Genome Sequence of Pseudomonas sp. Strain LAP_36, A Rhizosphere Bacterium Isolated from King George Island, Antarctica

Pseudomonas sp. strain LAP_36 was isolated from rhizosphere soil from Deschampsia antarctica on King George Island, South Shetland Islands, Antarctica. Here, we report on its draft genome sequence, which consists of 8,794,771 bp with 60.0% GC content and 8,011 protein-coding genes.

Salt Tolerance Mechanism of the Rhizosphere Bacterium JZ-GX1 and Its Effects on Tomato Seed Germination and Seedling Growth

Salinity is one of the strongest abiotic factors in nature and has harmful effects on plants and microorganisms. In recent years, the degree of soil salinization has become an increasingly serious problem, and the use of plant growth-promoting rhizobacteria has become an option to improve the stress resistance of plants. In the present study, the salt tolerance mechanism of the rhizosphere bacterium Rahnella aquatilis JZ-GX1 was investigated through scanning electron microscopy observations and analysis of growth characteristics, compatible solutes, ion distribution and gene expression. In addition, the effect of JZ-GX1 on plant germination and seedling growth was preliminarily assessed through germination experiments. R. aquatilis JZ-GX1 was tolerant to 0–9% NaCl and grew well at 3%. Strain JZ-GX1 promotes salt tolerance by stimulating the production of exopolysaccharides, and can secrete 60.6983 mg/L of exopolysaccharides under the high salt concentration of 9%. Furthermore, the accumulation of the compatible solute trehalose in cells as the NaCl concentration increased was shown to be the primary mechanism of resistance to high salt concentrations in JZ-GX1. Strain JZ-GX1 could still produce indole-3-acetic acid (IAA) and siderophores and dissolve inorganic phosphorus under salt stress, characteristics that promote the ability of plants to resist salt stress. When the salt concentration was 100 mmol/L, strain JZ-GX1 significantly improved the germination rate, germination potential, fresh weight, primary root length and stem length of tomato seeds by 10.52, 125.56, 50.00, 218.18, and 144.64%, respectively. Therefore, R. aquatilis JZ-GX1 is a moderately halophilic bacterium with good growth-promoting function that has potential for future development as a microbial agent and use in saline-alkali land resources.

Rhizosphere Bacterium Rhodococcus sp. P1Y Metabolizes Abscisic Acid to Form Dehydrovomifoliol

The phytohormone abscisic acid (ABA) plays an important role in plant growth and in response to abiotic stress factors. At the same time, its accumulation in soil can negatively affect seed germination, inhibit root growth and increase plant sensitivity to pathogens. ABA is an inert compound resistant to spontaneous hydrolysis and its biological transformation is scarcely understood. Recently, the strain Rhodococcus sp. P1Y was described as a rhizosphere bacterium assimilating ABA as a sole carbon source in batch culture and affecting ABA concentrations in plant roots. In this work, the intermediate product of ABA decomposition by this bacterium was isolated and purified by preparative HPLC techniques. Proof that this compound belongs to ABA derivatives was carried out by measuring the molar radioactivity of the conversion products of this phytohormone labeled with tritium. The chemical structure of this compound was determined by instrumental techniques including high-resolution mass spectrometry, NMR spectrometry, FTIR and UV spectroscopies. As a result, the metabolite was identified as (4RS)-4-hydroxy-3,5,5-trimethyl-4-[(E)-3-oxobut-1-enyl]cyclohex-2-en-1-one (dehydrovomifoliol). Based on the data obtained, it was concluded that the pathway of bacterial degradation and assimilation of ABA begins with a gradual shortening of the acyl part of the molecule.

Cyclic-di-GMP Regulates the Quorum-Sensing System and Biocontrol Activity of Pseudomonas fluorescens 2P24 through the RsmA and RsmE Proteins

ABSTRACT Pseudomonas fluorescens 2P24 is a rhizosphere bacterium that protects many crop plants against soilborne diseases caused by phytopathogens. The PcoI/PcoR quorum-sensing (QS) system and polyketide antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG) are particularly relevant to the strain’s biocontrol potential. In this study, we investigated the effects of c-di-GMP on the biocontrol activity of strain 2P24. The expression of the Escherichia coli diguanylate cyclase (YedQ) and phosphodiesterase (YhjH) in P. fluorescens 2P24 significantly increased and decreased the cellular concentration of c-di-GMP, respectively. The production of the QS signals N-acyl homoserine lactones (AHLs) and 2,4-DAPG was negatively regulated by c-di-GMP in 2P24. The regulatory proteins RsmA and RsmE were positively regulated by c-di-GMP. Genomic analysis revealed that 2P24 has 23 predicted proteins that contain c-di-GMP-synthesizing or -degrading domains. Among these proteins, C0J56_12915, C0J56_13325, and C0J56_27925 contributed to the production of c-di-GMP and were also involved in the regulation of the QS signal and antibiotic 2,4-DAPG production in P. fluorescens. Overexpression of C0J56_12915, C0J56_13325, and C0J56_27925 in 2P24 impaired its root colonization and biocontrol activities. Taken together, these results demonstrated that c-di-GMP played an important role in fine-tuning the biocontrol traits of P. fluorescens. IMPORTANCE In various bacteria, the bacterial second messenger c-di-GMP influences a wide range of cellular processes. However, the function of c-di-GMP on biocontrol traits in the plant-beneficial rhizobacteria remains largely unclear. The present work shows that the QS system and polyketide antibiotic 2,4-DAPG production are regulated by c-di-GMP through RsmA and RsmE proteins in P. fluorescens 2P24. The diguanylate cyclases (DGCs) C0J56_12915, C0J56_13325, and C0J56_27925 are especially involved in regulating the biocontrol traits of 2P24. Our work also demonstrated a connection between the Gac/Rsm cascade and the c-di-GMP signaling pathway in P. fluorescens.

Extracellular DNA and Outer Membrane Vesicles contribute to P. fluorescens SBW25 air-liquid interface biofilms.

<p>Outer membrane vesicles (OMVs) and extracellular DNA (eDNA) are important for biofilm formation for many bacteria. OMVs are a perfect transport system to deliver biofilm-related components including eDNA beyond the boundaries of cells, and eDNA itself is an important structural component of biofilms as well as enabling horizontal gene transfer and local adaptation. Both OMVs and eDNA are found in the biofilms produced by the opportunistic human pathogen P. aeruginosa and the plant pathogen P. syringae, but as yet, they have not been reported in the cellulose matrix-based biofilms produced by the related model rhizosphere bacterium Pseudomonas fluorescens SBW25.</p> <p>In this work we have gone back to re-assess the complexity of SBW25 biofilms by looking for evidence of OMVs and eDNA associated with biofilm–formation. OMVs were first imaged by SEM and LC-MC analysis used to identify 51 biofilm matrix-associated proteins of which 12 were also identified in biofilm OMVs. Interestingly, only 5 proteins were identified in both biofilm matrix and OMV samples, but not in planktonic OMVs, suggesting that these may be biofilm-specific components.  </p> <p>We also observed eDNA by CLSM in both the weak and poorly-attached Viscous Mass (VM) and robust and well-attached Wrinkly Spreader (WS) air-liquid (A-L) interface biofilms produced by wild-type SBW25 and the Wrinkly Spreader mutant. The eDNA fraction could be precipitated from biofilm cell-free supernatant samples which demonstrated that WS biofilms had two-fold–higher levels than VM biofilms. DNAse treatment effected the development of both types of biofilm and reduced the strength and attachment levels when added to mature VM and WS biofilms. Testing with exogenous DNA suggests that high molecular weight (HMW) DNA is involved in both strength and attachment, perhaps by surface conditioning and interactions with the primary cellulose matrix common to both biofilms. HMW eDNA could be isolated directly from biofilm supernatants whereas two different HMW size fractions could be isolated from OMVs, presumably, from the outer OMV surface because DNAse treatment led to a substantially reduced DNA signal. This suggest that eDNA persistence and degradation in SBW25 biofilms is complex and eDNA fractions may play different roles in biofilm development, protection and adaptation.</p>

Pleiotropic Effects of RsmA and RsmE Proteins in Pseudomonas Fluorescens 2P24

Background: Pseudomonas fluorescens 2P24 is a rhizosphere bacterium that produces 2,4-diacetyphloroglucinol (2,4-DAPG) as the decisive secondary metabolite to suppress soilborne plant diseases. The biosynthesis of 2,4-DAPG is strictly regulated by the RsmA family proteins RsmA and RsmE. However, mutation of both of rsmA and rsmE genes results in reduced bacterial growth.Results: In this study, we showed that overproduction of 2,4-DAPG in the rsmA rsmE double mutant influenced the growth of strain 2P24. This delay of growth could be partially reversal when the phlD gene was deleted or overexpression of the phlG gene encoding the 2,4-DAPG hydrolase in the rsmA rsmE double mutant. RNA-seq analysis of the rsmA rsmE double mutant revealed that a substantial portion of the P. fluorescens genome was regulated by RsmA family proteins. These genes are involved in the regulation of 2,4-DAPG production, cell motility, carbon metabolism, and type six secretion system.Conclusions: These results suggest that RsmA and RsmE are the important regulators of genes involved in the plant-associated strain 2P24 ecologic fitness and operate a sophisticated mechanism for fine-tuning the concentration of 2,4-DAPG in the cells.

Climate change alters beneficial crop-microbe-invertebrate interactions

Increasing levels of CO2 and tropospheric ozone (O3) due to climate change are contributing to reduced plant health and unstable crop yield production1. The inoculation of plant roots with beneficial fungi or bacteria can increase plant health2. However, this is often studied under very controlled conditions and it is unknown how climate change or interactions with other species can alter the resulting benefits. Here we show that the rhizosphere bacterium Acidovorax radicis N35 can increase plant growth and reduce insect growth – with increased impact in a high-stress elevated O3 environment, but reduced impact under elevated CO2. In a fully-factorial climate chamber experiment we disentangled the impacts of climate factors (elevated CO2 and elevated O3) and biotic interactions (plant cultivar, sap-feeding insects and earthworms) on cereal growth and insect suppression mediated by A. radicis N35. Earthworms promoted plant aboveground growth, whereas A. radicis N35 promoted root growth, and overall plant growth was higher when both species were present. However, earthworms also promoted insect growth and therefore increased plant damage through herbivory. While A. radicis N35 inoculation was able to mitigate these negative effects to some extent under an ambient environment this was lost under climate change conditions. Our results show that knowledge-based solutions for sustainable agriculture should include biotic interactions and must be tested across variable climate change scenarios in order to build resilient cropping systems.

Inhibition of Tomato Early Blight Disease by Culture Extracts of a Streptomyces puniceus Isolate from Mangrove Soil

This study investigates the potential of natural products derived from a mangrove rhizosphere bacterium in tomato early blight management. A Streptomyces puniceus strain L75 was isolated from the rhizosphere of Acanthus ilicifolius Linn in the Mai Po Reserve, Hong Kong. The crude ethyl acetate (EA) extract of L75 fermentation cultures has broad-spectrum antifungal bioactivities. L75 EA extract was significantly more effective in Alternaria solani growth inhibition at 25 μg/ml or lower compared with Mancozeb, with no observable negative impacts on tomato leaves or root development. Furthermore, L75 EA extract had significantly lower aquatic toxicity than Mancozeb at the same concentrations. L75 EA extract targets germ tube elongation of A. solani conidia, with a fungistatic mode of action. Liquid chromatography-quadrupole time-of-flight mass spectrometry analysis identified two possible antifungal compounds, Alteramide A and the Heat-Stable Antifungal Factor, which together contribute partially to the bioactivity of L75 EA extract. On detached tomato leaves, coinoculation of A. solani with L75 EA extract of 50, 25, or 5 μg/ml reduced diseased areas by ∼98, ∼90, and ∼48%, respectively, relative to the control after 5 days. This study demonstrates the potential of natural products from mangrove rhizosphere bacteria in agricultural applications.