Long-Term Changes in Soil Properties and Microbial Communities Are
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Inoculation with Mycorrhizal Fungi and Irrigation Management Shape the Bacterial and Fungal Communities and Networks in Vineyard Soils
microorganisms Article Inoculation with Mycorrhizal Fungi and Irrigation Management Shape the Bacterial and Fungal Communities and Networks in Vineyard Soils Nazareth Torres † , Runze Yu and S. Kaan Kurtural * Department of Viticulture and Enology, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA; [email protected] (N.T.); [email protected] (R.Y.) * Correspondence: [email protected] † Current address: Advanced Fruit and Grape Growing Group, Public University of Navarra, 31006 Pamplona, Spain. Abstract: Vineyard-living microbiota affect grapevine health and adaptation to changing environ- ments and determine the biological quality of soils that strongly influence wine quality. However, their abundance and interactions may be affected by vineyard management. The present study was conducted to assess whether the vineyard soil microbiome was altered by the use of biostimulants (arbuscular mycorrhizal fungi (AMF) inoculation vs. non-inoculated) and/or irrigation management (fully irrigated vs. half irrigated). Bacterial and fungal communities in vineyard soils were shaped by both time course and soil management (i.e., the use of biostimulants and irrigation). Regarding alpha diversity, fungal communities were more responsive to treatments, whereas changes in beta diversity were mainly recorded in the bacterial communities. Edaphic factors rarely influence bacte- rial and fungal communities. Microbial network analyses suggested that the bacterial associations Citation: Torres, N.; Yu, R.; Kurtural, were weaker than the fungal ones under half irrigation and that the inoculation with AMF led to S.K. Inoculation with Mycorrhizal the increase in positive associations between vineyard-soil-living microbes. Altogether, the results Fungi and Irrigation Management highlight the need for more studies on the effect of management practices, especially the addition Shape the Bacterial and Fungal of AMF on cropping systems, to fully understand the factors that drive their variability, strengthen Communities and Networks in Vineyard Soils. -
Effect of Vertical Flow Exchange on Microbial Community Dis- Tributions in Hyporheic Zones
Article 1 by Heejung Kim and Kang-Kun Lee* Effect of vertical flow exchange on microbial community dis- tributions in hyporheic zones School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea; *Corresponding author, E-mail: [email protected] (Received: November 2, 2018; Revised accepted: January 6, 2019) https://doi.org/10.18814/epiiugs/2019/019001 The effect of the vertical flow direction of hyporheic flux advance of hydrodynamic modeling has improved research of hydro- on the bacterial community is examined. Vertical velocity logical exchange processes at the hyporheic zone (Cardenas and Wil- change of the hyporheic zone was examined by installing son, 2007; Fleckenstein et al., 2010; Endreny et al., 2011). Also, this a piezometer on the site, and a total of 20,242 reads were zone has plentiful micro-organisms. The hyporheic zone constituents analyzed using a pyrosequencing assay to investigate the a dynamic hotspot (ecotone) where groundwater and surface water diversity of bacterial communities. Proteobacteria (55.1%) mix (Smith et al., 2008). were dominant in the hyporheic zone, and Bacteroidetes This area constitutes a flow path along which surface water down wells into the streambed sediment and groundwater up wells in the (16.5%), Actinobacteria (7.1%) and other bacteria phylum stream, travels for some distance before eventually mixing with (Firmicutes, Cyanobacteria, Chloroflexi, Planctomycetesm groundwater returns to the stream channel (Hassan et al., 2015). Sur- and unclassified phylum OD1) were identified. Also, the face water enters the hyporheic zone when the vertical hydraulic head hyporheic zone was divided into 3 points – down welling of surface water is greater than the groundwater (down welling). -
2019年第3季度在韩国注册的中国水产企业名单the List of Chinese
2019年第3季度在韩国注册的中国水产企业名单 The List of Chinese Registered Fishery Processing Establishments Export to Korea (Total 1347 , the third quarter of 2019,updated on 25 June, 2019) No. Est.No. 企业名称(中文) Est.Name 企业地址(中文) Est.Address 产品(Products) 北京市朝阳区崔各庄乡 The 23rd floor Sanyuan Property Jingmi Road 北京中洋环球金枪鱼有 1 1100/02010 Beijing Zhongyang Global Tuna Co.,Ltd 东辛店村京密路三元物 Dongxindian Village Cuigezhuang TownChaoyang Fishery Products 限公司 业院内23号楼 District Beijng 五洋海产(天津)有限 天津市塘沽区东江路 2 1200/02004 Ocean Products (Tian.Jin) Co., Ltd Dongjiang Road No.3849 Tanggu Tianjin Fishery Products 公司 3849号 欧盛实业(天津)有限 天津经济技术开发区渤 No.5, Bohai Road, Tianjin Economic & Technological 3 1200/02019 Ocean (Tianjin) Corporation Ltd. Fishery Products 公司 海路5号 Development Area, Tianjin 天津市颖明海湾食品有 天津市滨海新区中心渔 No.221 Yuehai RD., Binhai New Area Of The City 4 1200/02028 Tianjin Smart Gulf Foodstuffs Co.,Ltd. Fishery Products 限公司 港经济区悦海路221号 Center Fishing Port Economic Zone, Tianjin, China 天津市塘沽区海华水产 Tianjin Tanggu District Haihua Fishery Products Food 天津市塘沽区北塘镇水 No. 9, Shuichan Road, Beitang Town, Tanggu District, 5 1200/02048 Fishery Products 食品有限公司 Co., Ltd. 产路9号 Tianjin 天津百迅达进出口贸易 天津市津南区双桥河镇 South Dongnigu Village, Shuangqiaohe Town, Jinnan 6 1200/02063 Tianjin baixunda import and export trade Co., Ltd Fishery Products 有限公司 东泥沽村南 District, Tianjin, China 昌黎县筑鑫实业有限公 秦皇岛市昌黎县新开口 Economic Development Zone Xinkaikou Changli 7 1300/02228 Changli Zhuxin Enterprises Co., Ltd. Fishery Products 司 经济开发区 County Qinhuangdao 抚宁县渤远水产品有限 秦皇岛市抚宁县台营镇 Yegezhuang village taiying town funing county 8 1300/02229 Funing county boyuan aquatic products co.,ltd Fishery Products 公司 埜各庄村 Qinhuangdao city Hebei province 秦皇岛市江鑫水产冷冻 河北省秦皇岛北戴河新 Nandaihe Second District,Beidaihe New 9 1300/02236 Qinhuangdao Jiangxin Aquatic Food Products Co., Ltd. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Functions, Transmission and Emission of the Canopy Microbiota Tania Fort
Functions, transmission and emission of the canopy microbiota Tania Fort To cite this version: Tania Fort. Functions, transmission and emission of the canopy microbiota. Vegetal Biology. Univer- sité de Bordeaux, 2019. English. NNT : 2019BORD0338. tel-02869590 HAL Id: tel-02869590 https://tel.archives-ouvertes.fr/tel-02869590 Submitted on 16 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE PRESENTÉE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITE DE BORDEAUX ECOLE DOCTORALE SCIENCES ET ENVIRONNEMENTS ECOLOGIE ÉVOLUTIVE, FONCTIONNELLE, ET DES COMMUNAUTÉS Par Tania Fort Fonctions, transmission et émission du microbiote de la canopée Sous la direction de Corinne Vacher Soutenue le 10 décembre 2019 Membres du jury : Mme. Anne-Marie DELORT Directrice de recherche Institut de Chimie de Clermont-Ferrand Rapporteuse M. Stéphane Uroz Directeur de recherche INRA Nancy Rapporteur Mme. Patricia Luis Maître de conférence Université de Lyon 1 Rapporteuse Mme. Annabel Porté Directrice de recherche INRA Bordeaux Présidente Mme. Corinne Vacher Directrice de recherche INRA Bordeaux Directrice Fonctions, transmission et émission du microbiote de la canopée. Les arbres interagissent avec des communautés microbiennes diversifiées qui influencent leur fitness et le fonctionnement des écosystèmes terrestres. -
Country, Province 果园中文名chinese Name of Orchard 果园英文名
序号 所在地 Origin: Country, 果园中文名 果园英文名 果园中文地址 果园英文地址 注册登记号 水果品种 Number Location Province Chinese Name of Orchard English Name of Orchard Address in Chinese Address in English Registered Number Commodity 1 北京平谷 PINGGU,BEIJING 北京聚源果品产销合作果园 BEIJING JUYUAN ORCHARD FRUIT PRODUCTION AND MARKETING COOPERATION平谷区王辛庄镇 WANGXINZHUANG,PINGGU DISTRICT,BEIJING 1100GY001 PEACH 2 天津蓟州区 JIZHOU,TIANJIN 天津瑞年农业科技有限公司 TIANJIN RUINIAN AGRICULTURAL TECHNOLOGY CO., LTD. 天津市蓟州区罗庄子镇磨盘裕村 MOPANYU VILLAGE LUOZHUANGZI TOWN, JIZHOU DISTRICT, TIANJIN 1200GY001 PERSIMMON 3 天津静海区 JINGHAI,TIANJIN 天津市胜起农作物种植专业合作社 TIANJIN SHENGQI CROPS PROFESSIONAL COOPERATIVE 天津市静海区双塘镇朴楼村 BUN VILLAGE SHUANGTANG TOWN,JINGHAI DISTRICT TIANJIN 1200GY002 APPLE 4 河北辛集 XINJI,HEBEI 裕隆果园 YULONG ORCHARD 河北省辛集市张名府村 ZHANGMINGFU VILLAGE,XINJI CITY,HEBEI PROVINCE 1300GY002 PEAR 5 河北辛集 XINJI,HEBEI 泊庄果园 BOZHUANG ORCHARD 河北省辛集市泊庄村 BOZHUANG VILLAGE,XINJI CITY,HEBEI 1300GY004 PEAR 6 河北辛集 XINJI,HEBEI 吴家庄果园 WUJIAZHUANG ORCHARD 河北省辛集市吴家庄村 WUJIAZHUANG VILLAGE,XINJI CITY,HEBEI 1300GY005 PEAR 7 河北晋州 JINZHOU,HEBEI 吕家庄果园 LVJIAZHUANG ORCHARD 河北省晋州市马于镇吕家庄村 LVJIAZHUANG,MAYU TOWN, JINZHOU CITY,HEBEI PROVINCE 1300GY007 PEAR 8 河北晋州 JINZHOU,HEBEI 周家庄十队果园 ZHOUJIAZHUANG SHIDUI ORCHARD 河北省晋州市周家庄乡北捏盘村 BEINIEPAN,ZHOUJIAZHUANG TOWN,JINZHOU CITY,HEBEI PROVINCE 1300GY008 PEAR 9 河北晋州 JINZHOU,HEBEI 段家庄果园 DUANJIAZHUANG ORCHARD 河北省晋州市东寺吕乡段家庄村 DUANJIAZHUANG,DONGSILV TOWN,JINZHOU CITY,HEBEI PROVINCE 1300GY009 PEAR 10 河北晋州 JINZHOU,HEBEI 王家庄果园 WANGJIAZHUANG ORCHARD 河北省晋州市王家庄村 WANGJIAZHUANG VILLAGE,JINZHOU CITY,HEBEI PROVINCE 1300GY010 PEAR -
Isolation of Rhizobacteria in Southwestern Québec, Canada: An
Isolation of rhizobacteria in Southwestern Québec, Canada: An investigation of their impact on the growth and salinity stress alleviation in Arabidopsis thaliana and crop plants Di Fan Department of Plant Science Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec H9X 3V9 December 2017 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of DOCTOR OF PHILOSOPHY © Di Fan, Canada, 2017 Table of contents Abstract ................................................................................................. x Résumé ................................................................................................ xiii Acknowledegments ............................................................................. xv Preface ................................................................................................ xviii Contribution of authors ................................................................................ xviii Chapter 1................................................................................................. 1 Introduction ............................................................................................ 1 Chapter 2................................................................................................. 5 Literature Review ................................................................................... 5 2.1 What are root exudates? ......................................................................... -
Microbial Community Analysis in Soil (Rhizosphere) and the Marine (Plastisphere) Environment in Function of Plant Health and Biofilm Formation
Microbial community analysis in soil (rhizosphere) and the marine (plastisphere) environment in function of plant health and biofilm formation Caroline De Tender Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Biotechnology Promotors: Prof. Dr. Peter Dawyndt Department of Applied mathematics, Computer Science and Statistics Faculty of Science Ghent University Dr. Martine Maes Crop Protection - Plant Sciences Unit Institute for Agricultural, Fisheries and Food Research (ILVO) Ir. Lisa Devriese Fisheries – Animal Sciences Unit Insitute for Agricultural, Fisheries and Food Research (ILVO) Dank je wel! De allerlaatste woorden die geschreven worden voor deze thesis zijn waarschijnlijk de eerste die gelezen worden door velen. Ongeveer vier jaar geleden startte ik mijn doctoraat bij het ILVO. Met volle moed begon ik aan mijn avontuur. Het ging niet altijd even vlot en ik kan eerlijk bekennen dat meerdere grenzen verlegd zijn. Vooral de combinatie van twee onderwerpen bleek niet altijd evident en kostte me meer dan eens bloed, zweet en tranen. Daarentegen bracht het ook vele opportuniteiten. De enige dag kon ik aan het wroeten zijn in de serre, terwijl ik de dag erop op de Simon Stevin sprong (en dit mag letterlijk worden genomen!) om plastic uit zee te vissen. Ja, het was me wel het avontuur… Natuurlijk zou dit allemaal niet mogelijk geweest zijn zonder de hulp van een aantal geweldige mensen. In de eerste plaats, mijn promotoren: Prof. Peter Dawyndt, dr. Martine Maes en natuurlijk Lisa Devriese. Dank je wel om vier jaar geleden het vertrouwen te hebben om mij dit onderzoek toe te wijzen, me steeds in de juiste richting te duwen als ik het Noorden even kwijt was, maar ook voor de gezellige babbels op de bureau. -
Rice Plant–Soil Microbiome Interactions Driven by Root and Shoot Biomass
diversity Article Rice Plant–Soil Microbiome Interactions Driven by Root and Shoot Biomass Cristina P. Fernández-Baca 1, Adam R. Rivers 2 , Jude E. Maul 3 , Woojae Kim 1,4, Ravin Poudel 2, Anna M. McClung 1, Daniel P. Roberts 3, Vangimalla R. Reddy 5 and Jinyoung Y. Barnaby 1,* 1 Dale Bumpers National Rice Research Center, USDA Agricultural Research Service, Stuttgart, AR 72160, USA; [email protected] (C.P.F.-B.); [email protected] (W.K.); [email protected] (A.M.M.) 2 Genomics and Bioinformatics Research Unit, USDA Agricultural Research Service, Gainesville, FL 32608, USA; [email protected] (A.R.R.); [email protected] (R.P.) 3 Beltsville Agricultural Research Center, Sustainable Agricultural Systems Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA; [email protected] (J.E.M.); [email protected] (D.P.R.) 4 Rural Development Administration, National Institute of Crop Science, Wanju 55365, Korea 5 Beltsville Agricultural Research Center, Adaptive Cropping Systems Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA; [email protected] * Correspondence: [email protected]; Tel.: 1-301-504-8436 Abstract: Plant–soil microbe interactions are complex and affected by many factors including soil type, edaphic conditions, plant genotype and phenotype, and developmental stage. The rice rhizo- sphere microbial community composition of nine recombinant inbred lines (RILs) and their parents, Francis and Rondo, segregating for root and shoot biomass, was determined using metagenomic Citation: Fernández-Baca, C.P.; sequencing as a means to examine how biomass phenotype influences the rhizosphere community. Rivers, A.R.; Maul, J.E.; Kim, W.; Two plant developmental stages were studied, heading and physiological maturity, based on root Poudel, R.; McClung, A.M.; Roberts, and shoot biomass growth patterns across the selected genotypes. -
784 2016 1980 Moesm1
The mycobiome of root canal infections is correlated to the bacteriome. Clinical Oral Investigations Ilona F. Persoon1, Mark J. Buijs1, Ahmet R. Özok2, Wim Crielaard1, Bastiaan P. Krom1, Egija Zaura1, Bernd W. Brandt1 Affiliations:1Department of Preventive Dentistry; 2Department of Endodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, The Netherlands Correspondence: Ilona F. Persoon, [email protected] Table Abundance and prevalence of bacterial genera of root canal infections All teeth (N = 23) Apical samples (N = 22) Coronal samples (N = 23) Phylum Genus or higher level % Abundance Prevalence % Abundance Prevalence % Abundance Prevalence Bacteroidetes Prevotella 12.74 23 13.08 22 12.42 22 Firmicutes Lactobacillus 11.18 21 7.41 16 14.79 19 Actinobacteria Actinomyces 7.47 23 4.39 21 10.42 23 Fusobacteria Fusobacterium 7.20 23 9.33 21 5.16 22 Actinobacteria Atopobium 6.94 21 4.14 19 9.61 19 Firmicutes Streptococcus 4.39 23 4.62 19 4.17 23 Fusobacteria Leptotrichia 4.32 22 6.56 18 2.17 20 Bacteroidetes Phocaeicola 3.45 14 3.65 12 3.26 14 Synergistetes Pyramidobacter 2.85 6 3.66 4 2.07 4 Bacteroidetes Porphyromonas 2.68 19 3.21 15 2.18 16 Firmicutes Clostridiales Family XIII 2.50 20 2.97 18 2.05 17 Bacteroidetes Alloprevotella 2.37 17 2.21 12 2.52 12 TM7 Phylum TM7 1.92 18 1.62 13 2.21 18 Actinobacteria Actinobaculum 1.72 16 1.30 13 2.12 15 Firmicutes Parvimonas 1.59 22 2.24 20 0.97 19 Firmicutes Dialister 1.58 21 1.88 18 1.30 21 Firmicutes Pseudoramibacter 1.57 19 1.28 15 -
Alterations in the Gut Microbiota of Patients with Silica-Induced Pulmonary Fibrosis Yao Zhou1†, Lv Chen1†, Gaofeng Sun2, Ying Li3 and Ruixue Huang1*
Zhou et al. Journal of Occupational Medicine and Toxicology (2019) 14:5 https://doi.org/10.1186/s12995-019-0225-1 RESEARCH Open Access Alterations in the gut microbiota of patients with silica-induced pulmonary fibrosis Yao Zhou1†, Lv Chen1†, Gaofeng Sun2, Ying Li3 and Ruixue Huang1* Abstract Silicosis resulting from silica exposure is a global occupational disease characterized by severe pathological changes in progressive pulmonary fibrosis. Previous evidence has indicated that dysbiosis of the gut microbiota occurs after environmental dust exposure and is associated with certain diseases. The aims of this study are to elucidate the compositional and functional characteristics of the gut microbiota in early-stage silicosis and to understand their influence on pulmonary fibrosis. We investigated the gut microbial composition of fecal samples from 18 patients and 21 healthy subjects using 16S rRNA gene sequencing technology. Compared with the healthy subjects, reductions in the levels of Firmicutes and Actinobacteria were noted in patients with silicosis and progressive pulmonary fibrosis, as well as lower levels of Devosia, Clostridiales, AlloprevotellaandRikenellaceae_RC9. Lachnospiraceae and Lachnoclostridium levels were increased in patients with silicosis. GOC and KEGG analyses were used to predict that certain bacteria taxa play critical roles in the development of pulmonary fibrosis, including posttranslational modification, amino acid transport and metabolism, nucleotide transport and metabolism, and ribosomal structure and biogenesis. KEGG analysis showed that certain taxa participate in various roles including cancer, endocrine metabolism, immune system, signaling molecules and interaction, and transcription. Collectively, in this pilot study, microbiota changes have been represented in the gut of patients with silicosis. Although this change in gut microbiota have been represented, caution is needed when interpreting the findings since this is observational finding, not necessarily causative. -
Structural and Functional Differentiation of Bacterial Communities
www.nature.com/scientificreports OPEN Structural and functional diferentiation of bacterial communities in post-coal mining reclamation soils of South Africa: bioindicators of soil ecosystem restoration Obinna T. Ezeokoli1,2,3, Cornelius C. Bezuidenhout1, Mark S. Maboeta1, Damase P. Khasa3,4 & Rasheed A. Adeleke1,2* Soil microbial communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and role in soil ecosystem processes. Presently, information on structural and functional diferentiation of bacterial communities in post-coal mining reclamation soils of South Africa is sparse. Here, bacterial communities in three post-coal mining reclamation soils were investigated using community-level physiological profling (CLPP), enzyme activities, and next-generation sequencing of 16S rRNA gene. Inferences were drawn in reference to adjacent unmined soils. CLPP- based species diversity and proportionality did not difer signifcantly (P > 0.05) whereas activities of β-glucosidase, urease and phosphatases were signifcantly (P < 0.05) infuenced by site and soil history (reclaimed vs unmined). Bacterial communities were infuenced (PERMANOVA, P < 0.05) by soil history and site diferences, with several phylotypes diferentially abundant between soils. Contrastingly, predicted functional capabilities of bacterial communities were not diferent (PERMANOVA, P > 0.05), suggesting redundancy in bacterial community functions between reclamation and unmined soils. Silt content, bulk density, pH, electrical conductivity, Na and Ca signifcantly infuenced soil bacterial communities. Overall, results indicate that bacterial community structure refects underlying diferences between soil ecosystems, and suggest the restoration of bacterial diversity and functions over chronological age in reclamation soils. Te soil ecosystem supports numerous interactions between living and non-living matter.