Growth Promotion of Giant Duckweed Spirodela polyrhiza (Lemnaceae) by Ensifer sp. SP4 Through Enhancement of Nitrogen Metabolism and Photosynthesis.

Duckweeds (Lemnaceae) are representative producers in fresh aquatic ecosystems and also yield sustainable biomass for animal feeds, human foods, and biofuels, and contribute toward effective wastewater treatment; thus, enhancing duckweed productivity is a critical challenge. Plant-growth-promoting bacteria (PGPB) can improve the productivity of terrestrial plants; however, duckweed-PGPB interactions remain unclear and no previous study has investigated the molecular mechanisms underlying duckweed-PGPB interaction. Herein, a PGPB, Ensifer sp. strain SP4, was newly isolated from giant duckweed (Spirodela polyrhiza), and the interactions between S. polyrhiza and SP4 were investigated through physiological, biochemical, and metabolomic analyses. In S. polyrhiza and SP4 coculture, SP4 increased the nitrogen (N), chlorophyll, and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) contents and the photosynthesis rate of S. polyrhiza by 2.5-, 2.5-, 2.7-, and 2.4-fold, respectively. Elevated photosynthesis increased the relative growth rate and biomass productivity of S. polyrhiza by 1.5- and 2.7-fold, respectively. Strain SP4 significantly altered the metabolomic profile of S. polyrhiza, especially its amino acid profile. N stable isotope analysis revealed that organic N compounds were transferred from SP4 to S. polyrhiza. These N compounds, particularly glutamic acid, possibly triggered the increase in photosynthetic and growth activities. Accordingly, we propose a new model for the molecular mechanism underlying S. polyrhiza growth promotion by its associated bacteria Ensifer sp. SP4, which occurs through enhanced N compound metabolism and photosynthesis. Our findings show that Ensifer sp. SP4 is a promising PGPB for increasing biomass yield, wastewater purification activity, and CO2 capture of S. polyrhiza.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A two-component monooxygenase for continuous denitration and dechlorination of chlorinated 4-nitrophenol in Ensifer sp. strain 22-1.

The environmental fates of chlorinated 4-nitrophenols, 2,6-dichloro-4-nitrophenol (2,6-DCNP) and 2-chloro-4-nitrophenol (2C4NP), mediated via microbial catabolism have attracted great attention due to their high toxicity and persistence in the environment. In this study, a strain of Ensifer sp. 22-1 that was capable of degrading both 2,6-DCNP and 2C4NP was isolated from a halogenated aromatic-contaminated soil sample. A gene cluster cnpBADCERM was predicted to be involved in the catabolism of 2,6-DCNP and 2C4NP based on genome sequence analysis. A two-component monooxygenase CnpAB, composed of an oxygenase component (CnpA) and a reductase component (CnpB), was confirmed to catalyze the continuous denitration and dechlorination of 2,6-DCNP and 2C4NP to 6-chlorohydroxyquinol (6-CHQ) and hydroxyquinol (HQ), respectively. Knockout of cnpA resulted in the complete loss of the capacity for strain 22-1 to degrade 2,6-DCNP and 2C4NP. Homologous modeling and docking showed that Val155~Ala159, Phe206~Pro209 and Phe446~Arg461 of CnpA participated in the formation of the FAD-binding pocket, and Arg101, Val155 and Asn447 formed hydrogen bonds with 2,6-DCNP/2C4NP in the substrate-binding pocket. This work characterized a new two-component monooxygenase for 2,6-DCNP and 2C4NP, and enriched our understanding of the degradation mechanism of chlorinated nitrophenols (CNPs) by microorganisms.

The type 3 effector NopL of Sinorhizobium sp. strain NGR234 is a mitogen-activated protein kinase substrate.

Pathogenic bacteria utilize type 3 secretion systems to inject type 3 effectors (T3Es) into host cells, thereby subverting host defense reactions. Similarly, T3Es of symbiotic nitrogen-fixing rhizobia can affect nodule formation on roots of legumes. Previous work showed that NopL (nodulation outer protein L) of Sinorhizobium(Ensifer) sp. strain NGR234 is multiply phosphorylated in eukaryotic cells and that this T3E suppresses responses mediated by mitogen-activated protein (MAP) kinase signaling in yeast (mating pheromone signaling) and plant cells (expression of pathogenesis-related defense proteins). Here, we show that NopL is a MAP kinase substrate. Microscopic observations of fluorescent fusion proteins and bimolecular fluorescence complementation analysis in onion cells indicated that NopL is targeted to the nucleus and forms a complex with SIPK (salicylic acid-induced protein kinase), a MAP kinase of tobacco. In vitro experiments demonstrated that NopL is phosphorylatyed by SIPK. At least nine distinct spots were observed after two-dimensional gel electrophoresis, indicating that NopL can be hyperphosphorylated by MAP kinases. Senescence symptoms in nodules of beans (Phaseolus vulgaris cv. Tendergreen) were analyzed to determine the symbiotic effector activity of different NopL variants with serine to alanine substitutions at identified and predicted phosphorylation sites (serine-proline motif). NopL variants with six or eight serine to alanine substitutions were partially active, whereas NopL forms with 10 or 12 substituted serine residues were inactive. In conclusion, our findings provide evidence that NopL interacts with MAP kinases and reveals the importance of serine-proline motifs for effector activity during symbiosis.

Microcystin-degrading bacteria reduce bioaccumulation in Fragaria vulgaris and enhance fruit yield and quality.

In Morocco, red fruit production has thrived, primarily utilizing hydroponic methods to control crops, increase fruit yield and quality, and avoid soil-related problems. However, the irrigation of these expansive hydroponic farms relies heavily on water sourced from dams, many of which are contaminated with Microcystins (MCs). To address this contamination issue, ongoing research is focused on discovering effective and cost-efficient biological solutions for eliminating MCs. In this study, we isolate and identify bacterial strains capable of degrading MCs, evaluate the rate of degradation, and investigate how soil inoculated with these bacteria affects the accumulation of MCs in plant tissue. The partial 16S rRNA analyses of three bacterial sequences were conducted, identifying them through NCBI as follows: Ensifer sp. (B1) isolated from soil, Shinella sp. (B2) from a cyanobacterial bloom, and Stutzerimonas sp. (B3) from water. These bacteria exhibited the ability to degrade MCs, with approximately 34.75%, 73.75%, and 30.1% of the initial concentration (20 µg/L) being removed after a 6-day period for B1, B2, and B3, respectively. Moreover, strawberry plants were cultivated hydroponically in a greenhouse for a duration of 90 days. These plants were subjected to extracts of cyanobacteria containing 10 and 20 µg/L of Microcystins (MC), as well as water from an artificial lake contaminated with MC, both with and without the presence of isolated bacterial strains. Among these strains, Shinella sp. exhibited the highest efficacy in mitigating MC accumulation. Specifically, it resulted in a reduction of approximately 1.159 µg of MC per kilogram of root dry weight, leading to complete elimination in the leaves and fruits. The findings also indicated that the inoculation of perlite with the three MC-degrading bacterial strains significantly enhanced growth, photosynthetic pigments, yield, biochemical constituents, and quality attributes of strawberries (p ≤ 0.05). These promising outcomes suggest the potential of this approach for addressing the adverse impacts of crops irrigated with MC-contaminated water in future agricultural practices.

Genomic characterization of eight Ensifer strains isolated from pristine caves and a whole genome phylogeny of Ensifer (Sinorhizobium).

A total of eight Ensifer sp. strains were isolated from two pristine cave environments. One strain was isolated from a cave water pool located in the Wind Cave National Park, South Dakota, USA and the remaining seven strains were isolated from Lechuguilla Cave of Carlsbad Caverns National Park, New Mexico, USA. Whole genome sequencing and comparative genomic analyses of the eight isolates compared to various type strains from the genera Ensifer and Sinorhizobium demonstrates that although members in these genera can be phylogenetically separated into two distinct clades, the percentage of conserved proteins (POCP) between various type strains from Ensifer and Sinorhizobium are consistently higher than 50%, providing strong genomic evidence to support the classification of the genera Ensifer and Sinorhizobium into a single genus.