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de Matos JP, Ribeiro DF, da Silva AK, de Paula CH, Cordeiro IF, Lemes CGDC, Sanchez AB, Rocha LCM, Garcia CCM, Almeida NF, Alves RM, de Abreu VAC, Varani AM, Moreira LM. Diversity and potential functional role of phyllosphere-associated actinomycetota isolated from cupuassu (Theobroma grandiflorum) leaves: implications for ecosystem dynamics and plant defense strategies. Mol Genet Genomics 2024; 299:73. [PMID: 39066857 DOI: 10.1007/s00438-024-02162-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 06/25/2024] [Indexed: 07/30/2024]
Abstract
Exploring the intricate relationships between plants and their resident microorganisms is crucial not only for developing new methods to improve disease resistance and crop yields but also for understanding their co-evolutionary dynamics. Our research delves into the role of the phyllosphere-associated microbiome, especially Actinomycetota species, in enhancing pathogen resistance in Theobroma grandiflorum, or cupuassu, an agriculturally valuable Amazonian fruit tree vulnerable to witches' broom disease caused by Moniliophthora perniciosa. While breeding resistant cupuassu genotypes is a possible solution, the capacity of the Actinomycetota phylum to produce beneficial metabolites offers an alternative approach yet to be explored in this context. Utilizing advanced long-read sequencing and metagenomic analysis, we examined Actinomycetota from the phyllosphere of a disease-resistant cupuassu genotype, identifying 11 Metagenome-Assembled Genomes across eight genera. Our comparative genomic analysis uncovered 54 Biosynthetic Gene Clusters related to antitumor, antimicrobial, and plant growth-promoting activities, alongside cutinases and type VII secretion system-associated genes. These results indicate the potential of phyllosphere-associated Actinomycetota in cupuassu for inducing resistance or antagonism against pathogens. By integrating our genomic discoveries with the existing knowledge of cupuassu's defense mechanisms, we developed a model hypothesizing the synergistic or antagonistic interactions between plant and identified Actinomycetota during plant-pathogen interactions. This model offers a framework for understanding the intricate dynamics of microbial influence on plant health. In conclusion, this study underscores the significance of the phyllosphere microbiome, particularly Actinomycetota, in the broader context of harnessing microbial interactions for plant health. These findings offer valuable insights for enhancing agricultural productivity and sustainability.
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Affiliation(s)
- Jéssica Pereira de Matos
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Dilson Fagundes Ribeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Ana Karla da Silva
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Camila Henriques de Paula
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Isabella Ferreira Cordeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Angélica Bianchini Sanchez
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Camila Carrião Machado Garcia
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | | | | | - Alessandro M Varani
- Departamento de Biotecnologia Agropecuária e Ambiental, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil.
| | - Leandro Marcio Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
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2
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Wang H, Chen K, Jin H, Hu R. Interspecific Differences in Carbon and Nitrogen Metabolism and Leaf Epiphytic Bacteria among Three Submerged Macrophytes in Response to Elevated Ammonia Nitrogen Concentrations. PLANTS (BASEL, SWITZERLAND) 2024; 13:1427. [PMID: 38891236 PMCID: PMC11174776 DOI: 10.3390/plants13111427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024]
Abstract
Submerged macrophytes in eutrophic aquatic environments adapt to changes in ammonia nitrogen (NH4-N) levels by modifying their levels of free amino acids (FAAs) and soluble carbohydrates (SCs). As symbionts of submerged macrophytes, epiphytic bacteria have obvious host specificity. In the present study, the interspecific differences in the FAA and SC contents of Hydrilla verticillata (Linn. f.) Roylep, Vallisneria natans Hara and Chara braunii Gmelin and their leaf epiphytic bacterial communities were assessed in response to increased NH4-N concentrations. The results revealed that the response of the three submerged macrophytes to NH4-N stress involved the consumption of SCs and the production of FAAs. The NH4-N concentration had a greater impact on the variation in the FAA content, whereas the variation in the SC content was primarily influenced by the species. At the phylum level, the relative abundance of Nitrospirota on the leaves exhibited specific differences, with the order H. verticillata > V. natans > C. braunii. The dominant genera of epiphytic bacteria with denitrification effects on V. natans, H. verticillata and C. braunii leaves were Halomonas, Acinetobacter and Bacillus, respectively. When faced with NH4-N stress, the variation in epiphytic bacterial populations associated with ammonia oxidation and denitrification among submerged macrophytes could contribute to their divergent responses to heightened nitrogen levels.
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Affiliation(s)
- Heyun Wang
- Key Laboratory of Intelligent Health Perception and Ecological Restoration of River and Lake, Ministry of Education, Innovation Demonstration Base of Ecological Environment Geotechnical and Ecological Restoration of Rivers and Lakes, School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China; (K.C.)
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Lee S, Cho M, Sadowsky MJ, Jang J. Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater-A Review. J Microbiol 2023; 61:791-805. [PMID: 37594681 DOI: 10.1007/s12275-023-00067-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023]
Abstract
Nitrate (NO3-) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3- have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas (N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3--removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3- in several field studies. NO3- removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3- to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3- pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3- from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3- in WBR, and perspectives to enhance WBR performance in the future.
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Affiliation(s)
- Sua Lee
- Division of Biotechnology and Advanced Institute of Environment and Bioscience, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Min Cho
- Division of Biotechnology and Advanced Institute of Environment and Bioscience, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Michael J Sadowsky
- BioTechnology Institute, Department of Soil, Water and Climate, and Department of Microbial and Plant Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jeonghwan Jang
- Division of Biotechnology and Advanced Institute of Environment and Bioscience, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea.
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Wang Y, Li Q. Competition and interaction between DNRA and denitrification in composting ecosystems: insights from metagenomic analysis. BIORESOURCE TECHNOLOGY 2023; 381:129140. [PMID: 37169197 DOI: 10.1016/j.biortech.2023.129140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
This study investigated denitrification and dissimilatory nitrate reduction to ammonium (DNRA) competition for nitrite in composting of sugarcane pith and cow manure. Metagenomic analysis showed that Actinobacteria was the main DNRA microorganism. During heating phase and thermophilic phase, the abundances of denitrification functional genes (nirK and nirS decreased by 40.22% and 98.60%, respectively) and DNRA functional genes (nirB, nirD increased by 195.24% and 176.61%, and nrfA decreased by 45%, respectively) showed different trends. Interestingly, the abundance of nrfA increased by 250% during cooling and maturity phases. Mantel test revealed that competition between denitrification and DNRA microorganisms for NO2--N limited the succession of their respective communities (P < 0.01). Network analysis showed that unclassified Solirubrobacterales, Altererythrobacter and Microbacterium were the key microorganisms in DNRA microbial communities. The results provided new insights into the key microorganisms and their driving factors affecting DNRA and nitrogen management in the composting ecosystems.
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Affiliation(s)
- Yiwu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China; Key Laboratory of New Low-carbon Green Chemical Technology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning 530004, China.
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Timsy T, Behrendt U, Ulrich A, Foesel BU, Spanner T, Neumann-Schaal M, Wolf J, Schloter M, Horn MA, Kolb S. Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36861375 DOI: 10.1099/ijsem.0.005581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.
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Affiliation(s)
- Timsy Timsy
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Bärbel U Foesel
- Research Unit Molecular Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Spanner
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Park S, Cho T, Rhee M. Characterization of the nitrite production of mesophilic spore-forming bacteria during the handling of reconstituted infant formula. Food Res Int 2022; 156:111332. [DOI: 10.1016/j.foodres.2022.111332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 11/30/2022]
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Paenibacillus farraposensis sp. nov., isolated from a root nodule of Arachis villosa. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain UY79T was isolated from a root nodule of Arachis villosa, collected at the Esteros de Farrapos National Park, Río Negro, Uruguay. Cells were non-motile Gram-variable rods with central to subterminal oval to ellipsoidal endospores that swell the sporangia. Growth was observed in the range of 15–42 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0–8.0) and with up to 3 % (w/v) NaCl (optimum, 1–2 %). Strain UY79T was facultative anaerobic, catalase-positive and oxidase-negative. According to the results of 16S rRNA gene sequence analysis, UY79T belongs to the genus
Paenibacillus
and is closely related to
P. ottowii
MS2379T,
P. peoriae
BD-57T,
P. polymyxa
ATCC 842T and
P. brasilensis
PB172T, exhibiting 99.4, 99.0, 99.0 and 98.9% sequence identity, respectively. Average nucleotide identity and digital DNA–DNA hybridization values with the most closely related type strains were 74.3–88.6% and 38.2–48.7 %, respectively. Major fatty acids (>10 %) were anteiso-C15:0, iso-C15:0, and C16 : 0. Menaquinones MK-7 and MK-6 were the only isoprenoid quinones detected. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. Spermidine was the predominant polyamine. The DNA G+C content based on the draft genome sequence was 46.34 mol%. Based on the current polyphasic study, UY79T represents a novel species of the genus
Paenibacillus
, for which the name Paenibacillus farraposensis sp. nov. is proposed. The type strain is UY79T (=CCM 9147T=CGMCC 1.19038T).
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Baek J, Weerawongwiwat V, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W. Paenibacillus arenosi sp. nov., a siderophore-producing bacterium isolated from coastal sediment. Arch Microbiol 2022; 204:113. [PMID: 34982225 DOI: 10.1007/s00203-021-02735-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/02/2022]
Abstract
In this study, strain CAU 1523T, a novel Gram-positive-positive bacterium isolated from marine sediment collected from the coast of Busan, Republic of Korea, was characterized using a polyphasic taxonomic approach. This strain showed growth at a temperature range of 20-37 °C (optimum, 30 °C), a pH range of 6.5-9.5 (optimum, 7.5), and in the presence of 0-3% (w/v) NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequencing and 92 concatenated core genes indicated that CAU 1523T belonged to the genus Paenibacillus, sharing the highest sequence similarity with P. assamensis JCM 13186T (98.0%). CAU 1523T was differentiated from other Paenibacillus species by average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values, using cut-off values of 95-96%, 90%, and 70%, respectively, for closely related strains. The genome of CAU 1523T possessed various biosynthetic gene clusters, one of which encoded a putative siderophore-interacting protein. Siderophore production by the isolate was confirmed using the qualitative chrome azurol sulfonate (CAS) agar assay. Based on its phylogenetic and physiological characteristics, strain CAU 1523T represents a novel, siderophore-producing species within the genus Paenibacillus, for which the name Paenibacillus arenosi sp. nov. is proposed, with the type strain CAU 1523T (= KCTC 43108T = MCCC 1K04063T).
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Affiliation(s)
- Jihye Baek
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56216, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea.
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Timsy, Spanner T, Ulrich A, Kublik S, Foesel BU, Kolb S, Horn MA, Behrendt U. Pseudomonas campi sp. nov., a nitrate-reducing bacterium isolated from grassland soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34016249 DOI: 10.1099/ijsem.0.004799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2T=LMG 31521T=DSM 110222T) is proposed.
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Affiliation(s)
- Timsy
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Tobias Spanner
- Leibniz University Hannover, Institute of Microbiology, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Susanne Kublik
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Bärbel U Foesel
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Steffen Kolb
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Marcus A Horn
- Leibniz University Hannover, Institute of Microbiology, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Undine Behrendt
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
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Pandey CB, Kumar U, Kaviraj M, Minick KJ, Mishra AK, Singh JS. DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139710. [PMID: 32544704 DOI: 10.1016/j.scitotenv.2020.139710] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO3- occurs in two steps; in the first step, NO3- is reduced to NO2-; and in the second, unlike denitrification, NO2- is reduced to NH4+ without intermediates. There are two sets of NO3-/NO2- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N2O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N2O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO2-/NO3- ratio, and concentrations of ferrous iron (Fe2+) and sulfide (S2-). Under low-redox conditions, a high C/NO3- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO3- are equal, the NO2-/NO3- ratio modulates partitioning of NO3-, and a high NO2-/NO3- ratio favours DNRA. A high S2-/NO3- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO3- to NH4+, it is essential for protecting NO3- from leaching and gaseous (N2O) losses and enriches soils with readily available NH4+-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO3- pollution, enhance soil health and improve environmental quality.
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Affiliation(s)
- C B Pandey
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India.
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India.
| | - Megha Kaviraj
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - K J Minick
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - A K Mishra
- International Rice Research Institute, New Delhi 110012, India
| | - J S Singh
- Ecosystem Analysis Lab, Centre of Advanced Study in Botany, Banaras Hindu University (BHU), Varanasi 221005, India
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Heo J, Kim SJ, Kim JS, Hong SB, Kwon SW. Paenibacillus protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis. Int J Syst Evol Microbiol 2019; 70:989-994. [PMID: 31702533 DOI: 10.1099/ijsem.0.003860] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, strictly aerobic, endospore-forming and motile bacterium with peritrichous flagella was isolated from a gut sample of the larva of Protaetia brevitarsis seulensis at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. Growth was observed at 15-50 °C (optimum, 28-37 °C), pH 6.0-8.0 (pH 7.0) and only without NaCl. 16S rRNA gene sequence comparisons indicated that strain FW100M-2T had the highest similarity to type strains of Paenibacillus thailandensis S3-4AT (96.8 %) and Paenibacillus agaridevorans DSM 1355T (96.3 %), and had sequence similarity values less than 96.0 % to all other taxa. The phylogenetic tree showed that strain FW100M-2T fell into the genus Paenibacillus, and formed a cluster with P. thailandensis S3-4AT independent from other Paenibacillus species. Antesio-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 were detected as the major fatty acids. The only isoprenoid quinone was MK-7. Polar lipids of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and an unidentified lipid were present. The meso-diaminopimelic acid was present in the cell-wall peptidoglycan. The genomic DNA G+C content was 51.5 mol%. Hence, strain FW100M-2T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus protaetiae sp. nov. is proposed, with FW100M-2T (=KACC 19327T=NBRC 113071T) as the type strain.
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Affiliation(s)
- Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
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12
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Macêdo WV, Santos CED, Guerrero RDBS, Sakamoto IK, Amorim ELCD, Azevedo EB, Damianovic MHRZ. Establishing simultaneous nitrification and denitrification under continuous aeration for the treatment of multi-electrolytes saline wastewater. BIORESOURCE TECHNOLOGY 2019; 288:121529. [PMID: 31136891 DOI: 10.1016/j.biortech.2019.121529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 06/09/2023]
Abstract
Simultaneous nitrification and denitrification (SND) was established under continuous aeration (6 mgO2 L-1) aiming at achieving a feasible and simple operational strategy for treating multi-electrolyte saline wastewaters. Two Structured Fixed-Bed Reactors (SFBR) were used to assess SND performance with (Saline Reactor, SR) and without (Control Reactor, CR) salinity interference. Salinity was gradually increased (from 1.7 to 9 atm) based on the composition of water supplied in arid regions of Brazil. At 1.7 atm, N-NH4+ oxidation and Total Nitrogen (TN) removal efficiencies of 95.9 ± 2.8 and 65.76 ± 7.5%, respectively, were obtained. At osmotic pressure (OP) of 9 atm, the system was severely affected by specific salt toxicity and OP. High chemical oxygen demand (COD) removal efficiency was achieved at all operational conditions (97.2 ± 1.6 to 78.5 ± 4.6%). Salinity did not affect microbial diversity, although it modified microbial structure. Halotolerant genera were identified (Prosthecobacter, Chlamydia, Microbacterium, and Paenibacillus).
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Affiliation(s)
- Williane Vieira Macêdo
- Biological Processes Laboratory (LPB), University of São Paulo (USP), 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil.
| | - Carla E D Santos
- Biological Processes Laboratory (LPB), University of São Paulo (USP), 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
| | - Renata de Bello Solcia Guerrero
- Biological Processes Laboratory (LPB), University of São Paulo (USP), 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
| | - Isabel K Sakamoto
- Biological Processes Laboratory (LPB), University of São Paulo (USP), 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
| | | | - Eduardo Bessa Azevedo
- Environmental Technology Development Laboratory (LTDAmb), University of São Paulo (USP), 400 Trab. São Carlense Avenue, 13563-120 São Carlos, SP, Brazil
| | - Marcia Helena R Z Damianovic
- Biological Processes Laboratory (LPB), University of São Paulo (USP), 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
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13
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Chen S, Chen Y, Pei H, Hou Q. Biofilm development dynamics and pollutant removal performance of ceramsite made from drinking-water treatment sludge. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2019; 91:616-627. [PMID: 30742347 DOI: 10.1002/wer.1089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Alum-sludge ceramsite and denitrifying bacteria (XP-1, XP-2, CL-1, CL-3) were used as substrate and constructed biofilm for enhancing the removal of pollutants from wastewater. The results showed that, due to the large specific surface area, the maximum growth rate was 0.49 mg/(g·day) on the sludge ceramsite, and the mass of biofilm attached onto sludge ceramsite was 5.98 times higher than that when using commercial ceramsite as substrate. Better removal performance could be achieved with the combination of sludge ceramsite and bacteria, viz. 98.6%, 91.0%, and 85.8% reduction in total phosphorus (TP), total nitrogen (TN), and chemical oxygen demand (COD), respectively. Pseudo-first-order kinetics, pseudo-second-order kinetics, Monod kinetics, and multiple Monod kinetics combined with continuous-flow-stirred tank reactor (CFSTR) behavior were used to investigate the dynamics of the pollutant removal processes. The decrease in band brightness for bacteria attached onto sludge ceramsite was 11.5%, while it was more than 35.7% on commercial ceramsite during wastewater treatment according to results from denaturing gradient gel electrophoresis (DGGE). Sludge ceramsite played an important role in maintaining quantities and activities of denitrifying bacteria, and application of sludge ceramsite substrate and denitrifying bacteria was a reliable method to enhance the removals of phosphorus, nitrogen, and COD from domestic wastewater. PRACTITIONER POINTS: Alum-sludge ceramsite was a good substrate for phosphorus adsorption and denitrifying bacterial growth. There was 5.98 times more biofilm on sludge ceramsite than on commercial ceramsite The biofilm of denitrifying bacteria on sludge ceramsite was more stable. High removals of TP (98.6%), TN (90.1%) and COD (85.81%) were achieved.
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Affiliation(s)
- Shuaiqi Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Yang Chen
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Haiyan Pei
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
- Shandong Provincial Engineering Center on Environmental Science and Technology, Jinan, China
| | - Qingjie Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
- Shandong Provincial Engineering Center on Environmental Science and Technology, Jinan, China
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14
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Barbagli A, Jensen BN, Raza M, Schüth C, Rossetto R. Assessment of soil buffer capacity on nutrients and pharmaceuticals in nature-based solution applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:759-774. [PMID: 30415360 DOI: 10.1007/s11356-018-3515-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 10/17/2018] [Indexed: 06/09/2023]
Abstract
The ability of a soil to sustain infiltration rates and to attenuate pollutants is critical for the design and operation of Managed Aquifer Recharge/Soil Aquifer Treatment and phyto-treatment schemes, also referred to as "Blue Infrastructures". We investigated the buffering capacity of a sediment sample and a peat soil sample for nutrients and selected pharmaceutical compounds and its evolution under continuous infiltration of secondary treated wastewater (TWW) in column experiments. Samples were obtained from two blue infrastructures, the Sant'Alessio Induced River Bank Filtration plant and the San Niccolò large-scale phyto-treatment plant in Italy, and were mainly different in their organic carbon contents (0.9 and 48%, respectively). In the column experiments, a constant infiltration rate of about 0.5 L/d was maintained for 6 months. After 4 months of operation, diclofenac and carbamazepine were spiked into the TWW to evaluate their fate. Water quality was monitored by periodic water sampling from the column inflow, at sampling ports along the column length, and at the outflow. Hydraulic conductivity (K) was also monitored. The hydraulic conductivity of the Sant'Alessio sediment decreased by a factor of 10 during the first 10 days of infiltration and then stabilized, while for the San Niccolò K (initially lower) remained constant for 50 days until it decreased following a change of the redox condition in the column. The different redox conditions, due to the two different soils tested, influenced also the concentration and mobility of PO43-, Fe, Mn, and NPOC, and the speciation of the redox sensitive elements (nitrogen and sulfur). NOPC and phosphate were enriched during the filtration through San Niccolò peat soil (from 2 to 4 times, respectively), while they were buffered by the Sant'Alessio sediment (from 0.2 to 0.4 times, respectively). Diclofenac removal (69% and below 20% for San Niccolò and Sant'Alessio, respectively) was related to sorption and degradation processes and it was lower than the removal of carbamazepine in both soils (76 and 35%). The buffer capacity differences between the two soils were higher for diclofenac (62%) than carbamazepine (35%). Nevertheless, since no apparent degradation of carbamazepine was detected in both soils, its persistence in the soil may have a larger impact in case of desorption, posing contamination risk to groundwater. The results highlight the importance of the soils or sediments to be used as medium in such nature-based solutions for their operations. They also offer an approach to, e.g., tailor man-made soil layers in infiltration basins. We strongly suggest that soil characteristics and test duration are carefully considered in designing these infrastructures, when nature-based processes are the choice for dealing with reuse of treated wastewater management issues.
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Affiliation(s)
- Alessio Barbagli
- CGT Center for GeoTechnologies, University of Siena, Via Vetri Vecchi 34, 52027, San Giovanni Valdarno, Italy
| | - Benjamin Niklas Jensen
- Dr. Spang Ingenieurgesellschaft für Bauwesen, Geologie und Umwelttechnik mbH, Rosi-Wolfstein-Strasse 6, 58453, Witten, Germany
| | - Muhammad Raza
- Institute of Applied Geosciences, Technische Universität Darmstadt, Schnittspahnstr. 9, 64287, Darmstadt, Germany
- IWW Water Centre, Moritzstr. 26, 45476, Mülheim an der Ruhr, Germany
| | - Christoph Schüth
- Institute of Applied Geosciences, Technische Universität Darmstadt, Schnittspahnstr. 9, 64287, Darmstadt, Germany
- IWW Water Centre, Moritzstr. 26, 45476, Mülheim an der Ruhr, Germany
| | - Rudy Rossetto
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Via Santa Cecilia 3, 56127, Pisa, Italy.
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15
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Cho TJ, Rhee MS. Underrecognized niche of spore-forming bacilli as a nitrite-producer isolated from the processing lines and end-products of powdered infant formula. Food Microbiol 2018; 80:50-61. [PMID: 30704596 DOI: 10.1016/j.fm.2018.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/20/2018] [Accepted: 12/21/2018] [Indexed: 01/14/2023]
Abstract
Although nitrite in powdered milk formula (PIF) is a recognized health risk for infants, the presence of nitrite in PIF has only been investigated as a chemical contaminant during the inspection of end-products. The risk posed by microbial sources of nitrite during the PIF manufacturing process has not been considered. This is the first study to report the taxonomy and physiological characteristics of nitrite-producing bacteria isolated from PIF processing environments. All isolates identified as nitrite-producers (133 out of 501 strains collected over four years) from work-in-process and end-products of PIF were spore-forming bacilli. Nitrite-producing metabolism under PIF processing conditions was found in not only thermophilic isolates (3 Bacillus, 60 Geobacillus from 63 strains; 100%) but also in mesophilic isolates (65 Bacillus, 1 Anoxybacillus from 70 strains; 65.7%). Geobacillus was the only highly heat-resistant sporeformer and vigorous nitrite-producer exhibiting dramatic increases in nitrite over short periods of incubation (a maximum value within 3 h). High conversions of nitrate to nitrite (up to 88.8%) was also observed, highlighting bacteria as a key source of nitrite in PIF processing lines. Further research into the diversity of metabolic activity observed in this study can facilitate specialized management of nitrite-producers in PIF processing lines.
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Affiliation(s)
- Tae Jin Cho
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea.
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16
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Anderson CR, Peterson ME, Frampton RA, Bulman SR, Keenan S, Curtin D. Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum. PeerJ 2018; 6:e6090. [PMID: 30581677 PMCID: PMC6295159 DOI: 10.7717/peerj.6090] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/08/2018] [Indexed: 01/13/2023] Open
Abstract
Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO2 respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N2-N g-1 h-1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential.
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Affiliation(s)
- Craig R Anderson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Michelle E Peterson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Rebekah A Frampton
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Simon R Bulman
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Sandi Keenan
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Denis Curtin
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
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17
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Hwang WM, Ko Y, Kang K, Ahn TY. Paludirhabdus telluriireducens gen. nov., sp. nov. and Paludirhabdus pumila sp. nov., isolated from soil of a mountain wetland and emended description of Gorillibacterium massiliense. Int J Syst Evol Microbiol 2018; 68:3040-3046. [PMID: 30067175 DOI: 10.1099/ijsem.0.002946] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-stain-positive, endospore-forming, motile by means of peritrichous flagella, aerobic or facultative anaerobic, and rod-shaped bacteria that were designated ON8T and ON6T were isolated from soil collected from a mountain wetland in Gwang-ju, Republic of Korea. The isolates were catalase-positive and oxidase-negative. Cells of ON8T and ON6T grew at 15-35 °C (optimal 30 °C) and 15-40 °C (optimal 30 °C), respectively. The major menaquinone was MK-7 and the major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, iso-C15 : 0, C14 : 0 and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, aminophospholipid and phospholipid. Meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C contents of strains ON8T and ON6T were 50.6 and 53.5 mol%, respectively, and the 16S rRNA gene sequence analysis showed that the nearest phylogenetic neighbour of both strains was Gorillibacterium massiliense G5T (93.9 %), followed by the members of the genus Paenibacillus in the family Paenibacillaceae. The DNA-DNA hybridization relatedness value between ON8T and ON6T was 44.1 %, which indicated that they represented distinct species. Based on polyphasic characteristics, a novel genus is proposed with the name Paludirhabdus gen. nov., which consists of two species, Paludirhabdus telluriireducens sp. nov. (the type species; type strain ON8T=KACC 19267T=JCM 31958T) and Paludirhabdus pumila sp. nov. (type strain ON6T=KACC 19266T=JCM 31957T).
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Affiliation(s)
- Woon Mo Hwang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Yongseok Ko
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Tae-Young Ahn
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
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18
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Root-associated bacteria influencing mycelial growth of Tricholoma matsutake (pine mushroom). J Microbiol 2018; 56:399-407. [PMID: 29858828 DOI: 10.1007/s12275-018-7491-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/19/2018] [Accepted: 04/06/2018] [Indexed: 10/14/2022]
Abstract
Tricholoma matsutake is an ectomycorrhizal fungus usually associated with Pinus densiflora in South Korea. Fruiting bodies (mushrooms) of T. matsutake are economically important due to their attractive aroma; yet, T. matsutake is uncultivatable and its habitat is rapidly being eradicated due to global climate change. Root-associated bacteria can influence the growth of ectomycorrhizal fungi that co-exist in the host rhizosphere and distinctive bacterial communities are associated with T. matsutake. In this study, we investigated how these bacterial communities affect T. matsutake growth by isolating bacteria from the roots of P. densiflora colonized by ectomycorrhizae of T. matsutake and co-culturing rootassociated bacteria with T. matsutake isolates. Thirteen species of bacteria (27 isolates) were found in pine roots, all belonging to the orders Bacillales or Burkholderiales. Two species in the genus Paenibacillus promoted the growth of T. matsutake in glucose poor conditions, likely using soluble metabolites. In contrast, other bacteria suppressed the growth of T. matsutake using both soluble and volatile metabolites. Antifungal activity was more frequent in glucose poor conditions. In general, pine rhizospheres harbored many bacteria that had a negative impact on T. matsutake growth and the few Paenibacillus species that promoted T. matsutake growth. Paenibacillus species, therefore, may represent a promising resource toward successful cultivation of T. matsutake.
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19
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Uksa M, Buegger F, Gschwendtner S, Lueders T, Kublik S, Kautz T, Athmann M, Köpke U, Munch JC, Schloter M, Fischer D. Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:729-741. [PMID: 28892269 DOI: 10.1111/1758-2229.12588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, 13 C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in 13 C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in 13 C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear 13 C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.
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Affiliation(s)
- Marie Uksa
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
- Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Tillmann Lueders
- Institute for Groundwater Ecology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Timo Kautz
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Miriam Athmann
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Ulrich Köpke
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Jean Charles Munch
- Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
- Chair for Soil Science, Research Department Ecology and Ecosystem Management, Technische Universität München, D-85350 Freising-Weihenstephan, Germany
| | - Doreen Fischer
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
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20
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Shin SK, Kim E, Yi H. Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas. Int J Syst Evol Microbiol 2017; 68:58-63. [PMID: 29068277 DOI: 10.1099/ijsem.0.002444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, endospore-forming, rod-shaped, aerobic bacterium, designated LPB0068T, was isolated from a Pacific oyster (Crassostrea gigas) in Korea. This isolate was found to share the highest 16S rRNA gene sequence similarity with Paenibacillus macquariensis subsp. macquariensis DSM 2T (98.1 %) and Paenibacillus macquariensis subsp. defensor JCM 14954T (98.0 %). To establish the genomic relatedness of this isolate to its phylogenetic neighbours, its genome sequence and those of Paenibacillus antarcticus CECT 5836T, P. macquariensis subsp. macquariensis DSM 2T, P. macquariensis subsp. defensor JCM 14954T, and Paenibacillus glacialis DSM 22343T were determined. The low average nucleotide identity and digital DNA-DNA hybridization values exhibited by LPB0068T in relation to the other strains in this analysis revealed that it is distinct from other Paenibacillus species. The genome of strain LPB0068T consists of one chromosome and three circular plasmids, and had a DNA G+C content of 40.0 mol%. The major respiratory quinone was menaquinone-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified glycolipid, and two unidentified polar lipids. The major cellular fatty acids were anteiso-C15 : 0, C14 : 0, and C16 : 0. Based on genomic, phylogenetic, and phenotypic characteristics, this strain was clearly distinguished from other Paenibacillus species with validly published names and should therefore be classified as a novel species of the genus. The name Paenibacillus crassostreae sp. nov. is proposed, the type strain of which is LPB0068T (=KACC 18694T=JCM 31183T).
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Affiliation(s)
- Su-Kyoung Shin
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea
| | - Eunji Kim
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea.,School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
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Koskinen K, Rettberg P, Pukall R, Auerbach A, Wink L, Barczyk S, Perras A, Mahnert A, Margheritis D, Kminek G, Moissl-Eichinger C. Microbial biodiversity assessment of the European Space Agency's ExoMars 2016 mission. MICROBIOME 2017; 5:143. [PMID: 29070062 PMCID: PMC5657055 DOI: 10.1186/s40168-017-0358-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/27/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli lander was subject to strict requirements for microbial cleanliness according to the obligatory planetary protection policy. To reach the required cleanliness, the ExoMars 2016 flight hardware was assembled in a newly built, biocontrolled cleanroom complex at Thales Alenia Space in Turin, Italy. In this study, we performed microbiological surveys of the cleanroom facilities and the spacecraft hardware before and during the assembly, integration and testing (AIT) activities. METHODS Besides the European Space Agency (ESA) standard bioburden assay, that served as a proxy for the microbiological contamination in general, we performed various alternative cultivation assays and utilised molecular techniques, including quantitative PCR and next generation sequencing, to assess the absolute and relative abundance and broadest diversity of microorganisms and their signatures in the cleanroom and on the spacecraft hardware. RESULTS Our results show that the bioburden, detected microbial contamination and microbial diversity decreased continuously after the cleanroom was decontaminated with more effective cleaning agents and during the ongoing AIT. The studied cleanrooms and change room were occupied by very distinct microbial communities: Overall, the change room harboured a higher number and diversity of microorganisms, including Propionibacterium, which was found to be significantly increased in the change room. In particular, the so called alternative cultivation assays proved important in detecting a broader cultivable diversity than covered by the standard bioburden assay and thus completed the picture on the cleanroom microbiota. CONCLUSION During the whole project, the bioburden stayed at acceptable level and did not raise any concern for the ExoMars 2016 mission. The cleanroom complex at Thales Alenia Space in Turin is an excellent example of how efficient microbiological control is performed.
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Affiliation(s)
- Kaisa Koskinen
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Petra Rettberg
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna Auerbach
- Department for Microbiology, University of Regensburg, Regensburg, Germany
| | - Lisa Wink
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
| | - Simon Barczyk
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Alexandra Perras
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- Department for Microbiology, University of Regensburg, Regensburg, Germany
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | | | - Christine Moissl-Eichinger
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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Li J, Guo W, Shi M, Cao Y, Wang G. High-quality-draft genomic sequence of Paenibacillus ferrarius CY1 T with the potential to bioremediate Cd, Cr and Se contamination. Stand Genomic Sci 2017; 12:60. [PMID: 29046739 PMCID: PMC5634878 DOI: 10.1186/s40793-017-0273-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/21/2017] [Indexed: 11/23/2022] Open
Abstract
Paenibacillus ferrarius CY1T (= KCTC 33419T = CCTCC AB2013369T) is a Gram-positive, aerobic, endospore-forming, motile and rod-shaped bacterium isolated from iron mineral soil. This bacterium reduces sulfate (SO42-) to S2-, which reacts with Cd(II) to generate precipitated CdS. It also reduces the toxic chromate [Cr(VI)] and selenite [Se(VI)] to the less bioavailable chromite [Cr(III)] and selenium (Se0), respectively. Thus, strain CY1T has the potential to bioremediate Cd, Cr and Se contamination, which is the main reason for the interest in sequencing its genome. Here we describe the features of strain CY1T, together with the draft genome sequence and its annotation. The 9,184,169 bp long genome exhibits a G + C content of 45.6%, 7909 protein-coding genes and 81 RNA genes. Nine putative Se(IV)-reducing genes, five putative Cr(VI) reductase and nine putative sulfate-reducing genes were identified in the genome.
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Affiliation(s)
- Jingxin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Wei Guo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Manman Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yajing Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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Behrendt U, Kämpfer P, Glaeser SP, Augustin J, Ulrich A. Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov. Int J Syst Evol Microbiol 2016; 66:2354-2361. [PMID: 27030972 DOI: 10.1099/ijsem.0.001036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed.
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Affiliation(s)
- Undine Behrendt
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Department of Applied Microbiology, Justus-Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Jürgen Augustin
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany
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Zheng B, Zhang F, Dong H, Chai L, Shu F, Yi S, Wang Z, Cui Q, Dong H, Zhang Z, Hou D, Yang J, She Y. Draft genome sequence of Paenibacillus sp. strain A2. Stand Genomic Sci 2016; 11:9. [PMID: 26819653 PMCID: PMC4728784 DOI: 10.1186/s40793-015-0125-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/22/2015] [Indexed: 11/19/2022] Open
Abstract
Paenibacillus sp. strain A2 is a Gram-negative rod-shaped bacterium isolated from a mixture of formation water and petroleum in Daqing oilfield, China. This facultative aerobic bacterium was found to have a broad capacity for metabolizing hydrocarbon and organosulfur compounds, which are the main reasons for the interest in sequencing its genome. Here we describe the features of Paenibacillus sp. strain A2, together with the genome sequence and its annotation. The 7,650,246 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 54.2 % and contains 7575 protein-coding and 49 RNA genes, including 3 rRNA genes. One putative alkane monooxygenase, one putative alkanesulfonate monooxygenase, one putative alkanesulfonate transporter and four putative sulfate transporters were found in the draft genome.
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Affiliation(s)
- Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Fan Zhang
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing, China
| | - Hao Dong
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, China
| | - Lujun Chai
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing, China
| | - Fuchang Shu
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, China
| | - Shaojin Yi
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, China
| | - Zhengliang Wang
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, China
| | - Qingfeng Cui
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang, China
| | - Hanping Dong
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang, China
| | - Zhongzhi Zhang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Dujie Hou
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing, China
| | - Jinshui Yang
- College of Life Sciences, China Agricultural University, Beijing, China
| | - Yuehui She
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, China
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High-quality genome sequence and description of Paenibacillus dakarensis sp. nov. New Microbes New Infect 2016; 10:132-41. [PMID: 26958345 PMCID: PMC4773451 DOI: 10.1016/j.nmni.2016.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/18/2015] [Accepted: 01/14/2016] [Indexed: 12/03/2022] Open
Abstract
Strain FF9T was isolated in Dakar (Senegal) from a blood-culture taken from a 16-month-old child. MALDI-TOF analysis did not allow for identification. After sequencing, strain FF9T exhibited 98.18% similarity with the 16SrRNA sequence of Paenibacillus uliginis. A polyphasic study of phenotypic and genomic analyses showed that strain FF9T is Gram variable, catalase-positive, and presents a genome of 4,569,428 bp (one chromosome but no plasmid) with 4,427genes (4,352 protein-coding and 75 RNA genes (including 3 rRNA operons). The G+C content is 45.7%. On the basis of these genomic and phenotypic data analyses, we propose the creation of Paenibacillus dakarensis strain FF9T.
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26
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Wang DD, Kim YJ, Hoang VA, Nguyen NL, Singh P, Wang C, Chun-Yang D. Paenibacillus puernese sp. nov., a β-glucosidase-producing bacterium isolated from Pu'er tea. Arch Microbiol 2016; 198:211-7. [PMID: 26721586 DOI: 10.1007/s00203-015-1180-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/11/2015] [Accepted: 12/17/2015] [Indexed: 11/29/2022]
Abstract
A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain DCY97(T) was closely related to Paenibacillus dongdonensis KUDC0114(T) (98.0 %), Paenibacillus oceanisediminis L10(T) (97.7 %), and Paenibacillus barcinonensis BP-23(T) (97.2 %). The phenotypic and chemotaxonomic characteristics of strain DCY97(T) matched with the characteristics of members belonging to the genus Paenibacillus. The major identified polar lipids included phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant quinone was MK-7. The major fatty acids were anteiso-C15:0 (35.1 %), anteiso-C16:0 (19.0 %), and iso-C16:0 (13.9 %). The peptidoglycan cell wall was composed of meso-diaminopimelic acids, alanine, and D-glutamic acid. The genomic DNA G + C content was determined to be 46.7 mol%. The DNA-DNA relatedness between strain DCY97(T) and Paenibacillus dongdonensis KCTC 33221(T), Paenibacillus oceanisediminis KACC 16023(T), Paenibacillus barcinonensis KCTC 13019(T) were 27, 19, and 10 %, respectively. Based on the genotypic, phenotypic, and chemotaxonomic characteristics, strain DCY97(T) is considered as a novel species of the genus Paenibacillus, for which the name Paenibacillus puernese sp. nov. is proposed. The type strain is DCY97(T) (=KCTC 33596(T) = JCM 140369(T)).
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Affiliation(s)
- Dan-Dan Wang
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Yeon-Ju Kim
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Van-An Hoang
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Ngoc-Lan Nguyen
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Priyanka Singh
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Chao Wang
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Deok Chun-Yang
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea. .,Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea.
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27
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Nguyen NL, Kim YJ, Hoang VA, Kang JP, Singh P, Yang DC. Paenibacillus panaciterrae sp. nov., isolated from ginseng-cultivated soil. Int J Syst Evol Microbiol 2015; 65:4080-4086. [DOI: 10.1099/ijsem.0.000540] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A novel bacterium, designated DCY95T, was isolated from ginseng-cultivated soil in Quang Nam province, Vietnam. On the basis of 16S rRNA and gyrB gene sequence analysis, this isolate was assigned to the genus Paenibacillus and found to be closely related to Paenibacillus sacheonensis SY01T (97.1 % 16S rRNA gene sequence similarity) and Paenibacillus taihuensis THMBG22T (96.4 %). The partial gyrB gene of DCY95T possessed 69.6–83.9 % sequence identity to those of other members of the genus Paenibacillus. Strain DCY95T was Gram-reaction-negative, catalase-negative, oxidase-positive, strictly aerobic, rod-shaped and motile by means of peritrichous flagella. Ellipsoidal free spores or subterminal endospores were produced in sporangia. MK-7 was the diagnostic menaquinone. The cell-wall peptidoglycan contained meso-diamonopimelic acid as the diamino acid. Whole-cell sugars comprised ribose, mannose and glucose. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, and two unidentified phospholipids. The genomic DNA G+C content was 60.7 ± 0.9 mol%. Phenotypic and chemotaxonomic results placed strain DCY95T within the genus Paenibacillus. However, DNA–DNA relatedness values between strain DCY95T and P. sacheonensis KACC 14895T or P. taihuensis NBRC 108766T were lower than 36 %. The low DNA relatedness data in combination with phylogenetic and (GTG)5-PCR analyses, as well as biochemical tests, indicated that strain DCY95T could not be assigned to any recognized species. In conclusion, the results in this study support the classification of strain DCY95T as a representative of a novel species within the genus Paenibacillus, for which the name Paenibacillus panaciterrae is proposed. The type strain is DCY95T ( = KCTC 33581T = DSM 29477T).
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Affiliation(s)
- Ngoc-Lan Nguyen
- Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Yeon-Ju Kim
- Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Van-An Hoang
- Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Jong-Pyo Kang
- Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Priyanka Singh
- Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Deok-Chun Yang
- Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
- Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
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Behrendt U, Augustin J, Spröer C, Gelbrecht J, Schumann P, Ulrich A. Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium. Antonie van Leeuwenhoek 2015; 108:1457-1468. [PMID: 26437638 DOI: 10.1007/s10482-015-0601-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/28/2015] [Indexed: 11/28/2022]
Abstract
In the context of studying the influence of N-fertilization on N2 and N2O flux rates in relation to the soil bacterial community composition in fen peat grassland, a group of bacterial strains was isolated that performed dissimilatory nitrate reduction to ammonium and concomitantly produced N2O. The amount of nitrous oxide produced was influenced by the C/N ratio of the medium. The potential to generate nitrous oxide was increased by higher availability of nitrate-N. Phylogenetic analysis based on the 16S rRNA and the rpoB gene sequences demonstrated that the investigated isolates belong to the genus Proteus, showing high similarity with the respective type strains of Proteus vulgaris and Proteus penneri. DNA-DNA hybridization studies revealed differences at the species level. These differences were substantiated by MALDI-TOF MS analysis and several distinct physiological characteristics. On the basis of these results, it was concluded that the soil isolates represent a novel species for which the name Proteus terrae sp. nov. (type strain N5/687(T) =DSM 29910(T) =LMG 28659(T)) is proposed.
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Affiliation(s)
- Undine Behrendt
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, 15374, Müncheberg, Germany.
| | - Jürgen Augustin
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, 15374, Müncheberg, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Jörg Gelbrecht
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Central Chemical Laboratory, Müggelseedamm 301, 12587, Berlin, Germany
| | - Peter Schumann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, Eberswalder Str. 84, 15374, Müncheberg, Germany
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Paenibacillus populi sp. nov., a novel bacterium isolated from the rhizosphere of Populus alba. Antonie van Leeuwenhoek 2015; 108:659-66. [DOI: 10.1007/s10482-015-0521-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/27/2015] [Indexed: 10/23/2022]
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30
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Mishra SS, Markande AR, Keluskar RP, Karunasagar I, Nayak BB. Simultaneous nitrification and denitrification by novel heterotrophs in remediation of fish processing effluent. J Basic Microbiol 2015; 55:772-9. [DOI: 10.1002/jobm.201400783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 01/28/2015] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | | | - Binaya B. Nayak
- Central Institute of Fisheries Education (CIFE); Mumbai India
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Keita MB, Padhmananabhan R, Caputo A, Robert C, Delaporte E, Raoult D, Fournier PE, Bittar F. Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov. Stand Genomic Sci 2014; 9:1031-45. [PMID: 25197481 PMCID: PMC4149019 DOI: 10.4056/sigs.5189179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Strain G1(T) sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species within the genus Paenibacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic, Gram-negative, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856 protein-coding and 62 RNAs genes, including 60 tRNA genes.
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Affiliation(s)
| | | | - Aurélia Caputo
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Catherine Robert
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | | | - Didier Raoult
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
- King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | | | - Fadi Bittar
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
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Verbaendert I, Hoefman S, Boeckx P, Boon N, De Vos P. Primers for overlooked nirK, qnorB, and nosZ genes of thermophilic Gram-positive denitrifiers. FEMS Microbiol Ecol 2014; 89:162-80. [PMID: 24784780 DOI: 10.1111/1574-6941.12346] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/03/2014] [Accepted: 04/10/2014] [Indexed: 12/16/2022] Open
Abstract
Although efforts have been made the past few years, knowledge on genomic and phenotypic diversity and occurrence of the denitrification ability in Gram-positive bacteria are still fragmentary. Many environmental monitoring approaches have used nir, nor, and nos genes as marker genes for detection of denitrification or denitrifying bacteria. However, primers used in these methods often fail to detect the genes in specific bacterial taxa, such as Gram-positive denitrifiers. In this study, novel primer sets specifically targeting nirK, qnorB, and nosZ genes of the Firmicute genus Geobacillus were developed by genomic mining and tested in parallel with commonly used primers on a set of phylogenetically closely related denitrifying geobacilli. Novel nirK and qnorB sequences were recovered from all strains tested, whereas nosZ was detected in part of the strain set, which was in agreement with observed phenotypes. Interspecies and modest intraspecies variations in amplified fragment length polymorphism (AFLP) patterns were observed, verifying presence of genomic variation within the strain set. Our study shows that closely related Gram-positive denitrifiers may differ in denitrification phenotype and genotype. But foremost, novel primers targeting very divergent nirK, qnorB, and nosZ gene sequences of Gram-positive denitrifiers, are now available for cultivation-independent environmental surveys.
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Affiliation(s)
- Ines Verbaendert
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
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Meng P, Hu W, Pei H, Hou Q, Ji Y. Effect of different plant species on nutrient removal and rhizospheric microorganisms distribution in horizontal-flow constructed wetlands. ENVIRONMENTAL TECHNOLOGY 2014; 35:808-816. [PMID: 24645463 DOI: 10.1080/09593330.2013.852626] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Three macrophyte species, Phragmites australis, Arundo donax L., and Typha latifolia L. have been separately grown in a horizontal-flow (HF) constructed wetland (CW) fed with domestic wastewater to investigate effects of plant species on nutrient removal and rhizospheric microorganisms. All the three mesocosms have been in operation for eight months under the loading rates of 1.14 g Nm(-2) d(-1) and 0.014gP m(-2) d(-1). Appropriately 34-43% phosphorus (P) was removed in HF CWs, and no distinct difference was found among the plants. In the growing season, A. donax L. removed 31.19 gm(-2) of nitrogen (N), followed by P. australis (29.96 g m(-2)), both of which were significantly higher than T. latifolia L. (7.21 g m(-2). Depending on the species, plants absorbed 1.73-7.15% of the overall N, and 0.06-0.56% of the P input. At least 10 common dominant microorganisms were found in the rhizosphere of all the three plants, and 6 of the 10 kinds of bacteria had close relationship with denitrifying bacteria, implying that denitrifiers were dominant microorganism distributed in rhizosphere of wetland plants.
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Moissl-Eichinger C, Pukall R, Probst AJ, Stieglmeier M, Schwendner P, Mora M, Barczyk S, Bohmeier M, Rettberg P. Lessons learned from the microbial analysis of the Herschel spacecraft during assembly, integration, and test operations. ASTROBIOLOGY 2013; 13:1125-39. [PMID: 24313230 DOI: 10.1089/ast.2013.1024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Understanding microbial diversity in spacecraft assembly clean rooms is of major interest with respect to planetary protection considerations. A coordinated screening of different clean rooms in Europe and South America by three German institutes [Deutsches Zentrum für Luft- und Raumfahrt (DLR), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), and the Institute of Microbiology and Archaea Center, University of Regensburg] took place during the assembly, test, and launch operations of the Herschel spacecraft in 2006-2009. Through this campaign, we retrieved critical information regarding the microbiome within these clean rooms and on the Herschel spacecraft, which served as a model for upcoming ESA mission preparations. This "lessons learned" document summarizes and discusses the data we obtained during this sampling campaign. Additionally, we have taken the opportunity to create a database that includes all 16S rRNA gene sequences ever retrieved from molecular and cultivable diversity studies of spacecraft assembly clean rooms to compare the microbiomes of US, European, and South American facilities.
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Stapelmann K, Fiebrandt M, Raguse M, Awakowicz P, Reitz G, Moeller R. Utilization of low-pressure plasma to inactivate bacterial spores on stainless steel screws. ASTROBIOLOGY 2013; 13:597-606. [PMID: 23768085 PMCID: PMC3713438 DOI: 10.1089/ast.2012.0949] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 04/12/2013] [Indexed: 05/22/2023]
Abstract
A special focus area of planetary protection is the monitoring, control, and reduction of microbial contaminations that are detected on spacecraft components and hardware during and after assembly. In this study, wild-type spores of Bacillus pumilus SAFR-032 (a persistent spacecraft assembly facility isolate) and the laboratory model organism B. subtilis 168 were used to study the effects of low-pressure plasma, with hydrogen alone and in combination with oxygen and evaporated hydrogen peroxide as a process gas, on spore survival, which was determined by a colony formation assay. Spores of B. pumilus SAFR-032 and B. subtilis 168 were deposited with an aseptic technique onto the surface of stainless steel screws to simulate a spore-contaminated spacecraft hardware component, and were subsequently exposed to different plasmas and hydrogen peroxide conditions in a very high frequency capacitively coupled plasma reactor (VHF-CCP) to reduce the spore burden. Spores of the spacecraft isolate B. pumilus SAFR-032 were significantly more resistant to plasma treatment than spores of B. subtilis 168. The use of low-pressure plasma with an additional treatment of evaporated hydrogen peroxide also led to an enhanced spore inactivation that surpassed either single treatment when applied alone, which indicates the potential application of this method as a fast and suitable way to reduce spore-contaminated spacecraft hardware components for planetary protection purposes.
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Affiliation(s)
- Katharina Stapelmann
- Ruhr University Bochum (RUB), Institute for Electrical Engineering and Plasma Technology (AEPT), Bochum, Germany
| | - Marcel Fiebrandt
- Ruhr University Bochum (RUB), Institute for Electrical Engineering and Plasma Technology (AEPT), Bochum, Germany
| | - Marina Raguse
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Cologne (Köln), Germany
| | - Peter Awakowicz
- Ruhr University Bochum (RUB), Institute for Electrical Engineering and Plasma Technology (AEPT), Bochum, Germany
| | - Günther Reitz
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Cologne (Köln), Germany
| | - Ralf Moeller
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Cologne (Köln), Germany
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Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang YJ, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, Brumm P. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park. Stand Genomic Sci 2012; 6:381-400. [PMID: 23408395 PMCID: PMC3558958 DOI: 10.4056/sigs.2605792] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The isolate was initially classified as a Geobacillus sp. Y412MC10 based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species, and the organism was most closely related to Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other paenibacilli. The Y412MC10 genome shows a high level of synteny and homology to the draft sequence of Paenibacillus sp. HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes. This, combined with genomic CAZyme analysis, suggests an intestinal, rather than environmental origin for Y412MC10.
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Affiliation(s)
- David A. Mead
- Lucigen Corporation, Middleton, Wisconsin
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California
| | | | - David C. Bruce
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Sam Pitluck
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Olga Chertkov
- DOE Joint Genome Institute, Walnut Creek, California
| | - Xiaojing Zhang
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Cliff S. Han
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California
- Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Loren J. Hauser
- DOE Joint Genome Institute, Walnut Creek, California
- Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | | | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California
| | | | | | | | - Phillip Brumm
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
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Paenibacillus thermophilus sp. nov., a novel bacterium isolated from a sediment of hot spring in Fujian province, China. Antonie van Leeuwenhoek 2012; 102:601-9. [DOI: 10.1007/s10482-012-9755-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Accepted: 05/21/2012] [Indexed: 10/28/2022]
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Wang Y, Wiatrowski HA, John R, Lin CC, Young LY, Kerkhof LJ, Yee N, Barkay T. Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments. Biodegradation 2012; 24:33-46. [PMID: 22678127 DOI: 10.1007/s10532-012-9555-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 05/04/2012] [Indexed: 10/28/2022]
Abstract
The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress. We observed an inverse relationship between Hg concentrations and onset and rates of denitrification in nitrate enrichment cultures containing between 53 and 1.1 μM of inorganic Hg; higher Hg concentrations increasingly extended the time to onset of denitrification and inhibited denitrification rates. Microbial community complexity, as indicated by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA genes, declined with increasing Hg concentrations; at the 312 nM Hg treatment, a single tRFLP peak was detected representing a culture of Bradyrhizobium sp. that possessed the merA gene indicating a potential for Hg reduction. A culture identified as Bradyrhizobium sp. strain FRC01 with an identical 16S rRNA sequence to that of the enriched peak in the tRFLP patterns, reduced Hg(II) to Hg(0) and carried merA whose amino acid sequence has 97 % identity to merA from the Proteobacteria and Firmicutes. This study demonstrates that in subsurface sediment incubations, Hg may inhibit denitrification and that inhibition may be alleviated when Hg resistant denitrifying Bradyrhizobium spp. detoxify Hg by its reduction to the volatile elemental form.
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Affiliation(s)
- Yanping Wang
- Department of Biochemistry and Microbiology, Rutgers University, 223C Lipman Hall, 76 Lipman Dr., New Brunswick, NJ 08901, USA.
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Su W, Zhang L, Li D, Zhan G, Qian J, Tao Y. Dissimilatory nitrate reduction byPseudomonas alcaliphilawith an electrode as the sole electron donor. Biotechnol Bioeng 2012; 109:2904-10. [DOI: 10.1002/bit.24554] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 03/23/2012] [Accepted: 05/01/2012] [Indexed: 01/21/2023]
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Identification and characterization of psychrotolerant sporeformers associated with fluid milk production and processing. Appl Environ Microbiol 2012; 78:1853-64. [PMID: 22247129 DOI: 10.1128/aem.06536-11] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Psychrotolerant spore-forming bacteria represent a major challenge to the goal of extending the shelf life of pasteurized dairy products. The objective of this study was to identify prominent phylogenetic groups of dairy-associated aerobic sporeformers and to characterize representative isolates for phenotypes relevant to growth in milk. Analysis of sequence data for a 632-nucleotide fragment of rpoB showed that 1,288 dairy-associated isolates (obtained from raw and pasteurized milk and from dairy farm environments) clustered into two major divisions representing (i) the genus Paenibacillus (737 isolates, including the species Paenibacillus odorifer, Paenibacillus graminis, and Paenibacillus amylolyticus sensu lato) and (ii) Bacillus (n = 467) (e.g., Bacillus licheniformis sensu lato, Bacillus pumilus, Bacillus weihenstephanensis) and genera formerly classified as Bacillus (n = 84) (e.g., Viridibacillus spp.). When isolates representing the most common rpoB allelic types (ATs) were tested for growth in skim milk broth at 6°C, 6/9 Paenibacillus isolates, but only 2/8 isolates representing Bacillus subtypes, grew >5 log CFU/ml over 21 days. In addition, 38/40 Paenibacillus isolates but only 3/47 Bacillus isolates tested were positive for β-galactosidase activity (including some isolates representing Bacillus licheniformis sensu lato, a common dairy-associated clade). Our study confirms that Paenibacillus spp. are the predominant psychrotolerant sporeformers in fluid milk and provides 16S rRNA gene and rpoB subtype data and phenotypic characteristics facilitating the identification of aerobic spore-forming spoilage organisms of concern. These data will be critical for the development of detection methods and control strategies that will reduce the introduction of psychrotolerant sporeformers and extend the shelf life of dairy products.
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Verbaendert I, Boon N, De Vos P, Heylen K. Denitrification is a common feature among members of the genus Bacillus. Syst Appl Microbiol 2011; 34:385-91. [PMID: 21530125 DOI: 10.1016/j.syapm.2011.02.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/04/2011] [Accepted: 02/04/2011] [Indexed: 11/26/2022]
Abstract
Although several Gram-positive denitrifiers have been characterized in the past, there is still uncertainty about the occurrence of the denitrification trait among these bacteria. In an isolation campaign on luvisol soil, Bacillus spp. were among the most abundant retrieved cultured denitrifiers next to members of Rhizobiaceae family and genus Cupriavidus. Subsequent screening of 180 representatives of the genus Bacillus (encompassing more than half of the current validly described species diversity in Bacillus) was performed and demonstrated the potential for dissimilatory reduction of nitrogen compounds in 45 of the 87 investigated species, with 19 species containing denitrifying members. The influence of several electron donors and acceptors was tested. The use of more than one electron acceptor, e.g. both nitrate and nitrite, was crucial to detect the denitrification potential of reference strains. Complex electron donors, most suitable for aerobic growth, were ideal for denitrification testing, while retrieval of denitrifiers from the environment was facilitated by the use of defined electron donors, due to less interference of other anaerobic growers. The outcome of the isolation campaign and screening of reference strain set suggest that bacilli may be potential contributors to denitrification in terrestrial and possibly other ecosystems.
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Affiliation(s)
- Ines Verbaendert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
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Abstract
Denitrifying organisms are essential in removing fixed nitrogen pollutants from ecosystems (e.g. sewage sludge). They can be detrimental (e.g. for agricultural soil) and can also produce the greenhouse gas N2O (nitrous oxide). Therefore a more comprehensive understanding of this process has become increasingly important regarding its global environmental impact. Even though bacterial genome sequencing projects may reveal new data, to date the denitrification abilities and features in Gram-positive bacteria are still poorly studied and understood. The present review evaluates current knowledge on the denitrification trait in Gram-positive bacteria and addresses the likely existence of unknown denitrification genes. In addition, current molecular tools to study denitrification gene diversity in pure cultures and environmental samples seem to be highly biased, and additional novel approaches for the detection of denitrifying (Gram-positive) bacteria appear to be crucial in re-assessing the real diversity of denitrifiers.
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Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2011; 61:6-7. [PMID: 21224488 DOI: 10.1099/ijs.0.030452-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429-1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the 'correct names' (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no 'official character', other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2011. [DOI: 10.1099/ijs.0.030445-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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