1
|
Wu C, Zhang X, Fan Y, Ye J, Dong L, Wang Y, Ren Y, Yong H, Liu R, Wang A. Vertical transfer and functional characterization of cotton seed core microbiome. Front Microbiol 2024; 14:1323342. [PMID: 38264479 PMCID: PMC10803423 DOI: 10.3389/fmicb.2023.1323342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Microbiome within plant tissues is pivotal for co-evolution with host plants. This microbiome can colonize the plant, with potential transmission via seeds between parents and offspring, affecting seedling growth and host plant adaptability to the environment. Methods We employed 16S rRNA gene amplicon analysis to investigate the vertical distribution of core microbiome in cotton seeds across ecological niches [rhizosphere, root, stem, leaf, seed and seed-P (parental seed)] of the three cotton genotypes. Results The findings demonstrated a significant decrease in microbiome diversity and network complexity from roots, stems, and leaves to seeds. The microenvironment exerted a more substantial influence on the microbiome structure of cotton than the genotypes. The core endophytic microorganisms in cotton seeds comprised 29 amplicon sequence variants (ASVs) affiliated with Acidimicrobiia, Alphaproteobacteria, Bacilli, Bacteroidia, Clostridia, Gammaproteobacteria, and unclassified_Proteobacteria. These vertically transmitted taxa are widely distributed in cotton plants. Through 16S rRNA gene-based function prediction analysis of the cotton microbiome, we preliminarily understood that there are potential differences in metabolic capabilities and phenotypic traits among microbiomes in different microhabitats. Discussion In conclusion, this study demonstrated the crucial role of the microenvironment in influencing the cotton microbiome and offered insights into the structures and functions of the cotton seed microbiome, facilitating future crop yield enhancement through core seed microbiome regulation.
Collapse
Affiliation(s)
- Chongdie Wu
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Xin Zhang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yongbin Fan
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Jingyi Ye
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Lingjun Dong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - YuXiang Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - YinZheng Ren
- College of Life Sciences, Shihezi University, Shihezi, China
| | - HongHong Yong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Ruina Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Aiying Wang
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| |
Collapse
|
2
|
Bizjak T, Sellstedt A, Gratz R, Nordin A. Presence and activity of nitrogen-fixing bacteria in Scots pine needles in a boreal forest: a nitrogen-addition experiment. TREE PHYSIOLOGY 2023; 43:1354-1364. [PMID: 37073466 PMCID: PMC10423461 DOI: 10.1093/treephys/tpad048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Endophytic nitrogen-fixing bacteria have been detected and isolated from the needles of conifer trees growing in North American boreal forests. Because boreal forests are nutrient-limited, these bacteria could provide an important source of nitrogen for tree species. This study aimed to determine their presence and activity in a Scandinavian boreal forest, using immunodetection of nitrogenase enzyme subunits and acetylene-reduction assays of native Scots pine (Pinus sylvestris L.) needles. The presence and rate of nitrogen fixation by endophytic bacteria were compared between control plots and fertilized plots in a nitrogen-addition experiment. In contrast to the expectation that nitrogen-fixation rates would decline in fertilized plots, as seen, for instance, with nitrogen-fixing bacteria associated with bryophytes, there was no difference in the presence or activity of nitrogen-fixing bacteria between the two treatments. The extrapolated calculated rate of nitrogen fixation relevant for the forest stand was 20 g N ha-1 year-1, which is rather low compared with Scots pine annual nitrogen use but could be important for the nitrogen-poor forest in the long term. In addition, of 13 colonies of potential nitrogen-fixing bacteria isolated from the needles on nitrogen-free media, 10 showed in vitro nitrogen fixation. In summary, 16S rRNA sequencing identified the species as belonging to the genera Bacillus, Variovorax, Novosphingobium, Sphingomonas, Microbacterium and Priestia, which was confirmed by Illumina whole-genome sequencing. Our results confirm the presence of endophytic nitrogen-fixing bacteria in Scots pine needles and suggest that they could be important for the long-term nitrogen budget of the Scandinavian boreal forest.
Collapse
Affiliation(s)
- Tinkara Bizjak
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Anita Sellstedt
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Regina Gratz
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Annika Nordin
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| |
Collapse
|
3
|
Complete Genome Sequence of Achromobacter Strain ES-001, a Betaproteobacterium Associated with a Cellulolytic Soil Community. Microbiol Resour Announc 2021; 10:e0082821. [PMID: 34617787 PMCID: PMC8496361 DOI: 10.1128/mra.00828-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence of the soilborne bacterium Achromobacter strain ES-001, assembled from Illumina NextSeq and Nanopore MinION reads, is rich in genes predicted to encode iron, arsenic, and hydrocarbon metabolism, as well as type 6 secretion components. The sequenced genome will aid in determining the roles of noncellulolytic species in cellulose-enriched environments.
Collapse
|
4
|
Maquia ISA, Fareleira P, Videira e. Castro I, Soares R, Brito DRA, Mbanze AA, Chaúque A, Máguas C, Ezeokoli OT, Ribeiro NS, Marques I, Ribeiro-Barros AI. The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique. Microorganisms 2021; 9:microorganisms9081562. [PMID: 34442641 PMCID: PMC8400031 DOI: 10.3390/microorganisms9081562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/14/2022] Open
Abstract
(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.
Collapse
Affiliation(s)
- Ivete Sandra Alberto Maquia
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- TropiKMan Doctoral Program, NOVA SBE, 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, Maputo 3453, Mozambique;
| | - Paula Fareleira
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Isabel Videira e. Castro
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Ricardo Soares
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, Maputo 3453, Mozambique;
| | | | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, Maputo 3453, Mozambique; (A.C.); (N.S.R.)
| | - Cristina Máguas
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Obinna T. Ezeokoli
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein 9300, South Africa;
| | - Natasha Sofia Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, Maputo 3453, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- Correspondence: (I.M.); (A.I.R.-B.)
| | - Ana I. Ribeiro-Barros
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- Correspondence: (I.M.); (A.I.R.-B.)
| |
Collapse
|
5
|
Shao A, Sun Z, Fan S, Xu X, Wang W, Amombo E, Yin Y, Li X, Wang G, Wang H, Fu J. Moderately low nitrogen application mitigate the negative effects of salt stress on annual ryegrass seedlings. PeerJ 2020; 8:e10427. [PMID: 33344081 PMCID: PMC7719293 DOI: 10.7717/peerj.10427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/03/2020] [Indexed: 01/21/2023] Open
Abstract
Appropriate application of nitrogen (N) can alleviate the salt stress-induced damage on plants. This study explores the changes of nitrogen requirement in feeding annual ryegrass seedlings under mild salt concentrations (50 mM, 100 mM) plus its underlying mitigation mechanism. Results showed that low salt concentration decreased N requirement as observed from the increment in plant height and biomass at a relative low N level (2.0 mM not 5.0 mM). Under salt treatment, especially at 50 mM NaCl, the OJIP (Chl a fluorescence induction transient) curve and a series of performance indexes (PIABS, RC/CS0, ET0/CS0, ϕE0, ϕ0) peaked whereas DI0/RC, Vj and M0 were the lowest under moderately low N level (2.0 mM). In addition, under salt stress, moderately low N application could maintain the expression of NR (nitrate reductase) and GS (glutamine synthetase) encoding genes at a relatively stable level but had no effect on the expression of detected NRT (nitrate transporter) gene. The seedlings cultured at 2.0 mM N also exhibited the highest activity of CAT and POD antioxidant enzymes and the lowest MDA content and EL under relative low level of salt treatment. These results indicated that mild salt treatment of annual ryegrass seedlings might reduce N requirement while moderately low N application could promote their growth via regulating photosynthesis, alleviating ROS-induced (reactive oxygen species) damage and maintenance of N metabolism. These results also can provide useful reference for nitrogen application in moderation rather than in excess on annual ryegrass in mild or medium salinity areas through understanding the underlying response mechanisms.
Collapse
Affiliation(s)
- An Shao
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Zhichao Sun
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Xiao Xu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Erick Amombo
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Yanling Yin
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Xiaoning Li
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Guangyang Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Hongli Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, China
| |
Collapse
|
6
|
Maquia IS, Fareleira P, Videira e Castro I, Brito DRA, Soares R, Chaúque A, Ferreira-Pinto MM, Lumini E, Berruti A, Ribeiro NS, Marques I, Ribeiro-Barros AI. Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion. Microorganisms 2020; 8:E1291. [PMID: 32846974 PMCID: PMC7563409 DOI: 10.3390/microorganisms8091291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/19/2023] Open
Abstract
(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.
Collapse
Affiliation(s)
- Ivete Sandra Maquia
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
- TropiKMan Doctoral Program, Nova School of Business & Economics (Nova SBE), 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Paula Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Isabel Videira e Castro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Ricardo Soares
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - M. Manuela Ferreira-Pinto
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Erica Lumini
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Andrea Berruti
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Natasha S. Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Ana I. Ribeiro-Barros
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| |
Collapse
|
7
|
Mehmood MA, Zhao H, Cheng J, Xie J, Jiang D, Fu Y. Sclerotia of a phytopathogenic fungus restrict microbial diversity and improve soil health by suppressing other pathogens and enriching beneficial microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 259:109857. [PMID: 32072956 DOI: 10.1016/j.jenvman.2019.109857] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Sclerotinia sclerotiorum, a notorious soil-borne pathogen of various important crops, produces numerous sclerotia to oversummer in the soil. Considering that sclerotia may also be attacked by other microbes in the soil, we hypothesized that sclerotia in soil may affect the community of soil microbes directly and/or indirectly. In this study, we inoculated sclerotia of S. sclerotiorum in soil collected from the field to observe changes in microbial diversity over three months using 16S rRNA and ITS2 sequencing techniques. Alpha diversity indices exhibited a decline in the diversity of microbial communities, while permanova results confirmed a significant difference in the microbial communities of sclerotia-amended and non-amended soil samples. In sclerotia-amended soil, fungal diversity showed enrichment of antagonists such as Clonostachys, Trichoderma, and Talaromyces and a drastic reduction in the plant pathogenic microbes compared to the non-amended soil. Sclerotia not only activated the antagonists but also enhanced the abundance of plant growth-promoting bacteria, such as Chitinophaga, Burkholderia, and Dyella. Moreover, the presence of sclerotia curtailed the growth of several notorious plant pathogenic fungi belonging to various genera such as Fusarium, Colletotrichum, Cladosporium, Athelia, Alternaria, and Macrophomina. Thus, we conclude that S. sclerotiorum when dormant in soil can reduce the diversity of soil microbes, including suppressing plant pathogens and enriching beneficial microbes. To the best of our knowledge, this is the first time a plant pathogen has been found in soil that can significantly suppress other pathogens. Our findings may provide novel cues to understand the ecology of crop pathogens in soil and maintaining soil conditions that could be beneficial for constructing a healthy soil microorganism community required for mitigating soil-borne diseases.
Collapse
Affiliation(s)
- Mirza Abid Mehmood
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Department of Plant Pathology, Muhammad Nawaz Shareef University of Agriculture, Multan, Punjab, Pakistan
| | - Huizhang Zhao
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Jiasen Cheng
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Jiatao Xie
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Yanping Fu
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China.
| |
Collapse
|
8
|
Nie G, Huang T, Ma X, Huang L, Peng Y, Yan Y, Li Z, Wang X, Zhang X. Genetic variability evaluation and cultivar identification of tetraploid annual ryegrass using SSR markers. PeerJ 2019; 7:e7742. [PMID: 31579612 PMCID: PMC6756138 DOI: 10.7717/peerj.7742] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 08/25/2019] [Indexed: 11/20/2022] Open
Abstract
Annual ryegrass (Lolium multiflorum) is a widely used cool-season turf and forage grass with high productivity and ornamental characteristics. However, the abundant intra-cultivar genetic variability usually hampers the application of conventional techniques for cultivar identification. The objectives of this study were to: (1) describe an efficient strategy for identification of six tetraploid annual ryegrass cultivars and (2) investigate the genetic diversity based on SSR markers. A total of 242 reliable bands were obtained from 29 SSR primer pairs with an average of 8.3 bands for each primer pair and the average value of polymorphic information content (PIC) was 0.304. The result of analysis of molecular variance (AMOVA) revealed that 81.99% of the genetic variation occurred in within-cultivars and 18.01% among-cultivars. The principal coordinate analysis (PCoA) showed that the first two principal axes explain 8.57% (PC1) and 6.05% (PC2) of total variation, respectively. By using multi-bulk strategy based on different filtering thresholds, the results suggested that bands frequency of 40% could be used as a reliable standard for cultivar identification in annual ryegrass. Under this threshold, 12 SSR primer pairs (00-04A, 02-06G, 02-08C, 03-05A, 04-05B, 10-09E, 12-01A, 13-02H, 13-12D, 14-06F, 15-01C and 17-10D) were detected for direct identification of six tetraploid annual ryegrass cultivars, which could be incorporated into conservation schemes to protect the intellectual property of breeders, ensure purity for consumers, as well as guarantee effective use of cultivars in future.
Collapse
Affiliation(s)
- Gang Nie
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ting Huang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linkai Huang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Peng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanhong Yan
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhou Li
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xia Wang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
9
|
Aroua I, Abid G, Souissi F, Mannai K, Nebli H, Hattab S, Borgi Z, Jebara M. Identification of two pesticide-tolerant bacteria isolated from Medicago sativa nodule useful for organic soil phytostabilization. Int Microbiol 2018; 22:111-120. [PMID: 30810937 DOI: 10.1007/s10123-018-0033-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022]
Abstract
Plant-microbe interactions such as rhizobacteria legumes are interesting in organic farming that has undergone significant expansion in the world. The organic agriculture is as an environment-friendly technique and a sustainable alternative to intensive agricultural system. Three types of soil were chosen, organic (ORG), conventional (CON), and fallow land (NA) to isolate soil bacteria-nodulating Medicago sativa, in order to develop microbial inoculants for use in agricultural sustainable system. Soil analysis revealed significant higher amounts of total nitrogen, organic carbon, total phosphorus, and matter detected in ORG. As for heavy metals, ORG showed high Cu content due to the authorized chemical use in organic farming. A sample of 130 bacteria was isolated from Medicago sativa nodule, genetically characterized by PCR/RFLP of ribosomal 16S RNAs, and a great dominance of Sinorhizobium meliloti (88.4%, 73.8%, and 55.5%) is obtained among NA-, CON-, and ORG-managed soils, respectively. The ORG showed the high bacterial diversity with 13.3% of non-identified strains. The resistance against five pesticides (Prosper, Cuivox, Fungastop, Nimbecidine, and Maneb) revealed a maximum of inhibitory concentration about 10 mg l-1 of Prosper, 12 mg l-1 of Cuivox, 6 ml l-1 of Fungastop, 7.5 ml l-1of Nimbecidine, and 25 ml l-1 of Maneb. The analysis of the symbiotic properties and plant growth-promoting potential revealed two efficient strains significantly increased alfalfa dry weight through producing siderophores, phosphorus, and indole acetic acid (13.6 mg ml-1 and 19.9 mg ml-1 respectively). Hence, we identify two tolerant and efficient strains, Achromobacter spanium and Serratia plymuthica, isolated from Medicago sativa nodule with valuable potential able to phytostabilize pesticide-contaminated soils.
Collapse
Affiliation(s)
- Ibtissem Aroua
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia
| | - Ghassen Abid
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia
| | - Fatma Souissi
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia
| | - Khdiri Mannai
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia
| | - Houcem Nebli
- The Technical Center of Organic Agriculture in Chott Meriem, BP 54, 4042, Chott Meriem, Sousse, Tunisia
| | - Sabrine Hattab
- The Regional Center of Research in Horticulture and Organic Agriculture in Chott-Meriem Route Touristique, 4042, Chott Meriem, Tunisia
| | - Ziad Borgi
- The Technical Center of Organic Agriculture in Chott Meriem, BP 54, 4042, Chott Meriem, Sousse, Tunisia
| | - Moez Jebara
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia.
| |
Collapse
|
10
|
White JF, Kingsley KL, Verma SK, Kowalski KP. Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes. Microorganisms 2018; 6:microorganisms6030095. [PMID: 30227634 PMCID: PMC6164190 DOI: 10.3390/microorganisms6030095] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 12/20/2022] Open
Abstract
In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells—locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes—effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown.
Collapse
Affiliation(s)
- James F White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Kathryn L Kingsley
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Satish K Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP 221005, India.
| | - Kurt P Kowalski
- U.S. Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105-2807, USA.
| |
Collapse
|
11
|
Castellano-Hinojosa A, Pérez-Tapia V, Bedmar EJ, Santillana N. Purple corn-associated rhizobacteria with potential for plant growth promotion. J Appl Microbiol 2018; 124:1254-1264. [PMID: 29368373 DOI: 10.1111/jam.13708] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 11/21/2017] [Accepted: 01/18/2018] [Indexed: 12/13/2022]
Abstract
AIMS Purple corn (Zea mays var. purple amylaceum) is a native variety of the Peruvian Andes, cultivated at 3000 m since the pre-Inca times without N fertilization. We aimed to isolate and identify native plant growth-promoting rhizobacteria (PGPR) for future microbial-based inoculants. METHODS AND RESULTS Eighteen strains were isolated from the rhizosphere of purple corn plants grown without N fertilization in Ayacucho (Peru). The 16S rRNA gene clustered the 18 strains into nine groups that contained species of Bacillus, Stenotrophomonas, Achromobacter, Paenibacillus, Pseudomonas and Lysinibacillus. A representative strain from each group was selected and assayed for N2 fixation, phosphate solubilization, indole acetic and siderophore production, 1-aminocyclopropane-1-carboxylic acid deaminase activity and biocontrol abilities. Inoculation of purple corn plants with single and combined strains selected after a principal component analysis caused significant increases in root and shoot dry weight, total C and N contents of the plants. CONCLUSIONS PGPRs can support growth and crop production of purple corn in the Peruvian Andes and constitute the base for microbial-based inoculants. SIGNIFICANCE AND IMPACT OF THE STUDY This study enlarges our knowledge on plant-microbial interactions in high altitude mountains and provides new applications for PGPR inoculation in purple amylaceum corn, which is part of the staple diet for the native Quechua communities.
Collapse
Affiliation(s)
- A Castellano-Hinojosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Granada, Spain.,Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - V Pérez-Tapia
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Granada, Spain
| | - E J Bedmar
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - N Santillana
- Facultad de Ciencias Agrarias, Universidad Nacional de San Cristóbal de Huamanga, Ayacucho, Perú
| |
Collapse
|
12
|
Liu Q, Qi X, Yan H, Huang L, Nie G, Zhang X. Reference Gene Selection for Quantitative Real-Time Reverse-Transcriptase PCR in Annual Ryegrass (Lolium multiflorum) Subjected to Various Abiotic Stresses. Molecules 2018; 23:E172. [PMID: 29337852 PMCID: PMC6017817 DOI: 10.3390/molecules23010172] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/12/2018] [Accepted: 01/13/2018] [Indexed: 02/06/2023] Open
Abstract
To select the most stable reference genes in annual ryegrass (Lolium multiflorum), we studied annual ryegrass leaf tissues exposed to various abiotic stresses by qRT-PCR and selected 11 candidate reference genes, i.e., 18S rRNA, E2, GAPDH, eIF4A, HIS3, SAMDC, TBP-1, Unigene71, Unigene77, Unigene755, and Unigene14912. We then used GeNorm, NormFinder, and BestKeeper to analyze the expression stability of these 11 genes, and used RefFinder to comprehensively rank genes according to stability. Under different stress conditions, the most suitable reference genes for studies of leaf tissues of annual ryegrass were different. The expression of the eIF4A gene was the most stable under drought stress. Under saline-alkali stress, Unigene14912 has the highest expression stability. Under acidic aluminum stress, SAMDC expression stability was highest. Under heavy metal stress, Unigene71 expression had the highest stability. According to the software analyses, Unigene14912, HIS3, and eIF4A were the most suitable for analyses of abiotic stress in tissues of annual ryegrass. GAPDH was the least suitable reference gene. In conclusion, selecting appropriate reference genes under abiotic stress not only improves the accuracy of annual ryegrass gene expression analyses, but also provides a theoretical reference for the development of reference genes in plants of the genus Lolium.
Collapse
Affiliation(s)
- Qiuxu Liu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiao Qi
- National Animal Husbandry Service, Ministry of Agriculture, Beijing 100000, China.
| | - Haidong Yan
- Department of Horticulture, Virginia Polytechnic Institute and State University, 490 West Campus Dr., Blacksburg, VA 24061, USA.
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Gang Nie
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| |
Collapse
|
13
|
Castanheira NL, Dourado AC, Pais I, Semedo J, Scotti-Campos P, Borges N, Carvalho G, Barreto Crespo MT, Fareleira P. Colonization and beneficial effects on annual ryegrass by mixed inoculation with plant growth promoting bacteria. Microbiol Res 2017; 198:47-55. [DOI: 10.1016/j.micres.2017.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/22/2016] [Accepted: 01/23/2017] [Indexed: 12/20/2022]
|
14
|
Soares MA, Li HY, Kowalski KP, Bergen M, Torres MS, White JF. Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth. MICROBIAL ECOLOGY 2016; 72:407-417. [PMID: 27260154 DOI: 10.1007/s00248-016-0793-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/18/2016] [Indexed: 06/05/2023]
Abstract
We hypothesize that bacterial endophytes may enhance the competitiveness and invasiveness of Phragmites australis. To evaluate this hypothesis, endophytic bacteria were isolated from P. australis. The majority of the shoot meristem isolates represent species from phyla Firmicutes, Proteobacteria, and Actinobacteria. We chose one species from each phylum to characterize further and to conduct growth promotion experiments in Phragmites. Bacteria tested include Bacillus amyloliquefaciens A9a, Achromobacter spanius B1, and Microbacterium oxydans B2. Isolates were characterized for known growth promotional traits, including indole acetic acid (IAA) production, secretion of hydrolytic enzymes, phosphate solubilization, and antibiosis activity. Potentially defensive antimicrobial lipopeptides were assayed for through application of co-culturing experiments and mass spectrometer analysis. B. amyloliquefaciens A9a and M. oxydans B2 produced IAA. B. amyloliquefaciens A9a secreted antifungal lipopeptides. Capability to promote growth of P. australis under low nitrogen conditions was evaluated in greenhouse experiments. All three isolates were found to increase the growth of P. australis under low soil nitrogen conditions and showed increased absorption of isotopic nitrogen into plants. This suggests that the Phragmites microbes we evaluated most likely promote growth of Phragmites by enhanced scavenging of nitrogenous compounds from the rhizosphere and transfer to host roots. Collectively, our results support the hypothesis that endophytic bacteria play a role in enhancing growth of P. australis in natural populations. Gaining a better understanding of the precise contributions and mechanisms of endophytes in enabling P. australis to develop high densities rapidly could lead to new symbiosis-based strategies for management and control of the host.
Collapse
Affiliation(s)
- M A Soares
- Department of Botany and Ecology, Federal University of Mato Grosso, Cuiabá, Mato Grosso, 78060-900, Brazil.
| | - H-Y Li
- Faculty of Life Sciences and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan Province, China
| | - K P Kowalski
- US Geological Survey, Great Lakes Science Center, Ann Arbor, MI, USA
| | - M Bergen
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901-8520, USA
| | - M S Torres
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901-8520, USA
| | - J F White
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901-8520, USA
| |
Collapse
|
15
|
Potential of Endophytic Bacterium Paenibacillus sp. PHE-3 Isolated from Plantago asiatica L. for Reduction of PAH Contamination in Plant Tissues. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13070633. [PMID: 27347988 PMCID: PMC4962174 DOI: 10.3390/ijerph13070633] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/01/2016] [Accepted: 06/11/2016] [Indexed: 11/17/2022]
Abstract
Endophytes are ubiquitous in plants, and they may have a natural capacity to biodegrade polycyclic aromatic hydrocarbons (PAHs). In our study, a phenanthrene-degrading endophytic Paenibacillus sp. PHE-3 was isolated from P. asiatica L. grown in a PAH-contaminated site. The effects of environmental variables on phenanthrene biodegradation by strain PHE-3 were studied, and the ability of strain PHE-3 to use high molecular weight PAH (HMW-PAH) as a sole carbon source was also evaluated. Our results indicated that pH value of 4.0–8.0, temperature of 30 °C–42 °C, initial phenanthrene concentration less than 100 mg·L−1, and some additional nutrients are favorable for the biodegradation of phenanthrene by strain PHE-3. The maximum biodegradation efficiency of phenanthrene was achieved at 99.9% after 84 h cultivation with additional glutamate. Moreover, the phenanthrene biodegradation by strain PHE-3 was positively correlated with the catechol 2,3-dioxygenase activity (ρ = 0.981, p < 0.05), suggesting that strain PHE-3 had the capability of degrading HMW-PAHs. In the presence of other 2-, 3-ringed PAHs, strain PHE-3 effectively degraded HMW-PAHs through co-metabolism. The results of this study are beneficial in that the re-colonization potential and PAH degradation performance of endophytic Paenibacillus sp. PHE-3 may be applied towards reducing PAH contamination in plants.
Collapse
|
16
|
Castanheira N, Dourado A, Kruz S, Alves P, Delgado-Rodríguez A, Pais I, Semedo J, Scotti-Campos P, Sánchez C, Borges N, Carvalho G, Barreto Crespo M, Fareleira P. Plant growth-promoting Burkholderia
species isolated from annual ryegrass in Portuguese soils. J Appl Microbiol 2016; 120:724-39. [DOI: 10.1111/jam.13025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/25/2015] [Accepted: 12/09/2015] [Indexed: 02/05/2023]
Affiliation(s)
- N. Castanheira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | - A.C. Dourado
- iBET-Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | - S. Kruz
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- iBET-Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | - P.I.L. Alves
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- iBET-Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | | | - I. Pais
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| | - J. Semedo
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| | - P. Scotti-Campos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| | - C. Sánchez
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| | - N. Borges
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | - G. Carvalho
- UCBIO; REQUIMTE; Department of Chemistry; Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica Portugal
| | - M.T. Barreto Crespo
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- iBET-Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | - P. Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| |
Collapse
|
17
|
França L, Albuquerque L, Sánchez C, Fareleira P, da Costa MS. Ampullimonas aquatilis gen. nov., sp. nov. isolated from bottled mineral water. Int J Syst Evol Microbiol 2016; 66:1459-1465. [PMID: 26782963 DOI: 10.1099/ijsem.0.000903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates, designated B15.09-116T and B15.09-124, were recovered from bottled mineral water in Portugal. Based on 16S rRNA gene sequence analysis, these strains were related most closely to species of the genus Derxia (belonging to the family Alcaligenaceae) with pairwise sequence similarities of 93.0-93.6 %. The isolates were not pigmented and formed Gram-stain-negative, short, motile rod-shaped cells. The organisms were strictly aerobic, oxidase-positive and catalase-negative. These organisms also fixed N2. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 was the major respiratory quinone. The DNA G+C content of strain B15.09-116T was 49.8 mol%. Based on phylogenetic, physiological and biochemical characteristics the two strains are considered to represent a novel species of a new genus, for which the name Ampullimonas aquatilis gen. nov., sp. nov. is proposed. The type strain of Ampullimonas aquatilis is B15.09-116T ( = CECT 8581T = LMG 28208T).
Collapse
Affiliation(s)
- Luís França
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Claudia Sánchez
- Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Paula Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Milton S da Costa
- Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| |
Collapse
|
18
|
Castellano-Hinojosa A, Correa-Galeote D, Palau J, Bedmar EJ. Isolation of N2 -fixing rhizobacteria from Lolium perenne and evaluating their plant growth promoting traits. J Basic Microbiol 2015; 56:85-91. [PMID: 26781208 DOI: 10.1002/jobm.201500247] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/25/2015] [Indexed: 11/09/2022]
Abstract
Twenty one dinitrogen (N2 )-fixing bacteria were isolated from the rhizosphere of Lolium perenne grown for more than 10 years without N-fertilization. The nearly complete sequence of the 16S rRNA gene of each strain and pairwise alignments among globally aligned sequences of the 16S rRNA genes clustered them into nine different groups. Out of the 21 strains, 11 were members of genus Bacillus, 3 belonged to each one of genera Paenibacillus and Pseudoxanthomonas, and the remaining 2 strains to each one of genera Burkholderia and Staphylococcus, respectively. A representative strain from each group contained the nifH gene and fixed atmospheric N2 as determined by the acetylene-dependent ethylene production assay (acetylene reduction activity, ARA). The nine selected strains were also examined to behave as plant growth promoting bacteria (PGPRs) including their ability to act as a biocontrol agent. The nine representative strains produced indol acetic acid (IAA) and solubilized calcium triphosphate, five of them, strains C2, C3, C12, C15, and C16, had ACC deaminase activity, and strains C2, C3, C4, C12, C16, and C17 produced siderophores. Strains C13, C16, and C17 had the capability to control growth of the pathogen Fusarium oxysporum mycelial growth in vitro. PCA analysis of determined PGPR properties showed that ARA, ACC deaminase activity, and siderophore production were the most valuable as they had the maximal contribution to the total variance.
Collapse
Affiliation(s)
| | - David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Granada, Spain
| | - Josep Palau
- Professional Sportsverd Football S.L., Badalona, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Granada, Spain
| |
Collapse
|
19
|
Wang X, Ma X, Huang L, Zhang X. Identification of the valid reference genes for quantitative RT-PCR in annual ryegrass (Lolium multiflorum) under salt stress. Molecules 2015; 20:4833-47. [PMID: 25786166 PMCID: PMC6272566 DOI: 10.3390/molecules20034833] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/06/2015] [Accepted: 03/10/2015] [Indexed: 01/13/2023] Open
Abstract
Annual ryegrass (Lolium multiflorum) is a cool-season annual grass cultivated worldwide for its high yield and quality. With the areas of saline soil increasing, investigation of the molecular mechanisms of annual ryegrass tolerance under salt stress has become a significant topic. qRT-PCR has been a predominant assay for determination of the gene expression, in which selecting a valid internal reference gene is a crucial step. The objective of present study was to evaluate and identify suitable reference genes for qRT-PCR in annual ryegrass under salt stress. The results calculated by RefFinder indicated that eEF1A(s) was the most stable reference gene in leaves, whereas EF1-a was the least stable; meanwhile, TBP-1 was the most optimal in roots and in all samples, and the eIF-5A shouldn’t be utilized for normalization of the gene expression. eEF1A(s) is more suitable than TBP-1 as reference gene in leaves when verified with P5CS1 and Cyt-Cu/Zn SOD genes. We should choose optimal reference genes in specific tissues instead of the most stable one selected from different conditions and tissues.
Collapse
Affiliation(s)
- Xia Wang
- Grassland Science Department, Sichuan Agriculture University, Chengdu 611130, China.
| | - Xiao Ma
- Grassland Science Department, Sichuan Agriculture University, Chengdu 611130, China.
| | - Linkai Huang
- Grassland Science Department, Sichuan Agriculture University, Chengdu 611130, China.
| | - Xinquan Zhang
- Grassland Science Department, Sichuan Agriculture University, Chengdu 611130, China.
| |
Collapse
|
20
|
Desgarennes D, Garrido E, Torres-Gomez MJ, Peña-Cabriales JJ, Partida-Martinez LP. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species. FEMS Microbiol Ecol 2014; 90:844-57. [PMID: 25314594 DOI: 10.1111/1574-6941.12438] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 01/04/2023] Open
Abstract
Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta.
Collapse
Affiliation(s)
- Damaris Desgarennes
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados - Irapuato, Irapuato, México
| | | | | | | | | |
Collapse
|
21
|
Khan AL, Waqas M, Kang SM, Al-Harrasi A, Hussain J, Al-Rawahi A, Al-Khiziri S, Ullah I, Ali L, Jung HY, Lee IJ. Bacterial endophyte Sphingomonas sp. LK11 produces gibberellins and IAA and promotes tomato plant growth. J Microbiol 2014; 52:689-95. [PMID: 24994010 DOI: 10.1007/s12275-014-4002-7] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/27/2022]
Abstract
Plant growth promoting endophytic bacteria have been identified as potential growth regulators of crops. Endophytic bacterium, Sphingomonas sp. LK11, was isolated from the leaves of Tephrosia apollinea. The pure culture of Sphingomonas sp. LK11 was subjected to advance chromatographic and spectroscopic techniques to extract and isolate gibberellins (GAs). Deuterated standards of [17, 17-(2)H2]-GA4, [17, 17-(2)H2]-GA9 and [17, 17-(2)H2]-GA20 were used to quantify the bacterial GAs. The analysis of the culture broth of Sphingomonas sp. LK11 revealed the existence of physiologically active gibberellins (GA4: 2.97 ± 0.11 ng/ml) and inactive GA9 (0.98 ± 0.15 ng/ml) and GA20 (2.41 ± 0.23). The endophyte also produced indole acetic acid (11.23 ± 0.93 μM/ml). Tomato plants inoculated with endophytic Sphingomonas sp. LK11 showed significantly increased growth attributes (shoot length, chlorophyll contents, shoot, and root dry weights) compared to the control. This indicated that such phyto-hormones-producing strains could help in increasing crop growth.
Collapse
Affiliation(s)
- Abdul Latif Khan
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|