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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. -
Innovative Process for Granulation of Continuous Flow Conventional Activated Sludge
Innovative Process for Granulation of Continuous Flow Conventional Activated Sludge Bev Stinson, Ph.D AECOM, Global Wastewater Technology Leader May 9th 2019 2 2Introduction The objective of this presentation is to: • Introduce Aerobic Granular Sludge (AGS), including mechanisms for formation and benefits • Present performance data for a Nereda® SBR pilot • AECOM’s continuous-flow granular sludge process for BNR infra-stretching or footprint reductions 3 3What is Granular Sludge? – Sludge granule is a tightly aggregated mass of microorganisms in a matrix of extra polymeric substances (EPS) – A cross between floc and fixed film growth – Their large size (>0.2mm) and density allow for excellent settling characteristics = more compact WWTPs Reference: Sarma, S.J. et al., 2017. Finding knowledge gaps in aerobic granulation technology 4 4Granular Sludge Relies on Dominance Slow Growing Microorganisms – Treatment processes that rely on slow-growing bacteria are better at granulation – Anaerobic systems were the first granular sludge processes developed (Biothane™, Biobed™) to treat high strength soluble COD waste Anaerobic granules supporting acid formers & methanogen growth Reference: van Lier, J.B. et al., 2015. Celebrating 40 years anaerobic sludge bed reactors for industrial wastewater treatment 5 5 Granular ANAMMOX – The first Anaerobic Oxidizing Ammonia (ANAMMOX™) process was based on a granular sludge approach 6 6 Aerobic Granular Sludge – Developing aerobic granular sludge (AGS) for treating domestic wastewater has been more challenging -
Aerobic Granulation in a Sequencing Batch Reactor for the Treatment of Piggery Wastewater
Aerobic Granulation in a Sequencing Batch Reactor for the Treatment of Piggery Wastewater Dalei Zhang1*, Yanan Wang1, Hongwei Li1, Shaoran Wang2, Yumei Jing3 ABSTRACT: This study investigated the formation of aerobic granules strategy on the treatment of swine wastewater and found that fed with digested piggery wastewater. After 42 days of cultivation, small feeding ratio had a more significant effect on the removal of yellow granules with mean diameter of 0.4 mm were first observed in the phosphorus and nitrogen than on the removal of chemical reactor. Scanning electron microscope pictures showed the granules oxygen demand (COD). Huang et al. (2011) found that high were compact, round structures with clear outer shapes and mainly 2þ 2þ composed of filamentous bacteria. Maximum chemical oxygen demand concentrations of K and Ca would be helpful for removing and ammonia removal ratios were 90.1 and 91.7%, respectively. The nutrients in piggery wastewater. Previous studies have shown Monod equation, which was used to describe ammonium utilization, great improvements in treating piggery wastewater, but there are yielded a maximum rate of 6.25 mg (g volatile suspended solids)À1 hÀ1. still some problems that hinder treatment (Latif et al., 2011). The measurement of extracellular polymeric substances (EPS) content Rich nitrogenous compounds in the wastewater make active and three-dimensional excitation and emission matrix results showed biomass densification, granular processes, and, consequently, that the EPS concentration increased during the granulation process. microorganism retention in the reactor difficult, limiting the use Fluorescence in situ hybridization analysis showed significant amounts of upflow anaerobic sludge blanket (UASB) reactors. -
Horizontal Operon Transfer, Plasmids, and the Evolution of Photosynthesis in Rhodobacteraceae
The ISME Journal (2018) 12:1994–2010 https://doi.org/10.1038/s41396-018-0150-9 ARTICLE Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae 1 2 3 4 1 Henner Brinkmann ● Markus Göker ● Michal Koblížek ● Irene Wagner-Döbler ● Jörn Petersen Received: 30 January 2018 / Revised: 23 April 2018 / Accepted: 26 April 2018 / Published online: 24 May 2018 © The Author(s) 2018. This article is published with open access Abstract The capacity for anoxygenic photosynthesis is scattered throughout the phylogeny of the Proteobacteria. Their photosynthesis genes are typically located in a so-called photosynthesis gene cluster (PGC). It is unclear (i) whether phototrophy is an ancestral trait that was frequently lost or (ii) whether it was acquired later by horizontal gene transfer. We investigated the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provide the first unequivocal evidence for the horizontal transfer of the PGC. The 33 concatenated core genes of the PGC formed a robust phylogenetic tree and the comparison with single-gene trees demonstrated the dominance of joint evolution. The PGC tree is, however, largely incongruent with the species tree and at least seven transfers of the PGC are required to reconcile both phylogenies. 1234567890();,: 1234567890();,: The origin of a derived branch containing the PGC of the model organism Rhodobacter capsulatus correlates with a diagnostic gene replacement of pufC by pufX. The PGC is located on plasmids in six of the analyzed genomes and its DnaA- like replication module was discovered at a conserved central position of the PGC. A scenario of plasmid-borne horizontal transfer of the PGC and its reintegration into the chromosome could explain the current distribution of phototrophy in Rhodobacteraceae. -
Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean)
fmicb-09-00796 May 18, 2018 Time: 17:53 # 1 ORIGINAL RESEARCH published: 22 May 2018 doi: 10.3389/fmicb.2018.00796 Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean) Emmanuelle Gérard1*, Siham De Goeyse1, Mylène Hugoni2, Hélène Agogué3, Laurent Richard4, Vincent Milesi1, François Guyot5, Léna Lecourt1, Stephan Borensztajn1, Marie-Béatrice Joseph1, Thomas Leclerc1, Gérard Sarazin1, Didier Jézéquel1, Christophe Leboulanger6 and Magali Ader1 1 UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France, 2 Université Lyon 1, UMR CNRS 5557 / INRA 1418, Ecologie Microbienne, Villeurbanne, France, 3 UMR 7266 CNRS-Université de la Rochelle, LIttoral ENvironnement Et Sociétés, La Rochelle, France, Edited by: 4 School of Mining and Geosciences, Nazarbayev University, Astana, Kazakhstan, 5 Museum National d’Histoire Naturelle, Christophe Dupraz, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS Sorbonne Universités, Université Stockholm University, Sweden Pierre et Marie Curie, Institut de Recherche pour le Développement UMR 206, Paris, France, 6 UMR MARBEC, IRD, Ifremer, Reviewed by: CNRS, Université de Montpellier, Sète, France Trinity L. Hamilton, University of Minnesota Twin Cities, United States Lake Dziani Dzaha is a thalassohaline tropical crater lake located on the “Petite Terre” Virginia Helena Albarracín, Island of Mayotte (Comoros archipelago, Western Indian Ocean). Stromatolites are Center for Electron Microscopy (CIME), Argentina actively growing in the shallow waters of the lake shores. These stromatolites are *Correspondence: mainly composed of aragonite with lesser proportions of hydromagnesite, calcite, Emmanuelle Gérard dolomite, and phyllosilicates. -
Limibaculum Halophilum Gen. Nov., Sp. Nov., a New Member of the Family Rhodobacteraceae
TAXONOMIC DESCRIPTION Shin et al., Int J Syst Evol Microbiol 2017;67:3812–3818 DOI 10.1099/ijsem.0.002200 Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae Yong Ho Shin,1 Jong-Hwa Kim,1 Ampaitip Suckhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A Gram-stain-negative, cream-pigmented, aerobic, non-motile, non-spore-forming and short-rod-shaped bacterial strain, designated CAU 1123T, was isolated from mud from reclaimed land. The strain’s taxonomic position was investigated by using a polyphasic approach. Strain CAU 1123T grew optimally at 37 C and at pH 7.5 in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CAU 1123T formed a monophyletic lineage within the family Rhodobacteraceae with 93.8 % or lower sequence similarity to representatives of the genera Rubrimonas, Oceanicella, Pleomorphobacterium, Rhodovulum and Albimonas. The major fatty acids were C18 : 1 !7c and 11-methyl C18 : 1 !7c and the predominant respiratory quinone was Q-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, one unidentified aminolipid and one unidentified lipid. The DNA G+C content was 71.1 mol%. Based on the data from phenotypic, chemotaxonomic and phylogenetic studies, it is proposed that strain CAU 1123T represents a novel genus and novel species of the family Rhodobacteraceae, for which the name Limibaculumhalophilum gen. nov., sp. nov. The type strain is CAU 1123T (=KCTC 52187T, =NBRC 112522T). The family Rhodobacteraceae was first established by Garr- chemotaxonomic properties along with a detailed phyloge- ity et al. -
Granular Biofilms: Formation, Function, Application
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 7 June 2019 doi:10.20944/preprints201906.0053.v1 1 Review 2 Granular biofilms: formation, function, application, 3 and new trends as model microbial communities 4 Anna Christine Trego, Simon Mills and Gavin Collins 5 Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland 6 Galway, University Road, Galway, H91 TK33, Ireland. 7 Corresponding author: 8 Tel: 00353 (0) 91 49 31 63 9 e-mail: [email protected] 10 11 KEYWORDS: Anammox; Biofilms; Granulation; Methanogens; Microbial ecology; Sludge 12 granules; Wastewater 13 14 LIST OF ABBREVIATIONS 15 AD – Anaerobic digestion 16 AHL – N-acetyl-homoserine-lactone 17 Anammox – Anaerobic ammonium oxidation 18 AOB – Ammonia oxidising bacteria 19 cDNA – Complementary DNA 20 COD – Chemical oxygen demand 21 EGSB – Expanded granular sludge bed 22 EPS – Extracellular polymeric substances 23 FISH – Fluorescence in situ hybridization 24 HRT – Hydraulic retention time 25 HTS – High-throughput sequencing Page 1 © 2019 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 7 June 2019 doi:10.20944/preprints201906.0053.v1 1 mRNA – Messenger RNA 2 MS – Mass spectrometry 3 NMR – Nuclear magnetic resonance 4 NOB – Nitrite-oxidising bacteria 5 OLR – Organic loading rate 6 OTU – Operational taxonomic unit 7 PAO – Polyphosphate-accumulating organism(s) 8 qPCR – Quantitative PCR 9 rRNA – Ribosomal RNA 10 SBR – Sequencing batch reactor 11 -
Detection of Microbial 16S Rrna Gene in the Blood of Patients with Parkinson’S Disease
ORIGINAL RESEARCH published: 24 May 2018 doi: 10.3389/fnagi.2018.00156 Detection of Microbial 16S rRNA Gene in the Blood of Patients With Parkinson’s Disease Yiwei Qian 1†, Xiaodong Yang 1†, Shaoqing Xu 1, Chunyan Wu 2, Nan Qin 2*, Sheng-Di Chen 1* and Qin Xiao 1* 1Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, 2Department of Bioinformatics, Realbio Genomics Institute, Shanghai, China Emerging evidence suggests that the microbiota present in feces plays a role in Parkinson’s disease (PD). However, the alterations of the microbiome in the blood of PD patients remain unknown. To test this hypothesis, we conducted this case-control study to explore the microbiota compositions in the blood of Chinese PD patients. Microbiota communities in the blood of 45 patients and their healthy spouses were investigated using high-throughput Illumina HiSeq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene. The relationships between the microbiota in the blood and Edited by: PD clinical characteristics were analyzed. No difference was detected in the structure Jiawei Zhou, and richness between PD patients and healthy controls. The following genera were Institute of Neuroscience, Shanghai Institutes for Biological Sciences enriched in the blood of PD patients: Isoptericola, Cloacibacterium, Enhydrobacter (CAS), China and Microbacterium; whereas genus Limnobacter was enriched in the healthy controls Reviewed by: after adjusting for age, gender, body mass index (BMI) and constipation. Additionally, Liu Zhihua, University of Chinese Academy of the findings regarding these genera were validated in another independent group of Sciences (UCAS), China 58 PD patients and 57 healthy controls using real-time PCR targeting genus-specific Shuo Yang, Nanjing Medical University, China 16S rRNA genes. -
Descriptions of Amaricoccus Veronensis Sp. Nov., Amaricoccus Tamworthensis Sp
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1997, p. 727-734 Vol. 47, No. 3 0020-7713/97/$04.00 + 0 Copyright 0 1997, International Union of Microbiological Societies Amaricoccus gen. nov., a Gram-Negative Coccus Occurring in Regular Packages or Tetrads, Isolated from Activated Sludge Biomass, and Descriptions of Amaricoccus veronensis sp. nov., Amaricoccus tamworthensis sp. nov., Amaricoccus macauensis sp. nov., and Amaricoccus kaplicensis sp. nov. A. M. MASZENAN,’ R. J. SEVIOUR,l* B. K. C. PATEL,2 G. N. REES,3t AND B. M. McDOUGALLl Biotechnology Research Centre, La Trobe University, Bendigo, Ectoria 3550, Faculty of Science and Technology, Grifith University, Nathan, Brisbane, Queensland 4111, and Faculty of Applied Science, University of Canberra, Belconnen, Australian Capital Territory 261 6, Australia Three isolates of gram-negative bacteria, strains Ben 10ZT, Ben 103T, and Ben 104T,were obtained in pure culture by micromanipulation from activated sludge biomass from wastewater treatment plants in Italy, Australia, and Macau, respectively. These isolates all had a distinctive morphology; the cells were cocci that usually were arranged in tetrads. Based on this criterion, they resembled other bacteria from activated sludge previously called “G” bacteria. On the basis of phenotypic characteristics and the results of 16s ribosomal DNA sequence analyses, the three isolates were very similar to each other, but were sufficiently different from their closest phylogenetic relatives (namely, the genera Rhodobacter, Rhodovulum, and Paracoccus in the (Y subdivision of the Proteobacteria) to be placed in a new genus, Amaricoccus gen. nov. Each of the three isolates represents a new species of the genus Amaricoccus; strains Ben 10ZT, Ben 103T, and Ben 104T are named Amaricoccus veronensis, Amaricoccus tamworthensis, and Amaricoccus mucauensis, respectively. -
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. -
Ocean Acidification Reduces Induction of Coral Settlement by Crustose
Global Change Biology (2013) 19, 303–315, doi: 10.1111/gcb.12008 Ocean acidification reduces induction of coral settlement by crustose coralline algae NICOLE S. WEBSTER, SVEN UTHICKE, EMANUELLE S. BOTTE´ , FLORITA FLORES and ANDREW P. NEGRI Australian Institute of Marine Science, PMB 3, Townsville Mail Centre, Townsville, Qld 4810, Australia Abstract Crustose coralline algae (CCA) are a critical component of coral reefs as they accrete carbonate for reef structure and act as settlement substrata for many invertebrates including corals. CCA host a diversity of microorganisms that can also play a role in coral settlement and metamorphosis processes. Although the sensitivity of CCA to ocean acidificat- ion (OA) is well established, the response of their associated microbial communities to reduced pH and increased CO2 was previously not known. Here we investigate the sensitivity of CCA-associated microbial biofilms to OA and determine whether or not OA adversely affects the ability of CCA to induce coral larval metamorphosis. We experi- mentally exposed the CCA Hydrolithon onkodes to four pH/pCO2 conditions consistent with current IPCC predictions l for the next few centuries (pH: 8.1, 7.9, 7.7, 7.5, pCO2: 464, 822, 1187, 1638 atm). Settlement and metamorphosis of = l coral larvae was reduced on CCA pre-exposed to pH 7.7 (pCO2 1187 atm) and below over a 6-week period. Addi- tional experiments demonstrated that low pH treatments did not directly affect the ability of larvae to settle, but instead most likely altered the biochemistry of the CCA or its microbial associates. Detailed microbial community analysis of the CCA revealed diverse bacterial assemblages that altered significantly between pH 8.1 = l = l (pCO2 464 atm) and pH 7.9 (pCO2 822 atm) with this trend continuing at lower pH/higher pCO2 treatments. -
Settling Properties of Aerobic Granular Sludge (AGS) and Aerobic Granular Sludge Molasses (AGSM)
E3S Web of Conferences 34, 02022 (2018) https://doi.org/10.1051/e3sconf/20183402022 CENVIRON 2017 Settling properties of aerobic granular sludge (AGS) and aerobic granular sludge molasses (AGSM) Azlina Mat Saad1, Farrah Aini Dahalan1, Naimah Ibrahim1, Sara Yasina Yusuf 1, Siti Aqlima Ahmad2, and Khalilah Abdul Khalil3 1School of Environmental Engineering, Universiti Malaysia Perlis, Kompleks Pengajian Jejawi 3, 02600 Arau, Perlis, Malaysia 2Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, UPM 43400 Serdang, Selangor, Malaysia 3Department of Biomolecular Science, Faculty of Applied Sciences, Universiti Teknologi MARA, Seksyen 2, 40450 Shah Alam, Selangor, Malaysia Abstract. Aerobic granulation technology is applied to treat domestic and industrial wastewater. The Aerobic granular sludge (AGS) cultivated has strong properties that appears to be denser and compact in physiological structure compared to the conventional activated sludge. It offers rapid settling for solid:liquid separation in wastewater treatment. Aerobic granules were developed using sequencing batch reactor (SBR) with intermittent aerobic – anaerobic mode with 8 cycles in 24 hr. This study examined the settling velocity performance of cultivated aerobic granular sludge (AGS) and aerobic granular sludge molasses (AGSM). The elemental composition in both AGS and AGSM were determined using X- ray fluorescence (XRF). The results showed that AGSM has higher settling velocity 30.5 m/h compared to AGS. 1 Introduction Technology on wastewater treatment has improved over time based on various advanced processes to treat municipal and industrial wastewaters. Since the operational performance of the conventional activated sludge processes is limited by the aptitude of a clarifier for the solid;liquid separation of the activated sludge from the treated wastewater, Aerobic granular sludge (AGS) technology is an attractive option due to its settleability advantages.