Proposal of Mycetocola Gen. Nov. in the Family Microbacteriaceae and Three New Species, Mycetocola Saprophilus Sp
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Novel Bacterial Lineages Associated with Boreal Moss Species Hannah
bioRxiv preprint doi: https://doi.org/10.1101/219659; this version posted November 16, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 Novel bacterial lineages associated with boreal moss species 2 Hannah Holland-Moritz1,2*, Julia Stuart3, Lily R. Lewis4, Samantha Miller3, Michelle C. Mack3, Stuart 3 F. McDaniel4, Noah Fierer1,2* 4 Affiliations: 5 1Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, 6 Boulder, CO, USA 7 2Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, 8 USA 9 3Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ USA 10 4Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA 11 *Corresponding Author 12 13 Abstract 14 Mosses are critical components of boreal ecosystems where they typically account for a large 15 proportion of net primary productivity and harbor diverse bacterial communities that can be the major 16 source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have 17 limited understanding of how microbial communities vary across boreal moss species and the extent to 18 which local environmental conditions may influence the composition of these bacterial communities. 19 We used marker gene sequencing to analyze bacterial communities associated with eight boreal moss 20 species collected near Fairbanks, AK USA. We found that host identity was more important than site in 21 determining bacterial community composition and that mosses harbor diverse lineages of potential N2- 22 fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including 23 candidate phylum WPS-2). -
Rhodoglobus Vestalii Gen. Nov., Sp. Nov., a Novel Psychrophilic Organism Isolated from an Antarctic Dry Valley Lake
International Journal of Systematic and Evolutionary Microbiology (2003), 53, 985–994 DOI 10.1099/ijs.0.02415-0 Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake Peter P. Sheridan,1 Jennifer Loveland-Curtze,2 Vanya I. Miteva2 and Jean E. Brenchley2 Correspondence 1Department of Biological Sciences, PO Box 8007, Idaho State University, Pocatello, Vanya I. Miteva ID 83209, USA [email protected] 2Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA A novel, psychrophilic, Gram-positive bacterium (designated strain LV3T) from a lake near the McMurdo Ice Shelf, Antarctica, has been isolated and characterized. This organism formed red-pigmented colonies, had an optimal growth temperature of 18 ˚C and grew on a variety of media between ”2 and 21 ˚C. Scanning electron micrographs of strain LV3T that showed small rods with unusual bulbous protuberances during all phases of growth were of particular interest. The G+C content of the genomic DNA was approximately 62 mol%. The cell walls contained ornithine as the diamino acid. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cells grown at ”2 ˚C contained significant amounts of anteiso-C15 : 1. The major menaquinones found in strain LV3T were MK-11 and MK-12. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain LV3T was a member of the family Microbacteriaceae and related to, but distinct from, organisms belonging to the genera Agreia, Leifsonia and Subtercola.In addition, alignments of 16S rRNA sequences showed that the sequence of strain LV3T contained a 13 bp insertion that was found in only a few related sequences. -
Name: Mycetocola Lacteus Authors: Tsukamoto Et Al. 2001 Status: New
Compendium of Actinobacteria from Dr. Joachim M. Wink, University of Braunschweig Name: Mycetocola lacteus Authors: Tsukamoto et al. 2001 Status: New Species Literature: Int. J. Syst. Evol. Microbiol. 51:942 Risk group: 1 (German classification) Type strain: CM-10, DSM 15177, IFO 16278, NRRL B-24121 Author(s) Tsukamoto, T., Takeuchi, M., Shida, O., Murata, H., Shirata, A. Title Proposal of Mycetocola gen. nov. in the family Microbacteriaceae and three new species, Mycetocola saprophilus sp. nov., Mycetocola tolaasinivorans sp. nov. and Mycetocola lacteus sp. nov., isolated from cultivated mushroom, Pleurotus ostreatus . Journal Int. J. Syst. Evol. Microbiol. Volume 51 Page(s) 937-944 Year 2001 Copyright: PD Dr. Joachim M. Wink, HZI - Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany, Mail: [email protected]. Compendium of Actinobacteria from Dr. Joachim M. Wink, University of Braunschweig Genus: Mycetocola FH 6451 Species: lacteus Numbers in other collections: DSM 15177 Morphology: G R ISP 2 good beige A SP none none G R ISP 3 good beige A SP none none G R ISP 4 sparse A SP G R ISP 5 sparse A SP G R ISP 6 sparse A SP ISP 7 G R sparse A SP Melanoid pigment: - - - - NaCl resistance: % Lysozyme resistance: pH: Value- Optimum- Temperature : Value- Optimum- 28 °C Carbon utilization: Glu Ara Suc Xyl Ino Man Fru Rha Raf Cel - - - + - (+) (+) - - - Enzymes: 2 - 3 + 4 + 5 - 6 + 7 + 8 + 9 - 10 - 11 (+) 12 (+) 13 + 14 + 15 - 16 + 17 + 18 + 19 - 20 - Nit Pyz Pyr Pal βGur βGal αGlu βNag Esc Ure Gel - + + - - + + - + (+) - Comments: Beige on media 5429 and 5475 Copyright: PD Dr. -
Name: Mycetocola Saprophilus Authors: Tsukamoto Et Al. 2001
Compendium of Actinobacteria from Dr. Joachim M. Wink, University of Braunschweig Name: Mycetocola saprophilus Authors: Tsukamoto et al. 2001 Status: New Species Literature: Int. J. Syst. Evol. Microbiol. 51:942 Risk group: 1 (German classification) Type strain: CM-01, DSM 15178, IFO 16274, NRRL B-24119 Author(s) Tsukamoto, T., Takeuchi, M., Shida, O., Murata, H., Shirata, A. Title Proposal of Mycetocola gen. nov. in the family Microbacteriaceae and three new species, Mycetocola saprophilus sp. nov., Mycetocola tolaasinivorans sp. nov. and Mycetocola lacteus sp. nov., isolated from cultivated mushroom, Pleurotus ostreatus . Journal Int. J. Syst. Evol. Microbiol. Volume 51 Page(s) 937-944 Year 2001 Copyright: PD Dr. Joachim M. Wink, HZI - Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany, Mail: [email protected]. Compendium of Actinobacteria from Dr. Joachim M. Wink, University of Braunschweig Genus: Mycetocola FH 6452 Species: saprophilus Numbers in other collections: DSM 15178 Morphology: G R ISP 2 good beige A SP none none G R ISP 3 good beige A SP none none G R ISP 4 sparse A SP G R ISP 5 sparse A SP G R ISP 6 sparse A SP ISP 7 G R sparse A SP Melanoid pigment: - - - - NaCl resistance: % Lysozyme resistance: pH: Value- Optimum- Temperature : Value- Optimum- 28 °C Carbon utilization: Glu Ara Suc Xyl Ino Man Fru Rha Raf Cel - - (+) + - (+) (+) - - - Enzymes: 2 - 3 + 4 + 5 - 6 + 7 (+) 8 (+) 9 - 10 - 11 - 12 - 13 + 14 + 15 - 16 + 17 + 18 (+) 19 - 20 - Nit Pyz Pyr Pal βGur βGal αGlu βNag Esc Ure Gel - + + - - + + - - (+) - Comments: Sand yellow on medium 5429 and beige on 5475 Copyright: PD Dr. -
Corynebacterium Sp.|NML98-0116
1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album -
Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample
geosciences Article Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample Andrey A. Belov 1,*, Vladimir S. Cheptsov 1,2 , Elena A. Vorobyova 1,2, Natalia A. Manucharova 1 and Zakhar S. Ezhelev 1 1 Soil Science Faculty, Lomonosov Moscow State University, Moscow 119991, Russia; [email protected] (V.S.C.); [email protected] (E.A.V.); [email protected] (N.A.M.); [email protected] (Z.S.E.) 2 Space Research Institute, Russian Academy of Sciences, Moscow 119991, Russia * Correspondence: [email protected]; Tel.: +7-917-584-44-07 Received: 28 February 2019; Accepted: 8 April 2019; Published: 10 April 2019 Abstract: The arid Mojave Desert is one of the most significant terrestrial analogue objects for astrobiological research due to its genesis, mineralogy, and climate. However, the knowledge of culturable bacterial communities found in this extreme ecotope’s soil is yet insufficient. Therefore, our research has been aimed to fulfil this lack of knowledge and improve the understanding of functioning of edaphic bacterial communities of the Central Mojave Desert soil. We characterized aerobic heterotrophic soil bacterial communities of the central region of the Mojave Desert. A high total number of prokaryotic cells and a high proportion of culturable forms in the soil studied were observed. Prevalence of Actinobacteria, Proteobacteria, and Firmicutes was discovered. The dominance of pigmented strains in culturable communities and high proportion of thermotolerant and pH-tolerant bacteria were detected. Resistance to a number of salts, including the ones found in Martian regolith, as well as antibiotic resistance, were also estimated. -
Analysis of Cellulolytic and Hemicellulolytic Enzyme Activity
Insect Science (2010) 17, 291–302, DOI 10.1111/j.1744-7917.2010.01346.x ORIGINAL ARTICLE Analysis of cellulolytic and hemicellulolytic enzyme activity within the Tipula abdominalis (Diptera: Tipulidae) larval gut and characterization of Crocebacterium ilecola gen. nov., sp. nov., isolated from the Tipula abdominalis larval hindgut Theresa E. Rogers and Joy Doran-Peterson Microbiology Department, University of Georgia, Athens, Georgia, USA Abstract In forested stream ecosystems of the north and eastern United States, larvae of the aquatic crane fly Tipula abdominalis are important shredders of leaf litter detritus. T. abdominalis larvae harbor a dense and diverse microbial community in their hindgut that may aide in the degradation of lignocellulose. In this study, the activities of cellulolytic and hemicellulolytic enzymes were demonstrated from hindgut extracts and from bacterial isolates using model sugar substrates. One of the bacterial isolates was further characterized as a member of the family Microbacteriaceae. Taxonomic position of the isolate within this family was determined by a polyphasic approach, as is commonly employed for the separation of genera within the family Microbacteriaceae. The bacterial isolate is Gram- type positive, motile, non-sporulating, and rod-shaped. The G + C content of the DNA is 64.9 mol%. The cell wall contains B2γ type peptidoglycan, D- and L-diaminobutyric acid as the diamino acid, and rhamnose as the predominant sugar. The predominant fatty acids are 12-methyltetradecanoic acid (ai-C15:0) and 14-methylhexadecanoic acid (ai-C17:0). The isolate forms a distinct lineage within the family Microbacteriaceae, as determined by 16S rRNA sequence analysis. We propose the name Crocebacterium ilecola gen. -
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 -
Biodiversity and Habitats of Polar Region Polyhydroxyalkanoic Acid-Producing Bacteria: Bioprospection by Popular Screening Methods
G C A T T A C G G C A T genes Article Biodiversity and Habitats of Polar Region Polyhydroxyalkanoic Acid-Producing Bacteria: Bioprospection by Popular Screening Methods Małgorzata Marta Rogala 1 , Jan Gawor 2, Robert Gromadka 2 , Magdalena Kowalczyk 3 and Jakub Grzesiak 1,* 1 Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawi´nskiego5A, 02-106 Warszawa, Poland; [email protected] 2 Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawi´nskiego5A, 02-106 Warszawa, Poland; [email protected] (J.G.); [email protected] (R.G.) 3 Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawi´nskiego5A, 02-106 Warszawa, Poland; [email protected] * Correspondence: [email protected] Received: 30 June 2020; Accepted: 27 July 2020; Published: 31 July 2020 Abstract: Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. -
Large-Scale Replicated Field Study of Maize Rhizosphere Identifies Heritable Microbes
Large-scale replicated field study of maize rhizosphere identifies heritable microbes William A. Waltersa, Zhao Jinb,c, Nicholas Youngbluta, Jason G. Wallaced, Jessica Suttera, Wei Zhangb, Antonio González-Peñae, Jason Peifferf, Omry Korenb,g, Qiaojuan Shib, Rob Knightd,h,i, Tijana Glavina del Rioj, Susannah G. Tringej, Edward S. Bucklerk,l, Jeffery L. Danglm,n, and Ruth E. Leya,b,1 aDepartment of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; bDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; cDepartment of Microbiology, Cornell University, Ithaca, NY 14853; dDepartment of Crop & Soil Sciences, University of Georgia, Athens, GA 30602; eDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093; fPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853; gAzrieli Faculty of Medicine, Bar Ilan University, 1311502 Safed, Israel; hCenter for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093; iDepartment of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093; jDepartment of Energy Joint Genome Institute, Walnut Creek, CA 94598; kPlant, Soil and Nutrition Research, United States Department of Agriculture – Agricultural Research Service, Ithaca, NY 14853; lInstitute for Genomic Diversity, Cornell University, Ithaca, NY 14853; mHoward Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514; and nDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514 Edited by Jeffrey I. Gordon, Washington University School of Medicine in St. Louis, St. Louis, MO, and approved May 23, 2018 (received for review January 18, 2018) Soil microbes that colonize plant roots and are responsive to used for a variety of food and industrial products (16). -
Supplementary Information the Biodiversity and Geochemistry Of
Supplementary Information The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica Figure S1. Principal component analysis of the bacterial OTUs. Samples cluster according to habitats. Figure S2. Principal component analysis of the eukaryotic OTUs. Samples cluster according to habitats. Figure S3. Principal component analysis of selected trace elements that cause the separation (primarily Zr, Ba and Sr). Figure S4. Partial canonical correspondence analysis of the bacterial abundances and all non-collinear environmental variables (i.e., after identification and exclusion of redundant predictor variables) and without spatial effects. Samples from Lake 3 in Utsteinen clustered with higher nitrate concentration and samples from Dubois with a higher TC abundance. Otherwise no clear trends could be observed. Table S1. Number of sequences before and after quality control for bacterial and eukaryotic sequences, respectively. 16S 18S Sample ID Before quality After quality Before quality After quality filtering filtering filtering filtering PES17_36 79285 71418 112519 112201 PES17_38 115832 111434 44238 44166 PES17_39 128336 123761 31865 31789 PES17_40 107580 104609 27128 27074 PES17_42 225182 218495 103515 103323 PES17_43 219156 213095 67378 67199 PES17_47 82531 79949 60130 59998 PES17_48 123666 120275 64459 64306 PES17_49 163446 158674 126366 126115 PES17_50 107304 104667 158362 158063 PES17_51 95033 93296 - - PES17_52 113682 110463 119486 119205 PES17_53 126238 122760 72656 72461 PES17_54 120805 117807 181725 181281 PES17_55 112134 108809 146821 146408 PES17_56 193142 187986 154063 153724 PES17_59 226518 220298 32560 32444 PES17_60 186567 182136 213031 212325 PES17_61 143702 140104 155784 155222 PES17_62 104661 102291 - - PES17_63 114068 111261 101205 100998 PES17_64 101054 98423 70930 70674 PES17_65 117504 113810 192746 192282 Total 3107426 3015821 2236967 2231258 Table S2. -
Response of Gut Microbiota to Feed-Borne Bacteria Depends on Fish
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.24.265785; this version posted August 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Response of gut microbiota to feed-borne bacteria depends on fish 2 growth rate: a snapshot survey of farmed juvenile Takifugu obscurus 3 4 Xingkun Jin1, Ziwei Chen1, Yan Shi1, Jian-Fang Gui1,2, Zhe Zhao1*. 5 6 1Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 7 210098, Jiangsu, China; 2State Key Laboratory of Freshwater Ecology and 8 Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, 9 Chinese Academy of Sciences, Wuhan, 430072, Hubei, China. 10 11 Running title: Snapshot of gut microbiota in farmed obscure puffer 12 13 Authors’ Email address: 14 Xingkun Jin, [email protected] 15 Ziwei Chen, [email protected] 16 Yan Shi, [email protected] 17 Jian-Fang Gui, [email protected] 18 *To whom correspondence should be addressed: Zhe Zhao, Fax: +86 2583787653; 19 E-mail: [email protected]. 20 21 Keywords: aquaculture, ecological process, environment, feed-borne bacteria, fish 22 growth, obscure puffer 23 24 25 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.24.265785; this version posted August 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.