Origin and Fate of Nitrite in Model Ecosystems: Case Studies in Groundwater and Constructed Wetlands
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Fuscibacter Oryzae Gen. Nov., Sp. Nov., a Phosphate- Solubilizing Bacterium Isolated from the Rhizosphere of Rice Plant
Fuscibacter Oryzae Gen. nov., sp. nov., A Phosphate- Solubilizing Bacterium Isolated from the Rhizosphere of Rice Plant Geeta Chhetri Dongguk University Minchung Kang Dongguk University Jiyoun Kim Dongguk University Inhyup Kim Dongguk University Yoonseop So Dongguk University Taegun Seo ( [email protected] ) Dongguk Univesity https://orcid.org/0000-0001-9701-2806 Research Article Keywords: Fuscibacter oryzae, non-phototrophic, binary ssion, phosphate-solubilization, brown-pigment Posted Date: June 29th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-382391/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Antonie van Leeuwenhoek on July 17th, 2021. See the published version at https://doi.org/10.1007/s10482-021-01619-2. Page 1/18 Abstract An ovoid to rod shaped, white tobrown pigmented, facultative anaerobic, mesophilic, non-phototrophic, Gram-staining-negative, non-motile, multiply by binary ssion designated strain KVB23T, which was isolated from root of rice plant, near Ilsan, South Korea, was investigated for its taxonomic position by polyphasic approach. Optimal growth was found to occur at 30˚C, at pH 6.5 and in the absence of NaCl on R2A. Phylogenetic analysis based on the 16S rRNA gene sequence of strain KVB23Trevealed that it formed a distinct lineage, as a separate deep branch within the family Rhodobacteriaceae, with <96.5% sequence similarity to representatives of the genera Rhodobacter, Xinfangfangia, Tabrizicola, Falsirhodobacter, Haematobacter, Paenirhodobacter, Pseudorhodobacter and Pararhodobacter. Based in 16S rRNA sequences strain KVB23T was most closely related to Tabrizicola fusiformis KCTC 62105T (96.5%) and Rhodobacter thermarumKCTC 52712T(96.2%).The draft genome of strain KVB23Twas 3.80 bp long with a DNA G + C content of 63.1 %. -
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. -
ABSTRACT SEQUENCE ANALYSIS of 16Srrna, Rpob, Rpoc and Rpod
International Journal of Health Medicine and Current Research Vol. 4, Issue 04, pp.1478-1483, December, 2019 DOI: 10.22301/IJHMCR.2528-3189.1478 INTERNATIONAL JOURNAL ORIGINAL ARTICLE OF HEALTH MEDICINE AND Article can be accessed online on: http://www.ijhmcr.com CURRENT RESEARCH SEQUENCE ANALYSIS OF 16SrRNA, rpoB, rpoC AND rpoD GENES FROM THE GENUS RHODOBACTER Edwin Thomas Apituley1* and Amos Killay1 1Jurusan Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Pattimura, Ambon. ARTICLE INFO ABSTRACT Article History: Molecular sequence data analysis become important tool to inferred Received 10th Sep, 2019 Received in revised form evolutionary relationship and systematic ordering among among organism. It 11th Oct, 2019 complementing traditional method such as comparison of morpholocical and Accepted 13th Nov, 2019 biochemichal characteristics. In this article, three genes sequnces encoding RNA Published online 31th Dec, 2019 polymerase subunits and 16S rRNA gene sequence are discussed for their evolutionary relationship among species of Rhodobacter, a genus of phototrophic α-proteobacteria, and between Rhodobacter species and several Key words: reference microorganism. Level of sequence identity among gene sequence Rhodobacter, phylogenetic analysis, 16S rRNA, rpoB, rpoC, rpoD. showed the lowest variation was in 16SrRNA gene sequences, and the the highest was in rpoD gene sequence. Phylogenetic tree constructions were done using Neighbour joining method and Kimura – 2 Parameter model to measure *Correspondence to Author: genetic distance. Bootstrap analysis was also applied with 1000 repeats. Edwin Thomas Apituley Members of Rhodobacter genus were divided into two major clusters based on Jurusan Biologi Fakultas phylognetic analysis of 16S rRNA gene sequence. There is ambiguity of Matematika dan Ilmu Pengetahuan Alam Universitas Pattimura, Ambon. -
Removal of Biological Organics in High-Salinity Wastewater Produced from Methylcellulose Production and Subsequent Changes in the Microbial Community
Environ. Eng. Res. 2021; 26(4): 200187 pISSN 1226-1025 https://doi.org/10.4491/eer.2020.187 eISSN 2005-968X Research Removal of biological organics in high-salinity wastewater produced from methylcellulose production and subsequent changes in the microbial community GueSoo Jo1, SeongWan Hong1,2, HyunGu Kim2, Zhuliping3, DaeHee Ahn1,2,† 1Department of Environmental Engineering and Energy, Myongji University, Yongin 17058, Republic of Korea 2BlueBank Co., Ltd., Business Incubator Center, Myongji University, Yongin 17058, Republic of Korea 3Wuxi YDS Environmental Protection & Energy Saving Co., Ltd., Environmental Protection Technology Building, Yixing 214200, P.R. China ABSTRACT The wastewater generated in methylcellulose (MC) production is characterized by high salinity and pH due to the residual sodium and chlorine separated from the methyl group. It is difficult to treat wastewater using the conventional activated sludge method because the high concentration of salt interferes with the microbial activity. This study confirms the biological removal of organic matter from MC wastewater using sludge dominated by Halomonas spp., a halophilic microorganism. The influent was mixed with MC wastewater and epichlorohydrin (ECH) wastewater in a 1:9 ratio and operated using a sequencing batch reactor with a hydraulic retention time of 27.8 d based on the MC wastewater. The removal efficiency of chemical oxygen demand (COD) increased from 80.4% to 93.5%, and removal efficiency had improved by adding nutrients such as nitrogen and phosphorus to the wastewater. In terms of microbial community change, Halomonas spp. decreased from 43.26% to 0.11%, whereas Marinobacter spp. and Methylophaga spp. increased from 0.50% to 15.12% and 7.51%, respectively. -
(ST). the Table
1 SUPPLEMENTAL MATERIALS Growth Media Modern Condition Seawater Freshwater Light T°C Atmosphere AMCONA medium BG11 medium – Synechococcus – – Synechocystis – [C] in PAL [C] in the [C] in the Gas Nutrients Modern Nutrients (ppm) Medium Medium Ocean NaNO3 CO2 ~407.8 Na2SO4 25.0mM 29mM Nitrogen 50 Standard (17.65mM) μmol (ST) NaNO NaNO 20°C O ~209’460 Nitrogen 3 3 MgSO 0.304mM photon 2 (549µM) (13.7µM) 4 /m2s FeCl3 6.56µM 2nM Ammonium 0.6g/L ZnSO 254nM 0.5nM ferric stock N ~780’790 4 2 citrate (10ml NaMoO 105nM 105nM 4 green stock/1L) 2 Table S 1 Description of the experimental condition defined as Standard Condition (ST). The table 3 shows the concentrations of fundamental elements, such as C, N, S, and Fe used for the AMCONA 4 seawater medium (Fanesi et al., 2014) and BG11 freshwater medium (Stanier et al., 1971) flushing air 5 with using air pump (KEDSUM-310 8W pump; Xiolan, China) Growth Media Possible Proterozoic T° Condition Modified Seawater Modified Freshwater Light Atmosphere AMCONA medium BG11 medium C – Synechococcus – – Synechocystis – [C] in [C] in PPr Nutrients PPr Nutrients Medium Gas ppm Medium NH Cl Na SO 3mM Nitrogen 4 3 2 4 (0.0035mM) CO 2 10’000ppm (20%) NH Cl Possible (~ 2’450% Nitrogen 4 3 MgSO 0.035mM 50 with 20ml/ (100µM) 4 Proterozoic PAL) μmol 20° min (PPr) photon C O2 20’000ppm /m2s (in Air) (~ 10% FeCl 200nM with 5ml/ 3 PAL) Ammonium 0.6g/L stock min ferric 10ml N ZnSO 0.0nM 2 4 citrate green stock/1L (100%) Base gas with NaMoO4 10.5nM 200ml/min 6 Table S 2 Description of the experimental condition defined as Possible Proterozoic Condition (PPr). -
Tochko Colostate 0053N 15136.Pdf (4.934Mb)
THESIS PROCESSES GOVERNING THE PERFORMANCE OF OLEOPHILIC BIO-BARRIERS (OBBS) – LABORATORY AND FIELD STUDIES Submitted by Laura Tochko Department of Civil and Environmental Engineering In partial fulfillment of the requirements For the Degree of Master of Science Colorado State University Fort Collins, Colorado Fall 2018 Master’s Committee: Advisor: Tom Sale Joe Scalia Sally Sutton Copyright by Laura Elizabeth Tochko 2018 All Rights Reserved ABSTRACT PROCESSES GOVERNING THE PERFORMANCE OF OLEOPHILIC BIO-BARRIERS (OBBS) – LABORATORY AND FIELD STUDIES Petroleum sheens, a potential Clean Water Act violation, can occur at petroleum refining, distribution, and storage facilities located near surface water. In general, sheen remedies can be prone to failure due to the complex processes controlling the flow of light non-aqueous phase liquid (LNAPL) at groundwater/surface water interfaces (GSIs). Even a small gap in a barrier designed to resist the movement of LNAPL can result in a sheen of large areal extent. The cost of sheen remedies, exacerbated by failure, has led to research into processes governing sheens and development of the oleophilic bio-barrier (OBB). OBBs involve 1) an oleophilic (oil-loving) plastic geocomposite which intercepts and retains LNAPL and 2) cyclic delivery of oxygen and nutrients via tidally driven water level fluctuations. The OBB retains LNAPL that escapes the natural attenuation system through oleophilic retention and enhances the natural biodegradation capacity such that LNAPL is retained or degraded instead of discharging to form a sheen. Sand tank experiments were conducted to visualize the movement of LNAPL as a wetting and non-wetting fluid in a water-saturated tank. -
Rhabdonatronobacter Sediminivivens Gen. Nov., Sp. Nov. Isolated from the Sediment of Hutong Qagan Soda Lake
Rhabdonatronobacter Sediminivivens gen. nov., sp. nov. Isolated from the Sediment of Hutong Qagan Soda Lake Heng Zhou Institute of Microbiology Chinese Academy of Sciences Ming Yang Institute of Microbiology Chinese Academy of Sciences Qiong Xue Institute of Microbiology Chinese Academy of Sciences Shengjie Zhang Institute of Microbiology Chinese Academy of Sciences Jian Zhou Institute of Microbiology Chinese Academy of Sciences Dahe Zhao ( [email protected] ) Institute of Microbiology Chinese Academy of Sciences https://orcid.org/0000-0003-0312-6824 Hua Xiang Institute of Microbiology Chinese Academy of Sciences Research Article Keywords: Rhodobacteraceae, Rhabdonatronobacter, Soda lake, Whole genome sequence Posted Date: May 11th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-502262/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/15 Abstract A novel Gram-stain negative bacterium, designated IM2376T, was isolated from the sediment of Hutong Qagan Lake in Ordos, Inner Mongolia Autonomous Region of China. The strain IM2376T had the highest similarity with Roseinatronobacter thiooxidans DSM 13087T (96.18%) and Rhodobaca bogoriensis LBB1T (96.18%) of the family Rhodobacteraceae according to 16S rRNA gene sequence comparison. Genomic relatedness analyses showed that strain IM2376T was clearly distinguished from other species in the family Rhodobacteraceae, with average nucleotide identities, amino acid identities and in silico DNA-DNA hybridization values not more than 74.1%, 68.5% and 20.2%. The fatty acid was mainly composed of C18:1ω7c (64.86%), iso-C16:0 (16.33%) and C16: 1ω7c/C16:1ω6c (6.02%). The major polar lipid was diphosphatidyl glycerol, phosphatidylglycerol and phosphatidylcholine. -
A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria from Coastal Sediments
fmicb-12-675048 June 7, 2021 Time: 17:46 # 1 ORIGINAL RESEARCH published: 14 June 2021 doi: 10.3389/fmicb.2021.675048 A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments Zhaobin Huang1,2*, Shiqing Mo1, Lifei Yan1, Xiaomei Wei1, Yuanyuan Huang1, Lizhen Zhang1, Shuhui Zhang1, Jianzong Liu1, Qingqing Xiao1, Hong Lin1 and Yu Guo1 1 College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China, 2 Fujian Province Key Laboratory for the Development of Bioactive Material From Marine Algae, Quanzhou, China Molecular methods revealed that the majority of microbes in natural environments remains uncultivated. To fully understand the physiological and metabolic characteristics of microbes, however, culturing is still critical for microbial studies. Here, we Edited by: used bacterial community analysis and four culture media, namely, traditional Martin W. Hahn, marine broth 2216 (MB), water extracted matter (WEM), methanol extracted matter Research Institute of Limnology, Mondsee, Faculty of Biology, (MEM), and starch casein agar (SCA), to investigate the diversity of cultivated University of Innsbruck, Austria bacteria in coastal sediments. A total of 1,036 isolates were obtained in pure Reviewed by: culture, and they were classified into five groups, namely, Alphaproteobacteria Ryosuke Nakai, (52.51%), Gammaproteobacteria (23.26%), Actinobacteria (13.32%), Firmicutes, and National Institute of Advanced Industrial Science and Technology Bacteroidetes. Compared to other three media,