Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions.

The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.

Biodegradation of organophosphorus pesticide profenofos by the bacterium Bacillus sp. PF1 and elucidation of initial degradation pathway.

Among the organophosphate pesticides, the wide and indiscriminate use of profenofos (PFF) in agricultural and horticultural crops has resulted in serious environmental and animal health concerns and therefore demands an urgent need to develop a biological solution for its effective removal from the environment. For the bioremediation of PFF, a strain PF1, capable of utilizing profenofos as the sole source of carbon and energy was isolated from the soil samples of apple orchards of Shimla region of Himachal Pradesh, India. Based on the biochemical, FAME, and 16S rRNA gene analysis the bacterium PF1 was identified as Bacillus altitudinis (GenBank: MH986176). The strain was able to degrade 50µg mL-1 PFF up to 93% within 30 days of incubation at 28°C, pH 7.0. A linear regression analysis performed on the data-set revealed the statistical significance of the relationship between the growth of the bacterial population and the degradation of pesticides. The compound 4-Bromo-2-chlorophenol (BCP) was detected as one of the pathway metabolites which further were completely degraded to lower pathway metabolites. A probable PFF degradation pathway has been proposed which follows the path from PFF to BCP and ultimately enters into the TCA cycle. To the best of our knowledge, this is the first report of PFF biodegradation by any Bacillus species of western Himalayan origin exhibiting close phylogenetic association with Bacillus altitudinis. This indigenous bacterium can be useful to bio-remediate the PFF contaminated soil as this pesticide is extensively used in the different horticulture fields in Himachal Pradesh, India.

Transcriptome Analysis of Podoscypha petalodes Strain GGF6 Reveals the Diversity of Proteins Involved in Lignocellulose Degradation and Ligninolytic Function.

The present study reports transcriptomic profiling of a Basidiomycota fungus, Podoscypha petalodes strain GGF6 belonging to the family Podoscyphaceae, isolated from the North-Western Himalayan ranges in Himachal Pradesh, India. Podoscypha petalodes strain GGF6 possesses significant biotechnological potential as it has been reported for endocellulase, laccase, and other lignocellulolytic enzymes under submerged fermentation conditions. The present study attempts to enhance our knowledge of its lignocellulolytic potential as no previous omics-based analysis is available for this white-rot fungus. The transcriptomic analysis of P. petalodes GGF6 reveals the presence of 280 CAZy proteins. Furthermore, bioprospecting transcriptome signatures in the fungi revealed a diverse array of proteins associated with cellulose, hemicellulose, pectin, and lignin degradation. Interestingly, two copper-dependent lytic polysaccharide monooxygenases (AA14) and one pyrroloquinolinequinone-dependent oxidoreductase (AA12) were also identified, which are known to help in the lignocellulosic plant biomass degradation. Overall, this transcriptome profiling-based study provides deeper molecular-level insights into this Basidiomycota fungi, P. petalodes, for its potential application in diverse biotechnological applications, not only in the biofuel industry but also in the environmental biodegradation of recalcitrant molecules. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-022-01037-6.

Influence of cationic polyacrilamide flocculant on high-solids' anaerobic digestion of sewage sludge under thermophilic conditions.

Treatment of sewage sludge (SS) by biodegradable polyacrylamide-based flocculants (PAM) is considered to be an effective way to increase total solids' (TS) content prior to anaerobic digestion (AD). However, data on how PAM addition influences the efficiency of AD process are quite contradictory; moreover, no data are available for thermophilic AD (TAD). This study showed that at an optimal inoculum-to-substrate ratio (ISR, 55/45), PAM addition resulted in some decrease in initial methane production during the TAD of SS due to the formation of large flocs (up to 2-3 mm in diameter), which deteriorated the mass transfer. However, at non-optimal ISR (40/60), which led to the destabilization of TAD, PAM addition (40 mg/g TS) could restore the methanogenesis despite the inhibiting accumulation of volatile fatty acids (14-15 g/l) and pH drop (5.5). The observed positive effect of PAM-forced flocculation proposes a new interesting alternative for recovery of 'soured' reactors.

Biodegradation of di­n­butyl phthalate by psychrotolerant Sphingobium yanoikuyae strain P4 and protein structural analysis of carboxylesterase involved in the pathway.

A priority pollutant Phthalate Esters (PAEs) are widely used as plasticizers and are responsible mainly for carcinogenicity and endocrine disruption in human. For the bioremediation of PAEs, a psychrotolerant Sphingobium yanoikuyae strain P4, capable of utilizing many phthalates di­methyl phthalate (DMP), di­ethyl phthalate (DEP), di­n­butyl phthalate (DBP), di­isobutyl phthalate (DIBP), butyl benzyl phthalate (BBP), and few Polycyclic Aromatic Hydrocarbons as the sole source of carbon and energy was isolated from Palampur, Kangra, Himachal Pradesh, India. 100% utilization of DBP (1 g L-1) by the strain was observed within 24 h of incubation at 28 °C. Interestingly the strain also degraded DBP completely at 20 °C and 15 °C within 36 h and 60 h, respectively. Esterase involved in DBP degradation was found to be inducible in nature and intracellular. Comparative sequence analysis of carboxylesterase enzyme sequences revealed conserved motifs: G-X-S-X-G and -HGG- which were the characteristic peptide motifs reported in different esterases. Structural analysis showed that the enzyme belongs to serine hydrolase superfamily, which has an α/ß hydrolase fold. Interaction and binding of DBP to a catalytic Ser184 residue in the esterase enzyme were also analysed. In conclusion, carboxylesterase possess the required active site which may be involved in the catabolism of DBP.

Development and diversity of lactic acid producing bacteria and bifidobacteria in healthy full term Indian infants from Himachal Pradesh.

BACKGROUND/AIMS: The initial microbial colonization is a crucial step for the healthy development of an infant. Previous studies from India reported the dominance of target microbial species among Indian infants without any analysis on the diversity of target groups. This is the first study from India with an objective to investigate the establishment and diversity of lactic acid producing bacteria (LAB) and bifidobacteria in vaginally delivered, full term, breastfed infants for the first 4 months after birth. METHODS: Present study used polymerase chain reaction-denaturating gradient gel electrophoresis (PCR-DGGE) based sequence analysis of LAB and bifidobacteria in healthy infants. The results were used to compare the development and early colonization by LAB and bifidobacteria using diversity indices during the initial months of development of gut microbiota in infants. RESULTS: During the first 4 months, the Shannon diversity index (H) of LAB increased from 1.16 to 1.318 and for bifidobacteria the H increased from 0.975 to 1.293 (P<0.05). Higher Sorenson's pair wise similarity coefficient was observed for LAB and bifidobacteria during 2nd and the 3rd month. The species of the genera Enterococcus, Streptococcus, and Lactobacillus were dominant among the LAB group whereas Bifidobacterium breve was dominant species among Bifidobacterium group. CONCLUSIONS: Our results indicate that in breast fed infants, the microbial diversity of LAB and bifidobacteria increased during the period of study.

A simple HPLC-DAD method for simultaneous detection of two organophosphates, profenofos and fenthion, and validation by soil microcosm experiment.

Indiscriminate use of two broad spectrum pesticides, profenofos and fenthion, in agricultural system, often results in their accumulation in a non-target niche and leaching into water bodies. The present study, therefore, aims at developing a simple and rapid HPLC method that allows simultaneous extraction and detection of these two pesticides, especially in run-off water. Extraction of the two pesticides from spiked water samples using dichloromethane resulted in recovery ranging between 80 and 90%. An HPLC run of 20 min under optimized chromatographic parameters (mobile phase: methanol (75%) and water (25%); flow rate of 0.8 ml min-1; diode array detector at wavelength 210 nm) resulted in a significant difference in retention times of two pesticides (4.593 min) which allows a window of opportunity to study any possible intermediates/transformants of the parent compounds while evaluating run-off waters from agricultural fields. The HPLC method developed allowed simultaneous detection of profenofos and fenthion with a single injection into the HPLC system with 0.0328 mg l-1 (32.83 ng ml-1) being the limit of detection (LOD) and 0.0995 mg l-1 (99.5 ng ml-1) as the limit of quantification (LOQ) for fenthion; for profenofos, LOD and LOQ were 0.104 mg l-1 (104.50 ng ml-1) and 0.316 mg l-1 (316.65 ng ml-1), respectively. The findings were further validated using the soil microcosm experiment that allowed simultaneous detection and quantification of profenofos and fenthion. The findings indicate towards the practical significance of the methodology developed as the soil microcosm experiment closely mimics the agricultural run-off water under natural environmental conditions.

Molecular insights into the activity and mechanism of cyanide hydratase enzyme associated with cyanide biodegradation by Serratia marcescens.

The present study provides molecular insights into the activity and mechanism of cyanide hydratase enzyme associated with degradation of cyanide compounds, using Serratia marcescens RL2b as a model organism. Resting cells harvested after 20 h achieved complete degradation of 12 mmol l- 1 cyanide in approximately 10 h. High-performance liquid chromatography analysis of reaction samples revealed formation of formamide as the only end product, which confirmed the presence of cyanide hydratase activity in S. marcescens RL2b. Comparative structural analysis with the other nitrilase family proteins, which was carried out using a sequence of cyanide hydratase from a phylogenetically related strain S. marcescens WW4, also revealed subtle but significant differences in amino acid residues of the substrate-binding pocket and catalytic triad (Cys-Lys-Glu).

Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples.

Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.

Microbe-bio-Chemical Insight: Reviewing Interactions between Dietary Polyphenols and Gut Microbiota.

OBJECTIVE: Polyphenols are widespread constituents of different food commodities. These are regarded as essential micronutrients because of their well-documented health benefits. These health benefits depend on the amount of polyphenols consumed and their bioavailability in the gut. The microbial transformation of polyphenols in gut is poorly characterized, where, these polyphenols may act as promoting factors for proliferation of beneficial gut inhabitants and inhibiting the pathogenic species. CONCLUSION: The aim of this review is to present a holistic view on occurrence of polyphenols, their health benefits and influence of dietary polyphenols on gut microbiota.

Tricalcium phosphate solubilization and nitrogen fixation by newly isolated Aneurinibacillus aneurinilyticus CKMV1 from rhizosphere of Valeriana jatamansi and its growth promotional effect

Abstract Aneurinibacillus aneurinilyticus strain CKMV1 was isolated from rhizosphere of Valeriana jatamansi and possessed multiple plant growth promoting traits like production of phosphate solubilization (260 mg/L), nitrogen fixation (202.91 nmol ethylene mL-1 h-1), indole-3-acetic acid (IAA) (8.1 µg/mL), siderophores (61.60%), HCN (hydrogen cyanide) production and antifungal activity. We investigated the ability of isolate CKMV1 to solubilize insoluble P via mechanism of organic acid production. High-performance liquid chromatography (HPLC) study showed that isolate CKMV1 produced mainly gluconic (1.34%) and oxalic acids. However, genetic evidences for nitrogen fixation and phosphate solubilization by organic acid production have been reported first time for A. aneurinilyticus strain CKMV1. A unique combination of glucose dehydrogenase (gdh) gene and pyrroloquinoline quinone synthase (pqq) gene, a cofactor of gdh involved in phosphate solubilization has been elucidated. Nitrogenase (nif H) gene for nitrogen fixation was reported from A. aneurinilyticus. It was notable that isolate CKMV1 exhibited highest antifungal against Sclerotium rolfsii (93.58%) followed by Fusarium oxysporum (64.3%), Dematophora necatrix (52.71%), Rhizoctonia solani (91.58%), Alternaria sp. (71.08%) and Phytophthora sp. (71.37%). Remarkable increase was observed in seed germination (27.07%), shoot length (42.33%), root length (52.6%), shoot dry weight (62.01%) and root dry weight (45.7%) along with NPK (0.74, 0.36, 1.82%) content of tomato under net house condition. Isolate CKMV1 possessed traits related to plant growth promotion, therefore, could be a potential candidate for the development of biofertiliser or biocontrol agent and this is the first study to include the Aneurinibacillus as PGPR.

Tricalcium phosphate solubilization and nitrogen fixation by newly isolated Aneurinibacillus aneurinilyticus CKMV1 from rhizosphere of Valeriana jatamansi and its growth promotional effect.

Aneurinibacillus aneurinilyticus strain CKMV1 was isolated from rhizosphere of Valeriana jatamansi and possessed multiple plant growth promoting traits like production of phosphate solubilization (260mg/L), nitrogen fixation (202.91nmolethylenemL-1h-1), indole-3-acetic acid (IAA) (8.1µg/mL), siderophores (61.60%), HCN (hydrogen cyanide) production and antifungal activity. We investigated the ability of isolate CKMV1 to solubilize insoluble P via mechanism of organic acid production. High-performance liquid chromatography (HPLC) study showed that isolate CKMV1 produced mainly gluconic (1.34%) and oxalic acids. However, genetic evidences for nitrogen fixation and phosphate solubilization by organic acid production have been reported first time for A. aneurinilyticus strain CKMV1. A unique combination of glucose dehydrogenase (gdh) gene and pyrroloquinoline quinone synthase (pqq) gene, a cofactor of gdh involved in phosphate solubilization has been elucidated. Nitrogenase (nif H) gene for nitrogen fixation was reported from A. aneurinilyticus. It was notable that isolate CKMV1 exhibited highest antifungal against Sclerotium rolfsii (93.58%) followed by Fusarium oxysporum (64.3%), Dematophora necatrix (52.71%), Rhizoctonia solani (91.58%), Alternaria sp. (71.08%) and Phytophthora sp. (71.37%). Remarkable increase was observed in seed germination (27.07%), shoot length (42.33%), root length (52.6%), shoot dry weight (62.01%) and root dry weight (45.7%) along with NPK (0.74, 0.36, 1.82%) content of tomato under net house condition. Isolate CKMV1 possessed traits related to plant growth promotion, therefore, could be a potential candidate for the development of biofertiliser or biocontrol agent and this is the first study to include the Aneurinibacillus as PGPR.

Autochthonous microbial community associated with pine needle forest litterfall influences its degradation under natural environmental conditions.

The slow natural degradation of chir pine (Pinus roxburghii) needle litterfall and its accumulation on forest floors have been attributed to its lignocellulosic complexities of the biomass. The present study offers a microbiological insight into the role of autochthonous microflora associated with pine needle litterfall in its natural degradation. The denaturing gradient gel electrophoresis (DGGE) fingerprinting indicated actinomycetes (Saccharomonospora sp., Glycomyces sp., Agrococcus sp., Leifsonia sp., Blastocatella sp., and Microbacterium sp.) as a dominant microbial community associated with pine needle litterfall with the absence of fungal decomposers. On exclusion of associated autochthonous microflora from pine litterfall resulted in colonization by decomposer fungi identified as Penicillium chrysogenum and Aspergillus sp., which otherwise failed to colonize the litterfall under natural conditions. The results, therefore, indicated that the autochthonous microbial community of pine needle litterfall (dominated by actinomycetes) obstructs the colonization of litter-degrading fungi and subsequently hinders the overall process of natural degradation of litterfall.

Microbial diversity in an anaerobic digester with biogeographical proximity to geothermally active region.

Anaerobic digestion of agricultural biomass or wastes can offer renewable energy, to help meet the rise in energy demands. The performance of an anaerobic digester considerably depends upon the complex interactions between bacterial and archaeal microbiome, which is greatly influenced by environmental factors. In the present study, we evaluate a microbial community of digester located at two different geographical locations, to understand whether the biogeographical proximity of a digester to a geothermally active region has any influence on microbial composition. The comparative microbial community profiling, highlights coexistence of specific bacterial and archaeal representatives (especially, Prosthecochloris sp., Conexibacter sp., Crenarchaeota isolate (Caldivirga sp.), Metallosphaera sp., Pyrobaculum sp. and Acidianus sp.) in a digester with close proximity to geothermally active region (Site I) and their absence in a digester located far-off from geothermally active region (Site II). A Sörensen's index of similarity of 83.33% and 66.66% for bacterial and archaeal community was observed in both the reactors, respectively.

Retraction: Characterization of cellulolytic activities of newly isolated Thelephora sowerbyi from North-Western Himalayas on different lignocellulosic substrates.

Characterization of cellulolytic activities of newly isolated Thelephora sowerbyi from North-Western Himalayas on different lignocellulosic substrate J. Basic Microbiol. 2015, 55, 1-11 - DOI: 10.1002/jobm.201500107 The above article from the Journal of Basic Microbiology, published online on 08 June 2015 in Wiley Online Library as Early View (http://onlinelibrary.wiley.com/doi/10.1002/jobm.201500107/pdf), has been retracted by agreement between the authors, the Editor-in-Chief and Wiley-VCH GmbH & Co. KGaA. The retraction has been agreed because the microorganism studied in the described experiments has been identified as the fungus Cotylidia pannosa (Gene Accession No. KT008117) instead of Thelephora sowerbyi. The culture has been identified on the basis of the sequence of the amplified ITS region of the microorganism which was submitted by the authors to the NCBI database.