Molecular diversity of tannic acid degrading bacteria isolated from tannery soil

A comprehensive review on biological funnel mechanism in lignin valorization: Pathways and enzyme dynamics

Lignin, a significant byproduct of the paper and pulp industry, is attracting interest due to its potential utilization in biomaterial-based sectors and biofuel production. Investigating biological methods for converting lignin into valuable products is crucial for effective utilization and has recently gained growing attention. Several microorganisms effectively decomposed low molecular weight lignins, transforming them into intermediate compounds via upper and lower metabolic pathways. This review focuses on assessing bacterial metabolic pathways involved in the breakdown of lignin into aromatic compounds and their subsequent utilization by different bacteria through various metabolic pathways. Understanding these pathways is essential for developing efficient synthetic metabolic systems to valorize lignin and obtain valuable industrial aromatic chemicals. The concept of "biological funneling," which involves examining key enzymes, their interactions, and the complex metabolic pathways associated with lignin conversion, is crucial in lignin valorization. By manipulating lignin metabolic pathways and utilizing biological routes, many aromatic compounds can be synthesized within cellular factories. Although there is insufficient evidence regarding the complete metabolism of polyaromatic hydrocarbons by particular microorganisms, understanding lignin-degrading enzymes, regulatory mechanisms, and interactions among various enzyme systems is essential for optimizing lignin valorization. This review highlights recent advancements in lignin valorization, bio-funneling, multi-omics, and analytical characterization approaches for aromatic utilization. It provides up-to-date information and insights into the latest research findings and technological innovations. The review offers valuable insights into the future potential of biological routes for lignin valorization.

Do epiphytic lichens negatively impact their hosts through allelopathy? The effect of Evernia esorediosa on growth and biochemical processes of Larix gmelinii

The question of the nature of the interaction between epiphytic lichens and their host trees remains highly debated. Some authors showed cases of allelopathy, but this needs further investigation. Our study covers the effects caused by the epiphytic lichen Evernia esorediosa (Müll. Arg.) Du Rietz on growth and biochemical processes in Larix gmelinii (Rupr.) Rupr. ex Kuzen trees in cryolithozone boreal forests. Usnic acid (UA) is shown to migrate from the thalli of E. esorediosa in the bark and phloem of L. gmelinii, from which it is transported to the root system of the tree, and then UA is moved upward through the xylem into tree needles. Accumulation of UA in L. gmelinii needles causes the following effects: inhibition of photosynthesis, cellular respiration and oxidative phosphorylation. These disruptions could reflect on the tree growth processes. The L. gmelinii trees inhabited by the epiphytic lichen E. esorediosa were found to show lower radial and apical growth parameters. Our results show that E. esorediosa exhibits an allelopathic effect toward L. gmelinii through the migration of UA from the lichen thalli to the tissues of the tree, which led to inhibition of energetic processes in cells. This caused the tree growth to slow down and could ultimately lead to its death.

Anti-Oomycete Activity and Pepper Root Colonization of Pseudomonas plecoglossicida YJR13 and Pseudomonas putida YJR92 against Phytophthora capsici

Previously, Pseudomonas plecoglossicida YJR13 and Pseudomonas putida YJR92 from a sequential screening procedure were proven to effectively control Phytophthora blight caused by Phytophthora capsici. In this study, we further investigated the anti-oomycete activities of these strains against mycelial growth, zoospore germination, and germ tube elongation of P. capsici. We also investigated root colonization ability of the bacterial strains in square dishes, including cell motility (swimming and swarming motilities) and biofilm formation. Both strains significantly inhibited mycelial growth in liquid and solid V8 juice media and M9 minimal media, zoospore germination, and germ tube elongation compared with Bacillus vallismortis EXTN-1 (positive biocontrol strain), Sphingomonas aquatilis KU408 (negative biocontrol strain), and MgSO4 solution (untreated control). In diluted (nutrient-deficient) V8 juice broth, the tested strain populations were maintained at >108 cells/ml, simultaneously providing mycelial inhibitory activity. Additionally, these strains colonized pepper roots at a 106 cells/ml concentration for 7 days. The root colonization of the strains was supported by strong swimming and swarming activities, biofilm formation, and chemotactic activity towards exudate components (amino acids, organic acids, and sugars) of pepper roots. Collectively, these results suggest that strains YJR13 and YJR92 can effectively suppress Phytophthora blight of pepper through direct anti-oomycete activities against mycelial growth, zoospore germination and germ tube elongation. Bacterial colonization of pepper roots may be mediated by cell motility and biofilm formation together with chemotaxis to root exudates.

Metabolic activity and bioweathering properties of yeasts isolated from different supraglacial environments of Antarctica and Himalaya

Yeasts have been frequently isolated from cold habitats, but their contribution to essential ecological processes such as the mineralization of organic matter in these environments is less known. Here, the diversity, metabolic capability, and extracellular enzyme profiles of yeasts from snow, blue ice and cryoconite hole environments from East Antarctica and cryoconite holes from a glacier in Western Himalaya were determined. Eighty-six yeast strains isolated were affiliated to the genera Glaciozyma, Goffeauzyma, Mrakia, Phenoliferia, and Rhodotorula. Variations in the abundance, diversity, physiological properties, extracellular enzyme and carbon substrate utilization patterns of the isolated yeasts, reflect the specific environmental conditions from which they were isolated. Overall, 20-90% of the yeasts across all habitat types and geographical locations produced extracellular enzymes to degrade proteins, esters, carbohydrates, pectin, cellulose, lignin, and tannin. About 10 and 29% of the yeasts also exhibited ability to solubilize rock-minerals like phosphate and silicate, respectively. Additionally, selected isolates were able to metabolize 28-93% of the carbon substrates comprising different compound classes on Biolog YT plates. Overall, the ability of yeasts to use diverse organic compounds prevalent on the glacier surface, points to their ecological significance in the decomposition of organic matter, cycling of nutrients, and in the weathering of minerals in supraglacial environments. Moreover, their wide metabolic capabilities suggest that they can colonize new niches and environments when meltwater export during the summer that enables links with surrounding ecosystems.

Performance of Slow-Growing Male Muscovy Ducks Exposed to Different Dietary Levels of Quebracho Tannin

Simple Summary

Different inclusion levels of Quebracho tannin (QT) in the diet of growing male Muscovy ducks of a slow-growing type were explored under free-range conditions. As a result of the dietary treatments tested in this trial, the growth performance or the total blood proteins were not affected. By contrast, dietary QT did not lead birds to produce less moist excreta, as observed in other bird species, as a desirable aspect for intensively raised poultry. A marked improvement in carcass yield was observed as a desirable economic trait in the extensive slow-type duck farming system.

Abstract

The study of the nutritional effects of tannins is complex due to the large chemical diversity; consequently, in poultry nutrition the biological responses may vary greatly. The aim of the present study was to evaluate the effect of different levels of dietary Quebracho tannins (QT) on growth and production performance in slow-growing type Muscovy ducks. For this purpose, a 42-d trial was carried out on 126 male ducks (42-d old at start), fed on three levels of dietary QT inclusion in the diet (0% as control diet, vs. 1.5% vs. 2.5% on an as fed basis). Birds were reared under free-range conditions. A linear increase in feed intake as a function of QT inclusion in the diet was observed (p < 0.05). No difference as to final body weight, overall average daily weight gain (ADG) and total feed conversion ratio (FCR) in relation to dietary treatments was observed. Carcass yields were positively improved in QT birds (p < 0.05). No adverse responses were recorded in total blood protein and liver weight. Dietary QT might be safely used up by to 2.5% in 42- to 84-d aged male Muscovy ducks.

The construction of novel and efficient hafnium catalysts using naturally existing tannic acid for Meerwein-Ponndorf-Verley reduction

The conversion of carbonyl compounds into alcohols or their derivatives via the catalytic transfer hydrogenation (CTH) process known as Meerwein-Ponndorf-Verley reduction is an important reaction in the reaction chain involved in biomass transformation. The rational design of efficient catalysts using natural and renewable materials is critical for decreasing the catalyst cost and for the sustainable supply of raw materials during catalyst preparation. In this study, a novel hafnium-based catalyst was constructed using naturally existing tannic acid as the ligand. The prepared hafnium-tannic acid (Hf-TA) catalyst was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and thermogravimetry (TG). Hf-TA was applied in the conversion of furfuraldehyde (FD) to furfuryl alcohol (FA) using isopropanol (2-PrOH) as both the reaction solvent and the hydrogen source. Both preparation conditions and the effects of the reaction parameters on the performance of the catalyst were studied. Under the relatively mild reaction conditions of 70 °C and 3 h, FD (1 mmol) could be converted into FA with a high yield of 99.0%. In addition, the Hf-TA catalyst could be reused at least ten times without a notable decrease in activity and selectivity, indicating its excellent stability. It was proved that Hf-TA could also catalyze the conversion of various carbonyl compounds with different structures. The high efficiency, natural occurrence of tannic acid, and facile preparation process make Hf-TA a potential catalyst for applications in the biomass conversion field.

Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database

Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.

Microbial dynamics and metabolite changes in Chinese Rice Wine fermentation from sorghum with different tannin content

Chinese rice wine (CRW) is the oldest kind of wine in China and is mainly fermented by wheat Qu and yeast with rice, millet, etc. This gives CRW a unique quality, but the flavor components are complex. Its formation is related to microorganisms, but the link between CRW and microorganisms is poorly understood. Here, we used two kinds of sorghum (JZ22 and JB3, of which JZ22 has a higher tannin content) as the raw materials to brew and determined the structural and functional dynamics of the microbiota by metagenomics and flavor analyses. We detected 106 (JZ22) and 109 (JB3) volatile flavor compounds and 8 organic acids. By correlation analysis, we established 687 (JZ22) and 496 (JB3) correlations between the major flavor compounds and microbes. In JZ22, Blautia, Collinsella, Bifidobacterium, Faecalibacterium and Prevotella had the most correlations with flavor production. In JB3, the top 5 genera were Stenotrophomonas, Bdellovibrio, Solibacillus, Sulfuritalea and Achromobacter. In addition, more esters were detected, and more microorganisms correlated with ester generation in JZ22. This study provides a new idea for the micro ecological diversity of CRW fermented with sorghum. This is of significance for improving the quality and broadening the CRW varieties.

Diversity of lactic acid bacteria from Miang, a traditional fermented tea leaf in northern Thailand and their tannin-tolerant ability in tea extract

The microbiota of lactic acid bacteria (LAB) in thirty-five samples of Miang, a traditional fermented tea leaf product, collected from twenty-two different regions of eight provinces in upper northern Thailand was revealed through the culture-dependent technique. A total of 311 presumptive LAB strains were isolated and subjected to clustering analysis based on repetitive genomic element-PCR (rep-PCR) fingerprinting profiles. The majority of the strains belonged to the Lactobacillus genera with an overwhelming predominance of the Lb. plantarum group. Further studies of species-specific PCR showed that 201 of 252 isolates in the Lb. plantarum group were Lb. plantarum which were thus considered as the predominant LAB in Miang, while the other 51 isolates belonged to Lb. pentosus. In contrast to Lb. plantarum, there is a lack of information on the tannase gene and the tea tannin-tolerant ability of Lb. pentosus. Of the 51 Lb. pentosus isolates, 33 were found to harbor the genes encoding tannase and shared 93-99% amino acid identity with tannase obtained from Lb. pentosus ATCC 8041^T. Among 33 tannase gene-positive isolates, 23 isolates exhibited high tannin- tolerant capabilities when cultivated on de Man Rogosa and Sharpe agar-containing bromocresol purple (0.02 g/L, MRS-BCP) supplemented with 20% (v/v) crude tea extract, which corresponded to 2.5% (w/v) tannins. These Lb. pentosus isolates with high tannin-tolerant capacity are expected to be the high potential strains for functional tannase production involved in Miang fermentation as they will bring about certain benefits and could be used to improve the fermentation of tea products.

Environmental Pollution, Toxicity Profile and Treatment Approaches for Tannery Wastewater and Its Chemical Pollutants

Leather industries are key contributors in the economy of many developing countries, but unfortunately they are facing serious challenges from the public and governments due to the associated environmental pollution. There is a public outcry against the industry due to the discharge of potentially toxic wastewater having alkaline pH, dark brown colour, unpleasant odour, high biological and chemical oxygen demand, total dissolved solids and a mixture of organic and inorganic pollutants. Various environment protection agencies have prioritized several chemicals as hazardous and restricted their use in leather processing however; many of these chemicals are used and discharged in wastewater. Therefore, it is imperative to adequately treat/detoxify the tannery wastewater for environmental safety. This paper provides a detail review on the environmental pollution and toxicity profile of tannery wastewater and chemicals. Furthermore, the status and advances in the existing treatment approaches used for the treatment and/or detoxification of tannery wastewater at both laboratory and pilot/industrial scale have been reviewed. In addition, the emerging treatment approaches alone or in combination with biological treatment approaches have also been considered. Moreover, the limitations of existing and emerging treatment approaches have been summarized and potential areas for further investigations have been discussed. In addition, the clean technologies for waste minimization, control and management are also discussed. Finally, the international legislation scenario on discharge limits for tannery wastewater and chemicals has also been discussed country wise with discharge standards for pollution prevention due to tannery wastewater.

Distribution of tannin-'tolerant yeasts isolated from Miang, a traditional fermented tea leaf (Camellia sinensis var. assamica) in northern Thailand

Miang is a fermented food product prepared from the tea leaves of Camellia sinensis var. assamica, and is traditionally produced in mountainous areas of northern Thailand. Although Miang has a long history and reveals deep-rooted cultural involvement with local people in northern Thailand, little is known regarding its microbial diversity. Yeasts were isolated from 47 Miang samples collected from 28 sampling sites, including eight provinces in upper northern Thailand. A hundred and seven yeast isolates were recovered and identified within 14 species based on the comparison of the D1/D2 sequence of the large subunit (LSU) rRNA gene. Candida ethanolica was determined to be the dominant species that was frequently found in Miang together with minor resident yeast species. All yeast isolates demonstrated their tannin-tolerant capability when cultivated on yeast malt agar (YMA) containing 50g/l tannin, but nine isolates displayed clear zones forming around their colonies, e.g., Debaryomyces hansenii, Cyberlindnera rhodanensis, and Sporidiobolus ruineniae. The results obtained from a visual reading method of tannase revealed that all yeast isolates were positive for methyl gallate, indicating that they possess tannase activity. It is assumed that a tannin-tolerant ability is one of the most important factors for developing a yeast community in Miang. This research study is the first report to describe tannin-tolerant yeasts and yeast communities in traditionally fermented tea leaves.

Bacteria Present in Comadia redtenbacheri Larvae (Lepidoptera: Cossidae)

The external and internal culturable bacterial community present in the larvae of Comadia redtenbacheri Hammerschmidt, an edible insect, was studied. Characterization of the isolates determined the existence of 18 morphotypes and phylogenetic analysis of the 16S rRNA gene revealed the existence of Paenibacillus sp., Bacillus safensis, Pseudomonas sp., Bacillus pseudomycoides, Corynebacterium variabile, Enterococcus sp., Gordonia sp., Acinetobacter calcoaceticus, Arthrobacter sp., Micrococcus sp., and Bacillus cereus. Greater diversity of bacteria was found in those larvae obtained from vendors than in those directly taken from Agave plants in nature. Many of the larvae obtained from vendors presented signs of potential disease, and after the analysis, results showed a greater bacterial community compared with the larvae with a healthy appearance. This indicates that bacterial flora can vary in accordance with how the larvae are handled during extraction, collection, and transport.

Zearalenone degradation by two Pseudomonas strains from soil

This study describes the screening of soil bacteria for their capability to degrade zearalenone (ZEN), employing an enrichment technique in which ZEN is used as the sole carbon source. Two isolates that were able to degrade ZEN belonged to the genus Pseudomonas according to biochemical characterization and 16S rRNA gene sequence and were named as Pseudomonas alcaliphila TH-C1 and Pseudomonas plecoglossicida TH-L1, respectively. The results showed that the degradation rates of P. alcaliphila TH-C1 and P. plecoglossicida TH-L1 for ZEN (2 μg/ml) were 68 ± 0.85 % and 57 ± 0.73%, when incubated for 72 h at 30 °C in a rotary shaker (160 rpm) and detected by high-performance liquid chromatograms (HPLC). These results suggest that the two Pseudomonas strains are new bacterial resource for degrading ZEN and can provide a new approach for the detoxification of ZEN.

Biosynthesis, structural architecture and biotechnological potential of bacterial tannase: a molecular advancement

Tannin-rich materials are abundantly generated as wastes from several agroindustrial activities. Therefore, tannase is an interesting hydrolase, for bioconversion of tannin-rich materials into value added products by catalyzing the hydrolysis of ester and depside bonds and unlocked a new prospect in different industrial sectors like food, beverages, pharmaceuticals, etc. Microorganisms, particularly bacteria are one of the major sources of tannase. In the last decade, cloning and heterologous expression of novel tannase genes and structural study has gained momentum. In this article, we have emphasized critically on bacterial tannase that have gained worldwide research interest for their diverse properties. The present paper delineate the developments that have taken place in understanding the role of tannase action, microbial sources, various cultivation aspects, downstream processing, salient biochemical properties, structure and active sites, immobilization, efforts in cloning and overexpression and with special emphasis on recent molecular and biotechnological achievements.

Uncovering the Lactobacillus plantarum WCFS1 gallate decarboxylase involved in tannin degradation

Lactobacillus plantarum is a lactic acid bacterium able to degrade tannins by the subsequent action of tannase and gallate decarboxylase enzymes. The gene encoding tannase had previously been identified, whereas the gene encoding gallate decarboxylase is unknown. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of gallic-acid induced L. plantarum extracts showed a 54-kDa protein which was absent in the uninduced cells. This protein was identified as Lp_2945, putatively annotated UbiD. Homology searches identified ubiD-like genes located within three-gene operons which encoded the three subunits of nonoxidative aromatic acid decarboxylases. L. plantarum is the only bacterium in which the lpdC (lp_2945) gene and the lpdB and lpdD (lp_0271 and lp_0272) genes are separated in the chromosome. Combination of extracts from recombinant Escherichia coli cells expressing the lpdB, lpdC, and lpdC genes demonstrated that LpdC is the only protein required to yield gallate decarboxylase activity. However, the disruption of these genes in L. plantarum revealed that the lpdB and lpdC gene products are essential for gallate decarboxylase activity. Similar to L. plantarum tannase, which exhibited activity only in esters derived from gallic and protocatechuic acids, purified His6-LpdC protein from E. coli showed decarboxylase activity against gallic and protocatechuic acids. In contrast to the tannase activity, gallate decarboxylase activity is widely present among lactic acid bacteria. This study constitutes the first genetic characterization of a gallate decarboxylase enzyme and provides new insights into the role of the different subunits of bacterial nonoxidative aromatic acid decarboxylases.

Microbial community structure at different fermentation stages of kutajarista, a herbal formulation

Kutajarista is an Ayurvedic fermented herbal formulation prescribed for gastrointestinal disorders. This herbal formulation undergoes a gradual fermentative process and takes around 2 months for production. In this study, microbial composition at initial stages of fermentation of Kutajarista was assessed by culture independent 16S rRNA gene clone library approach. Physicochemical changes were also compared at these stages of fermentation. High performance liquid chromatography-mass spectrometry analysis showed that Gallic acid, Ellagic acid, and its derivatives were the major chemical constituents recovered in this process. At 0 day of fermentation, Lactobacillus sp., Acinetobacter sp., Alcaligenes sp., and Methylobacterium sp. were recovered, but were not detected at 8 day of fermentation. Initially, microbial diversity increased after 8 days of fermentation with 11 operational taxonomic units (OTUs), which further decreased to 3 OTUs at 30 day of fermentation. Aeromonas sp., Pseudomonas sp., and Klebsiella sp. dominated till 30 day of fermentation. Predominance of γ- Proteobacteria and presence of gallolyl derivatives at the saturation stage of fermentation implies tannin degrading potential of these microbes. This is the first study to highlight the microbial role in an Ayurvedic herbal product fermentation.

Cultivation-independent analysis of archaeal and bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into methane

Biogenic origin of the significant proportion of coal bed methane has indicated the role of microbial communities in methanogenesis. By using cultivation-independent approach, we have analysed the archaeal and bacterial community present in the formation water of an Indian coal bed at 600-700 m depth to understand their role in methanogenesis. Presence of methanogens in the formation water was inferred by epifluorescence microscopy and PCR amplification of mcrA gene. Archaeal 16S rRNA gene clone library from the formation water metagenome was dominated by methanogens showing similarity to Methanobacterium, Methanothermobacter and Methanolinea whereas the clones of bacterial 16S rRNA gene library were closely related to Azonexus, Azospira, Dechloromonas and Thauera. Thus, microbial community of the formation water consisted of predominantly hydrogenotrophic methanogens and the proteobacteria capable of nitrogen fixation, nitrate reduction and polyaromatic compound degradation. Methanogenic potential of the microbial community present in the formation water was elucidated by the production of methane in the enrichment culture, which contained 16S rRNA gene sequences showing close relatedness to the genus Methanobacterium. Microcosm using formation water as medium as well as a source of inoculum and coal as carbon source produced significant amount of methane which increased considerably by the addition of nitrite. The dominance of Diaphorobacter sp. in nitrite amended microcosm indicated their important role in supporting methanogenesis in the coal bed. This is the first study indicating existence of methanogenic and bacterial community in an Indian coal bed that is capable of in situ biotransformation of coal into methane.

Two-phase olive mill waste composting: community dynamics and functional role of the resident microbiota

In this study, physico-chemical modifications and community dynamics and functional role of the resident microbiota during composting of humid husk from a two-phase extraction system (TPOMW) were investigated. High mineralization and humification of carbon, low loss of nitrogen and complete degradation of polyphenols led to the waste biotransformation into a high-quality compost. Viable cell counts and denaturing gradient gel electrophoresis (DGGE) profiling of the 16S rRNA genes showed that the thermophilic phase was characterized by the strongest variations of cell number, the highest biodiversity and the most variable community profiles. The isolation of tannin-degrading bacteria (e.g. Lysinibacillus fusiformis, Kocuria palustris, Tetrathiobacter kashmirensis and Rhodococcus rhodochrous) suggested a role of this enzymatic activity during the process. Taken together, the results indicated that the composting process, particularly the thermophilic phase, was characterized by a rapid succession of specialized bacterial populations with key roles in the organic matter biotransformation.

Intraspecific genetic variability of Edwardsiella tarda strains from cultured turbot

Edwardsiella tarda is an enterobacterial fish pathogen that causes mortality in various fish species worldwide. In this study, we analyzed the intraspecific variability in a collection of E. tarda strains isolated from turbot. To do this we employed 4 polymerase chain reaction (PCR)-based methods: (1) random amplified polymorphic DNA (RAPD), (2) enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), (3) repetitive extragenic palindromic-PCR (REP-PCR) and (4) BOX-PCR. E. tarda isolates from different hosts were also included for comparison. E. tarda strains from turbot showed high molecular homogeneity when RAPD (primers P3 and P6), ERIC-PCR and BOX-PCR were employed. However, with regard to the REP-PCR and RAPD (primers P4 and P5) techniques, different genetic groups could be established within these isolates using either technique. The 2 RAPD types presented an 85% similarity, while those obtained with REP-PCR showed 74% similarity. Based on the results obtained, although a high genetic homogeneity was found in turbot isolates, the RAPD test (with primers P4 and P5) and REP-PCR were capable of discrimination within these strains, and they are therefore considered the most appropriate typing methods for studies of edwardsiellosis in turbot.

Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida

Gallic acid (3,4,5-trihydroxybenzoic acid, GA) is widely distributed in nature, being a major phenolic pollutant and a commonly used antioxidant and building-block for drug development. We have characterized the first complete cluster (gal genes) responsible for growth in GA in a derivative of the model bacterium Pseudomonas putida KT2440. GalT mediates specific GA uptake and chemotaxis, and highlights the critical role of GA transport in bacterial adaptation to GA consumption. The proposed GA degradation via the central intermediate 4-oxalomesaconic acid (OMA) was revisited and all enzymes involved have been identified. Thus, GalD is the prototype of a new subfamily of isomerases that catalyses a biochemical step that remained unknown, i.e. the tautomerization of the OMAketo generated by the GalA dioxygenase to OMAenol. GalB is the founding member of a new family of zinc-containing hydratases that converts OMAenol into 4-carboxy-4-hydroxy-2-oxoadipic acid (CHA). galC encodes the aldolase catalysing CHA cleavage to pyruvic and oxaloacetic acids. The presence of homologous gal clusters outside the Pseudomonas genus sheds light on the evolution and ecology of the gal genes in GA degraders. The gal genes were used for expanding the metabolic abilities of heterologous hosts towards GA degradation, and for engineering a GA cellular biosensor.

Effect of tannic acid on Lactobacillus plantarum wine strain during starvation: A proteomic study

The molecular mechanisms involved in tannic-acid (TA)-mediated cell growth retardation and viability prolongation of Lactobacillus plantarum VP08 strain were evaluated by a proteomic analysis of starved cells grown in the presence of TA or glucose as carbon source. The tannase activity and the cell growth retardation as well as viability prolongation were confirmed by enzymatic assay and growing tests, respectively. In order to gain information about the effect triggered at the molecular level by TA, total proteins (extracted from starved cells grown in 250 mg/L TA, or 2 g/L glucose) were analyzed by a 2D-PAGE/MS approach to detect differentially expressed proteins. A total of 15 spots were found to be down-regulated and 21 up-regulated in TA-grown cells. The results indicate an overall impact of TA on proteins involved in some cellular and metabolic pathways: glycolysis, amino acid metabolism, translation and protein folding. The modulation of specific proteins correlates with the positive effect of TA on the survival of tannase-positive L. plantarum.

Characterization of arsenic resistant and arsenopyrite oxidizing Acidithiobacillus ferrooxidans from Hutti gold leachate and effluents

Four arsenic resistant ferrous oxidizers were isolated from Hutti Gold Mine Ltd. (HGML) samples. Characterization of these isolates was done using conventional microbiological, biochemical and molecular methods. The ferrous oxidation rates with these isolates were 16, 48, 34 and 34 mg L(-1)h(-1) and 15, 47, 34 and 32 mg L(-1)h(-1) in absence and presence of 20 mM of arsenite (As3+) respectively. Except isolate HGM 8, other three isolates showed 2.9-6.3% inhibition due to the presence of 20 mM arsenite. Isolate HGM 8 was able to grow in presence of 14.7 g L(-1) of arsenite, with 25.77 mg L(-1)h(-1) ferrous oxidation rate. All the four isolates were able to oxidize iron and arsenopyrite from 20 g L(-1) and 40 g L(-1) refractory gold ore and 20 g L(-1) refractory gold concentrate. Once the growth was established pH adjustment was not needed inspite of ferrous oxidation, which could be due to concurrent oxidation of pyrite. Isolate HGM 8 showed the final cell count of as high as 1.12 x 10(8) cells mL(-1) in 40 g L(-1) refractory gold ore. The isolates were grouped into one haplotypes by amplified ribosomal DNA restriction analysis (ARDRA). The phylogenetic position of HGM 8 was determined by 16S rDNA sequencing. It was identified as Acidithiobacillus ferrooxidans and strain name was given as SRHGM 1.

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.

Exploration of soil bacterial communities for their potential as bioresource

Soil is a repository of diverse microorganisms, which has frequently been used to isolate and exploit microbes for industrial, environmental and agricultural applications. Knowledge about the structure and dynamics of bacterial communities in soil has been limited as only a small fraction of bacterial diversity is accessible to culture methods. Traditional enrichment techniques and the pure culture approach for microbiological studies have offered only a narrow portal for examining the soil microbial flora due to their limited selectivity. Therefore, the morphological and nutritional criteria used to describe bacterial community failed to provide a natural taxonomic order according to evolutionary relationship. Molecular methods under an emerging discipline of biology "molecular microbial ecology" are now helping in getting these constraints removed to some extent. Nucleic acid extraction from soil is the first crucial step in the application of most of the molecular techniques, which have largely been dominated by diverse variations of PCR. Due to its rapidity, sensitivity and specificity, PCR-based finger printing techniques have proved extremely useful in assessing the changes in microbial community structure. Such techniques can yield complex community profiles and can also provide useful phylogenetic information. Fluorescent in situ hybridization (FISH) can be used to evaluate the distribution and function of bacterial population in situ. DNA microarray techniques have also been developed and being frequently used for the evaluation of ecological role and phylogenetic affiliations of bacterial populations in the soil.

Enrichment for microbes living in association with plant tissues

AIMS

To investigate a cultivation-independent method of enrichment for microbes living in association with plant tissues.

METHODS AND RESULTS

A large quantity of leaves or seeds was enzymatically hydrolyzed, and the pellets were collected by differential centrifugation. Enzyme concentration, buffer and incubation time were optimized for release of plant-associated microbes. The relative abundance of plant nuclear DNA and bacterial DNA in the enriched sample was estimated by PCR amplification of genome-specific marker genes. The efficiency of microbe enrichment was estimated from the proportion of bacterium-derived clones and their restriction fragment length polymorphism (RFLP) types as detected by 16S rRNA gene-based techniques. With a higher ratio of bacterial to plant nuclear DNA, the enriched samples showed a considerably enhanced proportion of bacterium-derived clones and a wider sequence diversity of those clones.

CONCLUSIONS

The method described here proved to be remarkably effective in enriching for bacteria living in association with plant tissues.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method can be applied to study plant-associated microbes in the field of environmental molecular ecology and environmental metagenomics.

Formation of water-soluble metal cyanide complexes from solid minerals by Pseudomonas plecoglossicida

A few Pseudomonas species are able to form hydrocyanic acid (HCN), particularly when grown under glycine-rich conditions. In the presence of metals, cyanide can form water-soluble metal complexes of high chemical stability. We studied the possibility to mobilize metals as cyanide complexes from solid minerals using HCN-forming microorganisms. Pseudomonas plecoglossicida was cultivated in the presence of copper- and nickel-containing solid minerals. On powdered elemental nickel, fast HCN generation within the first 12 h of incubation was observed and water-soluble tetracyanaonickelate was formed. Cuprite, tenorite, chrysocolla, malachite, bornite, turquoise, millerite, pentlandite as well as shredded electronic scrap was also subjected to a biological treatment. Maximum concentrations of cyanide-complexed copper corresponded to a solubilization of 42% and 27% when P. plecoglossicida was grown in the presence of cuprite or tenorite, respectively. Crystal system, metal oxidation state and mineral hydrophobicity might have a significant influence on metal mobilization. However, it was not possible to allocate metal mobilization to a single mineral property. Cyanide-complexed gold was detected during growth on manually cut circuit boards. Maximum dicyanoaurate concentration corresponded to a 68.5% dissolution of the total gold added. These findings represent a novel type of microbial mobilization of nickel and copper from solid minerals based on the ability of certain microbes to form HCN.