Characterization and antimicrobial activity of endophytic fungi from medicinal plant Agave americana.

Endophytic microorganisms associated with medicinal plants are of particular interest as they are a potential source of new bioactive chemicals effective against novel emerging and drug-resistant pathogens. Agave americana is a tropical medicinal plant with antibacterial, antifungal, and anticancer properties. We studied the biodiversity of fungal endophytes of A. americana and their antimicrobial production potential. Isolated endophytic fungi were classified into 32 morphotypes (15 from stem and 17 from leaf) based on their cultural and morphological characteristics. Among the fungal crude extracts tested, 82% of isolates from the leaves and 80% of the isolates from the stem showed antibacterial activity against the bacterial strains (Escherichia coli ATTC 25902, Staphylococcus aureus ATTC 14775, and Bacillus subtilis NRRL 5109) tested. Extracts from four fungal isolates from leaves showed antifungal activity against at least one of the fungal strains (Candida albicans ATTC 10231 and Aspergillus fumigatus NRRL 5109) tested. Crude extracts of seven fungal isolates showed a zone of inhibition of more than 11 mm at 10 mgml-1 against both Gram-positive and Gram-negative bacteria tested. Penicillium, Colletotrichum, Curvularia, Pleosporales, Dothideomycetes, and Pleurotus are the main endophytes responsible for bioactive potential. These results indicate that A. americana harbors endophytes capable of producing antimicrobial metabolites.

Development of novel kinetic model based on microbiome and biochar for in-situ remediation of total petroleum hydrocarbons (TPHs) contaminated soil.

A novel kinetic model has been developed to explain the degradation of total petroleum hydrocarbons. Microbiome engineered biochar amendment may result in a synergistic impact on degradation of total petroleum hydrocarbons (TPHs). Therefore, the present study analyzed the potential of hydrocarbon-degrading bacteria A designated as Aeromonas hydrophila YL17 and B as Shewanella putrefaciens Pdp11 morphological characterized as rod shaped, anaerobic and gram-negative immobilized on biochar, and the degradation efficiency was measured by gravimetric analysis and gas chromatography-mass spectrometry (GC-MS). Whole genome sequencing of both strains revealed the existence of genes responsible for hydrocarbon degradation. In 60 days remediation setup, the treatment consisting of immobilization of both strains on biochar proved more efficient with less half-life and better biodegradation potentials compared to biochar without strains for decreasing the content of TPHs and n-alkanes (C12-C18). Enzymatic content and microbiological respiration showed that biochar acted as a soil fertilizer and carbon reservoir and enhanced microbial activities. The removal efficiency of hydrocarbons was found to be a maximum of 67% in soil samples treated with biochar immobilized with both strains (A + B), followed by biochar immobilized with strain B 34%, biochar immobilized with strain A 29% and with biochar 24%, respectively. A 39%, 36%, and 41% increase was observed in fluorescein diacetate (FDA) hydrolysis, polyphenol oxidase and dehydrogenase activities in immobilized biochar with both strains as compared to control and individual treatment of biochar and strains. An increase of 35% was observed in the respiration rate with the immobilization of both strains on biochar. While a maximum colony forming unit (CFU/g) was found 9.25 with immobilization of both strains on biochar at 40 days of remediation. The degradation efficiency was due to synergistic effect of both biochar and bacteria based amendment on the soil enzymatic activity and microbial respiration.

Advances in Biochar and PGPR engineering system for hydrocarbon degradation: A promising strategy for environmental remediation.

In soil, polycyclic aromatic hydrocarbons (PAHs) have resulted in severe environmental deterioration, compromised soil characteristics, and negatively affect all life forms, including humans. Developing appropriate and effective clean-up technology is crucial in solving the contamination issues. The traditional methods to treat PHAs contaminated soil are less effective and not ecofriendly. Bioremediation, based on bioaugmentation and biostimulation approaches, is a promising strategy for remediating contaminated soil. The use of plant growth-promoting rhizobacteria (PGPR) as a bioaugmentation tool is an effective technique for treating hydrocarbon contaminated soil. Plant growth-promoting rhizobacteria (PGPR) are group of rhizospheric bacteria that colonize the roots of plants. Biochar is a carbon-rich residue, which acts as a source of nutrients, and is also a bio-stimulating candidate to enhance the activities of oil-degrading bacteria. The application of biochar as a nutrient source to bioremediate oil-contaminated soil is a promising approach for reducing PHA contamination. Biochar induces polyaromatic hydrocarbons (PAHs) immobilization and removes the contaminants by various methods such as ion exchange electrostatic attractions and volatilization. In comparison, PGPR produce multiple types of biosurfactants to enhance the adsorption of hydrocarbons and mineralize the hydrocarbons with the conversion to less toxic substances. During the last few decades, the use of PGPR and biochar in the bioremediation of hydrocarbons-contaminated soil has gained greater importance. Therefore, developing and applying a PGPR-biochar-based remediating system can help manage hazardous PAH contaminated soil. The goal of this review paper is to (i) provide an overview of the PGPR mechanism for degradation of hydrocarbons and (ii) discuss the contaminants absorbent by biochar and its characteristics (iii) critically discuss the combined effect of PGPR and biochar for degradation of hydrocarbons by decreasing their mobility and bioavailability. The present review focuses on techniques of bioaugmentation and biostimulation based on use of PGPR and biochar in remediating the oil-contaminated soil.

Biodegradation of PAHs by Bacillus marsiflavi, genome analysis and its plant growth promoting potential.

The biodegradation of hazardous petroleum hydrocarbons has recently received a lot of attention because of its many possible applications. Bacillus marsiflavi strain was isolated from oil contaminated soil of Rawalpindi, Pakistan. Initial sequencing was done by 16s rRNA sequencing technique. Bac 144 had shown 78% emulsification index and 72% hydrophobicity content. Further, the strain displayed production of 15.5 mg/L phosphate sloubilization and 30.25 µg/ml indole acetic acid (IAA) in vitro assay. The strain showed 65% biodegradation of crude oil within 5 days by using Gas Chromatography-Mass Spectrometry (GC-MS) analysis. Whole Genome analysis of Bac 144 was performed by PacBio sequencing and results indicated that Bacillus marsiflavi Bac144 strain consisted of size of 4,417,505bp with closest neighbor Bacillus cereus ATCC 14579. The number of the coding sequence was 4662 and number of RNAs was 141. The GC content comprised 48.1%. Various genes were detected in genome responsible for hydrocarbon degradation and plant defense mechanism. The toxic effect of petroleum hydrocarbons in soil and its mitigation with Bac 144 was tested by soil experiment with three levels of oil contamination (5%, 10% and 15%). Soil enzymatic activity such as dehydrogenase and fluorescein diacetate (FDA) increased up to 49% and 40% with inoculation of Bac 144, which was considered to be correlated with hydrocarbon degradation recorded as 46%. An increase of 20%, 14% and 9% in shoot length of plant at 5%, 10% and 15% level of oil was recorded treated with Bac 144 as compared to untreated plants. A percent increase of 14.89%, 16.85%, and 13.87% in chlorophyll, carotenoid, and proline content of plant was observed by inoculation with Bac 144 under oil stress. Significant reduction of 14% and 18%, 21% was recorded in the malondialdehyde content of plant due to inoculation of Bac 144. A considerable increase of 21.33%, 19.5%, and 24.5% in super oxide dismutase, catalase, and peroxidase dismutase activity was also observed in plants inoculated with strain Bac 144. These findings suggested that Bac-144 can be considered as efficient candidate for bioremediation of hydrocarbons.

Biostimulation potential of biochar for remediating the crude oil contaminated soil and plant growth.

Crude oil contamination is a serious environmental threat to soil and plants growing in it. Biochar has the potential of biostimulation for remediation of crude oil-contaminated soil. Therefore, the current research was designed to analyze the bio-stimulatory impact of biochar for remediating the crude oil contaminated soil (10%, and 15%), and growth of maize under glasshouse conditions. Biochar was produced by pyrolysis of Australian pines at 350 °C. Soil incubations were done for 20 days. The results of soil analysis showed that the crude oil degradation efficiency of biochar was 34%. The soil enzymatic activities had shown 38.5% increase in fluorescein diacetate (FDA) hydrolysis and 55.6% increase in dehydrogenase activity in soil incubated with biochar in comparison to control. The soil microbial diversity was improved to 41% in biochar treated soil with respect to untreated one, while microbial respiration rate had shown a 33.67% increase in soil incubated with biochar with respect to control under oil stress. Gas Chromatography Mass spectrometry (GC-MS) analysis had shown the high content of low molecular weight hydrocarbons (C9-C13) in the soil incubated with biochar in comparison to untreated soil. Biochar showed a significant increase in fresh and dry biomass (25%, 14.61%), leaf area (10%), total chlorophyll (11%), water potential (21.6%), osmotic potential (21%), and membrane stability index (12.7%). Moreover, biochar treatment showed a higher increase in the contents of proline (29%), total amino acids (18%), soluble sugars (30.4%), and antioxidant enzymes like superoxide dismutase (16.5%), catalase (11%), and peroxidase (12%). Overall, the results of the present study suggest the bio-stimulating potential of biochar for degradation of hydrocarbons in crude oil contaminated soil and their growth-stimulating effects on maize.

Data on foliar nutrient concentration of invasive plants in the recipient habitat and their native habitat.

Higher foliar nitrogen concentration in plants is often attributed to higher biomass assimilation and subsequently higher plant growth rate. To understand the underlying mechanism of extensive growth rate of an invasive plant, Old World climbing fern (Lygodium microphyllum), we analyzed the leaf tissue samples from the native and invaded habitats. In each habitat we selected 3 different locations with varying habitat characteristics (soil type, land use history and coexisting vegetation). Plant aboveground tissue collected from each site were analyzed for macro and micro nutrients. Total C and N were measured with a Truspec CN Analyzer. Total Ca, Fe, Mg, K, Mn, and P in plant tissue samples were measured using inductively coupled plasma mass spectrometry (ICP -MS). Here we present the difference in foliar nutrient concentration of invasive plant species in their native habitats and invaded habitats.

Biodegradation of polyether algal toxins--isolation of potential marine bacteria.

Marine algal toxins such as brevetoxins, okadaic acid, yessotoxin, and ciguatoxin are polyether compounds. The fate of polyether toxins in the aqueous phase, particularly bacterial biotransformation of the toxins, is poorly understood. An inexpensive and easily available polyether structural analog salinomycin was used for enrichment and isolation of potential polyether toxin degrading aquatic marine bacteria from Florida bay area, and from red tide endemic sites in the South Florida Gulf coast. Bacterial growth on salinomycin was observed in most of the enrichment cultures from both regions with colony forming units ranging from 0 to 6×10(7) per mL. The salinomycin biodegradation efficiency of bacterial isolates determined using LC-MS ranged from 22% to 94%. Selected bacterial isolates were grown in media with brevetoxin as the sole carbon source to screen for brevetoxin biodegradation capability using ELISA. Out of the two efficient salinomycin biodegrading isolates MB-2 and MB-4, maximum brevetoxin biodegradation efficiency of 45% was observed with MB-4, while MB-2 was unable to biodegrade brevetoxin. Based on 16S rRNA sequence similarity MB-4 was found have a match with Chromohalobacter sp.

Barium toxicity effects in soybean plants.

Barium (Ba)-induced phytotoxicity at 100, 1000, or 5000 microM Ba in soybean plants (Glycine max) was investigated under hydroponic culture conditions. Soybean growth and leaf photosynthetic activity were significantly inhibited by all three levels of Ba treatments. In the case of photosynthetic activity, 5000 microM Ba treatment shutdown stomatal opening and perturbed carbon fixation metabolism and translocation. However, 100 and 1000 microM Ba treatments shut down stomatal opening and inhibited carbon fixation, but without perturbation of leaf carbon fixation-related metabolism. Potassium (K) absorption by soybean roots was also reduced in all three Ba treatments. This decreased K absorption reduced K localization at guard cells. Barium accumulation in guard cells also inhibited K transport from epidermal cells to guard cells. This lack of K in guard cells resulted in stomatal closure. As a result of inhibition of K transport into guard cells and stomatal shutdown, photosynthetic activity and plant productivity were inhibited. Our experiment indicates that Ba has phytotoxic effects on soybean plants by inhibiting photosynthesis.

An eco-informatics tool for microbial community studies: supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA.

Support vector machines (SVM) and K-nearest neighbors (KNN) are two computational machine learning tools that perform supervised classification. This paper presents a novel application of such supervised analytical tools for microbial community profiling and to distinguish patterning among ecosystems. Amplicon length heterogeneity (ALH) profiles from several hypervariable regions of 16S rRNA gene of eubacterial communities from Idaho agricultural soil samples and from Chesapeake Bay marsh sediments were separately analyzed. The profiles from all available hypervariable regions were concatenated to obtain a combined profile, which was then provided to the SVM and KNN classifiers. Each profile was labeled with information about the location or time of its sampling. We hypothesized that after a learning phase using feature vectors from labeled ALH profiles, both these classifiers would have the capacity to predict the labels of previously unseen samples. The resulting classifiers were able to predict the labels of the Idaho soil samples with high accuracy. The classifiers were less accurate for the classification of the Chesapeake Bay sediments suggesting greater similarity within the Bay's microbial community patterns in the sampled sites. The profiles obtained from the V1+V2 region were more informative than that obtained from any other single region. However, combining them with profiles from the V1 region (with or without the profiles from the V3 region) resulted in the most accurate classification of the samples. The addition of profiles from the V 9 region appeared to confound the classifiers. Our results show that SVM and KNN classifiers can be effectively applied to distinguish between eubacterial community patterns from different ecosystems based only on their ALH profiles.

Cascading ecological effects of low-level phosphorus enrichment in the Florida everglades.

Few studies have examined long-term ecological effects of sustained low-level nutrient enhancement on wetland biota. To determine sustained effects of phosphorus (P) addition on Everglades marshes we added P at low levels (5, 15, and 30 microg L(-1) above ambient) for 5 yr to triplicate 100-m flow-through channels in pristine marsh. A cascade of ecological responses occurred in similar sequence among treatments. Although the rate of change increased with dosing level, treatments converged to similar enriched endpoints, characterized most notably by a doubling of plant biomass and elimination of native, calcareous periphyton mats. The full sequence of biological changes occurred without an increase in water total P concentration, which remained near ambient levels until Year 5. This study indicates that Everglades marshes have a near-zero assimilative capacity for P without a state change, that ecosystem responses to enrichment accumulate over time, and that downstream P transport mainly occurs through biota rather than the water column.

Assessment of arsenic mobility in the soils of some golf courses in South Florida.

High concentrations of arsenic have been detected in soils and underlying groundwater of some South Florida golf courses, indicating the possible impact of the application of arsenic-containing herbicides. The mobility of arsenic in the soils from selected golf courses was studied using a simple two-step sequential extraction procedure. Sodium nitrate (0.1 M), potassium dihydrogen phosphate (0.1 M) and concentrated nitric acid were used to obtain mobile, mobilizable, and pseudo total arsenic fractions. Soils were separated into fine (<0.25 mm) and large (0.25-0.75 mm) particle size fractions. Arsenic contents were correlated with the distribution of iron (R2=0.4827), manganese (R2=0.7674) and aluminum (R2=5459) in the particle size fractions, while such correlation was not observed for soil organic matter, indicating that the oxides/hydroxides of iron, manganese and aluminum control the distribution of arsenic in these soils. Sodium nitrate and potassium dihydrogen phosphate extractants used in this study extracted large portions of arsenic from most soil samples studied. This is especially true for the fine fraction where the extractable arsenic ranged from 9.2 to 51.3% with an average of 28.7 +/- 13.3%, whereas in the large fraction, arsenic ranged from 7.2 to 24.7% with an average of 15.4 +/- 6.4%. These extractants, however, release only small amounts of iron, manganese, and aluminum. It seems likely that arsenic can be released by sodium nitrate and potassium dihydrogen phosphate without significant dissolution of the oxides/hydroxides of iron, manganese, and aluminum in these soil samples.