Palm Rhizosphere Research Articles

Isolation of Actinobacteria from Date Palm Rhizosphere with Enzymatic, Antimicrobial, Antioxidant, and Protein Denaturation Inhibitory Activities

Arid ecosystems constitute a promising source of actinobacteria producing new bioactive molecules. This study aimed to explore different biological activities of actinomycetes isolated from the rhizosphere of Phoenix dactylifera L. in the Ghardaia region, Algeria. A total of 18 actinobacteria were isolated and studied for their enzymatic and antimicrobial activities. All isolates shared cellulase and catalase activity; most of them produced amylase (94%), esterase (84%), lecithinase and lipoproteins (78%), caseinase (94%), and gelatinase (72%). The isolates could coagulate (56%) or peptonize (28%) skim milk. Overall, 72% of the isolates exhibited significant antibacterial activity against at least one test bacteria, while 56% demonstrated antifungal activity against at least one test fungi. Based on enzyme production and antimicrobial activity, isolate SGI16 was selected for secondary metabolite extraction by ethyl acetate. The crude extract of SGI16 was analyzed using DPPH and BSA denaturation inhibition tests, revealing significant antioxidant power (IC50 = 7.24 ± 0.21 μg mL−1) and protein denaturation inhibitory capacity (IC50 = 492.41 ± 0.47 μg mL−1). Molecular identification based on 16S rDNA analysis showed that SGI16 belonged to the genus Streptomyces. The findings highlight that date palms’ rhizosphere actinobacteria are a valuable source of biomolecules of biotechnological interest.

Comparative High-Throughput Sequencing Analysis of the Bacterial Community Associated with the Rhizosphere of Date Palm (Phoenix dactyllifera L.) Irrigated with Treated Wastewater and Groundwater

Water scarcity is a major agricultural issue in most arid and semi-arid regions of the world. Alternative water supplies, such as the reuse of wastewater for agricultural irrigation, have been introduced. However, little is known about their impact on the soil and rhizosphere microbiomes that receive irrigation. Therefore, this work evaluates the impact of treated wastewater (TWW) irrigation on the soil and rhizosphere bacterial communities of date palms in Al Madinah, Saudi Arabia. In this study, metagenomic DNA from the rhizosphere of the date palm was sequenced using Illumina high-throughput sequencing. According to the observed OTUs, Chao1 richness estimations, and Shannon diversity values, soils from groundwater-irrigated date palms showed higher microbial diversity than did soils from TWW-irrigated date palms. A total of 569 OTUs were generated; most of them (97.3%) were assigned into 15 different phyla, whereas 2.7% were marked as unclassified. DNA sequence analysis of the WWT-irrigated rhizosphere showed that the most abundant phyla were Firmicutes (43.6%), Bacteroidetes (17.3%), Proteobacteria (15.2%), and Actinobacteria (14.6%), representing more than 90.7% of the total community, while the soil of the rhizosphere irrigated with GW was dominated by Actinobacteria (44.1%), Proteobacteria (23.4%), Firmicutes (15.5%), and Gemmatimonadetes (4.9%). The most frequently observed species in the two soils were also different. The dominant species in TWW-irrigated soil was Planococcus plakortidis, which is prevalent in saline and moderately saline habitats and can play an important ecological role. The GW-irrigated rhizosphere exhibited higher levels of biocontrol bacteria, particularly Nocardioides mesophilus. These results provide a comprehensive understanding and insights into the population dynamics and microbiome of date palm rhizosphere. The findings show that the irrigation water quality has a significant impact on the microbiome composition. Identifying the microbial diversity is the first step toward determining the best way to use TWW in irrigation.

The effect of type and combination of fertilizers on eukaryotic microbiome of date palm rhizosphere

The date palm (Phoenix dactylifera) is an important cultivated crop in arid areas. Here, we studied the effect of plant genotype and type of fertilizers on the eukaryotic community structures of the date palm rhizosphere. Samples were collected from one wild population, five cultivars from two farms, and a factorial fertilizer experiment (organic, chemical, and biofertilizer) in Qatar. The eukaryotic communities were sequenced using a next-generation sequencing method. A total of 2422 Operational Taxonomic Units (OTUs) were identified as belonging to 15 phyla, Chlorophyta, Streptophyta, Imbricatea, Chytridiomycota, Ascomycota, Olpidiomycota, being dominant. The wild-type date palms showed a low number of OTUs compared to cultivated date palms, potentially due to the strong influence of soil salinity and low moisture level. However, the wild-type date palm hosted the highest number of unique OTUs. PCA revealed that the eukaryotic microbiome of the wild date palms was separated from the cultivated date palms and that the eukaryotic microbial diversity varied between date palm cultivars in similar environments. Using the highest amounts of biofertilizer and chemical fertilizer decreased the species diversity within the samples. However, a high concentration of biofertilizer combined with a low concentration of chemical fertilizers enhanced the eukaryotic diversity within the samples. We conclude that cultivar type (biotic factor), type of fertilizer, and dosage (abiotic factor) play significant roles in determining the microbiome diversity of the rhizosphere. The wild date palm population could potentially host salt and drought-tolerating eukaryotes that should be further investigated for future development of biofertilizers suitable for drylands.

Isolation and identification of a new Bacillus glycinifermentans strain from date palm rhizosphere and its effect on barley seeds under heavy metal stress.

Soil contamination by heavy metals is one of the major problems that adversely decrease plant growth and biomass production. Inoculation with the plant growth-promoting rhizobacteria (PGPR) can attenuate the toxicity of heavy metals and enhancing the plant growth. In this study, we evaluated the potential of a novel extremotolerant strain (IS-2T) isolated from date palm rhizosphere to improve barley seedling growth under heavy metal stress. The species-level identification was carried out using morphological and biochemical methods combined with whole genome sequencing. The bacterial strain was then used in vitro for inoculating Hordeum vulgare L. exposed to three different Cr, Zn, and Ni concentrations (0.5, 1, and 2mM) in petri dishes and different morphological parameters were assessed. The strain was identified as Bacillus glycinifermentans species. This strain showed high tolerance to pH (6-11), salt stress (0.2-2M), and heavy metals. Indeed, the minimum inhibitory concentrations at which bacterium was unable to grow were 4mM for nickel, 3mM for zinc, more than 8mM for copper, and 40mM for chromium, respectively. It was observed that inoculation of Hordeum vulgare L. under metal stress conditions with Bacillus glycinifermentans IS-2T stain improved considerably the growth parameters. The capacity of the IS-2T strain to withstand a range of abiotic stresses and improve barley seedling development under lab conditions makes it a promising candidate for use as a PGPR in zinc, nickel, copper, and chromium bioremediation.

Pengaruh Sifat Tanah Terhadap Kejadian dan Keparahan Penyakit pada Kelapa Sawit Main Nursery

Soil properties, both physical, chemical and biological, have a direct impact on the growth and health of oil palm seedlings. Fertile soil means the incidence and severity of plant diseases can be minimized. For this reason, research is needed to examine the influence of soil properties on the incidence and severity of disease in oil palm seedlings in the main nursery phase. The aim is to determine soil properties, both physical and chemical, that influence the incidence and severity of main nursery oil palm diseases. Implementation stages include taking soil samples and observing sick plants. The soil sample taken was the rhizosphere of main nursery oil palm. Data analysis uses Microsoft Excel to describe disease incidence and soil physical and chemical properties. The research results showed that in main nursery-B (MN-B) the incidence of disease attacks had a higher percentage compared to main nursery-A (MN-A). Physical and chemical properties of soil (N-available, P-available, C-organic, CEC) influence the incidence of disease attacks. The high content of available N and available P increases attacks by plant pests, while the high content of organic C and CEC can suppress pest attacks.

FIRST MOLECULAR CHARACTERIZATION OF DITYLENCHUS FILIMUS ANDERSON, 1983 (NEMATODA ANGUINIDAE) BASED ON THE POPULATION FROM IRAN

During a survey on the biodiversity of plant-parasitic nematodes in Khuzestan province (southwest Iran), Ditylenchus filimus was discovered in the rhizosphere of date palm. The morphological and morphometric data were provided for the recovered species. The morphological characters of Iranian population are in agreement with the type population and other populations of this species. Molecular phylogenetic analyses of the species with representatives of the family Anguinidae were discussed using partial sequences of the small subunit, D2-D3 expansion segments of the large subunit, and internal transcribed spacer regions of ribosomal DNA (SSU, LSU D2-D3 and ITS rDNA) based on Bayesian inference (BI). To the best of our knowledge, this is the first report of molecular characterization of this species. Key Words: 18S rDNA, D2-D3 LSU rDNA, ITS rDNA, Ditylenchus, morphometric data, phylogeny

Evaluation of the Mycorrhizal Potential of Date Palm (Phoenix dactylifera L.) Rhizosphere Soils in the Figuig Oasis (Southeastern Morocco).

Date palm, an important crop in Morocco and many other arid regions around the world, faces significant challenges from wind, water shortages, and salinization, which contribute to vegetation loss and soil degradation in the harsh environmental conditions of oasis ecosystems with low soil fertility. Protecting and regenerating these degraded lands is crucial for sustainable agriculture and improving the dryland ecosystem. Arbuscular mycorrhizal fungi (AMF) comprise a vital element in this dynamic within the microflora of the soil rhizosphere. This study evaluated the potential in mycorrhizal soil and identified AMF in date palm rhizospheres in eight locations within the Figuig oasis (southeastern Morocco). This study found that Extension and Zenaga had more mycorrhizal propagules than other locations. Replanted maize (Zea mays L.) in these soils exhibited higher mycorrhization rates (91-93%) compared to that in other locations, with the Lamaiz site registering the lowest rate (39%). The phosphorus content was negatively correlated with the AMF spore frequency, intensity, and density, while a positive correlation was detected between the soil pH and the AMF spore frequency and density. The morphological identification of spores revealed Glomus as the predominant species, along with Acaulospora and Sclerocystis. This study represents an initial step toward the potential application of these fungi in environmental conservation and sustainable agriculture in arid regions.

Bacterial community structure and predicted function in the rhizosphere of wild and cultivated date palms: Effects of Fertilizers on Composition and Functionality

This study investigated bacterial diversity in date palm rhizosphere and assessed the influence of different fertilizers on diversity using metagenomics. A total of 6356 Operational Taxonomic Units (OTUs) and 1164425 sequences were analyzed across 27 samples. The findings revealed variations in microbial community phylogeny among similar cultivars from different farms, except for the Khalas cultivar, suggesting minor influence of genotype on microbial community structure. Wild date palms exhibited more unique OTUs, in contrast, cultivated date palms had a higher number of OTUs and diversity. Moreover, different fertilizer treatments had varying effects on bacterial diversity. For example, organic and bio-organic fertilizers positively influenced specific bacterial groups, including delta-proteobacteria, acidobacteria-Gp3, Anaerolinaea, and Clostridia. Conversely, combining high concentrations of chemical fertilizers with other types did not show significant effects. Classes such as Bacilli, Nitrospira, Deltaproteobacteria, Spartobacteria, and Thermomacrobia exhibited high relative abundances in treatments with high chemical fertilizer concentrations. Our analysis revealed potential pathways related to carbon, nitrogen, phosphorus, phenol, sulfur, and antimicrobial compounds. Interestingly, these pathways and functions varied across different date palm cultivars. Our findings suggest that date palm cultivars shape the rhizosphere by selectively influencing bacterial communities consistently across other locations. These modulated bacterial communities can potentially provide enhanced benefits to the host. Importantly, this study was the first to investigate the soil bacterial diversity of wild date palms, giving valuable insights into the microbial community associated with this specific context.

Study of Arbuscular Mycorrhizal Fungi population in the rhizosphere of oil palm planted on 4 different soil types in Central Kalimantan Indonesia

Arbuscular mycorrhizal fungi (AMF) are naturally found in the soil. The population of this fungus is influenced by environmental factors such as soil type. Different soil types have different characteristics and will affect the AMF population in the soil. Therefore, this study was carried out to determine the AMF population in the soil based on the number of spores in the rhizosphere of oil palm planted in 4 different soil types, namely Dystrudepts, Paleudults, Haplohumods, and Haplosaprists. Soil samples were taken from each soil type at 4 sample points. At each sample point, soil samples were taken from 5 adjacent oil palm trees. Rhizosphere soil samples were taken at 4 points inside the oil palm circle at a depth of up to 15 cm and 4 points from the outside and then composited to represent 1 sample point for inside and outside the circle. Extraction of AMF spores from soil samples was carried out by the wet sieving method. The results showed that the average number of AMF spores per 50 g of rhizosphere soil from inside and outside the oil palm circle were 66,7 and 53,5 spores for Dystrudepts, 115,5 and 91,5 spores for Paleudults, 27 and 71,8 spores for Haplohumods, and 83,3 and 55 spores for Haplosaprists respectively. In Dystrudepts, Paleudults, and Haplosaprists soil types, the number of spores in the rhizosphere of oil palm inside the circle was higher than outside. On the other hand, for Haplohumods soil types, the number of spores inside the circle was lower than outside the circle.

Exploration of indigenous arbuscular mycorrhizal fungi on Arenga pinnata Merr in post-mining land

Mining activities have a positive impact that can generate income for the state, but the activities also cause negative impacts in the form of soil damage, vegetation and animal losses to disrupt the ecosystems. Therefore, it is necessary to carry out a reclamation with revegetation using local plant species. PT Berau Coal has conducted revegetation using a local sugar palm plant (Arenga pinnata). The success of sugar palm plant growth in post-mining reclamation land is influenced by several factors, one of it is the symbiosis of the arbuscula mycorrhizal fungi (AMF) with the sugar palm planted by PT Berau Coal. The purpose of this study was to determine the diversity of indigenous spores in the arenga rhizosphere and root colonization of sugar palm plants. Identification of the AMF diversity was carried out by observing the soil taken from the palm rhizosphere with a depth of 0-20 cm and 20-40 cm. Isolation of spores using the wet pouring technique method with centrifuges and AMF spores were identified using the INVAM methods. The observation of AMF colonization on plant roots was carried out through the root staining technique with the Clapp modification method. The results showed that the AMF spores were found in 3 AMF genera at the observation site, namely genus Glomus (15 sp), Acaulospora (3 sp), and Gigaspora (1 sp). The highest spore abundance is genus Glomus sp at a soil depth of 0-20 cm. The AMF structures found colonizing the roots of sugar palm plants are hyphae, vesicles, and spores.

Contrasting genome patterns of two pseudomonas strains isolated from the date palm rhizosphere to assess survival in a hot arid environment.

The plant growth-promoting rhizobacteria (PGPRs) improve plant growth and fitness by multiple direct (nitrogen fixation and phosphate solubilization) and indirect (inducing systematic resistance against phytopathogens, soil nutrient stabilization, and maintenance) mechanisms. Nevertheless, the mechanisms by which PGPRs promote plant growth in hot and arid environments remain poorly recorded. In this study, a comparative genome analysis of two phosphate solubilizing bacteria, Pseudomonas atacamensis SM1 and Pseudomonas toyotomiensis SM2, isolated from the rhizosphere of date palm was performed. The abundance of genes conferring stress tolerance (chaperones, heat shock genes, and chemotaxis) and supporting plant growth (plant growth hormone, root colonization, nitrogen fixation, and phosphate solubilization) were compared among the two isolates. This study further evaluated their functions, metabolic pathways, and evolutionary relationship. Results show that both bacterial strains have gene clusters required for plant growth promotion (phosphate solubilization and root colonization), but it is more abundant in P. atacamensis SM1 than in P. toyotomiensis SM2. Genes involved in stress tolerance (mcp, rbs, wsp, and mot), heat shock, and chaperones (hslJ and hslR) were also more common in P. atacamensis SM1. These findings suggest that P. atacamensis SM1could have better adaptability to the hot and arid environment owing to a higher abundance of chaperone genes and heat shock proteins. It may promote plant growth owing to a higher load of root colonization and phosphate solubilization genes and warrants further in vitro study.

Investigation of Microbial Community Structure and Diversity in the Rhizosphere of Date Palm (Phoenix Dactylifera L.), Sukkari Cultivar

The rhizosphere microbial community of a plant plays a pivotal role in mediating plant and soil health. This study was conducted to unravel the rhizosphere microbial structure and community of Sukkari date palm trees. The soil collected from the rhizosphere was subjected to metagenomic analysis. The results revealed that most of the sequences (62%) were identified as bacteria: 48% were unknown bacteria, 5% were Actinobacteria, and 9% were Proteobacteria. Microorganisms belonging to eukaryotes were 25% of the microbial community, represented by 21% Streptophyta and 4% Ciliopora and 5% of the sequences were Archaea. These analyses were followed by functional enzyme analysis, which identified microbial metabolism in diverse environments related to nine carbohydrate and energy pathways; seven pathways were associated with degradation, and nine metabolic pathways were associated with amino acid metabolism. The comparison of community analysis with our previous study provided distinct differences even in the same plants with various cultivars.

Morphological characterization of Trichoderma spp. isolated from the oil palm rhizosphere in peat soils and its potential as a biological control for Ganoderma boninense in vitro

Trichoderma sp. is a saprophytic fungus found in various environments, one of which is in the rhizosphere of oil palm plants which can be used to control Ganoderma and increase the resistance of oil palm plants from stem rot disease. This study aimed to characterize the morphology of Trichoderma spp. origin of peat land in oil palm plantations in Kampar Regency and screening the potential in controlling Ganoderma sp. Trichoderma spp. from oil palm rhizosphere was collected from the smallholder oil palm plantations in Deli Makmur Village, Kampar, Indonesia. This research was conducted by several observations, such as the hypovirulence test; identification of the morphology of Trichoderma spp. fungus; growth and diameter test of Trichoderma spp. fungus; test of the inhibitory ability of Trichoderma spp. fungus against Ganoderma sp. LPTUNRI-Gan002 isolate; test for hyperparasitism of the fungus Trichoderma spp., which has high antagonistic power against Ganoderma sp. isolate. Six Trichoderma spp. isolates had morphological characteristics similar to two species, i.e., Trichoderma harzianum (LPTUNRI-Trc001, Trc004, Trc005, and Trc006 isolates) and Trichoderma asperellum (LPTUNRI-Trc002 and Trc003). LPTUNRI-Trc003 had the highest diameter (90 mm), growth rate (32.66 mm/day), and the highest ability to suppress Ganoderma sp. LPTUNRI-Gan002 (91.03%) compared to the other five isolates.

Applications of Arbuscular Mycorrhiza Fungi to Improve Growth of Oil Palm Seedlings and Disease Resistance Against Ganoderma sp.

Currently, basal stem rot disease incident in oil palm caused by the Ganoderma sp. increasing rapidly. Arbuscular mycorrhizal fungi (AMF) are one of the types of mycorrhizae that are useful for plants as they can increase plant growth and resistance to disease. Therefore, this study aimed to determine whether the application of AMF to oil palm seedlings was able to increase the growth and resistance of oil palm seedlings against Ganoderma sp. The study used a factorial treatment design (4x2) with 5 replications arranged according to a completely randomized block design. The first factor was the type of AMF, namely without AMF (m0), Glomus sp. (m1), Entrophospora sp. (m2), and a mixture of Glomus sp. with Entrophospora sp. (m3). The second factor was soil from the oil palm rhizosphere that was attacked by Ganoderma sp., namely sterilized soil (g0) and unsterilized soil (g1). The data obtained were analyzed using analysis of variance and the mean separation was tested using the Least Significant Difference test at the 5% level. The results showed that all AMF treatments (m1, m2, and m3) increased the growth of oil palm seedlings compared to controls. Ganoderma sp. present in the planting medium has not inhibited the growth of oil palm seedlings (both control and those applied with AMF) as there is no Ganoderma sp. infection in the roots of oil palm seedlings observed at the end of the study (5 months after planting)

Metagenomic profile and nutrient concentrations in yellowing affected and healthy arecanut palm rhizosphere (Areca catechu L.)

Metagenomic profile and nutrient concentrations in yellowing affected and healthy arecanut palm rhizosphere (Areca catechu L.)

Exploration And Characterization Of Fungi From Oil Palm Rhizosphere (Elaeis Guneensis Jacq) On People's Plantations In Kuantan Singingi Regency

The rhizosphere is an excellent habitat for microbial growth because plant roots provide a variety of organic materials that generally stimulate microbial growth. This study aimed to explore and determine the character of fungi from oil palm rhizosphere (Elaeis guneensis Jacq) on smallholder plantations in Kuantan Singingi Regency. This research was conducted at the Islamic University of Kuantan Singingi. The method used was an experimental method carried out in two stages. The first stage was a random sampling survey. The sample was then taken to the Basic Laboratory of the Faculty of Agriculture, Kuantan Singingi Islamic University for analysis. They are Singingi Hilir District, Kuantan Mudik District, Kuantan Tengah District, Benai District, Pangean District and Sintajo Raya District. The most isolates were found in Singingi Hilir sub-district, the plant age was 2 years and the fertile soil was blackish brown. The least number of isolates was found at the age of 10 years, even though the soil was fertile. The age of the plant affected the microbial activity in the rhizosphere. The older the plant the microbial activity decreased. Therefore, it caused the number of isolates found to be small. Characteristics of isolates isolated at a younger plant age were more varied in color.

Microbial Diversity Characteristics of Areca Palm Rhizosphere Soil at Different Growth Stages.

The rhizosphere microflora are key determinants that contribute to plant health and productivity, which can support plant nutrition and resistance to biotic and abiotic stressors. However, limited research is conducted on the areca palm rhizosphere microbiota. To further study the effect of the areca palm’s developmental stages on the rhizosphere microbiota, the rhizosphere microbiota of areca palm (Areca catechu) grown in its main producing area were examined in Wanning, Hainan province, at different vegetation stages by an Illumina Miseq sequence analysis of the 16S ribosomal ribonucleic acid and internal transcribed spacer genes. Significant shifts of the taxonomic composition of the bacteria and fungi were observed in the four stages. Burkholderia-Caballeronia-Paraburkholderia were the most dominant group in stage T1 and T2; the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were decreased significantly from T1 to T2; and the genera Acidothermus and Bacillus were the most dominant in stage T3 and T4, respectively. Meanwhile, Neocosmospora, Saitozyma, Penicillium, and Trichoderma were the most dominant genera in the stage T1, T2, T3, and T4, respectively. Among the core microbiota, the dominant bacterial genera were Burkholderia-Caballeronia-Paraburkholderia and Bacillus, and the dominant fungal genera were Saitozyma and Trichoderma. In addition, we identified five bacterial genera and five fungal genera that reached significant levels during development. Finally, we constructed the OTU (top 30) interaction network of bacteria and fungi, revealed its interaction characteristics, and found that the bacterial OTUs exhibited more extensive interactions than the fungal OTUs. Understanding the rhizosphere soil microbial diversity characteristics of the areca palm could provide the basis for exploring microbial association and maintaining the areca palm’s health.

Identification of Arbuscular Mychorizae Fungi on Oil Palm in Bireuen, Aceh

Abstract
 
 Oil palm plantations in Aceh , especially in Bireuen, are generally planted on red-yellow podzolic soil types. Arbuscular mycorrhizal fungi (AMF) are fungi who are symbiotically associated with 97% of plant species. This study aims to identify the type and population of mycorrhizal spores from oil palm rhizosphere soil samples using culture trapping techniques (maize, sorghum, kudzu). This research was carried out in a greenhouse and Experimental Field, Faculty of Agriculture, Islamic National University of Indonesia, Bireuen, Aceh. Isolation, identification and observation of AMF colonization on plant roots was carried out at the Laboratory of Soil Biology, Faculty of Agriculture, Syiah Kuala University. The parameters included the number of arbuscular mycorrhizal fungi spores and the percentage of root colonization using the trapping culture method. The trapping culture method used 50 g of soil samples on oil palm rhizosphere which aged 5 months, 7 years, 9 years and 12 years. The results showed that the most dominant mycorrhizae found was the Glomus type. The mycorrhizae spores types found in the trapping culture were Glomus, Acaulospora and Gigaspora. The host plant that produced the most AMF spores was sorghum, while the highest AMF colonization of the three host plants was found in the roots of maize plants (78%) with very high criteria.
 Keywords: Oil palm, Culture trapping, AMF

Actinoplanes flavus sp. nov., a novel cellulase-producing actinobacterium isolated from coconut palm rhizosphere soil

A novel cellulase-producing actinomycete, designated strain NEAU-H7T, was isolated from coconut palm rhizosphere soil collected from Wenchang City, Hainan Province, PR China. A polyphasic taxonomic study was carried out to establish the status of this strain. Results of 16S rRNA gene sequence analysis indicated that strain NEAU-H7T belonged to the genus Actinoplanes, with highest similarity to Actinoplanes hulinensis NEAU-M9T (99.2 % 16S rRNA gene sequence similarity). The diagnostic sugars in cell hydrolysates were determined to be ribose, galactose and mannose. The major fatty acids (>10%) were C16 : 0, C18 : 1 ω9c and C18 : 0. The predominant menaquinones were identified as MK-9(H4) and MK-9(H6). The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and two phosphatidylinositol mannosides. The amino acid of the cell-wall peptidoglycan was determined to be meso-diaminopimelic acid. The DNA G+C content was 71.2 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain NEAU-H7T formed a stable phyletic line with A. hulinensis NEAU-M9T. However, whole-genome phylogeny showed strain NEAU-H7T formed a stable phyletic line with A. hulinensis NEAU-M9T (99.2%), Actinoplanes campanulatus DSM 43148T (98.6%), Actinoplanes capillaceus DSM 44859T (98.3%) and Actinoplanes lobatus DSM 43150T (97.6%). The digital DNA-DNA hybridization (dDDH) results between them were 53.6 (50.9-56.2), 54.1 (51.3-56.9), 53.1 (50.3-55.9) and 52.9 % (50.1-55.6 %), and whole-genome average nucleotide identity (ANI) values between them were 93.7, 93.6, 93.5 and 93.5 %. The low dDDH and ANI values demonstrated that strain NEAU-H7T could be distinguished from its reference strains. Moreover, genomic analysis indicated that the strain NEAU-H7T had the potential to decompose cellulose and produce bioactive compounds. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, strain NEAU-H7T is proposed to represent a novel species of the genus Actinoplanes, with the name Actinoplanes flavus sp. nov. The type strain is NEAU-H7T (=CCTCC AA 2020034T=DSM 112042T).

Genome analysis of a salinity adapted Achromobacter xylosoxidans rhizobacteria from the date palm

Rhizospheric bacteria play an indispensable role in plant growth, development, and stress response in plants. This project aims to isolate and functionally characterize plant-growth-promoting rhizobacteria (PGPR) from date palm (Phoenix dactylifera L.) rhizosphere, to investigate its potential uses as a biofertilizer in date palm. Here, we report an Achromobacter xylosoxidans SQU-1 (SQU-1), as a rhizobacteria strain isolated from date palms grown under salinity. The strain was visualized using electron microscopy, identified using protein profiling and 16 S rRNA gene sequencing, functionally characterized, and its genome was sequenced, assembled, and annotated. The results showed that SQU-1 is a Gram-negative flagellated strain and possesses several plant-growth-promoting traits, including the ability to solubilize micronutrients such as zinc, potassium, phosphorus and to produce ammonia, iron siderophores, indole acetic acid (IAA) phytohormone, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. SQU-1 was also able to significantly enhance date palm seed germination and Arabidopsis growth under normal and saline conditions. Whole-genome sequencing of SQU-1 revealed a total of 6,441,875 bp reads that were assembled into 15 scaffolds. Genome sequence analysis indicated the presence of 5968 open reading frames (ORFs), including 5848 coding genes, 56 pseudogenes, and 64 rRNA DNA sequences. Sequence and cluster of orthologous groups (COG) analysis of SQU-1 enabled the identification of potential genes involved in plant growth-promoting characteristics such as ACC DEAMINASE (acdS), D-CYSTEINE DESULFHYDRASE, and various siderophore production and transporter genes. In conclusion, SQU-1 can be a good candidate for a sustainable agricultural system that aims at producing date fruits under saline conditions with minimal usage of chemical fertilizers.