Production of dimethyldiselenide from methaneseleninic acid by soil bacteria.

The increasing prevalence of antibiotic-resistant bacteria is a global threat to public health. Agricultural use of antibiotics is believed to contribute to the spread of antibiotic resistance, but the mechanisms by which many agricultural practices influence resistance remain obscure. Although manure from dairy farms is a common soil amendment in crop production, its impact on the soil microbiome and resistome is not known. To gain insight into this impact, we cultured bacteria from soil before and at 10 time points after application of manure from cows that had not received antibiotic treatment. Soil treated with manure contained a higher abundance of β-lactam-resistant bacteria than soil treated with inorganic fertilizer. Functional metagenomics identified β-lactam-resistance genes in treated and untreated soil, and indicated that the higher frequency of resistant bacteria in manure-amended soil was attributable to enrichment of resident soil bacteria that harbor β-lactamases. Quantitative PCR indicated that manure treatment enriched the blaCEP-04 gene, which is highly similar (96%) to a gene found previously in a Pseudomonas sp. Analysis of 16S rRNA genes indicated that the abundance of Pseudomonas spp. increased in manure-amended soil. Populations of other soil bacteria that commonly harbor β-lactamases, including Janthinobacterium sp. and Psychrobacter pulmonis, also increased in response to manure treatment. These results indicate that manure amendment induced a bloom of certain antibiotic-resistant bacteria in soil that was independent of antibiotic exposure of the cows from which the manure was derived. Our data illustrate the unintended consequences that can result from agricultural practices, and demonstrate the need for empirical analysis of the agroecosystem.

Pseudomonas sp. K82 is a soil bacterium that can degrade and use monocyclic aromatic compounds including aniline, 3-methylaniline, 4-methylaniline, benzoate and p-hydroxybenzoate as its sole carbon and energy sources. In order to understand the impact of these aromatic compounds on metabolic pathways in Pseudomonas sp. K82, proteomes obtained from cultures exposed to different substrates were displayed by two-dimensional gel electrophoresis and were compared to search for differentially induced metabolic enzymes. Column separations of active fractions were performed to identify major biodegradation enzymes. More than thirty proteins involved in biodegradation and other types of metabolism were identified by electrospray ionization-quadrupole time of flight mass spectrometry. The proteome analysis suggested that Pseudomonas sp. K82 has three main metabolic pathways to degrade these aromatic compounds and induces specific metabolic pathways for each compound. The catechol 2,3-dioxygenase (CD2,3) pathway was the major pathway and the catechol 1,2-dioxygenase (beta-ketoadipate) pathway was the secondary pathway induced by aniline (aniline analogues) exposure. On the other hand, the catechol 1,2-dioxygenase pathway was the major pathway induced by benzoate exposure. For the degradation of p-hydroxybenzoate, the protocatechuate 4,5-dioxygenase pathway was the major degradation pathway induced. The nuclear magnetic resonance analysis of substrates demonstrated that Pseudomonas sp. K82 metabolizes some aromatic compounds more rapidly than others (benzoate > p-hydroxybenzoate > aniline) and that when combined, p-hydroxybenzoate metabolism is repressed by the presence of benzoate or aniline. These results suggest that proteome analysis can be useful in the high throughput study of bacterial metabolic pathways, including that of biodegradation, and that inter-relationships exist with respect to the metabolic pathways of aromatic compounds in Pseudomonas sp. K82.

Soil and water bacteria in general, and members of the genus Pseudomonas in particular, exhibit a fascinating wealth of exotic properties not found in commensal and parasitic bacteria, such as Escherichia coli. They are, for example, able to degrade and use as sources of carbon and energy a wide range of organic compounds, including some that are quite noxious and otherwise biocidal (e.g., phenol). Moreover, soil bacteria are able to evolve rapidly new metabolic activities in response to changes in environmental conditions, e.g., to evolve new pathways for the degradation of synthetic industrial compounds (xenobiotics) such as pesticides, that are newly applied to the environment (1). The rapidity of evolution of new pathways is particularly surprising because many pathways, e.g. those for the catabolism of aromatic hydrocarbons, involve a large number of enzymatic steps and often more than twice that number of polypeptides (2). It is hardly surprising, therefore, that many catabolic pathways are specified by plasmids (3), elements known to be instrumental for rapid genetic change in bacteria (4).

Agricultural pesticides are one of the indispensable materials used to meet increasing demand of food crops. Consequently, pesticides find their way to various ecosystems resulting in detrimental pollution problems. Chlorpyrifos is a predominantly used organophosphorus pesticide leading to harmful effects including abnormal cell division. Scientific attempt to eliminate these contaminants from the environment using biodegradation approach has been appreciated. Soil bacteria capable of utilizing chlorpyrifos are potential bioremediation candidates. In context to the same, the present study isolated six bacteria growing in presence of chlorpyrifos as sole carbon source from agricultural soils. The obtained bacterial isolates characterized based on their morphological characteristics, biochemical reactions were found to be Pseudomonas spp. JR16, Pseudomonas spp. J1, Pseudomonas spp. J2, Pantoea spp. J3, Enterobacter spp. J4 and Kocuria spp. J5. Among these, the most potential of them viz., Pseudomonas spp. JR16, was further proceeded for molecular identification and was observed to be the Pseudomonas putida JR16. The influence of different chlorpyrifos concentration, various carbon sources, metals sources, temperature and pH on the growth of Pseudomonas putida JR16 was assessed for developing optimum conditions for on field application of the strain for biodegradation of chlorpyrifos.

Bioaccumulation of Cd2+ in soil bacteria might represent an important route of metal transfer to associated mycorrhizal fungi and plants and may have potential as a tool to accelerate Cd2+ extraction in the bioremediation of contaminated soils. The present study examined the bioaccumulation of Cd2+ in 15 bacterial strains representing three phyla (Firmicutes, Proteobacteria, and Bacteroidetes) that were isolated from the rhizosphere, ectomycorrhizae, and fruitbody of ectomycorrhizal fungi. The strains Pseudomonas sp. IV-111-14, Variovorax sp. ML3-12, and Luteibacter sp. II-116-7 displayed the highest biomass productivity at the highest tested Cd2+ concentration (2 mM). Microscopic analysis of the cellular Cd distribution revealed intracellular accumulation by strains Massilia sp. III–116-18, Pseudomonas sp. IV-111-14, and Bacillus sp. ML1-2. The quantities of Cd measured in the interior of the cells ranged from 0.87 to 1.31 weight % Cd. Strains originating from the rhizosphere exhibited higher Cd2+ accumulation efficiencies than strains from ectomycorrhizal roots or fruitbodies. The high Cd tolerances of Pseudomonas sp. IV-111-16 and Bacillus sp. ML1-2 were attributed to the binding of Cd2+ as cadmium phosphate. Furthermore, silicate binding of Cd2+ by Bacillus sp. ML1-2 was observed. The tolerance of Massilia sp. III-116-18 to Cd stress was attributed to a simultaneous increase in K+ uptake in the presence of Cd2+ ions. We conclude that highly Cd-tolerant and Cd-accumulating bacterial strains from the genera Massilia sp., Pseudomonas sp., and Bacillus sp. might offer a suitable tool to improve the bioremediation efficiency of contaminated soils.Electronic supplementary materialThe online version of this article (doi:10.1007/s11356-014-3489-0) contains supplementary material, which is available to authorized users.

Diazotrophic bacteria in root-free soil and in the root zone of pine ( Pinus sylvestris L.) and oak ( Quercus robur L.)

How bacterial feeding fauna affects colonization and survival of bacteria in soil is not well understood, which constrains the applicability of bacterial inoculants in agriculture. This study aimed to unravel how food quality of bacteria and bacterial feeders with different feeding habits (the selective feeding flagellate Cercomonas longicauda versus the non-selective feeding nematode Caenorhabditis elegans) influence the abundance of two bacteria that compete for resources in simple model communities. Microcosms consisted of either one gfp-tagged bacterial strain (Pseudomonas fluorescens DSM50090 or one of two biocontrol strains P. fluorescens CHA0 or Pseudomonas sp. DSS73) or combinations of two bacterial strains. DSM50090 is a suitable food bacterium, DSS73 is of intermediate food quality, and CHA0 is inedible to the bacterial feeders. Bacterial and protozoan cell numbers were measured by flow cytometry. In the presence of flagellates, CHA0 increased its abundance as compared to the other biocontrol strain DSS73 or to DSM50090, which were both eaten by the flagellates. In contrast, the number of CHA0 declined as compared to DSS73 when the model community was subjected to nematode predation pressure. Hence, the results suggested that the outcome of competition among bacteria depended on their ability to cope with the prevailing bacterial predator.

SummaryThe application of potassium (K)‐releasing microorganisms is a promising approach for increasing K availability in soil. The objectives of this study were to isolate and characterize the K‐releasing bacteria (KRB) and to evaluate their contribution to the solubilization of K from muscovite and biotite, and to the assimilation of released K by tomato in a pot culture experiment. Soil samples were screened in both solid and liquid Aleksandrov media to isolate bacteria with the potential to release K from biotite and muscovite. Our results fromin‐vitroexperiments revealed that more K was released in treatments with KRB than in the uninoculated media (control). Under the best conditions an increase of 188 and 127% was obtained for biotite and muscovite, respectively; among the isolates with the largest releasing ability it was 49 mg l−1. The most efficient bacteria were identified as thePseudomonasgenus. Results of the pot culture experiment showed that the concentration and content of K in plant tissue were considerably more than those in any of the controls with no living organisms present. Results revealed that significantly more biomass was accumulated and K acquired in most pots treated with bacterial strains than in the control, especially forPseudomonassp. strain S10‐3. This treatment increased K concentation and content by more than 50 and 70%, respectively, in tomato aerial tissue. Further research is necessary to examine the effects of these bacterial strains on the mobilization of K‐bearing minerals under field conditions.HighlightsThe aim was to determine if bacterial isolates can accelerate K release from micas for plants.We investigated the potential of some isolated bacteria to solubilize K from muscovite and biotite.Identification of efficient isolates showed that KRB belonged to thePseudomonasgenus.Pseudomonassp. strain S10‐3 increased K concentration in tomato aerial tissue by more than 50%.

Ngoc Linh ginseng (Panax vietnamensis Ha et Grushv.) is an endemic species in Vietnam and was discovered at the Ngoc Linh mountain (Kon Tum/Quảng Nam). Investigations showed that the soil with a thick layer of humus was the ideal condition for growth and development of Ngoc Linh ginseng. Therefore research on microbial flora as well as cellulose-degrading bacteria in ginseng soil may elucidate factors contributing to acclimatized cultivation of this ginseng in Vietnam. From the soil sample with cultivated Ngoc Linh ginseng in Quang Nam, five bacteria strains with cellulose-degrading activities were isolated (QN1, QN2, QN3, QN4, QN5 with respectively hydrolyzed CMC halos diameters of 10, 11, 22, 7, 22 mm) with cellulase activities of 1,31; 1,23; 2,99; 0,99; 2,51 U/ml. The combination of 16S rRNA gene sequences and cultured/biochemical characteristics of the bacteria showed that the five bacteria strains was classified to be Pseudomonas sp. QN1; Pseudomonas sp. QN4; Bacillus sp. QN2; Bacillus sp. QN3; Roseomonas sp. QN5.

Ecological studies on coccoid bacteria in a pine forest soil—II. growth of bacteria introduced into soil

Soil salinity is a significant global issue that adversely affects plant growth by reducing the availability of essential nutrients, leading to deficiencies. This presents challenges for the production of medicinal plants, as their value relies on nutrient-dependent metabolites. To address this, bioremediation strategies using living organisms have gained attention. Native bacteria in saline soils offer a sustainable way to restore soil health and mitigate salt stress. This study investigates the impact of native rhizosphere soil bacteria on the growth and nutritional value of Aloe vera. We screened four bacterial isolates from the rhizosphere of A. vera plants grown in saline soil in the Mathura region of Uttar Pradesh, India, focusing on their nutrient-solubilizing abilities. These bacterial strains demonstrated phosphate solubilization, potassium solubilization, siderophore production, indole-3-acetic acid (IAA) production, and protease activity. Using partial 16S rRNA gene sequencing, bacterial isolates were identified as Paenibacillus sp., Arthrobacter sp., Pseudomonas sp., and Bacillus sp. Subsequently, a pot experiment was conducted to augment the population of these bacteria in the soil and to evaluate their impact on A. vera’s growth and nutritional value. The bacteria were applied both individually and as a consortium. To assess the impact of these inoculations, the nutrient content of leaf gel and various soil health parameters were measured. The results showed that the application of the bacterial consortium yielded higher number of leaves (47%), leaf fresh weight (74%), gel content (33%), and nutritional properties as compared to control treatment (non-inoculated). Furthermore, bacterial inoculation significantly enhanced soil enzymatic activity and increased the soluble nitrate and phosphate content in the experimental soil. In conclusion, the presence of these bacteria in the rhizosphere of A. vera, along with their nutrient-solubilizing activities, enhances nutrient uptake and metabolite synthesis in the host plant under saline soil conditions.

To exploit alginate lyase which could degrade bacterial alginates, degenerate PCR and long range-inverse PCR (LR-IPCR) were used to isolate alginate lyase genes from soil bacteria. Gene algL, an alginate lyase-encoding gene from Pseudomonas sp. QD03 was cloned, and it was composed of a 1122 bp open reading frame (ORF) encoding 373 amino acid residues with the calculated molecular mass of 42.2 kDa. The deduced protein had a potential N-terminal signal peptide of 20 amino acid residues that was consistent with its proposed periplasmic location. Gene algL was expressed in pET24a (+)/E. coli BL21 (DE3) system. The recombinant AlgL was purified to electrophoretic homogeneity using affinity chromatography. The molecular weight of AlgL was estimated to be 42.8 kDa by SDS-PAGE. AlgL exhibited maximal activity at pH 7.5 and 37 °C. Na+, K+, Ca2+ and Ba2+ significantly enhanced the activity of AlgL. AlgL could degrade alginate and mannuronate blocks, but hardly degrade guluronate blocks. In particular, AlgL could degrade acetylated alginate of Pseudomonas aeruginosa FRD1 (approximately 0.54 mol of O-acetyl group per mol of alginate). It might be possible to use alginate lyase AlgL as an adjuvant therapeutic medicine for the treatment of disease associated with P. aeruginosa infection.

A mesophilic bacterium capable of Low-Molecular-Weight Polyethylene (LMWPE) biodegradation was isolated from a beach soil having been contaminated extensively with crude oil. The isolated strain was rod-shaped gram negative bacterium and was identified as Pseudomonas sp. E4 through the 16S rDNA sequencing. The biodegradability test in the compost inoculated with the isolated strain for LMWPE having weight-average-molecularweight (Mw) in the range of 1,700~23,700 indicated that 4.9~28.6 % of the carbon was mineralized into CO2 after 80 days at 37°C. The biodegradability decreased with increase in Mw of LMWPE. In comparison to other previous works which reported biodegradation of pre-oxidized polyethylene, we investigated biodegradation of non-oxidized LMWPE whose Mw was well above the Mw upper limit penetrable through microbial membrane. The smooth surface of LMWPE sheet became eroded as a result of the biodegradation, and the degree of the surface erosion became more pronounced for LMWPE with lower molecular weight in line with the biodegradability test results. The alkane hydroxylase gene (alkB) of Pseudomonas sp. E4 was expressed in Escherichia coli BL21 and the recombinant E. coli BL21 mineralized 19.3% of the carbon of LMWPE into CO2 during the biodegradation in the compost at 37°C for 80 days, while the recipient cell was not active at all toward the LMWPE biodegradation, indicating that the alkB from Pseudomonas sp. E4 plays a central role in the LMWPE degradation even in the absence of the other specific enzymes like rubredoxin and rubredoxin reductase.

Recent publications indicate that inter-specific interactions between soil bacteria may strongly affect the behavior of the strains involved, e.g., by increased production of antibiotics or extracellular enzymes. This may point at an enhanced competitive ability due to inter-specific triggering of gene expression. However, it is not known if such inter-specific interactions also occur during competition for carbon which is the normal situation in soil. Here, we report on competitive interactions between two taxonomically non-related bacterial strains, Pseudomonas sp. A21 and Pedobacter sp. V48, that were isolated from a dune soil. The strains showed strong effects on each other's behavior and gene expression patterns when growing together under carbon-limited conditions on agar. The most pronounced observed visual changes in mixed cultures as compared to monocultures were (1) strong inhibition of a bioindicator fungus, suggesting the production of a broad-spectrum antibiotic, and (2) the occurrence of gliding-like movement of Pedobacter cells. Two independent techniques, namely random arbitrary primed-PCR (RAP-PCR) and suppressive subtractive hybridization (SSH), identified in total 24 genes that had higher expression in mixed cultures compared to monocultures. Microbial interactions were clearly bidirectional, as differentially expressed genes were detected for both bacteria in mixed cultures. Sequence analysis of the differentially expressed genes indicated that several of them were most related to genes involved in motility and chemotaxis, secondary metabolite production and two-component signal transduction systems. The gene expression patterns suggest an interference competition strategy by the Pseudomonas strain and an escape/explorative strategy by the Pedobacter strain during confrontation with each other. Our results show that the bacterial strains can distinguish between intra- and inter-specific carbon competition.

Commercial formulations of an insecticide, hexachlorocyclohexane (HCH), currently used on a large scale in India, contain {alpha}-, {beta}-, {gamma}-, {delta}- and other isomers. According to earlier reports these HCH isomers persist in aerobic soil and water systems, but disappear rapidly from predominantly anaerobic ecosystems such as flooded soils and lake sediments. Bacterial strains (facultative or strict anaerobes), isolated from these anaerobic systems rapidly degraded {alpha}- and/or {gamma}-isomer, but not {beta}- and {delta}-isomers of HCH under anaerobic conditions. Recent reports show that bacteria mainly Pseudomonads, isolated from aerobic soils could degrade not only {gamma}-isomer, but also {alpha}- and {beta}-isomers of HCH under aerobic conditions. There is no report of the degradation of {delta}-HCH in pure culture by either aerobic bacteria although it is a common constituent in widely used commercial formulations of HCH. The authors report the rapid degradation of {delta}-HCH by a Pseudomonas sp. under aerobic conditions.