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The Growth of Vallisneria natans and Its Epiphytic Biofilm in Simulated Nutrient-Rich Flowing Water. WATER 2022. [DOI: 10.3390/w14142236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This paper investigates the effects of water flow on the growth and physiological indicators of the submerged macrophyte, Vallisneria natans, and the bacteria and algae community composition on its epiphytic biofilm-covered leaves. The authors set up a simulated flowing water laboratory experiment testing high nitrogen (N) and phosphorus (P) concentrations. Total chlorophyll and dissolved oxygen (DO) was significantly enhanced, and turbidity was reduced, thereby accelerating the growth of V. natans. These experiments were compared to another set of observations on a static group. The accumulation of malonaldehyde (MDA) in the dynamic groups was significantly higher than that in the static group. As an antioxidant stress response, the total superoxide dismutase (T-SOD) was also induced in plants exposed to nutrient-rich flowing water. The results of 16S rRNA high-throughput sequencing analyses showed that the water flow increased the bacteria community diversity of biofilm-producing bacteria with N and P removing bacteria, carbon cycle bacteria, and plant growth-promoting rhizobacteria on the epiphytic biofilm. This research determined that water flow alleviates the adverse effects of eutrophication when V. natans grows in water containing high N and P concentrations. Water flow also inhibits the growth of cyanobacteria (also referred to as blue-green algae) in epiphytic biofilm. The ecological factor of water flow, such as water disturbance and aeration measures, could alleviate the adverse effect of eutrophic water by providing a new way to restore submerged macrophytes, such as V. natans, in eutrophic water.
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Characterization and assessment of two biocontrol bacteria against Pseudomonas syringae wilt in Solanum lycopersicum and its genetic responses. Microbiol Res 2017; 206:43-49. [PMID: 29146259 DOI: 10.1016/j.micres.2017.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 11/22/2022]
Abstract
Pseudomonas and Bacillus species are attractive due to their potential bio-control application against plant bacterial pathogens. Pseudomonas aeruginosa strain D4 and Bacillus stratosphericus strain FW3 were isolated from mine tailings in South Korea. In these potent bacterial strains, we observed improved antagonistic activity against Pseudomonas syringae DC3000. These strains produced biocatalysts for plant growth promotion, and in vivo examination of Solanum lycopersicum included analysis of disease severity, ion leakage, chlorophyll content, and H2O2 detection. In addition, regulation of the defense genes pathogen-related protein 1a (PR1a) and phenylalanine ammonia lyase (PAL) was compared with treated plants and untreated control plants. The results suggest that these two bacterial strains provide protection against plant pathogens via direct and indirect modes of action and could be used as a bio-control agent.
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Draft Genome Sequence of a Diazotrophic, Plant Growth-Promoting Rhizobacterium of the Pseudomonas syringae Complex. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01023-16. [PMID: 27660794 PMCID: PMC5034145 DOI: 10.1128/genomea.01023-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genome sequence of Pseudomonas syringae GR12-2, a nitrogen-fixing, plant growth–promoting bacterium, isolated from the rhizosphere of an Arctic grass. The 6.6-Mbp genome contains 5,676 protein-coding genes, including a nitrogen-fixation island similar to that in P. stutzeri.
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Herrera Paredes S, Lebeis SL. Giving back to the community: microbial mechanisms of plant–soil interactions. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12684] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sur Herrera Paredes
- Department of Biology Howard Hughes Medical Institute, Curriculum in Bioinformatics and Computational Biology University of North Carolina Chapel Hill North Carolina 27599‐3280 USA
| | - Sarah L. Lebeis
- Department of Microbiology University of Tennessee Knoxville Tennessee 37996‐0845 USA
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Sloan SS, Lebeis SL. Exercising influence: distinct biotic interactions shape root microbiomes. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:32-36. [PMID: 26116973 DOI: 10.1016/j.pbi.2015.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 06/04/2023]
Abstract
Root microbiomes are formed from diverse microbial soil settings with extraordinary consistency, suggesting both defined mechanisms of assembly and specific microbial activity. Recent improvements in sequencing technologies, data analysis techniques, and study design, allow definition of the microbiota within these intimate and important relationships with increasing accuracy. Comparing datasets provides powerful insights into the overlap of plant microbiomes, as well as the impacts of surrounding plants and microbes on root microbiomes and long-term soil conditioning. Here we address how recent studies tease apart the impact of various biotic interactions, including: plant-plant, plant-microbe, and microbe-microbe on root microbiome composition.
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Affiliation(s)
- Sarah Stuart Sloan
- Department of Microbiology, University of Tennessee, Knoxville, United States
| | - Sarah L Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, United States.
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Lebeis SL. The potential for give and take in plant-microbiome relationships. FRONTIERS IN PLANT SCIENCE 2014; 5:287. [PMID: 24999348 PMCID: PMC4064451 DOI: 10.3389/fpls.2014.00287] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/02/2014] [Indexed: 05/18/2023]
Abstract
Mutualistic microbes present in plant-associate microbial communities provide a variety of benefits for their host, including reciprocal exchange of nutrients and/or protection from biotic and abiotic environmental stresses. Plant microbiomes have remarkably robust composition in comparison to the complex and dynamic microbial environments from which they form, suggesting finely tuned discrimination by the plant host. Here the intersection between the plant immune system and microbiomes will be explored, both as a possible means of shaping community membership and as a consequence elicited by certain colonizing microbes. Notably, the advent of massive parallel sequencing technologies allows the investigation of these beneficial microbial functions within whole community settings, so we can now ask how engagement of the immune response influences subsequent microbial interactions. Thus, we are currently poised for future work defining how the plant immune system impacts microbiomes and consequently host health, allowing us to better understand the potential of plant productivity optimization within complex microbial surroundings.
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Affiliation(s)
- Sarah L. Lebeis
- *Correspondence: Sarah L. Lebeis, Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA e-mail:
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Walker V, Bruto M, Bellvert F, Bally R, Muller D, Prigent-Combaret C, Moënne-Loccoz Y, Comte G. Unexpected phytostimulatory behavior for Escherichia coli and Agrobacterium tumefaciens model strains. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:495-502. [PMID: 23360460 DOI: 10.1094/mpmi-12-12-0298-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plant-beneficial effects of bacteria are often underestimated, especially for well-studied strains associated with pathogenicity or originating from other environments. We assessed the impact of seed inoculation with the emblematic bacterial models Agrobacterium tumefaciens C58 (plasmid-cured) or Escherichia coli K-12 on maize seedlings in nonsterile soil. Compared with the noninoculated control, root biomass (with A. tumefaciens or E. coli) and shoot biomass (with A. tumefaciens) were enhanced at 10 days for 'PR37Y15' but not 'DK315', as found with the phytostimulator Azospirillum brasilense UAP-154 (positive control). In roots as well as in shoots, Agrobacterium tumefaciens and E. coli triggered similar (in PR37Y15) or different (in DK315) changes in the high-performance liquid chromatography profiles of secondary metabolites (especially benzoxazinoids), distinct from those of Azospirillum brasilense UAP-154. Genome sequence analysis revealed homologs of nitrite reductase genes nirK and nirBD and siderophore synthesis genes for Agrobacterium tumefaciens, as well as homologs of nitrite reductase genes nirBD and phosphatase genes phoA and appA in E. coli, whose contribution to phytostimulation will require experimental assessment. In conclusion, the two emblematic bacterial models had a systemic impact on maize secondary metabolism and resulted in unexpected phytostimulation of seedlings in the Azospirillum sp.-responsive cultivar.
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Butler MI, Stockwell PA, Black MA, Day RC, Lamont IL, Poulter RTM. Pseudomonas syringae pv. actinidiae from recent outbreaks of kiwifruit bacterial canker belong to different clones that originated in China. PLoS One 2013; 8:e57464. [PMID: 23555547 PMCID: PMC3583860 DOI: 10.1371/journal.pone.0057464] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 01/21/2013] [Indexed: 12/23/2022] Open
Abstract
A recently emerged plant disease, bacterial canker of kiwifruit (Actinidia deliciosa and A. chinensis), is caused by Pseudomonas syringae pv. actinidiae (PSA). The disease was first reported in China and Japan in the 1980s. A severe outbreak of PSA began in Italy in 2008 and has spread to other European countries. PSA was found in both New Zealand and Chile in 2010. To study the evolution of the pathogen and analyse the transmission of PSA between countries, genomes of strains from China and Japan (where the genus Actinidia is endemic), Italy, New Zealand and Chile were sequenced. The genomes of PSA strains are very similar. However, all strains from New Zealand share several single nucleotide polymorphisms (SNPs) that distinguish them from all other PSA strains. Similarly, all the PSA strains from the 2008 Italian outbreak form a distinct clonal group and those from Chile form a third group. In addition to the rare SNPs present in the core genomes, there is abundant genetic diversity in a genomic island that is part of the accessory genome. The island from several Chinese strains is almost identical to the island present in the New Zealand strains. The island from a different Chinese strain is identical to the island present in the strains from the recent Italian outbreak. The Chilean strains of PSA carry a third variant of this island. These genomic islands are integrative conjugative elements (ICEs). Sequencing of these ICEs provides evidence of three recent horizontal transmissions of ICE from other strains of Pseudomonas syringae to PSA. The analyses of the core genome SNPs and the ICEs, combined with disease history, all support the hypothesis of an independent Chinese origin for both the Italian and the New Zealand outbreaks and suggest the Chilean strains also originate from China.
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Affiliation(s)
- Margi I Butler
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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Guo Q, Li S, Lu X, Li B, Stummer B, Dong W, Ma P. phoRsequences as a phylogenetic marker to differentiate the species in theBacillus subtilisgroup. Can J Microbiol 2012; 58:1295-305. [DOI: 10.1139/w2012-106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillus subtilis and its closely related species are indistinguishable from one another by morphological characteristics and 16S rDNA sequences. In this study, the partial phoR sequence was tested to determine the phylogenetic relationship of species in the B. subtilis group. Degenerate primers were developed according to the relatively conserved nucleotide sequences of phoR and the linked gene phoP in the B. subtilis group. The primers amplified a 1100 bp phoR fragment from strains representative of 6 species in the B. subtilis group. Based on the sequenced fragments, 26 type strains comprising these 6 species were clearly distinguished. At the intraspecies level, the phoR sequence similarities were 90%–100%, but at the interspecies level, the phoR sequence similarities were 32.8%–75%. Compared with the gyrB sequence, the phoR sequences showed a larger divergence especially at the interspecies levels. Therefore, the phoR sequence may be an efficient alternative marker for phylogenetic and taxonomic analysis of species in the B. subtilis group. Twenty-three Bacillus undomesticated isolates were tested for identification and phylogenetic analysis based on the phoR and gyrB sequences. The 23 isolates could be clearly delineated into 4 distinct groups, 10 as B. subtilis, 3 as B. mojavensis, 2 as B. atrophaeus, and 8 as B. amyloliquefaciens.
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Affiliation(s)
- Qinggang Guo
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Shezeng Li
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Xiuyun Lu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Baoqing Li
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Belinda Stummer
- CSIRO Sustainable Agriculture National Research Flagship/CSIRO Ecosystem Sciences, PMB2, Glen Osmond, SA, 5064, Australia
| | - Weixin Dong
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Ping Ma
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
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Ghequire MGK, Li W, Proost P, Loris R, De Mot R. Plant lectin-like antibacterial proteins from phytopathogens Pseudomonas syringae and Xanthomonas citri. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:373-380. [PMID: 23760822 DOI: 10.1111/j.1758-2229.2012.00331.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The genomes of Pseudomonas syringae pv. syringae 642 and Xanthomonas citri pv. malvacearum LMG 761 each carry a putative homologue of the plant lectin-like bacteriocin (llpA) genes previously identified in the rhizosphere isolate Pseudomonas putida BW11M1 and the biocontrol strain Pseudomonas fluorescens Pf-5. The respective purified recombinant proteins, LlpAPss642 and LlpAXcm761 , display genus-specific antibacterial activity across species boundaries. The inhibitory spectrum of the P. syringae bacteriocin overlaps partially with those of the P. putida and P. fluorescens LlpAs. Notably, Xanthomonas axonopodis pv. citri str. 306 secretes a protein identical to LlpAXcm761 . The functional characterization of LlpA proteins from two different phytopathogenic γ-proteobacterial species expands the lectin-like bacteriocin family beyond the Pseudomonas genus and suggests its involvement in competition among closely related plant-associated bacteria with different lifestyles.
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Affiliation(s)
- Maarten G K Ghequire
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium Laboratory of Molecular Immunology, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium Molecular Recognition Unit, Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, 1050 Brussel, Belgium
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Chen M, Li X, Yang Q, Chi X, Pan L, Chen N, Yang Z, Wang T, Wang M, Yu S. Soil eukaryotic microorganism succession as affected by continuous cropping of peanut--pathogenic and beneficial fungi were selected. PLoS One 2012; 7:e40659. [PMID: 22808226 PMCID: PMC3393692 DOI: 10.1371/journal.pone.0040659] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 06/11/2012] [Indexed: 11/18/2022] Open
Abstract
Peanut is an important oil crop worldwide and shows considerable adaptability but growth and yield are negatively affected by continuous cropping. Soil micro-organisms are efficient bio-indicators of soil quality and plant health and are critical to the sustainability of soil-based ecosystem function and to successful plant growth. In this study, 18S rRNA gene clone library analyses were employed to study the succession progress of soil eukaryotic micro-organisms under continuous peanut cultivation. Eight libraries were constructed for peanut over three continuous cropping cycles and its representative growth stages. Cluster analyses indicated that soil micro-eukaryotic assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. Six eukaryotic groups were found and fungi predominated in all libraries. The fungal populations showed significant dynamic change and overall diversity increased over time under continuous peanut cropping. The abundance and/or diversity of clones affiliated with Eurotiales, Hypocreales, Glomerales, Orbiliales, Mucorales and Tremellales showed an increasing trend with continuous cropping but clones affiliated with Agaricales, Cantharellales, Pezizales and Pyxidiophorales decreased in abundance and/or diversity over time. The current data, along with data from previous studies, demonstrated that the soil microbial community was affected by continuous cropping, in particular, the pathogenic and beneficial fungi that were positively selected over time, which is commonplace in agro-ecosystems. The trend towards an increase in fungal pathogens and simplification of the beneficial fungal community could be important factors contributing to the decline in peanut growth and yield over many years of continuous cropping.
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Affiliation(s)
- Mingna Chen
- Shandong Peanut Research Institute, Qingdao, China
| | - Xiao Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Qingli Yang
- Shandong Peanut Research Institute, Qingdao, China
| | - Xiaoyuan Chi
- Shandong Peanut Research Institute, Qingdao, China
| | - Lijuan Pan
- Shandong Peanut Research Institute, Qingdao, China
| | - Na Chen
- Shandong Peanut Research Institute, Qingdao, China
| | - Zhen Yang
- Shandong Peanut Research Institute, Qingdao, China
| | - Tong Wang
- Shandong Peanut Research Institute, Qingdao, China
| | - Mian Wang
- Shandong Peanut Research Institute, Qingdao, China
| | - Shanlin Yu
- Shandong Peanut Research Institute, Qingdao, China
- * E-mail:
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