scholarly journals Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad

2021 ◽  
Vol 9 (6) ◽  
pp. 1167
Author(s):  
Amanda C. Ramdass ◽  
Sephra N. Rampersad
Keyword(s):  
Crude Oil ◽  
Contaminated Soils ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Industrial Applications ◽  
Microbial Composition ◽  
Sequence Comparisons ◽  
Multiple Sequence ◽  
Terrestrial Environments

Trinidad and Tobago is the largest producer of oil and natural gas in Central America and the Caribbean. Natural crude oil seeps, in addition to leaking petroleum pipelines, have resulted in chronic contamination of the surrounding terrestrial environments since the time of petroleum discovery, production, and refinement in Trinidad. In this study, we isolated microbes from soils chronically contaminated with crude oil using a culture-dependent approach with enrichment. The sampling of eight such sites located in the southern peninsula of Trinidad revealed a diverse microbial composition and novel oil-degrading filamentous fungi and yeast as single-isolate degraders and naturally occurring consortia, with specific bacterial species not previously reported in the literature. Multiple sequence comparisons and phylogenetic analyses confirmed the identity of the top degraders. The filamentous fungal community based on culturable species was dominated by Ascomycota, and the recovered yeast isolates were affiliated with Basidiomycota (65.23%) and Ascomycota (34.78%) phyla. Enhanced biodegradation of petroleum hydrocarbons is maintained by biocatalysts such as lipases. Five out of seven species demonstrated extracellular lipase activity in vitro. Our findings could provide new insights into microbial resources from chronically contaminated terrestrial environments, and this information will be beneficial to the bioremediation of petroleum contamination and other industrial applications.

scholarly journals The diversity of fungi consortium isolated from polluted soil for degrading petroleum hydrocarbon

2021 ◽  
Vol 22 (11) ◽  
Author(s):  
RIRYN NOVIANTY ◽  
ANNISA HIDAYAH ◽  
SARYONO SARYONO ◽  
AMIR AWALUDDIN ◽  
NOVA WAHYU PRATIWI ◽  
...  
Keyword(s):  
Crude Oil ◽  
Petroleum Hydrocarbon ◽  
Oil Spills ◽  
Petroleum Industry ◽  
Degradation Process ◽  
Petroleum Products ◽  
Industrial Applications ◽  
Polluted Soil ◽  
Gas Chromatography Mass Spectrometry ◽  
Terrestrial Environments

Abstract. Novianty R, Saryono, Awaluddin A, Pratiwi NW, Hidayah A, Juliantari E. 2021. The diversity of fungi consortium isolated from polluted soil for degrading petroleum hydrocarbon. Biodiversitas 22: 5077-5084. One of the major problems in the petroleum industry nowadays is crude oil spills. Riau Province, Sumatra is one of the largest oil producers in Indonesia. Accidental releases of petroleum products are of particular concern to the environment. The process of drilling and refining petroleum generates a large amount of oil sludge. One of the effective technologies used in the waste degradation process is bioremediation using certain microorganisms. The prime objective of the current research was to evaluate the efficiency of fungi consortiums in crude oil degradation in Bumi Siak Pusako-Pertamina Hulu, Indonesia. There are three potential fungi isolates as petroleum hydrocarbon degradation agents with four consortium variations. The parameter values of Optical Density (OD), pH, and diluted CO2 were measured on 0, 4, 8, and 16 days. To evaluate the fungal biodegradation activity using Gas Chromatography-Mass Spectrometry (GC-MS). The result showed that consortium II (KF II) has the highest potential to degrade petroleum hydrocarbon (50.61%). The visual GC-MS examination confirmed a decrease in the peak area for eight hydrocarbon compounds, indicating the efficiency of the fungi in the oil decomposition and dismantling of hydrocarbons. Our findings may provide new information on native fungal resources from chronically contaminated terrestrial environments, and will be useful for petroleum-contaminated bioremediation and other industrial applications.  

scholarly journals Study on a Fermented Whole Wheat: Phenolic Content, Activity on PTP1B Enzyme and In Vitro Prebiotic Properties

Molecules ◽  
2019 ◽  
Vol 24 (6) ◽  
pp. 1120 ◽  
Author(s):  
Diletta Balli ◽  
Maria Bellumori ◽  
Paolo Paoli ◽  
Giuseppe Pieraccini ◽  
Monica Di Paola ◽  
...  
Keyword(s):  
Lactobacillus Reuteri ◽  
Tyrosine Phosphatase ◽  
Bacterial Species ◽  
Food Ingredient ◽  
Microbial Composition ◽  
Acidic Hydrolysis ◽  
Inhibitory Power ◽  
Methyl Ferulate ◽  
First Time

Fermented cereals, staple foods in Asia and Africa, are recently receiving a growing interest in Western countries. The object of this work is the characterization of a fermented wheat used as a food ingredient and dietary supplement. To this aim, the phenolic composition, the activity on protein tyrosine phosphatase 1B (PTP1B), an enzyme overexpressed in type-II diabetes, the in vitro prebiotic properties on Lactobacillus reuteri and the microbial composition were investigated. Basic and acidic hydrolysis were tested for an exhaustive recovery of bound phenols: the acidic hydrolysis gave best yields. Methyl ferulate and neocarlinoside were identified for the first time in wheat. The inhibitory power of the extracts of several batches were investigated on PTP1B enzyme. The product was not able to inhibit the enzyme, otherwise, for the first time, a complete inhibition was observed for schaftoside, a major C-flavonoid of wheat. The microbial composition was assessed identifying Lactobacillus, Enterococcus, and Pediococcus as the main bacterial species. The fermented wheat was a suitable substrate for the grown of L. reuteri, recognized for its health properties in the human gut. The proposed method for phenols is easier compared to those based on strong basic hydrolysis; our results assessed the bound phenols as the major fraction, differently from that suggested by the literature for fermented cereals.

scholarly journals Characterization of Hydrocarbon Utilizing Bacteria and Fungi Associated with Crude Oil Contaminated Soil

2020 ◽  
pp. 54-69
Author(s):  
D. N. Ogbonna ◽  
S. I. Douglas ◽  
V. G. Awari
Keyword(s):  
Crude Oil ◽  
Contaminated Soil ◽  
Contaminated Soils ◽  
Heterotrophic Bacteria ◽  
Anthropogenic Activities ◽  
Bacterial Species ◽  
Soil Conditions ◽  
Penicillium Species ◽  
Hydrocarbon Utilizing Bacteria

Many substances known to have toxic properties are regularly introduced into the environment through human activity. These substances which include hydrocarbons range in degree of toxicity and danger to human health. Frequent oil spills incidents have become a problem to ecological protection efforts. Conventional methods to remove, reduce or mitigate toxic substances introduced into soil via anthropogenic activities suffer setbacks due to the level of risk involved but bioremediation offers an alternative method to detoxify contaminants especially if the soil conditions are amended with organic nutrients or growth enhancing co-substrates. This study was therefore aimed characterizing hydrocarbon utilizing microorganisms associated with crude oil contaminated soils. Soils were obtained from the Rivers State University Agricultural farm contaminated deliberately with crude oil and allowed for 21 days to mimic the natural polluted soil. Sample collection and analyses were carried out according to standard microbiological procedures while characterization of the isolates was done using genomic studies. The results of microbial counts obtained from the soil samples for total heterotrophic bacteria ranged from 2.10 x108 to 2.58 x108 cfu/g, Total heterotrophic fungi had 1.6 x105 to 2.0 x105 cfu/g while the hydrocarbon utilizing bacteria ranged from 8.0 x103 to 5.0 x104 cfu/g and total hydrocarbon utilizing fungi ranged from 9.0 x103 to 7.0 x104 cfu/g in the contaminated soil. Five hydrocarbon utilizing bacterial species were identified as Staphylococcus saprophyticus, Bacillus amyloliquefaciens, Pseudomonas aeruginosa, Comamonas testosteroni and Chryseobacterium cucumeris while five hydrocarbon utilizing fungal species were identified as Penicillium citrinum, Penicillium brocae, Fusarium solani, Kodamaea ohmeri and Lentinus squarrosulus. Bacillus and Penicillium species were predominantly isolated from the soil. This may be due to the ability of the organisms to produce spores, which may shield them from the toxic effects of the hydrocarbons. Since these organisms are able to utilize crude oil as their sole carbon source. Hence, can be used for bioremediation of crude oil polluted environment.

scholarly journals Characterization and Functional Test of Canine Probiotics

2021 ◽  
Vol 12 ◽  
Author(s):  
Hyun-Jun Jang ◽  
Seungwoo Son ◽  
Jung-Ae Kim ◽  
Min Young Jung ◽  
Yeon-jae Choi ◽  
...  
Keyword(s):  
Animal Health ◽  
Clinical Results ◽  
Industrial Applications ◽  
Bacterial Strains ◽  
Host Animal ◽  
Microbial Composition ◽  
Beneficial Effects ◽  
Acid And Bile Tolerance

Probiotics can modulate the composition of gut microbiota and benefit the host animal health in multiple ways. Lactic acid bacteria (LAB), mainly Lactobacillus and Bifidobacterium species, are well-known microbes with probiotic potential. In the present study, 88 microbial strains were isolated from canine feces and annotated. Among these, the four strains CACC517, 537, 558, and 566 were tested for probiotic characteristics, and their beneficial effects on hosts were evaluated both in vitro and in vivo; these strains exhibited antibiosis, antibiotic activity, acid and bile tolerance, and relative cell adhesion to the HT-29 monolayer cell line. Byproducts of these strains increased the viability and decreased oxidative stress in mouse and dog cell lines (RAW264.7 and DH82, respectively). Subsequently, when the probiotics were applied to the clinical trial, changes in microbial composition and relative abundance of bacterial strains were clearly observed in the experimental animals. Experimental groups before and after the application were obviously separated from PCA analysis of clinical results. Conclusively, these results could provide comprehensive understanding of the effects of probiotic strains (CACC517, 537, 558, and 566) and their industrial applications.

scholarly journals Molecular Characterization and Differential Expression of an Aromatic Heptaketide Producing Type III Plant Polyketide Synthase From Himalayan Rhubarb

2021 ◽  
Author(s):  
Shahzad A. Pandith ◽  
Niha Dhar ◽  
Sumedha Bhosale ◽  
Vitthal T. Barvkar ◽  
Sumeer Razdan ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Uv Light ◽  
Phylogenetic Analyses ◽  
Transcript Abundance ◽  
Single Copy ◽  
Medical Systems ◽  
Regeneration System ◽  
Multiple Sequence ◽  
Type Iii

Abstract Rheum australe (Himalayan Rhubarb, Polygonaceae) is an endangered medicinal and vegetable herb with known efficacy in different traditional medical systems. The age-old remedying properties of this perennial species are ascribed to the bio-active phytoconstituents viz anthraquinones, stilbenoids, chromones and dietary flavonoids. These metabolites share a major contribution of their synthesis from polyketide pathway which primarily involves the intricate Type III polyketide synthases (PKSs). In this context, present study was focussed on characterization of an important PKS member aloesone synthase (RaALS) known to catalyze six polyketide extensions of the starter acetyl CoA to generate aloesone. A full-length cDNA (1176 bp, ~ 42 kDa) was cloned and heterologously expressed in microbial hosts. Multiple sequence alignment and phylogenetic analyses revealed that RaALS shares high degree of similarity with orthologous PKSs. Model validation and donor-acceptor interactions were assessed using homology modeling and molecular docking studies. Further, southern blotting determined the existence of RaALS as single copy gene. qRT-PCR analyses revealed that higher expression of RaALS in leaves followed by stem and root corroborated well with the metabolite accumulation. Its expression was also found to be regulated by altitude. Additionally, an in vitro regeneration system was developed to evaluate the effect of various abiotic stressors viz methyl jasmonate, salicylic acid and UV light on the transcript abundance of RaALS vis-à-vis identified putative cis-regulatory promoter elements using genome walking approach. The study would act as a prelude to utilize this medical herb for prospective metabolic engineering attempts aimed at augmenting bio-active metabolite production for commercial purposes.

scholarly journals Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica

2017 ◽  
Vol 83 (8) ◽  
Author(s):  
Victoria Mesa ◽  
Alejandro Navazas ◽  
Ricardo González-Gil ◽  
Aida González ◽  
Nele Weyens ◽  
...  
Keyword(s):  
Plant Growth ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Field Application ◽  
Contaminated Site ◽  
Arsenic Content ◽  
Content Type ◽  
Arsenic Uptake

ABSTRACT The aim of this study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by the autochthonous pseudometallophyte Betula celtiberica. The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica's microbiome was dominated by taxa related to Flavobacteriales, Burkholderiales, and Pseudomonadales, especially the Pseudomonas and Flavobacterium genera. A total of 54 cultivable rhizobacteria and 41 root endophytes, mainly affiliated with the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, were isolated and characterized with respect to several potentially useful features for metal plant accumulation, such as the ability to promote plant growth, metal chelation, and/or mitigation of heavy-metal stress. Seven bacterial isolates were further selected and tested for in vitro accumulation of arsenic in plants; four of them were finally assayed in field-scale bioaugmentation experiments. The exposure to arsenic in vitro caused an increase in the total nonprotein thiol compound content in roots, suggesting a detoxification mechanism through phytochelatin complexation. In the contaminated field, the siderophore and indole-3-acetic acid producers of the endophytic bacterial consortium enhanced arsenic accumulation in the leaves and roots of Betula celtiberica, whereas the rhizosphere isolate Ensifer adhaerens strain 91R mainly promoted plant growth. Field experimentation showed that additional factors, such as soil arsenic content and pH, influenced arsenic uptake in the plant, attesting to the relevance of field conditions in the success of phytoextraction strategies. IMPORTANCE Microorganisms and plants have developed several ways of dealing with arsenic, allowing them to resist and metabolize this metalloid. These properties form the basis of phytoremediation treatments and the understanding that the interactions of plants with soil bacteria are crucial for the optimization of arsenic uptake. To address this in our work, we initially performed a microbiome analysis of the autochthonous Betula celtiberica plants growing in arsenic-contaminated soils, including endosphere and rhizosphere bacterial communities. We then proceeded to isolate and characterize the cultivable bacteria that were potentially better suited to enhance phytoextraction efficiency. Eventually, we went to the field application stage. Our results corroborated the idea that recovery of pseudometallophyte-associated bacteria adapted to a large historically contaminated site and their use in bioaugmentation technologies are affordable experimental approaches and potentially very useful for implementing effective phytoremediation strategies with plants and their indigenous bacteria.

Production of Novel Bioactive Compounds by the Bacteria Associated with Some Marine Sponges of Gulf of Mannar and Palk Bay, Southeast Coast of India

2018 ◽  
Vol 6 (8) ◽  
pp. 183
Author(s):  
V. Ramadas ◽  
G. Chandralega
Keyword(s):  
Bioactive Compounds ◽  
Bacterial Species ◽  
Marine Sponges ◽  
Marine Organisms ◽  
Gulf Of Mannar ◽  
Bacterial Symbionts ◽  
Palk Bay ◽  
Excellent Source

Sponges, exclusively are aquatic and mostly marine, are found from the deepest oceans to the edge of the sea. There are approximately 15,000 species of sponges in the world, of which, 150 occur in freshwater, but only about 17 are of commercial value. A total of 486 species of sponges have been identified in India. In the Gulf of Mannar and Palk Bay a maximum of 319 species of sponges have been recorded. It has been proved that marine organisms are excellent source of bioactive secondary metabolites and number of compounds of originated from marine organisms had been reported to possess in-vitro and in-vivo immuno stimulatory activity. Extracts from 20 sponge species were tested for bacterial symbionts and bioactive compounds were isolated from such associated bacterial species in the present study.

Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects

2020 ◽  
Vol 27 (5) ◽  
pp. 400-410
Author(s):  
Valentina De Luca ◽  
Luigi Mandrich
Keyword(s):  
Gene Evolution ◽  
Sequence Divergence ◽  
High Specificity ◽  
Industrial Applications ◽  
Point Of View ◽  
Enzyme Promiscuity ◽  
Primary Activity ◽  
Starting Point ◽  
Main Activity

: Enzymes are among the most studied biological molecules because better understanding enzymes structure and activity will shed more light on their biological processes and regulation; from a biotechnological point of view there are many examples of enzymes used with the aim to obtain new products and/or to make industrial processes less invasive towards the environment. Enzymes are known for their high specificity in the recognition of a substrate but considering the particular features of an increasing number of enzymes this is not completely true, in fact, many enzymes are active on different substrates: this ability is called enzyme promiscuity. Usually, promiscuous activities have significantly lower kinetic parameters than to that of primary activity, but they have a crucial role in gene evolution. It is accepted that gene duplication followed by sequence divergence is considered a key evolutionary mechanism to generate new enzyme functions. In this way, promiscuous activities are the starting point to increase a secondary activity in the main activity and then get a new enzyme. The primary activity can be lost or reduced to a promiscuous activity. In this review we describe the differences between substrate and enzyme promiscuity, and its rule in gene evolution. From a practical point of view the knowledge of promiscuity can facilitate the in vitro progress of proteins engineering, both for biomedical and industrial applications. In particular, we report cases regarding esterases, phosphotriesterases and cytochrome P450.

Amino Acids Sequence-based Analysis of Arginine Deiminase from Different Prokaryotic Organisms: An In Silico Approach

2020 ◽  
Vol 14 (3) ◽  
pp. 235-246
Author(s):  
Sara Abdollahi ◽  
Mohammad H. Morowvat ◽  
Amir Savardashtaki ◽  
Cambyz Irajie ◽  
Sohrab Najafipour ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
In Silico ◽  
Bacterial Species ◽  
Arginine Deiminase ◽  
Antitumor Effects ◽  
Multiple Sequence ◽  
In Silico Studies

Background: Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginineauxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. Objective: Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deiminase proteins from different bacterial species through in silico analysis. Methods: The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. Results: The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 conserved patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. Conclusion: The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes.

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