1
|
May-Mutul CG, López-Garrido MA, O’Connor-Sánchez A, Peña-Ramírez YJ, Labrín-Sotomayor NY, Estrada-Medina H, Ferrer MM. Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens. PLANTS (BASEL, SWITZERLAND) 2022; 11:3098. [PMID: 36432829 PMCID: PMC9699097 DOI: 10.3390/plants11223098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.
Collapse
Affiliation(s)
- Carla G. May-Mutul
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miguel A. López-Garrido
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Aileen O’Connor-Sánchez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico
| | - Yuri J. Peña-Ramírez
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Natalia Y. Labrín-Sotomayor
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Héctor Estrada-Medina
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miriam M. Ferrer
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| |
Collapse
|
2
|
Complete Genome and Plasmid Sequences of the Psychrotolerant Aureimonas Strain SA4125, Isolated from Antarctic Moss Vegetation. Microbiol Resour Announc 2021; 10:e0087821. [PMID: 34647799 PMCID: PMC8515883 DOI: 10.1128/mra.00878-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The complete genome sequences of Aureimonas sp. strain SA4125 and its native plasmid pSA4125 were determined. The genome sequence comprises 4,968,066 bp, with a GC content of 66.0%, and contains 4,691 coding DNA sequences (CDSs), 3 rRNA operons, and 50 tRNAs. The native plasmid comprises 131,777 bp, with a GC content of 62.3%, and contains 138 CDSs.
Collapse
|
3
|
Huang H, Punnarak P, Zhang Q, Piumsomboon A, Wang L, Li W, Chen S, Chen G, Ou D. Aureimonas mangrovi sp. nov., a marine alphaproteobacterium isolated from mangrove sediment in Thailand. Int J Syst Evol Microbiol 2021; 71. [PMID: 34224346 DOI: 10.1099/ijsem.0.004820] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, designated as 1-4-3T and 1-4-4, were isolated from a mangrove sediment cultured with coastal seawater. The cells were Gram-stain-negative, motile, short, rod-shaped bacteria with flagella. Growth occurred at 4-37 °C, pH 7.0-9.0, and 0-7% NaCl. The predominant fatty acids of the novel strains were C18 : 1 ω7c, C19 : 0 cyclo ω8c, C18 : 0, and C16 : 0. A phylogenetic analysis based on 16S rRNA gene sequences and whole genome phylogeny analysis based on distance matrix revealed an affiliation between the two strains and the genus Aureimonas, with closest sequence similarity to A. populi 4M3-2T (96.41 and 96.64% similarity, respectively) and A. glaciistagni (96.01 and 96.23% similarity, respectively). The DNA G+C content of strain 1-4-3T was 66.80 mol%. Strain 1-4-3T displayed low DNA-DNA relatedness to A. populi 4M3-2T, with an average nucleotide identity value of 77.47 % and digital DNA-DNA hybridization value of 22.83 %. Genotypic, chemotaxonomic, and phenotypic data indicate that strains 1-4-3T and 1-4-4 represent a novel species of the genus Aureimonas, for which we propose the name Aureimonas mangrovi sp. nov. The type strain is 1-4-3T (=LMG 31693T=CGMCC 1.18507T).
Collapse
Affiliation(s)
- Hao Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok 10330, Thailand
| | - Qinghua Zhang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | | | - Lei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Weiwen Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Shunyang Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Danyun Ou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| |
Collapse
|
4
|
Webster G, Mullins AJ, Cunningham-Oakes E, Renganathan A, Aswathanarayan JB, Mahenthiralingam E, Vittal RR. Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India. FEMS Microbiol Ecol 2021; 96:5876344. [PMID: 32710748 PMCID: PMC7422900 DOI: 10.1093/femsec/fiaa147] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Bacterial endophytes are found in the internal tissues of plants and have intimate associations with their host. However, little is known about the diversity of medicinal plant endophytes (ME) or their capability to produce specialised metabolites that may contribute to therapeutic properties. We isolated 75 bacterial ME from 24 plant species of the Western Ghats, India. Molecular identification by 16S rRNA gene sequencing grouped MEs into 13 bacterial genera, with members of Gammaproteobacteria and Firmicutes being the most abundant. To improve taxonomic identification, 26 selected MEs were genome sequenced and average nucleotide identity (ANI) used to identify them to the species-level. This identified multiple species in the most common genus as Bacillus. Similarly, identity of the Enterobacterales was also distinguished within Enterobacter and Serratia by ANI and core-gene analysis. AntiSMASH identified non-ribosomal peptide synthase, lantipeptide and bacteriocin biosynthetic gene clusters (BGC) as the most common BGCs found in the ME genomes. A total of five of the ME isolates belonging to Bacillus, Serratia and Enterobacter showed antimicrobial activity against the plant pathogen Pectobacterium carotovorum. Using molecular and genomic approaches we have characterised a unique collection of endophytic bacteria from medicinal plants. Their genomes encode multiple specialised metabolite gene clusters and the collection can now be screened for novel bioactive and medicinal metabolites.
Collapse
Affiliation(s)
- Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Alex J Mullins
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Edward Cunningham-Oakes
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Arun Renganathan
- Department of Studies in Microbiology, University of Mysore, Karnataka, 570006, Mysore, India
| | | | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Ravishankar Rai Vittal
- Department of Studies in Microbiology, University of Mysore, Karnataka, 570006, Mysore, India
| |
Collapse
|
5
|
Wang HL, Hopfer H, Cockburn DW, Wee J. Characterization of Microbial Dynamics and Volatile Metabolome Changes During Fermentation of Chambourcin Hybrid Grapes From Two Pennsylvania Regions. Front Microbiol 2021; 11:614278. [PMID: 33505380 PMCID: PMC7829364 DOI: 10.3389/fmicb.2020.614278] [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] [Received: 10/05/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
Microbial diversity present on grapes in wineries, and throughout fermentation has been associated with important metabolites for final wine quality. Although microbiome-metabolome associations have been well characterized and could be used as indicators of wine quality, the impact of regionality on the microbiome and metabolome is not well known. Additionally, studies between microbiome and metabolome have been conducted on single species grape such as Vitis vinifera instead of other species and interspecific hybrids. Although the Pennsylvania wine industry is relatively young compared to California, the industry has been experiencing rapid growth over the past decade and is expected to continue to grow in the future. Pennsylvania's climate of cold winters and high levels of rainfall throughout the growing season favors cultivation of interspecific hybrid grapes such as Vitis ssp. Chambourcin, one of the most commonly grown hybrid varieties in the state. Chambourcin is a prime candidate for studying the impact of regionality on microbiome-metabolome interactions as interspecific hybrid varieties could shape the future of winemaking. Here, we identify for the first time the regional distribution of microbial communities and their interactions with volatile metabolome during fermentation (0-20 days) by integrating high throughput Illumina sequencing (16S and ITS) and headspace-solid phase microextraction-gas chromatography-mass spectrometry. Analyzing 88 samples from nine wineries in the Central and East Pennsylvania regions, we observed high microbial diversity during early stages of fermentation (1-4 days) where non-Saccharomyces yeasts such as Starmerella and Aureobasidium and non-Oenococcus bacteria, Sphingomonas, likely contribute to microbial terroir to the resulting wines. Furthermore, key differentiators between two regions in Pennsylvania, as identified by LEfSe analysis, include the fungal genera Cladosporium and Kazachstania and the bacterial genera Lactococcus and Microbacterium. Moreover, 29 volatile fermentation metabolites were discriminated significantly (variable importance in projection > 1) between the two regions as shown by Partial Least Squares-Discriminant Analysis. Finally, Spearman's correlation identified regional differences of microbial-metabolite associations throughout fermentation that could be used for targeted microbiome manipulation to improve wine quality and preserve regionality. In summary, these results demonstrate the microbial signatures during fermentation and differential microorganisms and metabolites further support impact of regionality on Chambourcin wines in Pennsylvania.
Collapse
Affiliation(s)
- Hung Li Wang
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - Helene Hopfer
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
- Sensory Evaluation Center, The Pennsylvania State University, State College, PA, United States
| | - Darrell W. Cockburn
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
- Microbiome Center, HUCK Institute for Life Sciences, The Pennsylvania State University, State College, PA, United States
| | - Josephine Wee
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
- Microbiome Center, HUCK Institute for Life Sciences, The Pennsylvania State University, State College, PA, United States
| |
Collapse
|
6
|
Madhaiyan M, Saravanan VS, Wirth JS, Alex THH, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants. Antonie van Leeuwenhoek 2020; 113:1617-1632. [PMID: 32949307 DOI: 10.1007/s10482-020-01468-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
In this study, two endophytic bacterial strains designated JS21-1T and S6-262T isolated from leaves of Elaeis guineensis and stem tissues of Jatropha curcas respectively, were subjected for polyphasic taxonomic approach. On R2A medium, colonies of strains JS21-1T and S6-262T are orange and yellow, respectively. Phylogenetic analyses using 16S rRNA gene sequencing and whole-genome sequences placed the strains in distinct clades but within the genus Sphingomonas. The DNA G + C content of JS21-1T and S6-262T were 67.31 and 66.95%, respectively. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values of strains JS21-1T and S6-262T with phylogenetically related Sphingomonas species were lower than 95% and 70% respectively. The chemotaxonomic studies indicated that the major cellular fatty acids of the strain JS21-1T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C14:0 2OH; strain S6-262T possessed summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was Q10, and the unique polyamine observed was homospermidine. The polar lipid profile comprised of mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and certain uncharacterised phospholipids and lipids. Based on this polyphasic evidence, strains JS21-1T and S6-262T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov. are proposed, respectively. The type strain of Sphingomonas palmae sp. nov. is JS21-1T (= DSM 27348T = KACC 17591T) and the type strain of Sphingomonas gellani sp. nov. is S6-262T (= DSM 27346T = KACC 17594T).
Collapse
Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
| | | | - Joseph S Wirth
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Tan Hian Hwee Alex
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - William B Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA, 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
| |
Collapse
|
7
|
Baek J, Kim JH, Lee JS, Sukhoom A, Kim W. Aureimonas fodinaquatilis sp. nov., isolated from coal mine wastewater. Arch Microbiol 2020; 202:2655-2661. [PMID: 32715322 DOI: 10.1007/s00203-020-01988-8] [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: 03/04/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
A Gram stain-negative, aerobic, non-motile, short, rod-shaped bacterial strain CAU 1482T was isolated from coal mine wastewater in Hongcheon, Korea. It grew well at 30 °C, pH 8.5, 2% NaCl (w/v). 16S rRNA-based phylogeny indicated that CAU 1482T forms a distinct lineage within Aureimonas with high similarity to Aureimonas frigidaquae CW5T (98.2%), Aureimonas altamirensis S21BT (98.0%), and Aureimonas glaciei B5-2T (96.3%). The predominant cellular fatty acids were C18:1 2-OH, C16:0, C18:1 ω7c, and/or C18:1 ω6c (summed feature 8), with Q-10 as the major isoprenoid quinone. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified aminolipids, and three unidentified lipids. The 3.9-Mb genome included 8 contigs and 3599 protein-coding genes with a 56.7 mol% G + C content. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CAU 1482T and closely related strains of A. frigidaquae CW5T and A. altamirensis S21BT were 72.2‒72.4% and 18.7‒18.8%, respectively. These phenotypic, chemotaxonomic, and phylogenetic data support CAU 1482T as a novel Aureimonas species, for which the name Aureimonas fodinaquatilis sp. nov. is proposed. The type strain is CAU 1482T (= KCTC 62995T = NBRC 113692T).
Collapse
Affiliation(s)
- Jihye Baek
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Ampaitip Sukhoom
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
8
|
Aureimonas psammosilene sp. nov., isolated from the roots of Psammosilene tunicoides. Arch Microbiol 2020; 202:1939-1944. [DOI: 10.1007/s00203-020-01872-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/15/2020] [Accepted: 04/01/2020] [Indexed: 10/24/2022]
|
9
|
Madhaiyan M, See-Too WS, Ee R, Saravanan VS, Wirth JS, Alex THH, Lin C, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Chitinasiproducens palmae gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from leaf tissues of oil palm (Elaeis guineensis Jacq.). Int J Syst Evol Microbiol 2020; 70:2640-2647. [DOI: 10.1099/ijsem.0.004084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23T, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of
Burkholderiaceae
revealed that strain JS23T formed a distinct evolutionary lineage independent of other taxa within the family
Burkholderiaceae
. The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1
ω7c /C16 : 1
ω6c) and summed feature 8 (C18 : 1
ω7c /C18 : 1
ω6c). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA–DNA hybridization clearly distinguished strain JS23T from the closely related genera
Burkholderia
,
Caballeronia
,
Mycetohabitans
,
Mycoavidus
,
Pandoraea
,
Paraburkholderia
,
Robbsia
and
Trinickia
. Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0–68.4 and 28.2–45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23T to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23T is proposed to represent a novel species of a new genus within the family
Burkholderiaceae
, for which the name Chitinasiproducens palmae gen. nov., sp. nov., is proposed with the type strain of JS23T (= DSM 27307T=KACC 17592T).
Collapse
Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Joseph S. Wirth
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Tan Hian Hwee Alex
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Cai Lin
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B. Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| |
Collapse
|
10
|
Madhaiyan M, Saravanan VS, Blom J, Smits THM, Rezzonico F, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.). Int J Syst Evol Microbiol 2020; 70:841-848. [DOI: 10.1099/ijsem.0.003834] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wadenswil, Switzerland
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wadenswil, Switzerland
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B. Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| |
Collapse
|
11
|
Aureimonas leprariae sp. nov., Isolated from a Lepraria sp. Lichen. Curr Microbiol 2019; 77:313-319. [PMID: 31802200 DOI: 10.1007/s00284-019-01826-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/25/2019] [Indexed: 10/25/2022]
Abstract
A Gram-negative, motile, aerobic and coccoid rod-shaped bacterium, designated strain YIM132180T, was isolated from a Lepraria sp. lichen collected from Pu'er, Yunnan Province, China. The strain grew at 15-35 °C (optimum, 25-28 °C), at 0-2% (w/v) NaCl (optimum, 0-1%) and at pH 6.0-9.0 (optimum, pH 7.0). The 16S rRNA gene sequence showed that strain YIM132180T had highest similarity (96.4%) with Aureimonas endophytica 2T4P-2-4T, followed by Aureimonas ureilytica NBRC 106430T (95.7%) and Aureimonas rubiginis CC-CFT034T (95.6%). Phylogenetic analysis showed that the strain grouped with species of the genus Aureimonas. The genomic sequence was 4,779,519 bp and contained 4584 coding sequences (CDSs), 54 RNA genes, 3 complete rRNA genes and 47 tRNA genes. The major fatty acids (>10%) of strain YIM132180T were C18:1ω7c, C-16:0 and C19:0 cyclo ω8c. The predominant menaquinone was ubiquinone 10 (Q-10). The polar lipid profile comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, amino lipid, lipid and most importantly sulfoquinovosyldiacylglycerol (SQDG). Based on the draft genome sequence, the G +C content of strain YIM132180T was 68.4 mol%. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic, and phylogenetic analyses, showed that strain YIM132180T represents a novel species of the genus Aureimonas, for which the name Aureimonas leprariae sp. nov. is proposed. The type strain is YIM 132180T (=KCTC 72462T = CGMCC 1.17389T).
Collapse
|
12
|
Tuo L, Yan XR. Aureimonas flava sp. nov., a novel endophytic bacterium isolated from leaf of Acrostichum aureum. Int J Syst Evol Microbiol 2019; 69:846-851. [DOI: 10.1099/ijsem.0.003252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Li Tuo
- 2Zunyi Engineering Research Center of Physical Testing and Chemical Analysis, Zunyi Medical University, Zunyi 563006, PR China
- 1Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563006, PR China
| | - Xiao-Rui Yan
- 1Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563006, PR China
- 2Zunyi Engineering Research Center of Physical Testing and Chemical Analysis, Zunyi Medical University, Zunyi 563006, PR China
| |
Collapse
|
13
|
Li FN, Liao S, Guo M, Tuo L, Yan X, Li W, Jin T, Lee SMY, Sun CH. Mangrovicella endophytica gen. nov., sp. nov., a new member of the family Aurantimonadaceae isolated from Aegiceras corniculatum. Int J Syst Evol Microbiol 2018; 68:2838-2845. [PMID: 30010526 DOI: 10.1099/ijsem.0.002907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, motile and short-rod-shaped bacterium, designated strain 5T4P-12-1T, was isolated from a piece of surface-sterilized bark of Aegiceras corniculatum collected from Cotai Ecological Zones in Macao, China and tested by a polyphasic approach to clarify its taxonomic position. Strain 5T4P-12-1T grew optimally with 0-1 % (w/v) NaCl at 30 °C and at pH 7.0-8.0. The 16S rRNA gene sequence of strain 5T4P-12-1T had the highest similarity (96.7 %) to Aureimonas altamirensis DSM 21988T. Phylogenic analysis based on 16S rRNA gene sequences and coding sequences of 98 protein clusters showed that the strain represented a novel genus of the family Aurantimonadaceae. The predominant quinone system of strain 5T4P-12-1T was ubiquinone 10. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unidentified aminophospholipid, three unidentified aminolipids, three unidentified phospholipids and three unidentified lipids. The major fatty acids (>10 % of total fatty acids) were C18 : 1ω7c (55.4 %) and C18 : 1 2-OH (15.6 %). The DNA G+C content of strain 5T4P-12-1T was 66.5 mol%. Based on the phylogenic, phenotypic and chemotaxonomic features, strain 5T4P-12-1T is considered to represent a novel species of a new genus in the family Aurantimonadaceae, for which the name Mangrovicella endophytica gen. nov., sp. nov. is proposed. The type strain is 5T4P-12-1T (=KCTC 62053T=CGMCC 1.16279 T).
Collapse
Affiliation(s)
- Fei-Na Li
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Shuilin Liao
- 2BGI-Shenzhen, Beishan, Industrial Zone, Shenzhen 518083, PR China
- 3China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, PR China
- 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, PR China
| | - Min Guo
- 5State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, PR China
| | - Li Tuo
- 6Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563003, PR China
| | - Xinyu Yan
- 7China Pharmaceutical University, Nanjing 210009, PR China
| | - Wenlian Li
- 7China Pharmaceutical University, Nanjing 210009, PR China
| | - Tao Jin
- 2BGI-Shenzhen, Beishan, Industrial Zone, Shenzhen 518083, PR China
- 3China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, PR China
| | - Simon Ming-Yuen Lee
- 5State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, PR China
| | - Cheng-Hang Sun
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| |
Collapse
|
14
|
Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment. Front Microbiol 2018; 9:144. [PMID: 29487575 PMCID: PMC5816784 DOI: 10.3389/fmicb.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.
Collapse
Affiliation(s)
- Ebru L. Aydogan
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Gerald Moser
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Müller
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| |
Collapse
|
15
|
Li Y, Xu G, Lin C, Wang X, Piao CG. Aureimonas populi sp. nov., isolated from poplar tree bark. Int J Syst Evol Microbiol 2018; 68:487-491. [DOI: 10.1099/ijsem.0.002479] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yong Li
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Guangtang Xu
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Caili Lin
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xizhuo Wang
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Chun-gen Piao
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| |
Collapse
|
16
|
Madhaiyan M, Alex THH, Cho H, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L. Int J Syst Evol Microbiol 2017; 67:5150-5158. [PMID: 29087271 DOI: 10.1099/ijsem.0.002434] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yellow-pigmented isolates, S5-249T and L9-754T, originating from surface-sterilized plant tissues of Jatropha curcas L. (Jatropha) cultivars were characterized using a polyphasic taxonomic approach. Strains S5-249T and L9-754T had 16S rRNA genes sharing 94.2 % sequence similarity with each other and 91.6-97.2 % sequence similarity with those of other species in the genus Sphingomonas, suggesting that they represent two potentially novel species. The 16S rRNA gene sequences of strains S5-249T and L9-754T shared the highest similarity to that of Sphingomonas sanguinis NBRC 13937T (96.1 and 97.2 %, respectively). The genomic DNA G+C contents of strains S5-249T and L9-754T were 66.9 and 68.5 mol%, respectively. The respiratory quinone was determined to be Q-10, and the major polyamine was homospermidine. Strains S5-249T and L9-754T contained summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), C16 : 1, C14 : 0 2-OH and summed feature 4 (C16 : 1ω7t, iso-C15 : 0 2-OH and C16 : 1ω7c) as the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The average nucleotide identity (ANI) values between S. sanguinis NBRC 13937T and the two type strains (S5-249T and L9-754T) were 72.31 and 77.73 %, respectively. Digital DNA-DNA hybridization (dDDH) studies between the novel strains (S5-249T and L9-754T) and other species of the genus Sphingomonas were well below the thresholds used to discriminate between bacterial species. The results of dDDH and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the species of the genus Sphingomonas with validly published names. These data strongly support the classification of the strains as representatives of novel species, for which we propose the names Sphingomonas jatrophae sp. nov. (type strain S5-249T=DSM 27345T=KACC 17593T) and Sphingomonas carotinifaciens sp. nov. (type strain L9-754T=DSM 27347T=KACC 17595T).
Collapse
Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Tan Hian Hwee Alex
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Hayoung Cho
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| |
Collapse
|
17
|
Aureimonas endophytica sp. nov., a novel endophytic bacterium isolated from Aegiceras corniculatum. Int J Syst Evol Microbiol 2017; 67:2934-2940. [DOI: 10.1099/ijsem.0.002046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
18
|
Liu BB, Wang HF, Li QL, Zhou XK, Zhang YG, Xiao M, Li QQ, Zhang W, Li WJ. Aurantimonas endophytica sp. nov., a novel endophytic bacterium isolated from roots of Anabasis elatior (C. A. Mey.) Schischk. Int J Syst Evol Microbiol 2016; 66:4112-4117. [DOI: 10.1099/ijsem.0.001320] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bing-Bing Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Hong-Fei Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- College of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Qiu-Li Li
- College of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Xing-Kui Zhou
- China Tobacco Yunnan Industrial Co., Ltd, Kunming 650231, PR China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qing-Qing Li
- Life Science College, Southwest Forestry University, Kunming 650224, PR China
- Kunming Xianghao Technology Co., Ltd, Kunming 650204, PR China
| | - Wei Zhang
- China Tobacco Yunnan Industrial Co., Ltd, Kunming 650231, PR China
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| |
Collapse
|
19
|
Aydogan EL, Busse HJ, Moser G, Müller C, Kämpfer P, Glaeser SP. Aureimonas galii sp. nov. and Aureimonas pseudogalii sp. nov. isolated from the phyllosphere of Galium album. Int J Syst Evol Microbiol 2016; 66:3345-3354. [DOI: 10.1099/ijsem.0.001200] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ebru L. Aydogan
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Gerald Moser
- Institut für Pflanzenökologie (IFZ), Justus-Liebig-Universität Giessen, D-39392 Giessen, Germany
| | - Christoph Müller
- Institut für Pflanzenökologie (IFZ), Justus-Liebig-Universität Giessen, D-39392 Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Stefanie P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| |
Collapse
|
20
|
Madhaiyan M, Poonguzhali S, Saravanan VS, Duraipandiyan V, Al-Dhabi NA, Pragatheswari D, Santhanakrishnan P, Kim SJ, Weon HY, Kwon SW. Streptomyces pini sp. nov., an actinomycete isolated from phylloplane of pine (Pinus sylvestris L.) needle-like leaves. Int J Syst Evol Microbiol 2016; 66:4204-4210. [PMID: 27469580 DOI: 10.1099/ijsem.0.001336] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel siderophore-producing actinomycete, designated PL19T, was isolated from the Scots-pine needle-like leaves collected from TNAU campus, Coimbatore, India. The isolate was chemoorganotrophic in nutrition and able to grow at 30 °C, and the optimum pH and NaCl facilitated the growth pH 6-11 and 0-8 % (w/v), respectively. The cells are filamentous and the mycelia formed are basically of wide and intricately branched substrate mycelium from which aerial mycelia arises, later gets differentiated into spores that are warty and arranged spirally. The 16S rRNA gene of strain PL19T was sequenced and was highly similar to the type strains of species of the genus Streptomyces, including Streptomyces barkulensis RC1831T (98.8 % pairwise similarity), Streptomyces fenghuangensis GIMN4.003T (98.2 %), Streptomyces nanhaiensis SCSIO 01248T (98.0 %), Streptomyces radiopugnans R97T (97.9 %), Streptomyces atacamensis C60T (97.8 %) and Streptomyces macrosporus NBRC 14749T (97.2 %), all of which were subjected to taxonomical characterization using a polyphasic approach. The strains showed unique carbon utilization patterns, and it possesses iso-C16 : 0 anteiso-C15 : 0 and anteiso-C17 : 0 as a major cellular fatty acids. The cell-wall was dominated with ll-type diaminopimelic acid, and the menaquinone type was MK-9(H6, H8). These chemotaxonomic evidences placed strain PL19T within the genus Streptomyces. The determination of G+C ratio (69.5 mol%) and DNA-DNA hybridization values (13.4-31.8 % with the phylogenetically related species) helped in further hierarchical classification of strain PL19T. Based on morphological, physiological and chemotaxonomic data as well as DNA-DNA hybridization values, strain PL19T could be distinguished from the evolutionarily closest species currently available. All these collective data show that strain PL19T represents a novel species of the genus Streptomyces, for which the name Streptomyces pini sp. nov. is proposed. The type strain is PL19T (=NRRL B-24728T=ICMP 17783T).
Collapse
Affiliation(s)
- Munusamy Madhaiyan
- Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Republic of Singapore.,Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India.,Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Republic of Singapore
| | | | - Veeramuthu Duraipandiyan
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box. 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box. 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Dhandapani Pragatheswari
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India.,School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Palani Santhanakrishnan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| |
Collapse
|
21
|
Cho Y, Lee I, Yang YY, Baek K, Yoon SJ, Lee YM, Kang SH, Lee HK, Hwang CY. Aureimonas glaciistagni sp. nov., isolated from a melt pond on Arctic sea ice. Int J Syst Evol Microbiol 2015; 65:3564-3569. [DOI: 10.1099/ijsem.0.000453] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, motile, aerobic and rod-shaped bacterial strain, PAMC 27157T, was isolated from a melt pond on sea ice in the Chukchi Sea. Phylogenetic analysis of the 16S rRNA gene sequence of strain PAMC 27157T revealed an affiliation to the genus Aureimonas with the closest sequence similarity (96.2 %) to that of Aureimonas phyllosphaerae. Strain PAMC 27157T grew optimally at 30 °C and pH 7.0 in the presence of 3.5 % (w/v) NaCl. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, sulfoquinovosyldiacylglycerol and an unidentified aminolipid. The major cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 83.1 %) and the major respiratory quinone was Q-10. The genomic DNA G+C content was 69.1 mol%. The combined phylogenetic, phenotypic and chemotaxonomic data showed that strain PAMC 27157T could be clearly distinguished from species of the genus Aureimonas with validly published names. Thus, strain PAMC 27157T should be classified as representing a novel species in the genus Aureimonas, for which the name Aureimonas glaciistagni sp. nov. is proposed. The type strain is PAMC 27157T ( = KCCM 43049T = JCM 30183T).
Collapse
Affiliation(s)
- Yirang Cho
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305-4216, USA
| | - Inae Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Yoon Y. Yang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Kiwoon Baek
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Soo J. Yoon
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Yung M. Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Sung-Ho Kang
- Division of Polar Ocean Environment, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Hong K. Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Chung Y. Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| |
Collapse
|
22
|
Liang J, Liu J, Zhang XH. Jiella aquimaris gen. nov., sp. nov., isolated from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:1127-1132. [PMID: 25589737 DOI: 10.1099/ijs.0.000067] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic and rod-shaped motile bacterium with peritrichous flagella, designated strain LZB041(T), was isolated from offshore surface seawater of the East China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LZB041(T) formed a lineage within the family ' Aurantimonadaceae' that was distinct from the most closely related genera Aurantimonas (96.0-96.4% 16S rRNA gene sequence similarity) and Aureimonas (94.5-96.0%). Optimal growth occurred in the presence of 1-7% (w/v) NaCl, at pH 7.0-8.0 and at 28-37 °C. Ubiquinone-10 was the predominant respiratory quinone. The major fatty acids (>10% of total fatty acids) were C(18 : 1)ω7c and/or C(18 : 1)ω6c (summed feature 8) and cyclo-C(19 : 0)ω8c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unknown aminolipid, one unknown phospholipid and one unknown polar lipid. The DNA G+C content of strain LZB041(T) was 71.3 mol%. On the basis of polyphasic analysis, strain LZB041(T) is considered to represent a novel species of a new genus in the class Alphaproteobacteria , for which the name Jiella aquimaris gen. nov., sp. nov. is proposed. The type strain of the type species is LZB041(T) ( = JCM 30119(T) = MCCC 1K00255(T)).
Collapse
Affiliation(s)
- Jing Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Ji Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.,College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| |
Collapse
|
23
|
Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant. Int J Syst Evol Microbiol 2014; 64:3160-3167. [DOI: 10.1099/ijs.0.064154-0] [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 phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19T was distinct from other taxa within the class
Alphaproteobacteria
. Strain E19T showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera
Rhizobium
(≤93.5 %),
Labrenzia
(≤93.1 %),
Stappia
(≤93.1 %),
Aureimonas
(≤93.1 %) and
Mesorhizobium
(≤93.0 %) and was most closely related to
Rhizobium rhizoryzae
(93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19T was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19T ( = LMG 27460T = KACC 17263T).
Collapse
Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| |
Collapse
|
24
|
Bao Z, Sasaki K, Okubo T, Ikeda S, Anda M, Hanzawa E, Kakizaki K, Sato T, Mitsui H, Minamisawa K. Impact of Azospirillum sp. B510 inoculation on rice-associated bacterial communities in a paddy field. Microbes Environ 2013; 28:487-90. [PMID: 24256970 PMCID: PMC4070703 DOI: 10.1264/jsme2.me13049] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Rice seedlings were inoculated with Azospirillum sp. B510 and transplanted into a paddy field. Growth in terms of tiller numbers and shoot length was significantly increased by inoculation. Principal-coordinates analysis of rice bacterial communities using the 16S rRNA gene showed no overall change from B510 inoculation. However, the abundance of Veillonellaceae and Aurantimonas significantly increased in the base and shoots, respectively, of B510-inoculated plants. The abundance of Azospirillum did not differ between B510-inoculated and uninoculated plants (0.02-0.50%). These results indicate that the application of Azospirillum sp. B510 not only enhanced rice growth, but also affected minor rice-associated bacteria.
Collapse
Affiliation(s)
- Zhihua Bao
- Graduate School of Life Sciences, Tohoku University
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Madhaiyan M, Peng N, Te NS, Hsin I C, Lin C, Lin F, Reddy C, Yan H, Ji L. Improvement of plant growth and seed yield in Jatropha curcas by a novel nitrogen-fixing root associated Enterobacter species. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:140. [PMID: 24083555 PMCID: PMC3879406 DOI: 10.1186/1754-6834-6-140] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/26/2013] [Indexed: 05/13/2023]
Abstract
BACKGROUND Jatropha curcas L. is an oil seed producing non-leguminous tropical shrub that has good potential to be a fuel plant that can be cultivated on marginal land. Due to the low nutrient content of the targeted plantation area, the requirement for fertilizer is expected to be higher than other plants. This factor severely affects the commercial viability of J. curcas. RESULTS We explored the feasibility to use endophytic nitrogen-fixing bacteria that are native to J. curcas to improve plant growth, biomass and seed productivity. We demonstrated that a novel N-fixing endophyte, Enterobacter sp. R4-368, was able to colonize in root and stem tissues and significantly promoted early plant growth and seed productivity of J. curcas in sterilized and non-sterilized soil. Inoculation of young seedling led to an approximately 57.2% increase in seedling vigour over a six week period. At 90 days after planting, inoculated plants showed an average increase of 25.3%, 77.7%, 27.5%, 45.8% in plant height, leaf number, chlorophyll content and stem volume, respectively. Notably, inoculation of the strain led to a 49.0% increase in the average seed number per plant and 20% increase in the average single seed weight when plants were maintained for 1.5 years in non-sterilized soil in pots in the open air. Enterobacter sp. R4-368 cells were able to colonize root tissues and moved systemically to stem tissues. However, no bacteria were found in leaves. Promotion of plant growth and leaf nitrogen content by the strain was partially lost in nifH, nifD, nifK knockout mutants, suggesting the presence of other growth promoting factors that are associated with this bacterium strain. CONCLUSION Our results showed that Enterobacter sp. R4-368 significantly promoted growth and seed yield of J. curcas. The application of the strains is likely to significantly improve the commercial viability of J. curcas due to the reduced fertilizer cost and improved oil yield.
Collapse
Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Ni Peng
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Ngoh Si Te
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Cheng Hsin I
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Cai Lin
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Fu Lin
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Chalapathy Reddy
- Joil Pte Ltd, 1 Research Link National University of Singapore, Singapore 117604, Republic of Singapore
| | - Hong Yan
- Joil Pte Ltd, 1 Research Link National University of Singapore, Singapore 117604, Republic of Singapore
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| |
Collapse
|
26
|
Madhaiyan M, Jin TY, Roy JJ, Kim SJ, Weon HY, Kwon SW, Ji L. Pleomorphomonas
diazotrophica sp. nov., an endophytic N-fixing bacterium isolated from root tissue of Jatropha curcas L. Int J Syst Evol Microbiol 2013; 63:2477-2483. [DOI: 10.1099/ijs.0.044461-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic, non-motile, pleomorphic, Gram-negative and nitrogen-fixing bacterial strain, designated R5-392T, was isolated from surface-sterilized root tissue of Jatropha curcas. The organism grew optimally at 30 °C in media containing 1 % (w/v) NaCl and at pH 6.0–8.0. The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 63.2 mol%. Analysis of the 16S rRNA gene sequence suggested that strain R5-392T is affiliated with the order
Rhizobiales
within the class
Alphaproteobacteria
and is most closely related to
Pleomorphomonas oryzae
F-7T (98.8 % similarity) and
Pleomorphomonas koreensis
Y9T (98.3 % similarity). Analysis of partial nifH gene sequences also revealed a monophyletic lineage within the class
Alphaproteobacteria
, and strain R5-392T was most closely related to
P. oryzae
F-7T (98 %). Highest nitrogenase activity was detected in the presence of low-level organic nitrogen or in the presence of nitrogenase co-factors (Fe/Mo) in N-free media. Phenotypic and chemotaxonomic data suggest that strain R5-392T represents a novel species within the genus
Pleomorphomonas
, for which the name
Pleomorphomonas
diazotrophica sp. nov. is proposed. The type strain is R5-392T ( = KACC 16233T = DSM 25022T).
Collapse
Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| | - Tan Yuan Jin
- Raffles Institution, 1 Raffles Institution Lane, Singapore 575954
| | - Joseph Jegan Roy
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| | - Soo-Jin Kim
- Korean Agricultural Culture Collection (KACC), Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration (RDA), Suwon 441-707, Republic of Korea
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection (KACC), Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration (RDA), Suwon 441-707, Republic of Korea
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration (RDA), Suwon 441-707, Republic of Korea
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| |
Collapse
|