at the continental driven solely by differences in environmental conditions across scale as reported in plant and animal communities (12, 13, 16). space, a hypothesis summed up by microbiologists as, “every- thing is everywhere—the environmental selects” (10). Under this Results and Discussion model, a distance-decay curve is observed because environmen- We characterized AOB community composition by cloning and tal variables tend to be spatially autocorrelated, and organisms Sanger sequencing of 16S rRNA gene regions targeted by two with differing niche preferences are selected from the available primer sets. Here we focus on the results from a subset of those pool of taxa as the environment changes with distance. sequences from the order Nitrosomonadales, generated using β Dispersal limitation can also give rise to -diversity, as it per- primers specific for AOB within the β-Proteobacteria class (17). fl mits historical contingencies to in uence present-day biogeo- The second primer set (18) generated longer sequences from graphic patterns. For example, neutral niche models, in which an organism’s abundance is not influenced by its environmental preferences, predict a distance-decay curve (8, 11). On relatively Author contributions: J.B.H.M. and M.C.H.-D. designed research; J.B.H.M., J.A.E., K.P., and short time scales, stochastic births and deaths contribute to M.C.H.-D. performed research; J.B.H.M., S.D.A., and M.C.H.-D. analyzed data; and J.B.H.M. a heterogeneous distribution of taxa (ecological drift). On longer and M.C.H.-D. wrote the paper. time scales, stochastic genetic processes allow for taxon di- The authors declare no conflict of interest. versification across the landscape (evolutionary drift). If dispersal This article is a PNAS Direct Submission. is limiting, then current environmental or biotic conditions will Freely available online through the PNAS open access option. not fully explain the distance-decay curve, and thus geographic Data deposition: The sequences reported in this paper have been deposited in the Gen- distance will be correlated with community similarity even after Bank database (accession nos. HQ271472–HQ276885 and HQ276886–HQ283075). controlling for other factors (2). 1To whom correspondence should be addressed. E-mail: [email protected]. For macroorganisms, the relative contribution of environ- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. mental factors or dispersal limitation to β-diversity depends on 1073/pnas.1016308108/-/DCSupplemental. 7850–7854 | PNAS | May 10, 2011 | vol. 108 | no. 19 www.pnas.org/cgi/doi/10.1073/pnas.1016308108 Downloaded by guest on September 27, 2021 Fig. 1. The 13 marshes sampled (see Table S1 for details). Marshes com- pared with one another within regions are circled. (Inset) The arrangement of sampling points within marshes. Six points were sampled along a 100-m transect, and a seventh point was sampled ∼1 km away. Two marshes in the Northeast United States (outlined stars) were sampled more intensively, along four 100-m transects in a grid pattern. a broader range of Proteobacteria, but yielded similar results Fig. 2. Distance-decay curves for the Nitrosomadales communities. The (Fig. S1 and Tables S2 and S3). dashed, blue line denotes the least-squares linear regression across all spatial Across all samples, we identified 4,931 quality Nitrosomadales scales. The solid lines denote separate regressions within each of the three sequences, which grouped into 176 OTUs (operational taxo- spatial scales: within marshes, regional (across marshes within regions circled in nomic units) using an arbitrary 99% sequence similarity cutoff. Fig. 1), and continental (across regions). The slopes of all lines (except the solid fi This cutoff retained a high amount of sequence diversity, but light blue line) are signi cantly less than zero. The slopes of the solid red lines are significantly different from the slope of the all scale (blue dashed) line. minimized the chance of including diversity because of se- quencing or PCR errors. Most (95%) of the sequences appear closely related either to the marine Nitrosospira-like clade, somonadales community similarity. Geographic distance con- known to be abundant in estuarine sediments (e.g., ref. 19) or to tributed the largest partial regression coefficient (b = 0.40, marine bacterium C-17, classified as Nitrosomonas (20) (Fig. S2). P < 0.0001), with sediment moisture, nitrate concentration, plant Pairwise community similarity between the samples was calcu- cover, salinity, and air and water temperature contributing to ECOLOGY
Load more

Recommended publications
  • APP201895 APP201895__Appli
    APPLICATION FORM DETERMINATION Determine if an organism is a new organism under the Hazardous Substances and New Organisms Act 1996 Send by post to: Environmental Protection Authority, Private Bag 63002, Wellington 6140 OR email to: [email protected] Application number APP201895 Applicant Neil Pritchard Key contact NPN Ltd www.epa.govt.nz 2 Application to determine if an organism is a new organism Important This application form is used to determine if an organism is a new organism. If you need help to complete this form, please look at our website (www.epa.govt.nz) or email us at [email protected]. This application form will be made publicly available so any confidential information must be collated in a separate labelled appendix. The fee for this application can be found on our website at www.epa.govt.nz. This form was approved on 1 May 2012. May 2012 EPA0159 3 Application to determine if an organism is a new organism 1. Information about the new organism What is the name of the new organism? Briefly describe the biology of the organism. Is it a genetically modified organism? Pseudomonas monteilii Kingdom: Bacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: Pseudomonas monteilii Elomari et al., 1997 Binomial name: Pseudomonas monteilii Elomari et al., 1997. Pseudomonas monteilii is a Gram-negative, rod- shaped, motile bacterium isolated from human bronchial aspirate (Elomari et al 1997). They are incapable of liquefing gelatin. They grow at 10°C but not at 41°C, produce fluorescent pigments, catalase, and cytochrome oxidase, and possesse the arginine dihydrolase system.
    [Show full text]
  • 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
    [Show full text]
  • Stop AA Length Cluster ID Order Family Genus RBS
    Replicon Start Stop AA Lengthlpha-Score Cluster IDHasNR HasPro Order Family Genus RBS NC_008573 190900 191019 39 100 7 FALSE TRUE Alteromonadales Shewanellaceae Shewanella FALSE NC_009438 285981 286100 39 100 7 FALSE TRUE Alteromonadales Shewanellaceae Shewanella FALSE NC_009778 42140404214159 39 100 7 FALSE TRUE Enterobacteriales Enterobacteriaceae Cronobacter FALSE NC_009649 79985 79866 39 100 7 FALSE TRUE Enterobacteriales Enterobacteriaceae Klebsiella FALSE NC_009838 134371 134490 39 100 7 FALSE TRUE Enterobacteriales Enterobacteriaceae Escherichia FALSE NC_010468 37346433734524 39 100 7 FALSE TRUE Enterobacteriales Enterobacteriaceae Escherichia FALSE NC_006856 1475 1579 34 100 67 FALSE FALSE Enterobacteriales Enterobacteriaceae Salmonella FALSE NC_010410 3640820 3640924 34 100 67 FALSE FALSE Pseudomonadales Moraxellaceae Acinetobacter FALSE NC_010488 122800 122696 34 100 67 FALSE FALSE Enterobacteriales Enterobacteriaceae Escherichia FALSE NC_008344 679346 679233 37 100 60 FALSE FALSE Nitrosomonadales Nitrosomonadaceae Nitrosomonas FALSE NC_004741 2605885 2605772 37 100 60 FALSE FALSE Enterobacteriales Enterobacteriaceae Shigella FALSE NC_008344 2385914 2386027 37 100 60 FALSE FALSE Nitrosomonadales Nitrosomonadaceae Nitrosomonas FALSE NC_009085 792681 792794 37 100 60 FALSE FALSE Pseudomonadales Moraxellaceae Acinetobacter FALSE NC_008344 683849 683736 37 100 57 FALSE FALSE Nitrosomonadales Nitrosomonadaceae Nitrosomonas FALSE NC_004741 2610384 2610271 37 100 57 FALSE FALSE Enterobacteriales Enterobacteriaceae Shigella FALSE NC_008344
    [Show full text]
  • Microbial Nitrogen Metabolism in Chloraminated Drinking Water
    bioRxiv preprint doi: https://doi.org/10.1101/655316; this version posted June 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Microbial Nitrogen Metabolism in Chloraminated Drinking Water 2 Reservoirs 3 4 Sarah C Potgietera, Zihan Daic, Stefanus N Ventera, Makhosazana Sigudud and Ameet J 5 Pintob* 6 7 a Rand Water Chair in Water Microbiology, Department of Microbiology and Plant 8 Pathology, University of Pretoria, South Africa 9 b Department of Civil and Environmental Engineering, Northeastern University, Boston, USA 10 c College of Science and Engineering, School of Engineering, University of Glasgow, UK 11 d Scientific Services, Rand Water, Vereeniging, South Africa 12 13 *corresponding author: Dr Ameet J Pinto 14 Email address: [email protected] 15 16 17 18 19 20 21 22 23 24 25 bioRxiv preprint doi: https://doi.org/10.1101/655316; this version posted June 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 26 Abstract 27 Nitrification is a common concern in chloraminated drinking water distribution systems. The 28 addition of ammonia promotes the growth of nitrifying organisms, causing the depletion of 29 chloramine residuals and resulting in operational problems for many drinking water utilities. 30 Therefore, a comprehensive understanding of the microbially mediated processes behind 31 nitrogen metabolism together with chemical water quality data, may allow water utilities to 32 better address the undesirable effects caused by nitrification.
    [Show full text]
  • Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
    Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.
    [Show full text]
  • Jellyfish Life Stages Shape Associated Microbial Communities
    fmicb-09-01534 July 10, 2018 Time: 16:16 # 1 ORIGINAL RESEARCH published: 12 July 2018 doi: 10.3389/fmicb.2018.01534 Jellyfish Life Stages Shape Associated Microbial Communities, While a Core Microbiome Is Maintained Across All Michael D. Lee1, Joshua D. Kling1, Rubén Araya2 and Janja Ceh2,3,4* 1 Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States, 2 Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile, 3 Laboratory of Microbial Complexity and Functional Ecology, Institute of Antofagasta, University of Antofagasta, Antofagasta, Chile, 4 Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile The key to 650 million years of evolutionary success in jellyfish is adaptability: with alternating benthic and pelagic generations, sexual and asexual reproductive modes, multitudes of body forms and a cosmopolitan distribution, jellyfish are likely to have established a plenitude of microbial associations. Here we explored bacterial Edited by: assemblages in the scyphozoan jellyfish Chrysaora plocamia (Lesson 1832). Life stages Russell T. Hill, involved in propagation through cyst formation, i.e., the mother polyp, its dormant cysts University of Maryland Center for Environmental Science, (podocysts), and polyps recently excysted (excysts) from podocysts – were investigated. United States Associated bacterial assemblages were assessed using MiSeq Illumina paired-end tag Reviewed by: sequencing of the V1V2 region of the 16S rRNA gene. A microbial core-community was Detmer Sipkema, Wageningen University & Research, identified as present through all investigated life stages, including bacteria with closest Netherlands relatives known to be key drivers of carbon, nitrogen, phosphorus, and sulfur cycling. Jean-Christophe Auguet, Moreover, the fact that half of C.
    [Show full text]
  • Investigation of Biofilms Formed on Steelmaking Slags in Marine
    International Journal of Molecular Sciences Article Investigation of Biofilms Formed on Steelmaking Slags in Marine Environments for Water Depuration Akiko Ogawa 1,* , Reiji Tanaka 2, Nobumitsu Hirai 1, Tatsuki Ochiai 1, Ruu Ohashi 1, Karin Fujimoto 1, Yuka Akatsuka 1 and Masanori Suzuki 3 1 National Institute of Technology (KOSEN), Suzuka College, Shiroko-cho, Suzuka, Mie 510-0294, Japan; [email protected] (N.H.); [email protected] (T.O.); [email protected] (R.O.); [email protected] (K.F.); [email protected] (Y.A.) 2 Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan; [email protected] 3 Graduate School of Engineering, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-(0)59-368-1768 Received: 21 July 2020; Accepted: 18 September 2020; Published: 22 September 2020 Abstract: Steelmaking slags are a promising resource as artificial seaweed beds for the reconstitution of marine environments. To grow seaweed well, the formation of biofilms is an essential process in biofouling. This study focused on the formation of initial biofilms on steelmaking slag samples and analyzed the resulting bacterial communities using the next-generation sequencing technique. Three types of steelmaking slag were submerged in an area of Ise Bay in Mie Prefecture, Japan, for 3 and 7 days in the summer and winter seasons to allow the formation of biofilms. The bacterial communities of these biofilms were richer in sulfur-oxidizing bacteria compared to the biofilms formed on polyurethane sponges.
    [Show full text]
  • Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
    Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food.
    [Show full text]
  • Supplement of Hydrol
    Supplement of Hydrol. Earth Syst. Sci., 23, 139–154, 2019 https://doi.org/10.5194/hess-23-139-2019-supplement © Author(s) 2019. This work is distributed under the Creative Commons Attribution 4.0 License. Supplement of Microbial community changes induced by Managed Aquifer Recharge ac- tivities: linking hydrogeological and biological processes Carme Barba et al. Correspondence to: Carme Barba ([email protected]) The copyright of individual parts of the supplement might differ from the CC BY 4.0 License. 1 Supplementary material 2 Hydrochemical analyses of water samples - - -2 - 3 Samples for Cl , NO3 , SO4 and HCO3 analysis were filtered through 0.2-µm nylon filters, 4 stored at 4⁰C and analyzed using high performance liquid chromatography (HPLC) with a 5 WATERS 515 HPLC pump, IC-PAC anion columns, and a WATERS 432 detector. Samples for the 6 determination of cations were filtered through a 0.2-µm filter, acidified in the field with 1% 7 HNO3- and stored at 4⁰C. Cations were analyzed using inductively coupled plasma-optical 8 emission spectrometry (ICP-OES, Perkin-Elmer Optima 3200 RL). Samples for DOC analysis 9 were filtered through a 0.45-µm nylon filter and collected in muffled (450⁰C, 4.30 h) glass 10 bottles, acidified and stored at 4⁰C. In addition, water for TOC determination was sampled and 11 stored at 4⁰C. TOC and DOC were analyzed with an infrared detector using the NPOC method 12 (Shimadzu TOC-Vcsh). 13 Molecular analyses for liquid and soil samples 14 Liquid samples were filtered through 0.22-µm GV Durapore® membrane filters (Merck 15 Millipore, USA) and stored at -80ºC.
    [Show full text]
  • Application of Hierarchical Oligonucleotide Primer Extension (HOPE) to Assess Relative Abundances of Ammonia- and Nitrite-Oxidiz
    Scarascia et al. BMC Microbiology (2017) 17:85 DOI 10.1186/s12866-017-0998-2 RESEARCH ARTICLE Open Access Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria Giantommaso Scarascia, Hong Cheng, Moustapha Harb and Pei-Ying Hong* Abstract Background: Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. Results: The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance.
    [Show full text]
  • International Journal of Systematic and Evolutionary Microbiology
    University of Plymouth PEARL https://pearl.plymouth.ac.uk 01 University of Plymouth Research Outputs University of Plymouth Research Outputs 2017-05-01 Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and four new families within the orders Nitrosomonadales and Rhodocyclales Boden, R http://hdl.handle.net/10026.1/8740 10.1099/ijsem.0.001927 International Journal of Systematic and Evolutionary Microbiology All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. International Journal of Systematic and Evolutionary Microbiology Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov. Transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and 4 new families within the orders Nitrosomonadales and Rhodocyclales. --Manuscript Draft-- Manuscript Number: IJSEM-D-16-00980R2 Full Title: Reclassification of Thiobacillus aquaesulis (Wood & Kelly,
    [Show full text]
  • Microbial Diversity and Evidence of Sulfur- and Ammonium-Based Chemolithotrophy in Movile Cave
    The ISME Journal (2009) 3, 1093–1104 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej ORIGINAL ARTICLE Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave Yin Chen1,5, Liqin Wu2,5, Rich Boden1, Alexandra Hillebrand3, Deepak Kumaresan1, He´le`ne Moussard1, Mihai Baciu4, Yahai Lu2 and J Colin Murrell1 1Department of Biological Sciences, University of Warwick, Coventry, UK; 2College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; 3Institute of Speleology ‘Emil Racovita’, Bucharest, Romania and 4The Group of Underwater and Speleological Exploration, Bucharest, Romania Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/ oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monoox- ygenase). Sulfur oxidizers from both Gammaproteobacteria and Betaproteobacteria were detected in 16S rRNA, soxB and RuBisCO gene libraries. DNA-based stable-isotope probing analyses using 13 C-bicarbonate showed that Thiobacillus spp. were most active in assimilating CO2 and also implied that ammonia and nitrite oxidizers were active during incubations. Nitrosomonas spp. were detected in both 16S rRNA and amoA gene libraries from the ‘heavy’ DNA and sequences related to nitrite- oxidizing bacteria Nitrospira and Candidatus ‘Nitrotoga’ were also detected in the ‘heavy’ DNA, which suggests that ammonia/nitrite oxidation may be another major primary production process in this unique ecosystem. A significant number of sequences associated with known methylotrophs from the Betaproteobacteria were obtained, including Methylotenera, Methylophilus and Methylo- vorus, supporting the view that cycling of one-carbon compounds may be an important process within Movile Cave.
    [Show full text]