The use of 16s rDNA methods in soil microbial ecology

Optimized extraction methodology for phenolic compounds in soil and plant tissues: Their implications in plant growth and gall formation

Phenolic compounds, abundant secondary metabolites in plants, profoundly influence soil ecosystems, plant growth, and interactions with herbivores. Phenolic in soil microorganisms have the potential to impact a wide range of activities in plant-soil interactions. However, the existing methods for measuring microbial activity are typically time-consuming, intricate, and expensive. In this study, we propose modifications to the method used for the extraction and quantification of various types of phenolics in soil and plant tissues. There have been substantial advancements in research aimed at extracting, identifying, and quantifying phenolic compounds in the plant and soil samples. This study discusses the use of different methodologies in the analysis of phenolic compounds. In addition, we investigated the effect of phenolics on plant growth and cues in gall-forming under environmental disturbances.•This method is the optimum way to extract phenolic from soil and microbial activity in bulk and rhizosphere soil.•It can be used on any soil type and plant tissue, metabolites extracted from living organisms.

Effect of phenolics on soil microbe distribution, plant growth, and gall formation

Phenolic compounds, abundant secondary metabolites in plants, profoundly influence soil ecosystems, plant growth, and interactions with herbivores. In this study, we explore the intricate relationships between phenolics, soil microbes, and gall formation in Ageratina adenophora (A. adenophora), an invasive plant species in China known for its allelopathic traits. Using metabolomic and microbial profiling, significant differences in soil microbial composition and metabolite profiles were observed between bulk and rhizosphere soil samples. Phenolics influenced bacterial communities, with distinct microbial populations enriched in each soil type. Additionally, phenolics impacted soil metabolic processes, with variations observed in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis between different soil treatments. Analysis of phenolic content in plant and soil samples revealed considerable variations, with higher concentrations observed in certain plant tissues and soil types. Bioactive phenols extracted from plant and soil samples were identified using gas chromatography/mass spectrometry (GC-MS), providing insights into the diverse chemical composition of these compounds. Furthermore, the effects of phenolics on plant growth and gall formation were investigated. Phenols exhibited both stimulatory and inhibitory effects on plant growth, with optimal concentrations promoting emergence but higher concentrations hindering growth. Gall formation was influenced by phenolic concentrations, leading to structural alterations in stem tissue and gall morphology. Histochemical analysis revealed starch and lipid accumulation in gall tissues, indicating metabolic changes induced by phenolics. The presence of phenolics disrupted tissue structures and influenced vascular bundle orientation in gall tissues. Overall, our study highlights the multifaceted roles of phenolic compounds in soil ecosystems, plant development, and gall formation, facilitating the utilization of secondary metabolites in agriculture.

Shifts in metabolic patterns of soil bacterial communities on exposure to metal engineered nanomaterials

The explosive growth in nanomaterial use will bring about their increased release into terrestrial ecosystems. Metal engineered nanomaterials (ENMs) that gain entry into these environments may alter the composition and activities of resident natural bacterial communities. To assess changes in community level physiological profiles (CLPP) of microbial communities in soils exposed to metal ENMs, Biolog EcoPlates were used in this exploratory comparative study. The CLPP is a rapid screening technique to characterise functional differences among heterotrophic microbial communities based on variable substrate utilization. The impacts of three metal ENMs, silver, titanium dioxide and zinc oxide, on bacterial communities were investigated using three soil types from Maharashtra, India. Metabolic diversity of bacterial communities was impacted in the soils in presence of silver and zinc oxide, but not in presence of titanium dioxide nanoparticles. Diversity indices, viz., Shannon's index, Evenness index and Simpson's index also showed significant differences in the presence of silver and zinc oxide nanoparticles. Principal component analysis revealed changes in metabolic profiles in the presence of silver nanoparticles. This study also shows that testing ecotoxicity of nanoparticles using readily culturable bacteria is a practical approach.

Contribution of soil variables to bacterial community composition following land use change in Napahai plateau wetlands

Land use changes have significant modifications on soil conditions, which is likely to induce alterations in the soil bacterial communities. Little is known about the respective contributions of soil variables to these changes in bacterial communities. For this study, high-throughput sequencing technology was applied to measure the change in bacterial community compositions under the effects of soil variables across three land-use types (i.e., reference, degraded, and agricultural wetlands) in the Napahai plateau. Compared with the reference wetland, a pronounced decrease (1.5-5.3 times) in soil water content, soil organic matter, and total and available nitrogen was observed in degraded and agricultural wetlands. However, a conspicuous increase (1.3-5.7 times) was found for the total and available phosphorus, and potassium. Land use also strongly affected the taxonomic composition of soil bacterial assemblages, changing the normalized ratio of Acidobacteria to Proteobacteia, or to δ-proteobacteia. Soil properties had different contributions to the variations in abundance composition of bacterial community. Soil available phosphorus and potassium were the best predictors for changes in bacterial community composition, explaining 80.9% and 82% of the variations, respectively. In contrast, soil organic matter, carbon/nitrogen, total phosphorus, and total and available nitrogen accounted for 58.7-72.7% of the variations in bacterial community composition. Soil pH (24.6%) and soil water content (40.4%) had a minor contribution. Our data suggested that the compositional alterations of microbial communities following land-use change were likely realized through modifications in the availability of primary soil nutrients in the Napahai plateau wetlands.

Whole-cell biocatalytic of Bacillus cereus WZZ006 strain to synthesis of indoxacarb intermediate: (S)-5-Chloro-1-oxo-2,3-dihydro-2-hydroxy-1H-indene-2-carboxylic acid methyl ester

In this study, a newly isolated strain screened from the indoxacarb-rich agricultural soils, Bacillus cereus WZZ006, has a high stereoselectivity to racemic substrate 5-chloro-1-oxo-2,3-dihydro-2-hydroxy-1H-indene-2-carboxylic acid methyl ester. (S)-5-chloro-1-oxo-2,3-dihydro-2-hydroxy-1H-indene-2-carboxylic acid methyl ester was obtained by bio-enzymatic resolution. After the 36-hour hydrolysis in 50-mM racemic substrate under the optimized reaction conditions, the e.e._s was up to 93.0% and the conversion was nearly 53.0% with the E being 35.0. Therefore, B cereus WZZ006 performed high-level ability to produce (S)-5-chloro-1-oxo-2,3-dihydro-2-hydroxy-1H-indene-2-carboxylic acid methyl ester. This study demonstrates a new biocatalytic process route for preparing the indoxacarb chiral intermediates and provides a theoretical basis for the application of new insecticides in agricultural production.

Streptomyces kebangsaanensis sp. nov., an endophytic actinomycete isolated from an ethnomedicinal plant, which produces phenazine-1-carboxylic acid

A spore-forming streptomycete designated strain SUK12(T) was isolated from a Malaysian ethnomedicinal plant. Its taxonomic position, established using a polyphasic approach, indicates that it is a novel species of the genus Streptomyces. Morphological and chemical characteristics of the strain were consistent with those of members of the genus Streptomyces. Analysis of the almost complete 16S rRNA gene sequence placed strain SUK12(T) in the genus Streptomyces where it formed a distinct phyletic line with recognized species of this genus. The strain exhibited highest sequence similarity to Streptomyces corchorusii DSM 40340(T) (98.2 %) followed by Streptomyces chrestomyceticus NRRL B-3310(T) (98.1 %). The G+C content of the genomic DNA was 74 mol%. Chemotaxonomic data [MK-9(H8) as the major menaquinone; LL-diaminopimelic acid as a component of cell-wall peptidoglycan; C12 : 0, C14 : 0, C15 : 0 and C17 : 1 as the major fatty acids; phospholipid type II] supported the affiliation of strain SUK12(T) to the genus Streptomyces. The results of the phylogenetic analysis and phenotypic data derived from this and previous studies allowed the genotypic and phenotypic differentiation of strain SUK12(T) from the related species of the genus Streptomyces. The DNA-DNA relatedness value between strain SUK12(T) and S. corchorusii DSM 40340(T) is 18.85±4.55 %. Strain SUK12(T) produces phenazine-1-carboxylic acid, known as tubermycin B, an antibacterial agent. It is proposed, therefore, that strain SUK12(T) ( = DSM 42048(T) = NRRL B-24860(T)) be classified in the genus Streptomyces as the type strain of Streptomyces kebangsaanensis sp. nov.

Carl woese: from biophysics to evolutionary microbiology

This article is a tribute to Carl R. Woese, a biophysicist turned evolutionary microbiologist who passed away on December 30, 2012. We focus on his life, achievements, the discovery of Archaea and contributions to the development of molecular phylogeny. Further, the authors share their views and the lessons learnt from Woese's life with the microbiologists in India. We also emphasize the need for interdisciplinary collaboration and interaction for the progress and betterment of science.

Thermodynamic characterization of a highly thermoactive extracellular pectate lyase from a new isolate Bacillus pumilus DKS1

An extracellular pectate lyase (EC 4.2.2.2) was purified from the culture filtrate of a newly isolated Bacillus pumilus DKS1 grown in pectin containing medium. Using ion-exchange and gel filtration chromatography, this enzyme was purified and found to have a molecular weight of around 35kDa. The purified enzyme exhibited maximal activity at a temperature of 75 degrees C and pH 8.5. The presence of 1mM calcium and manganese enhanced pectate lyase activity and was strongly inhibited by zinc, nickel and EDTA. The thermal inactivation studies revealed an entropy-enthalpy compensation pattern below a critical temperature. The alkaliphilicity and high thermostability of this pectate lyase may have potential implications in fibre degumming.

Bacterial diversity of East Calcutta Wet land area: possible identification of potential bacterial population for different biotechnological uses

The extent of microbial diversity in nature is still largely unknown, suggesting that there might be many more useful products yet to be identified from soil microorganisms. This insight provides the scientific foundation for a renewed interest in examining soil microorganisms for novel commercially important products. This has led us to access the metabolic potential of soil microorganisms via cultivation strategy. Keeping this in mind, we have performed a culture-dependent survey of important soil bacterial community diversity in East Calcutta Wetland area (Dhapa Landfill Area). We describe isolation of 38 strains, their phenotypic and biochemical characterization, and finally molecular identification by direct sequencing of polymerase chain reaction (PCR)-amplified 16S rRNA gene products. We have isolated and identified strains able to fix nitrogen, produce extracellular enzymes like protease, cellulase, xylanase, and amylase, and solubilize inorganic phosphates. Some isolates can synthesize extracellular insecticidal toxins. We find a good correlation between biochemical and phenotypic behavior and the molecular study using 16S rRNA gene of the isolates. Furthermore, our findings clearly indicate the composition of cultivable soil bacteria in East Calcutta Wetland Area.