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This investigation employed 16S rRNA amplicon sequencing to understand microbial dynamics during a 2-month field-scale oil-impacted soil remediation in the Niger Delta. Surface soil (0.0–0.5 m) had extractable total petroleum hydrocarbons (ETPH) concentrations of 6231 mg/kg and subsurface samples from 1.0 m, 1.5 m and 2.0 m depths had 4836 mg/kg, 9112 mg/kg and 7273 mg/kg, respectively. Proteobacteria dominated the bacterial community of the oil-polluted soil and comprised mainly Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Alpha diversity analysis revealed the presence of hydrocarbons reduced microbial diversity. Principal coordinate analysis indicated that the community structure continually changed following variations in the ETPH concentrations. Mycobacterium, Burkholderia, Methylobacterium and Bacillus were among the core operational taxonomic units (OTUs) detected during remediation. Significant variation in predicted pathway abundance, particularly pathways for fatty acid metabolism, propanoate, benzoate, polycyclic aromatic hydrocarbons, naphthalene and xenobiotics degradation, was more apparent in samples obtained during remediation than in the reference control

Compounds present in oil sludge such as polycyclic aromatic hydrocarbons (PAHs) are known to be cytotoxic, mutagenic and potentially carcinogenic. Microorganisms including bacteria and fungi have been reported to degrade oil sludge components to innocuous compounds such as carbon dioxide, water and salts. In the present study, we isolated different bacteria with PAH-degrading capabilities from compost prepared from oil sludge and animal manures. These bacteria were isolated on a mineral base medium and mineral salt agar plates. A total of 31 morphologically distinct isolates were carefully selected from 5 different compost treatments for identification using polymerase chain reaction (PCR) of the 16S rRNA gene with specific primers (universal forward 16S-P1 PCR and reverse 16S-P2 PCR). The amplicons were sequenced and sequences were compared with the known nucleotides from the GenBank. The phylogenetic analyses of the isolates showed that they belong to 3 different clades; Firmicutes, Proteobacteria and Actinobacteria. These bacteria identified were closely related to the generaBacillus, Arthrobacter, Staphylococcus, Brevibacterium, Variovorax, Paenibacillus, Ralstonia and Geobacillus.The results showed thatBacillus species were predominant in all composts. Based on the results of the degradation of the PAHs in the composts and results of previous studies on bacterial degradation of hydrocarbons in oil, the characteristics of these bacterial isolates suggests that they may be responsible for the breakdown of PAHs of different molecular weights in the composts. Thus, they may be potentially useful for bioremediation of oil sludge during compost bioremediation.

Crop fungal infections such as those caused by Fusarium species often result in yield loss pre- and post-harvest and during storage, contaminate food and exacerbate food insecurity. Synthetic fungicides are becoming less attractive as they pose health risks to consumers and are not environmentally friendly. As an alternative to synthetic fungicides, medicinal plant species may present sustainable and affordable sources of environmentally friendly fungicides for controlling plant diseases. This study was aimed at evaluating the in vitro antifungal activity of different medicinal plant extracts individually or in combination against Fusarium proliferatum, F. solani, F. verticillioides and F. graminearum. Different solvent (water, acetone and ethyl acetate) extracts obtained from the leaves of thirteen medicinal plant species were evaluated for antifungal activity using the micro-plate dilution assay. Their combined effect was evaluated by determining their fractional inhibitory concentration index (FICI). When evaluated individually, acetone extracts obtained from Combretum erythrophyllum, Harpephyllum caffrum and Quercus acutissima were the most active extracts inhibiting the growth of all the four pathogens with minimum inhibitory concentration (MIC) values less than 0.1 mg/ml. Out of 204 extract combinations evaluated, 150 extract combinations demonstrated either synergistic or additive antifungal activity. among the best combinations, combined acetone extracts of Harpephyllum caffrum and Combretum erythrophyllum showed strong synergistic antifungal activity against F. graminearum, F. proliferatum and F. verticillioides (MIC values of 0.02 mg/ml, 0.002 mg/ml and 0.001 mg/ml, respectively), and strong additive antifungal activity against F. solani (MIC = 0.02 mg/ml). The approach of using medicinal plant extracts from renewable plant parts either individually or in combination is sustainable, affordable, environmentally friendly and may be more beneficial in the fight against crop pathogenic diseases, particularly in organic farming.

BACKGROUND: The uncontrolled overproduction of fruit and vegetable waste causes serious environmental challenges such as emission of greenhouse gases. Anaerobic digestion (AD) is becoming a widely adopted technology for treatment of food waste with the concomitant production of biogas. This study investigated the link between microbial community structure and biogas production when using cow dung and mixed fruit and vegetable waste (MFVW) as substrates. RESULTS: Semi‐continuous stir tank reactors were used for AD of cow dung and MFVW over a period of 40 days. The highest accumulative methane yield (112.9 L) was obtained from co‐ digestion, intermediate yield (59.5 L) was obtained from cow dung and lowest yield (6.1 L) from MFVW at the end of the digestion experiment. Polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE) revealed higher bacterial and archaeal diversity indices in co‐digestion in comparison to mono‐digestion of cow dung and MFVW. High‐throughput sequence analyses showed that operational taxonomic units (OTUs) belonging to the phyla Bacteroidetes, followed by Firmicutes, Actinobacteria and Proteobacteria were dominant in all treatments. CONCLUSION: The results of the study demonstrated that the enhanced methane production in co‐digestion could be attributed to the neutral pH and partial shift of archaea from Methanosaeta to Methanosarcina rich communities. © 2019 Society of Chemical Industry

Highlights • Serratia marcescens 39_H1 could enhance the hydrolysis of lignocellulosic biomass. • Serratia marcescens 39_H1 is a plant growth promoting organism. • Genome analysis showed diverse potential biotechnological application of organism. • This is an original report on the hydrolytic and acidogenic attributes ofSerratia marcescens 39_H1 for biogas production., Here, we report a high quality annotated draft genome of Serratia marcescens 39_H1, a Gram-negative facultative anaerobe that was isolated from an anaerobic digester. The strain exhibited hydrolytic/acidogenic properties by significantly improving methane production when used as a single isolate inoculum during anaerobic digestion of water hyacinth and cow dung. The total genome size of the isolate was 5,106,712 bp which corresponds to an N50 of 267,528 and G + C content of 59.7 %. Genome annotation with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) predicted a total of 4,908 genes of which 4,755 were protein coding genes; there were no plasmids detected. A number of genes associated with hydrolytic/acidogenic activities as well as other metabolic activities were identified and discussed.

Ready-to-eat foods (RTEs) are foods consumed without any further processing. They are widely consumed as choice meals especially by school-aged children and the fast-paced working class in most low- and middle-income countries (LMICs), where they contribute substantially to the dietary intake. Depending on the type of processing and packaging material, RTEs could be industrially or traditionally processed. Typically, RTE vendors are of low literacy level, as such, they lack knowledge about good hygiene and food handling practices. In addition, RTEs are often vended in outdoor environments such that they are exposed to several contaminants of microbial origin. Depending on the quantity and type of food contaminant, consumption of contaminated RTEs may result in foodborne diseases and several other adverse health effects in humans. This could constitute major hurdles to growth and development in LMICs. Therefore, this review focuses on providing comprehensive and recent occurrence and impact data on the frequently encountered contaminants of microbial origin published in LMICs within the last decade (2009 to 2018). We have also suggested viable food safety solutions for preventing and controlling the food contamination and promoting consumer health.

The study investigated microbial population dynamics and petroleum hydrocarbon degradation during 56-day landfarming bioremediation of crude oil-polluted soil at a Community in Niger Delta Nigeria. Landfarming involved the addition of fresh top soil from unpolluted soil to the polluted soil followed by periodic ploughing. Active oleophilic bacteria identified by 16S rRNA sequencing were screened with 2,6-dichlorophenol indophenol (DCPIP) redox indicator for their degradation profile. Physicochemical parameters monitored during landfarming included the extractable Total Petroleum Hydrocarbons (TPH), Polycyclic Aromatic Hydrocarbons (PAHs), pH and heavy metals. TPH was more than 9000 mg/kg which exceeded the Department of Petroleum Resources’ (DPR's) intervention value of 5000 mg/kg. Total viable counts of culturable heterotrophic and hydrocarbon utilizing bacteria in the polluted soil pre-landfarming were between 0.2 and 0.5 × 103 cfu/g. Monitoring of microbial population dynamics on days 0, 9, 18, 36 and 56 revealed an increase in hydrocarbon utilizing bacterial population from 104 up to 107 cfu/g which correlated significantly (R = 0.88; p = 0.05) with TPH reduction to below 700 mg/kg by day 56 when bioremediation experiment ended. Pseudomonas aeruginosa was the most efficient diesel degrader which showed 100% DCPIP decolourization. Acinetobacter, Myroides, Pseudomonas and Bacillus were central in the degradation of the long chain hydrocarbon fraction in the spill site. The fungal classes recovered included Eurotiomycetes, Saccharomycetes and Sordariomycetes. The findings from this study showed that the addition of virgin top soil to a compromised and chemically stressed soil is a green and eco-friendly strategy for enriching microbial degradative activities without addition of chemical fertilizers.

At present, there is no comprehensive soil quality assessment practice for soil stockpiles in the South African coal mining industry. Soil microorganisms and enzymes are suitable indicators for soil quality monitoring. Therefore, this study investigated the microbial community and enzyme (beta-glucosidase and urease) activities in soil stockpiles of opencast coal mines in the coal-rich region of South Africa. Soil stockpiles of three opencast coal mines were sampled at depths of 0–20 cm (‘topsoil’) and >20 cm (‘subsoil’) across three seasons. Beta-glucosidase and urease activities were mostly higher in soil stockpiles than in unmined soils and were significantly influenced (P < 0.05) by the interaction of site and seasonal factors. However, analyses of PCR-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of partial 16S rRNA gene and internally transcribed spacer 2 (ITS2) sequences revealed higher microbial diversity in unmined (reference) soils compared to soil stockpiles across all seasons. Redundancy analysis further revealed that microbial communities of topsoil were not significantly (P > 0.05) influenced by soil properties, whereas microbial communities of subsoils were significantly (P < 0.05) influenced by pH, organic carbon, total nitrogen and phosphorus contents. Furthermore, operational taxonomic units (OTUs) belonging to genera of known phytobeneficial species such as Azomonas, Aureobasidium, Phialocephala, Phoma and Sordariomycetes were detected in these soils. Overall, results suggest that the microbial community structure and diversity observed in stockpiles is impaired (compared to the unmined site), although variations in the microbial community structure of soil stockpiles across seasons are site-specific. The impaired microbial community of stockpiles may have negative implications on soil biological processes driven by microbes; especially those that are critical for nutrient cycling and ecosystem sustainability. More importantly, such alteration in soil biodiversity may impair post-mining land use capability of stockpile soils

Anthropogenic disturbances of soil environments predispose loss of soil ecosystem functions, including its habitat support function. In this study, the potential ecosystem support and habitat functions of soils from stockpiles and post-mining reclamation areas (ranging from 3 to 25 years) in two coal mining sites were assessed using Eisenia andrei bioassays. Endpoints such as avoidance response, mortality, relative growth rate and fecundity were determined. By taking into cognisance the ages of the reclamation areas, inference was drawn on the potential restoration of ecosystem support functions over the years since reclamation. Mortality and fecundity of earthworms did not suggest limited support functions of control and test soils. Net avoidance response (AR) indicated significant differences (P < 0.05) among treatments with only the net AR in a 3-year old reclaimed soil >80%. Earthworms generally preferred (P < 0.05) undisturbed (“reference”) soils to OECD and test soils. Furthermore, trends in AR suggested a negative effect (P < 0.05) of anthropogenic disturbance and a general improvement of soil habitat function in older reclaimed areas. Of all endpoints, the avoidance test was the most sensitive, which generally reflected the differences in soil physicochemical properties among test soils. Although high intra-site variations in soil properties suggest lack of strict adherence to best reclamation practices, coal mining soil environments are not ecologically derelict with regards to supporting biocoenosis

Lignin is an abundant biomass-derived polymer that can be utilized as an antimicrobial agent. However, its antimicrobial properties depend on the method used for its extraction. Amongst the extracted lignin, lignin-based materials including nanomaterials are often favoured due to their unique properties and mode of action in suppressing microbial growth by targeting the cell membrane of bacteria. This lignin is generally obtained through chemical extraction from a variety of natural sources using different methods. However, their extraction methods, in relation to their antibacterial properties, have not been well documented. Here, we present an overview of alternative methods of extracting lignin and their potential influence on antimicrobial properties of the lignin. Shortcomings of the extraction methods as well as potential solutions for process optimisation are also discussed.

This study offers a Nature-based Solutions (NbS) for the recovery of long-term oil-polluted soils. An NPK-type substituted organic fertilizer (SOF) was formulated using available nature-based materials, and its effect on bacterial diversity, richness and community composition investigated during the remediation of a long-term crude oil-impacted soil. Results obtained were compared to a control and a chemical fertilizer (CF) treatment. The rate of total petroleum hydrocarbons (TPH) degradation was observed to be highest in the SOF treatment (0.022 d – 1) compared to the CF (0.016 d – 1) and control treatments (0.001 d – 1). Improvement of bacterial diversity in the SOF treatment significantly correlated with pH and soil organic matter (SOM). Proteobacteria was the dominant phylum across all the treatment systems. Acidocella was dominant in both the control and CF treatments, while Brevundimonas and Alcanivorax were the most abundant genera in the SOF treatment. The bacterial community structure and composition were significantly differentiated (PERMANOVA, p ≤ 0.01) in the different treatment processes. Constrained redundancy analysis revealed that pH, SOM, calcium, TPH and potassium influences the bacterial community composition. Analysis of bacterial community interaction suggests that there was higher efficiency in information processing and chemical transmission in the SOF treatment compared to the CF treatment. PICRUSt2-based functional prediction revealed that dissimilatory/assimilatory nitrate reduction and denitrification were among biomarkers in the nutrient amended treatments, while enzymes for nitrogen fixation were differentially abundant in the control treatment. Overall, the findings of this study suggest that the formulated NbS-fertilizer might stimulate more rapid biodegradation by improving soil nutrients and the proliferation of diverse microbial species in oil-polluted soils.

Arbuscular mycorrhizal (AM) fungi contribute to the restoration of soil ecological functions and processes during ecosystem development. Here, diversity and differentiation of AM fungi in rhizosphere soils and roots of the dominant vegetation along a post-coal mining reclamation soil chronosequence of 3, 11, 15, 19 and 24 years after reclamation were investigated. High-throughput sequence analysis of partial Glomeromycotan 18S rRNA in soils and roots revealed a high number of core operational taxonomic units (OTUs) across chronosequence. Arbuscular mycorrhizal fungal (AMF) OTU richness, Shannon-Weiner index and species dominance were not significantly different across soil and root but were significantly (P < 0.05) correlated with ammonium, nitrate, silt fraction, litter, pH, foliar and/or basal covers. AMF community structure was significantly different (P < 0.05) across unmined and reclamation chronosequence soils, with differentiation between younger reclaimed areas (3 and 11 years) and older reclamation ages (19 and 24 years) in multivariate space. In contrast, structural differentiation in the AMF community colonising the single plant-host across the chronosequence was not significant (PERMANOVA, P > 0.05), although community composition and structure were heterogeneous within 3–11 years but similar within 15–24 years. Seven Glomeromycotan genera were detected in soil and roots, including the relatively dominant Glomus genus, and the differentially abundant Acaulospora, Diversispora, Paraglomus and Scutellospora in either earlier or later years since post-mining reclamation. Canonical correspondence analysis revealed that nitrates (NO3-N), clay content and bulk density significantly influenced (P < 0.05) the AMF community structure in soil, whereas, the AMF community in root was not significantly influenced (P > 0.05) by environmental variables. Overall, the study suggests that AMF community differentiation reflect ecosystem development over chronological space-time. Thus, AMF species differentiation may be included as part of a minimum dataset for monitoring ecosystem restoration following post-mining reclamation