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Liu J, Xu H, Wang Z, Liu J, Gong X. Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae). Microorganisms 2023; 11:2364. [PMID: 37764208 PMCID: PMC10537169 DOI: 10.3390/microorganisms11092364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes.
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Affiliation(s)
- Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Xu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Zhaochun Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
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2
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Jahan R, McDonald IR. Diversity of Methylobacterium species associated with New Zealand native plants. FEMS Microbiol Lett 2023; 370:fnad124. [PMID: 37985695 PMCID: PMC10699869 DOI: 10.1093/femsle/fnad124] [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: 05/24/2023] [Revised: 09/26/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens, and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species.
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Affiliation(s)
- Rowshan Jahan
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
| | - Ian R McDonald
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
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3
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Li S, Dong L, Han JR, Shi GY, Lu CY, Xu L, Lian WH, Alkhalifah DHM, Hozzein WN, Li WJ. Longitalea arenae gen. nov., sp. nov. and Longitalea luteola sp. nov., two new members of the family Chitinophagaceae isolated from desert soil. Arch Microbiol 2022; 204:499. [PMID: 35849221 DOI: 10.1007/s00203-022-03119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Two strains designated as SYSU D01084T and SYSU D00799T, were isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells of both strains were Gram-stain-negative, strictly aerobic, long-rod-shaped, oxidase- and catalase-negative, motile or non-motile. Colonies were circular, translucent, convex, smooth and light-yellow in color on R2A agar. The two isolates were found to grow at 4-50 ºC, at pH 6.0-8.0 and with 0-1.0% (w/v) NaCl. Analysis of their 16S rRNA gene sequences indicated that they belonged to the family Chitinophagaceae, and closely related to the genera Paraflavitalea, Niastella, Pseudoflavitalea and Flavitalea. The two novel strains shared 98.1% 16S rRNA sequence similarity and represent different species on the basis of low average nucleotide identity (ANI, 83.8%) and digital DNA-DNA hybridization (dDDH, 51.4%) values. The genomic DNA G + C contents of strains SYSU D01084T and SYSU D00799T were 46.0 and 45.6%, respectively. Phylogenetic trees showed that the two isolates were clustered in an individual lineage and not grouped consistently into any specific genus. The polar lipids contained of phosphatidylethanolamine, four unidentified aminolipids, two unidentified aminoglycolipids, and three or four unidentified lipids. The predominant respiratory quinone was MK-7 and the major fatty acids (> 10%) were identified as iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. Based on the combined phenotypic, genomic and phylogenetic analyses, the two strains represent two novel species of a new genus in the family Chitinophagaceae, for which the name Longitalea gen. nov. is proposed, comprising the type species Longitalea arenae sp. nov. (type strain SYSU D01084T = CGMCC 1.18641T = MCCC 1K05006T = KCTC 82283T) and Longitalea luteola sp. nov. (type strain SYSU D00799T = MCCC 1K04987T = KCTC 82282T = NBRC 114888T).
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.,School of Life Sciences, Jiaying University, Meizhou, 514015, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Guo-Yuan Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dalal Hussien M Alkhalifah
- Biology Department, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 11564, Kingdom of Saudi Arabia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, 999088, Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering. SUSTAINABILITY 2022. [DOI: 10.3390/su14148764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The metagenomic whole genome shotgun sequencing (mWGS) approach was used to detect signatures of the rhizosphere microbiomes of Dipterygium glaucum and surrounding bulk soil microbiomes, and to detect differential microbial responses due to watering. Preliminary results reflect the reliability of the experiment and the rationality of grouping microbiomes. Based on the abundance of non-redundant genes, bacterial genomes showed the highest level, followed by Archaeal and Eukaryotic genomes, then, the least abundant viruses. Overall results indicate that most members of bacteria have a higher abundance/relative abundance (AB/RA) pattern in the rhizosphere towards plant growth promotion, while members of eukaryota have a higher pattern in bulk soil, most likely acting as pathogens. The results also indicate the contribution of mycorrhiza (genus Rhizophagus) in mediating complex mutualistic associations between soil microbes (either beneficial or harmful) and plant roots. Some of these symbiotic relationships involve microbes of different domains responding differentially to plant root exudates. Among these are included the bacterial genus Burkholderia and eukaryotic genus Trichoderma, which have antagonistic activities against the eukaryotic genus Fusarium. Another example involves Ochrobactrum phage POA1180, its bacterial host and plant roots. One of the major challenges in plant nutrition involves other microbes that manipulate nitrogen levels in the soil. Among these are the microbes that perform contraversal actions of nitrogen fixation (the methanogen Euryarchaeota) and ammonia oxidation (Crenarchaeota). The net nitrogen level in the soil is originally based on the AB/RA of these microbes and partially on the environmental condition. Watering seems to influence the AB/RA of a large number of soil microbes, where drought-sensitive microbes (members of phyla Acidobacteria and Gemmatimonadetes) showed an increased AB/RA pattern after watering, while others (Burkholderia and Trichoderma) seem to be among microbes assisting plants to withstand abiotic stresses. This study sheds light on the efficient use of mWGS in the taxonomic assignment of soil microbes and in their response to watering. It also provides new avenues for improving biotic and abiotic resistance in domestic plant germplasm via the manipulation of soil microbes.
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Akter S, Park JH, Rahman MM, Huq MA. Niastella soli sp. nov., isolated from rhizospheric soil of a persimmon tree. Int J Syst Evol Microbiol 2021; 71. [PMID: 34252019 DOI: 10.1099/ijsem.0.004870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1-0.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-29T was able to grow at 20-37 °C, at pH 5.0-8.5 and at 0-2.0 % NaCl. Cell growth occurred on nutrient agar and R2A agar. The strain was positive in both oxidase and catalase tests. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Niastella and was closely related to Niastella vici DJ57T (97.7 % similarity), Niastella koreensis GR20-10T (97.1 %) and Niastella yeongjuensis GR20-13T (97.0 %). Strain MAH-29T has a draft genome size of 8 876 333 bp (31 contigs), annotated with 6920 protein-coding genes, 61 tRNA and four rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-29T and three closely related type strains were in the range of 78.2-83.2 % and 22.1-27.0 %, respectively. The genomic DNA G+C content was 43.8 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of DNA-DNA hybridization results, genotypic analysis and chemotaxonomic and physiological data, strain MAH-29T represents a novel species within the genus Niastella, for which the name Niastella soli sp. nov. is proposed, with MAH-29T (=KACC 19969T=CGMCC 1.16606T) as the type strain.
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Affiliation(s)
- Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam 461-701, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam 461-701, Republic of Korea
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
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6
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Okazaki K, Tsurumaru H, Hashimoto M, Takahashi H, Okubo T, Ohwada T, Minamisawa K, Ikeda S. Community Analysis-based Screening of Plant Growth-promoting Bacteria for Sugar Beet. Microbes Environ 2021; 36. [PMID: 33907063 PMCID: PMC8209457 DOI: 10.1264/jsme2.me20137] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clone libraries of bacterial 16S rRNA genes (a total of 1,980 clones) were constructed from the leaf blades, petioles, taproots, and lateral roots of sugar beet (Beta vulgaris L.) grown under different fertilization conditions. A principal coordinate analysis revealed that the structures of bacterial communities in above- and underground tissues were largely separated by PC1 (44.5%). The bacterial communities of above-ground tissues (leaf blades and petioles) were more tightly clustered regardless of differences in the tissue types and fertilization conditions than those of below-ground tissues (taproots and lateral roots). The bacterial communities of below-ground tissues were largely separated by PC2 (26.0%). To survey plant growth-promoting bacteria (PGPBs), isolate collections (a total of 665 isolates) were constructed from the lateral roots. As candidate PGPBs, 44 isolates were selected via clustering analyses with the combined 16S rRNA gene sequence data of clone libraries and isolate collections. The results of inoculation tests using sugar beet seedlings showed that eight isolates exhibited growth-promoting effects on the seedlings. Among them, seven isolates belonging to seven genera (Asticcacaulis, Mesorhizobium, Nocardioides, Sphingobium, Sphingomonas, Sphingopyxis, and Polaromonas) were newly identified as PGPBs for sugar beet at the genus level, and two isolates belonging to two genera (Asticcacaulis and Polaromonas) were revealed to exert growth-promoting effects on the plant at the genus level for the first time. These results suggest that a community analysis-based selection strategy will facilitate the isolation of novel PGPBs and extend the potential for the development of novel biofertilizers.
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Affiliation(s)
- Kazuyuki Okazaki
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | | | | | - Hiroyuki Takahashi
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | | | - Takuji Ohwada
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine
| | | | - Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
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7
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Cervantes-Avilés P, Caretta CA, Brito EMS, Bertin P, Cuevas-Rodríguez G, Duran R. Changes in bacterial diversity of activated sludge exposed to titanium dioxide nanoparticles. Biodegradation 2021; 32:313-326. [PMID: 33811584 DOI: 10.1007/s10532-021-09939-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/24/2021] [Indexed: 11/29/2022]
Abstract
The rapid growth of the use of nanomaterials in different modern industrial branches makes the study of the impact of nanoparticles on the human health and environment an urgent matter. For instance, it has been reported that titanium dioxide nanoparticles (TiO2 NPs) can be found in wastewater treatment plants. Previous studies have found contrasting effects of these nanoparticles over the activated sludge process, including negative effects on the oxygen uptake. The non-utilization of oxygen reflects that aerobic bacteria were inhibited or decayed. The aim of this work was to study how TiO2 NPs affect the bacterial diversity and metabolic processes on an activated sludge. First, respirometry assays of 8 h were carried out at different concentrations of TiO2 NPs (0.5-2.0 mg/mL) to measure the oxygen uptake by the activated sludge. The bacterial diversity of these assays was determined by sequencing the amplified V3-V4 region of the 16S rRNA gene using Illumina MiSeq. According to the respirometry assays, the aerobic processes were inhibited in a range from 18.5 ± 4.8% to 37.5 ± 2.0% for concentrations of 0.5-2.0 mg/mL TiO2 NPs. The oxygen uptake rate was affected mainly after 4.5 h for concentrations higher than 1.0 mg/mL of these nanoparticles. Results indicated that, in the presence of TiO2 NPs, the bacterial community of activated sludge was altered mainly in the genera related to nitrogen removal (nitrogen assimilation, nitrification and denitrification). The metabolic pathways prediction suggested that genes related to biofilm formation were more sensitive than genes directly related to nitrification-denitrification and N-assimilation processes. These results indicated that TiO2 NPs might modify the bacteria diversity in the activated sludge according to their concentration and time of exposition, which in turn impact in the performance of the wastewater treatment processes.
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Affiliation(s)
- Pabel Cervantes-Avilés
- Departamento de Ingeniería Civil and Ambiental, DI-CGT, Universidad de Guanajuato, Av. Juárez 77, Col. Centro, 36000, Guanajuato, Gto, Mexico.,Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Reserva Territorial Atlixcayotl, vía Atlixcayotl 5718, 72453, Puebla, Pue, Mexico
| | - César Augusto Caretta
- Departamento de Astronomía, DCNE-CGT, Universidad de Guanajuato, Callejón de Jalisco S/N, Col. Valenciana, 36023, Guanajuato, Gto, Mexico
| | - Elcia Margareth Souza Brito
- Departamento de Ingeniería Civil and Ambiental, DI-CGT, Universidad de Guanajuato, Av. Juárez 77, Col. Centro, 36000, Guanajuato, Gto, Mexico.
| | - Pierre Bertin
- Institut de Biologie Intégrative de la Cellule, Université Paris Sud, Batiment 400, 91400, Orsay, France
| | - Germán Cuevas-Rodríguez
- Departamento de Ingeniería Civil and Ambiental, DI-CGT, Universidad de Guanajuato, Av. Juárez 77, Col. Centro, 36000, Guanajuato, Gto, Mexico
| | - Robert Duran
- Equipe Environment et Microbiologie, MELODY Group, IPREM UMR CNRS 5254, Université de pau et des pays de l'Adour, BP 1155, 64013, Pau Cedex, France
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Lin H, Liu C, Li B, Dong Y. Trifolium repens L. regulated phytoremediation of heavy metal contaminated soil by promoting soil enzyme activities and beneficial rhizosphere associated microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123829. [PMID: 33254810 DOI: 10.1016/j.jhazmat.2020.123829] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/28/2023]
Abstract
Rhizosphere soil physiochemical properties, enzyme activities and rhizosphere associated microbial communities are of the central importance for modulating phytoremediation in heavy metal contaminated soil. In this study, the rhizosphere micro-ecological characteristics of phytoremediation in seven groups of contaminated soil with different heavy metal species and concentrations were examined. The results showed that heavy metal-enrichment inhibited plant growth, but enhanced both anions (Cr2O72-) and cations (Cd2+ and Pb2+) uptake with corresponding mean values ranging from 19.37 to 168.74 mg/kg in roots and 10.89-86.53 mg/kg in shoots. Trifolium repens L. planting was able to compensate the lost caused by the heavy metal on the soil organic matter, available N, available P, available K and enzyme activities as well. According to the cluster, some species like Lysobacter, Kaistobacter and Pontibacter, was significantly related to heavy metal accumulation while others such as Flavisolibacter, Adhaeribacter and Bacillus promoted plant growth. The importance of root-associated microbial community could relatively regulate plant growth and heavy metal uptake. Our study not only illustrated the correlation among rhizosphere micro-ecological parameters, and the possible mechanisms of phytoremediation regulation, but also provide clear strategy for improving the phytoremediation efficiency.
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Affiliation(s)
- Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing 100083, China.
| | - Chenjing Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Yingbo Dong
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing 100083, China.
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Abstract
A Gram-stain-negative, aerobic, non-flagellated and filamentous-shaped bacterium, HX-16-21T, was isolated from activated sludge. Strain HX-16-21T was able to degrade gentisate, protocatechuic acid and p-hydroxybenzoic acid and herbicides quizalofop-p-ethyl and diclofop-methyl. The strain shared 97.2 % 16S rRNA gene sequence similarity to
Niastella vici
CCTCC AB 2015052T and less than 97 % similarities to other type strains. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HX-16-21T belonged to the genus
Niastella
and formed a subclade with
N. vici
CCTCC AB 2015052T. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and six unidentified lipids. The major fatty acids were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The predominant respiratory quinone was menaquinone 7 (MK-7). The draft genome of strain HX-16-21T was 8.1 Mb, and the G+C content was 43.5 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain HX-16-21T and
N. vici
CCTCC AB 2015052T were 80.6 and 26.8 %, respectively. Based on both phenotypic and phylogenetic evidence, strain HX-16-21T is considered to represent a novel species in the genus
Niastella
, for which the name Niastella caeni sp. nov. is proposed. The type strain is HX-16-21T (=KCTC 72288T=ACCC 61580T).
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Agnolucci M, Palla M, Cristani C, Cavallo N, Giovannetti M, De Angelis M, Gobbetti M, Minervini F. Beneficial Plant Microorganisms Affect the Endophytic Bacterial Communities of Durum Wheat Roots as Detected by Different Molecular Approaches. Front Microbiol 2019; 10:2500. [PMID: 31736925 PMCID: PMC6834690 DOI: 10.3389/fmicb.2019.02500] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/17/2019] [Indexed: 11/18/2022] Open
Abstract
This study aimed at characterising the endophytic bacterial communities living in durum wheat roots, as affected by wheat cultivar and inoculation of the Arbuscular mycorrhizal fungus Funneliformis mosseae IMA1 and the wheat root endophytic bacterium Lactobacillus plantarum B.MD.R.A2. These microorganisms were inoculated, alone or in combination, in durum wheat (cultivars Odisseo and Saragolla). Non-inoculated plants of each cultivar represented the controls. Forty-three days after sowing, roots were deprived of the epiphytic microbiota and subjected to DNA extraction. The DNA was used as template in PCR-DGGE analysis of the 16S rRNA gene (variable region V3–V5) and 16S (region V1–V3) metagenetics. Odisseo and Saragolla root endophytic bacterial biotas differed for number of OTUs and composition. In detail, Pseudomonas was higher in Odisseo than in Saragolla. The inoculation of F. mosseae and L. plantarum increased the abundance of Pseudomonas, some Actinobacteria (e.g., Streptomyces, Microbacterium, two genera including several plant growth promoting (PGP) strains) and Bacteroidetes in both cultivars. However, the endophytic bacterial biota of Saragolla roots inoculated just with lactobacilli did not differ from that of the control. The inoculation of Saragolla with F. mosseae, alone or in combination with lactobacilli, led to higher abundance of Rhodococcus, belonging to Actinobacteria and encompassing PGP strains. First, this work showed that F. mosseae and L. plantarum shape the endophytic bacterial biota of durum wheat roots. Abundance of some OTUs was affected by the microbial inoculation, depending on the cultivar. This result represents a starting point for exploitation of beneficial endophytes of wheat roots.
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Affiliation(s)
- Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Michela Palla
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Caterina Cristani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Noemi Cavallo
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Fabio Minervini
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
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11
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Wang C, Zhang R, Liu BT, Liu CL, Du ZJ. Paracnuella aquatica gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring. Int J Syst Evol Microbiol 2019; 69:2360-2366. [PMID: 31140961 DOI: 10.1099/ijsem.0.003476] [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: 01/27/2023] Open
Abstract
A Gram-stain-negative, rod-shaped bacterium (designated strain N24T) with gliding motility was isolated from thermal spring water sampled at Xi'an, PR China. Cells were 0.4-0.8 µm wide and 1.8-7.8 µm long. Optimal growth occurred at 33 °C and pH 7.0 on Reasoner's 2A (R2A) agar. Strain N24T could produce exopolysaccharide on R2A agar at 33 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain N24T formed a distinct phyletic lineage within the family Chitinophagaceae and was most closely related to members of the genera Flavisolibacter, Cnuella, Niveitalea, Flavitalea, Flaviaesturariibacter and Niastella with 91.7-93.9 % 16S rRNA gene sequence similarities. The major fatty acids of strain N24T were iso-C15 : 0 (31.8 %), iso-C17 : 0 3-OH (16.1 %) and iso-C15 : 1 G (12.9 %). The polar lipid profile consisted of phosphatidylethanolamine, two aminolipids and six unknown lipids; the quinone system consisted of menaquinone-7 (MK-7). The genomic G+C content was 49.3 mol%. On the basis of the evidence presented in this study, strain N24T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Paracnuella aquatica gen. nov., sp. nov. is proposed. The type species is N24T (=KCTC 62083T=MCCC 1H00301T).
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Affiliation(s)
- Chong Wang
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Rui Zhang
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Bang-Tao Liu
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Chun-Li Liu
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- State key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
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12
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Lv YY, Gao ZH, Xia F, Chen MH, Qiu LH. Puia dinghuensis gen. nov., sp. nov., isolated from monsoon evergreen broad-leaved forest soil. Int J Syst Evol Microbiol 2017; 67:4639-4645. [DOI: 10.1099/ijsem.0.002346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ying-ying Lv
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zeng-hong Gao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Fan Xia
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Mei-hong Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Li-hong Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
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13
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Yan ZF, Lin P, Wang YS, Gao W, Li CT, Kook MC, Yi TH. Niastella hibisci sp. nov., isolated from rhizosphere soil of mugunghwa, the Korean national flower. Int J Syst Evol Microbiol 2016; 66:5218-5222. [DOI: 10.1099/ijsem.0.001498] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zheng-Fei Yan
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do, 46-701, Republic of Korea
| | - Pei Lin
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do, 46-701, Republic of Korea
| | - Yu-Shuai Wang
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do, 46-701, Republic of Korea
| | - Wei Gao
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do, 46-701, Republic of Korea
| | - Chang-Tian Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, PR China
| | - Moo-Chang Kook
- Department of Marine Biotechnology, Anyang University, Incheon 417833, Republic of Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do, 46-701, Republic of Korea
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14
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Siddiqi MZ, Im WT. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2016; 66:3449-3455. [DOI: 10.1099/ijsem.0.001216] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
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15
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Chen L, Wang D, Yang S, Wang G. Niastella vici sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2016; 66:1768-1772. [DOI: 10.1099/ijsem.0.000943] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lu Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PRChina
| | - Dan Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PRChina
| | - Sining Yang
- No. 1 Middle School Affiliated to Central China Normal University, Wuhan, Hubei 430223, PRChina
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PRChina
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16
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Kim SJ, Ahn JH, Weon HY, Hong SB, Seok SJ, Kim JS, Kwon SW. Niastella gongjuensis sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol 2015; 65:3115-3118. [PMID: 26296587 DOI: 10.1099/ijsem.0.000387] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, non-flagellated, long rod or rod-shaped bacterial strain, 5GH22-11(T), was isolated from a soil sample of a greenhouse in Gongju, Republic of Korea. According to 16S rRNA gene sequence analysis, strain 5GH22-11(T) showed the highest sequence similarities with Niastella populi THYL-44(T) (97.1%), Niastella koreensis GR20-10T (95.7%) and Niastella yeongjuensis GR20-13(T) (95.6%), and < 3% sequence similarity with all other species with validly published names. The phylogenetic tree also showed strain 5GH22-11(T) formed a compact cluster with members of the genus Niastella. DNA-DNA hybridization revealed strain 5GH22-11(T) is a novel species, showing far less than 70% DNA-DNA relatedness with Niastella populi THYL-44(T). Strain 5GH22-11(T) contained iso-C15 : 0 (34.3%), iso-C17 : 0 3-OH (24.8%) and iso-C15 : 1 G (18.2%) as the major fatty acids; phosphatidylethanolamine, six unknown aminolipids, two unknown lipids and one unknown phospholipid as the polar lipids; and MK-7 as the predominant isoprenoid quinone. The DNA G+C content was 41.4 mol%. Based on these phylogenetic, physiological and chemotaxonomic data, it was demonstrated that strain 5GH22-11(T) represents a novel species of the genus Niastella, for which the name Niastella gongjuensis sp. nov. is proposed. The type strain is 5GH22-11(T) ( = KACC 17339(T) [corrected] = JCM 19941(T)).
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Affiliation(s)
- Soo-Jin Kim
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Jae-Hyung Ahn
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Soon-Ja Seok
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
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17
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Kang JY, Chun J, Seo JW, Kim CH, Jahng KY. Flaviaesturariibacter amylovorans gen. nov., sp. nov., a starch-hydrolysing bacterium, isolated from estuarine water. Int J Syst Evol Microbiol 2015; 65:2209-2214. [PMID: 25858251 DOI: 10.1099/ijs.0.000249] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated GCR0105(T), was isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment, located in JEOLlabuk-do, South Korea. Cells of strain GCR0105(T) were Gram-stain-negative, non-motile and rod-shaped. Colonies of strain GCR0105(T) were pale yellow-pigmented on R2A agar and nutrient agar media, and were able to grow at 15-30 °C (optimum 25 °C) and pH 6.5-8.5 (optimum pH 7.5). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GCR0105(T) was related most closely to Flavisolibacter ginsengisoli Gsoil 643(T) (93.14% similarity). The polar lipid profile of strain GCR0105(T) comprised phosphatidylethanolamine, two unknown aminolipids, an unknown aminophospholipid and four unknown lipids. The DNA G+C content of strain GCR0105(T) was 42.9 mol% and the respiratory quinone was MK-7.On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain GCR0105(T) represents a novel species in a new genus within the family Chitinophagaceae, for which the name Flaviaesturariibacter amylovorans gen. nov., sp. nov. is proposed. The type strain of Flaviaesturariibacter amylovorans is GCR0105(T) ( = KACC 16454(T) = JCM 17919(T)).
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Affiliation(s)
- Ji Young Kang
- Department of Life Sciences, Chonbuk National University, Jeonju-si, 561-756, Republic of Korea.,Industrial Microbiology and Bioprocess Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea
| | - Jeesun Chun
- Department of Life Sciences, Chonbuk National University, Jeonju-si, 561-756, Republic of Korea
| | - Jeong-Woo Seo
- Industrial Microbiology and Bioprocess Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea
| | - Chul Ho Kim
- Industrial Microbiology and Bioprocess Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea
| | - Kwang Yeop Jahng
- Department of Life Sciences, Chonbuk National University, Jeonju-si, 561-756, Republic of Korea
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18
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Zhao R, Chen XY, Li XD, Tian Y, Kong BH, Chen ZL, Li YH. Cnuella takakiae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides. Int J Syst Evol Microbiol 2014; 64:607-612. [DOI: 10.1099/ijs.0.055749-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, rod-shaped and non-spore-forming bacterium, designated strain RG1-1T, was isolated from Takakia lepidozioides collected from Gawalong glacier in Tibet, China, and characterized by using a polyphasic taxonomic approach. The predominant fatty acids of strain RG1-1T were iso-C15 : 0 (19.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 17.0 %), C16 : 0 (9.9 %) and iso-C17 : 0 3-OH (9.4 %); its major polar lipids were phosphatidylethanolamine, four unidentified aminolipids, one unidentified phospholipid, one unidentified aminoglycolipid, one unidentified glycolipid, and three unidentified lipids. Strain RG1-1T contained MK-7 as the dominant menaquinone, and the G+C content of its genomic DNA was 49.1 mol%. Strain RG1-1T exhibited the highest 16S rRNA gene sequence similarity (91.8 %) with
Flavisolibacter ginsengiterrae
Gsoil 492T and
Flavisolibacter ginsengisoli
Gsoil 643T. Phylogenetic analysis showed that strain RG1-1T was a member of the family
Chitinophagaceae
, phylum
Bacteroidetes
. On the basis of 16S rRNA gene sequence analysis, and phenotypic and chemotaxonomic data, strain RG1-1T is considered to represent a novel species of a novel genus, for which the name Cnuella takakiae gen. nov., sp. nov. is proposed. The type strain is RG1-1T ( = CGMCC 1.12492T = DSM 26897T).
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Affiliation(s)
- Ran Zhao
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Xin Yao Chen
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Xue Dong Li
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Yang Tian
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Bi He Kong
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Zhi Ling Chen
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Yan Hong Li
- College of Life Science, Capital Normal University, Beijing 100048, PR China
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19
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Hanada S, Tamaki H, Nakamura K, Kamagata Y. Crenotalea thermophila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring. Int J Syst Evol Microbiol 2014; 64:1359-1364. [PMID: 24436064 DOI: 10.1099/ijs.0.058594-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic aerobic bacterium designated strain STH-1-Y1(T) was isolated from sulfur-turf in a Japanese hot spring (Okuhodaka hot spring, Gifu Pref.). Colonies of strain STH-1-Y1(T) were yellow and low convex morphology with a slightly irregular fringe. Cells were slender long rods, 0.4-0.6 µm wide and 1.2-3.0 µm long. The isolate was an obligate aerophilic organism, and could not grow by fermentation or nitrate respiration. The isolate had a thermophilic trait, and could grow at 35-60 °C and pH 5.5-7.5; maximum growth occurred at 55 °C and pH 7.0 with a doubling time of 1.9 h. The Biolog and API tests suggested that strain STH-1-Y1(T) was able to use various sugars such as glucose, lactose, mannose, maltose, trehalose, cellobiose and sucrose, but could not use sugar alcohols other than glycerol, i.e. adonitol, arabitol, erythritol, inositol, mannitol, sorbitol and xylitol. Lactate and glutamate could be used, but other fatty acids, i.e. acetate, citrate, propionate and succinate could not. Gelatin, casein, starch and glycogen were hydrolysed, but neither chitin nor agar was degraded. Cells lacked flexirubin and showed oxidase and catalase activities. The major respiratory quinone was menaquinone-7 (MK-7), and major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 0 and anteiso-C15 : 0. No unsaturated fatty acids were detected. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain STH-1-Y1(T) was closely related to the family Chitinophagaceae within the phylum Bacteroidetes. However, the isolate was evenly distant from all members in this family with sequence similarities of 87-89 %. These significantly low sequence similarities strongly suggested that strain STH-1-Y1(T) represents a novel species in a new genus of the family Chitinophagaceae within the phylum Bacteroidetes. Based on phenotypic and phylogenetic characteristics, the name Crenotalea thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is STH-1-Y1(T) ( = JCM 11541(T) = DSM 14807(T)).
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Affiliation(s)
- Satoshi Hanada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kazunori Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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20
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Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, MacKenzie AD, Vyssotski M, Ryan JLJ, Hanssen EG, Moreau JW, Stott MB. Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes. Int J Syst Evol Microbiol 2014; 64:1264-1270. [PMID: 24425740 DOI: 10.1099/ijs.0.057463-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, thermophilic, moderately acidophilic, non-spore-forming bacterium, strain P373(T), was isolated from geothermally heated soil at Waikite, New Zealand. Cells were filamentous rods, 0.2-0.4 µm in diameter and grew in chains up to 80 µm in length. On the basis of 16S rRNA gene sequence similarity, strain P373(T) was shown to belong to the family Chitinophagaceae (class Sphingobacteriia) of the phylum Bacteroidetes, with the most closely related cultivated strain, Chitinophaga pinensis UQM 2034(T), having 87.6 % sequence similarity. Cells stained Gram-negative, and were catalase- and oxidase-positive. The major fatty acids were i-15 : 0 (10.8 %), i-17 : 0 (24.5 %) and i-17 : 0 3-OH (35.2 %). Primary lipids were phosphatidylethanolamine, two unidentified aminolipids and three other unidentified polar lipids. The presence of sulfonolipids (N-acyl-capnines) was observed in the total lipid extract by mass spectrometry. The G+C content of the genomic DNA was 47.3 mol% and the primary respiratory quinone was MK-7. Strain P373(T) grew at 35-63 °C with an optimum temperature of 60 °C, and at pH 5.5-8.7 with an optimum growth pH of 7.3-7.4. NaCl tolerance was up to 5 % (w/v) with an optimum of 0.1-0.25 % (w/v). Cell colonies were non-translucent and pigmented vivid yellow-orange. Cells displayed an oxidative chemoheterotrophic metabolism. The distinct phylogenetic position and the phenotypic characteristics separate strain P373(T) from all other members of the phylum Bacteroidetes and indicate that it represents a novel species in a new genus, for which the name Thermoflavifilum aggregans gen. nov., sp. nov. is proposed. The type strain of the type species is P373(T) ( = ICMP 20041(T) = DSM 27268(T)).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, Canada
| | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Karen M Houghton
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Jean F Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | | | | | - Jason L J Ryan
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Eric G Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
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21
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Leandro T, França L, Nobre MF, Rainey FA, da Costa MS. Heliimonas saccharivorans gen. nov., sp. nov., a member of the family
Chitinophagaceae
isolated from a mineral water aquifer, and emended description of
Filimonas lacunae. Int J Syst Evol Microbiol 2013; 63:3793-3799. [DOI: 10.1099/ijs.0.050021-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates, with optimum growth temperature and pH of about 30 °C and 6.0–7.0, were recovered from a borehole head of a mineral water aquifer in Portugal. The closest relatives based on 16S rRNA gene sequence analysis were species of genera of the family
Chitinophagaceae
. Strains L2-4T and L2-109 formed translucent colonies and non-motile pleomorphic cells. Strains were strictly aerobic, and oxidase- and catalase-positive. The major fatty acids of strains L2-4T and L2-109 were 17 : 0 iso 3-OH, 15 : 0 iso and 15 : 1 iso G. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid, four unidentified aminophospholipids, four unidentified aminolipids and three unidentified polar lipids. Menaquinone 7 was the only respiratory quinone. The G+C content of the DNA of strains L2-4T and L2-109 was 42.0 and 41.4 mol%, respectively. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, strains L2-4T ( = CECT 8122T = LMG 26919T) and L2-109 ( = CECT 8121 = LMG 26920) are considered to represent a novel species of a new genus, for which the name Heliimonas saccharivorans gen. nov., sp. nov. is proposed. The type strain of Heliimonas saccharivorans is L2-4T. Due to additional results obtained in this study an emended description of
Filimonas lacunae
is provided.
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Affiliation(s)
- Tânia Leandro
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Luís França
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M. Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Fred A. Rainey
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
| | - Milton S. da Costa
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
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