Novel multifunctional plant growth-promoting bacteria isolated from the oil palm rhizosphere under long-term organic matter application

Most agricultural products are presently cultivated on marginal lands with poor soil properties and unfavorable environmental conditions (diseases and abiotic stresses), which can threaten plant growth and yield. Plant growth-promoting bacteria (PGPB) are beneficial bacteria that promote plant growth and biomass and act as biocontrols against diseases and stress. However, most isolated PGPBs have a single function and low survival rates owing to their limited growth behaviors. In this study, we isolated multifunctional PGPB from oil palm rhizosphere, quantitatively measured their activities, and evaluated their effectiveness in Brassica rapa (Komatsuna) cultivation. This is the first study to report the isolation of three multifunctional PGPB strains with ammonium production, phosphate-potassium-silicate solubilization, and indole-3-acetic acid (IAA) production from the oil palm rhizosphere, namely Kosakonia oryzendophytica AJLB38, Enterobacter quasimori AJTS77, and Lelliottia jeotgali AJTS83. Additionally, these strains showed antifungal activity against the oil palm pathogen Ganoderma boninense. These strains grow under high temperature, acidic and alkaline pH, and high salt concentration, which would result in their proliferation in various environmental conditions. The cultivation experiments revealed these strains improved the growth and biomass with half the dosage of chemical fertilizer application, which was not significantly different to the full dosage. Furthermore, the overall plant growth-promoting activities in quantitative assays and overall B. rapa growth in cultivation experiments were statistically correlated, which could contribute to the prediction of plant growth promotion without plant cultivation experiments. Thus, the selected PGPB could be valuable as a biofertilizer to improve soil health and quality and promote agricultural sustainability.

Microbial metabolism of caffeine and potential applications in bioremediation

With increasing global consumption of caffeine-rich products, such as coffee, tea, and energy drinks, there is also an increase in urban and processing waste full of residual caffeine with limited disposal options. This waste caffeine has been found to leach into the surrounding environment where it poses a threat to microorganisms, insects, small animals, and entire ecosystems. Growing interest in harnessing this environmental contaminant has led to the discovery of 79 bacterial strains, eight yeast strains, and 32 fungal strains capable of metabolizing caffeine by N-demethylation and/or C-8 oxidation. Recently observed promiscuity of caffeine-degrading enzymes in vivo has opened up the possibility of engineering bacterial strains capable of producing a wide variety of caffeine derivatives from a renewable resource. These engineered strains can be used to reduce the negative environmental impact of leached caffeine-rich waste through bioremediation efforts supplemented by our increasing understanding of new techniques such as cell immobilization. Here, we compile all of the known caffeine-degrading microbial strains, discuss their metabolism and related enzymology, and investigate their potential application in bioremediation.

Culturing the desert microbiota

Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that Arthrobacter subterraneus, Arthrobacter tecti, Pseudarthrobacter phenanthrenivorans, Pseudarthrobacter psychrotolerans, and Massilia agri are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera Arthrobacter/Pseudarthrobacter and Kocuria, and a relative underestimation of the genera Blastococcus and Domibacillus by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in Pseudomonadota (Proteobacteria).

Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera

Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.

Pseudomonas ovata sp. nov., Isolated from the Skin of the Tail of Farmed Murray cod (Maccullochella peelii peelii) with a Profound Ulceration

A Gram-negative, strictly aerobic, motile, rod-shaped bacterium with monopolar flagellum, designated as F51^T, was isolated from the skin ulcer of farmed Murray cod sampled from Zhejiang Province, China. Strain F51^T grew at 4-37 °C (optimal temperature, 28 °C), pH 5.0-8.5 (optimal pH, 7.5) and NaCl concentration of 0-6.0% (w/v) (optimal concentration, 2.0%). Phylogenetic analysis based on average nucleotide identity (76.2-78.4%) and in silico DNA-DNA hybridization (22.3-23.2%) values revealed that strain F51^T forms a distinct lineage in the clade of genus Pseudomonas with less than 98.9% 16S rRNA gene sequence similarity to type strains of the genus and represents a novel species related most closely to Pseudomonas floridensis LMG 30013^T. Three housekeeping genes (rpoB, rpoD and gyrB) of strain F51^T were analysed to further confirm that the isolate is distinctly delineated from related Pseudomonas species. Chemotaxonomic analysis indicated that the sole respiratory quinone of strain F51^T is Q-9; its predominant cellular fatty acids are C_16:0, summed feature 3 (iso-C_15:0 2-OH and/or C_16:1ω7c), summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) and C_10:0 3-OH; and its major polar lipids consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids, three unidentified phospholipids and an unidentified aminophosphoglycolipid. This composition is typical of the chemotaxonomic attributes of Pseudomonas. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain F51^T is considered to represent a novel species for which the name Pseudomonas ovata sp. nov. is proposed. The type strain is F51^T (= KCTC 62133^T = MCCC 1K03458^T).

Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard

We analyzed the genome sequence of an endophytic bacterial strain Pseudomonas putida TJI51 isolated from mango bark tissues. Next generation DNA sequencing and short read de novo assembly generated the 5,805,096 bp draft genome of P. putida TJI51. Out of 6,036 protein coding genes in P. putida TJI51 sequences, 4,367 (72%) were annotated with functional specifications, while the remaining encoded hypothetical proteins. Comparative genome sequence analysis revealed that the P. putida TJI51genome contains several regions, not identified in so far sequenced P. putida genomes. Some of these regions were predicted to encode enzymes, including acetylornithine deacetylase, betaine aldehyde dehydrogenase, aldehyde dehydrogenase, benzoylformate decarboxylase, hydroxyacylglutathione hydrolase, and uroporphyrinogen decarboxylase. The genome of P. putida TJI51 contained three nonribosomal peptide synthetase gene clusters. Genome sequence analysis of P. putidaTJI51 identified this bacterium as an endophytic resident. The endophytic fitness might be linked with alginate, which facilitates bacterial colonization in plant tissues. Genome sequence analysis shed light on the presence of a diverse spectrum of metabolic activities and adaptation of this isolate to various niches.

Cytotoxicity and inflammatory potential of two Pseudomonas mosselii strains isolated from clinical samples of hospitalized patients

BACKGROUND

The genus Pseudomonas includes a heterogeneous set of microorganisms that can be isolated from many different niches and nearly 100 different strains have been described. The best characterized bacterium is Pseudomonas aeruginosa which is the primary agent of opportunistic infection in humans, causing both acute and chronic infections. Other species like fluorescens, putida or mosselii have been sporadically isolated from hospitalized patients but their association with the pathology often remains unclear.

RESULTS

This study focuses on the cytotoxicity and inflammatory potential of two strains of Pseudomonas mosselii (ATCC BAA-99 and MFY161) that were recently isolated from clinical samples of hospitalized patients. The behavior of these bacteria was compared to that of the well-known opportunistic pathogen P. aeruginosa PAO1. We found that P. mosselii ATCC BAA-99 and MFY161 are cytotoxic towards Caco-2/TC7 cells, have low invasive capacity, induce secretion of human β-defensin 2 (HBD-2), alter the epithelial permeability of differentiated cells and damage the F-actin cytoskeleton.

CONCLUSIONS

These data bring new insights into P. mosselii virulence, since this bacterium has often been neglected due to its rare occurrence in hospital.

Pseudomonas zeshuii sp. nov., isolated from herbicide-contaminated soil

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain BY-1(T), was isolated from a soil sample from the city of Qiqihar in Heilongjiang Province, PR China. Strain BY-1(T) grew optimally at pH 7.0 and 30-35 °C in the presence of 0.5% (w/v) NaCl. Analysis of 16S rRNA gene sequences revealed that strain BY-1(T) fell within the radiation of the genus Pseudomonas, and showed highest 16S rRNA gene sequence similarities to Pseudomonas luteola IAM 13000(T) (99.5%) and Pseudomonas duriflava HR2(T) (97.3%); the levels of sequence similarity with respect to other recognized species of the genus Pseudomonas were <96.7%. Strain BY-1(T) showed low DNA-DNA relatedness values with Pseudomonas luteola IAM 13000(T) (29 ± 3.1%) and Pseudomonas duriflava HR2(T) (21 ± 1.5 %). The G+C content of the genomic DNA of strain BY-1(T) was 55.3 mol%. The major fatty acids were C(18:1), C(16:0) and summed feature 3 (C(16:1)ω6c and/or C(16:1)ω7c). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major ubiquinone was Q-9. Data obtained in this study indicated that this isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas zeshuii sp. nov. is proposed. The type strain is BY-1(T) (=KACC 15471(T)=ACCC 05688(T)).

Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor

Two Gram-negative, rod-shaped, motile, aerobic bacterial strains designated HY-14(T) and HY-24 were isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. The strains could not grow with 5 % (w/v) NaCl, did not produce acid from d-glucose or utilize d-glucose, gluconate or citrate as a sole carbon source. Summed feature 3 and C(16 : 0) were the most abundant fatty acids; hydroxyl fatty acids C(12 : 0) 3-OH and C(10 : 0) 3-OH were also present. Fatty acid C(12 : 0) 2-OH was absent. The DNA G+C contents of strains HY-14(T) and HY-24 were 50.6+/-0.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains HY-14(T) and HY-24 formed a monophyletic clade within the genus Pseudomonas. The highest sequence similarities were to Pseudomonas pseudoalcaligenes DSM 50188(T) (95.9 %). On the basis of phenotypic and phylogenetic properties, strains HY-14(T) and HY-24 are proposed as a novel species of the genus Pseudomonas, for which the name Pseudomonas caeni sp. nov. is proposed. The type strain is HY-14(T) (=KCTC 22292(T)=CCTCC AB208156(T)).