Impact of petroleum hydrocarbon contamination on the indigenous soil microbial community

Soil pH and Rice Chlorophyll Content as Indicators of Grain Productivity and Microbial Community in Acid-Exposed Paddy Mesocosms

The objective of this study was to evaluate the applicability of soil pH and chlorophyll content as predictive indicators of damage in paddy fields affected by HCl spills, based on causal relationships. Five doses of HCl (e.g., 1, 50, 100, 200, and 500-fold of PNEC) were added to the paddy mesocosm during the rice heading stage. In the 7th week after the acid addition, rice grain quality (e.g., 1000-grain weight and filled grain ratio), soil microbial diversity (e.g., Operational Taxonomic Units (OTUs) and Shannon index), and soluble nutrients (e.g., NH4+, NO3-, SiO2, P2O5, and basic cations) were measured. Causal relationships among variables were analyzed using the Partial Least Square Path Model (PLS-PM). At the dose of 500×PNEC, all rice plants lodged when pH < 4. At 100×PNEC and 200×PNEC, the number of immature grains increased, resulting in a reduction in grain quality of over 18%. At 200×PNEC, the microbial OTUs and the Shannon index decreased by 30%. Notably, the proportion of Planctomycetes, the dominant phylum in the control soil, decreased. The reduction of Planctomycetes led to excessive NH4+ accumulation in the soil, which leads to an undesirable increase of chlorophyll content thereby deteriorating grain quality. The causal relationship suggests that information of soil pH and leaf chlorophyll can aid us in predicting damage for grain quality and microbial diversity.

Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil

Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.

Advanced bioremediation by an amalgamation of nanotechnology and modern artificial intelligence for efficient restoration of crude petroleum oil-contaminated sites: a prospective study

Crude petroleum oil spillage is becoming a global concern for environmental pollution and poses a severe threat to flora and fauna. Bioremediation is considered a clean, eco-friendly, and cost-effective process to achieve success among the several technologies adopted to mitigate fossil fuel pollution. However, due to the hydrophobic and recalcitrant nature of the oily components, they are not readily bioavailable to the biological components for the remediation process. In the last decade, nanoparticle-based restoration of oil-contaminated, owing to several attractive properties, has gained significant momentum. Thus, intertwining nano- and bioremediation can lead to a suitable technology termed 'nanobioremediation' expected to nullify bioremediation's drawbacks. Furthermore, artificial intelligence (AI), an advanced and sophisticated technique that utilizes digital brains or software to perform different tasks, may radically transfer the bioremediation process to develop an efficient, faster, robust, and more accurate method for rehabilitating oil-contaminated systems. The present review outlines the critical issues associated with the conventional bioremediation process. It analyses the significance of the nanobioremediation process in combination with AI to overcome such drawbacks of a traditional approach for efficiently remedying crude petroleum oil-contaminated sites.

Differences in geological conditions have reshaped the structure and diversity of microbial communities in oily soils

High-throughput sequencing was used to study the microbial community structure diversity changes in oil-contaminated soils under different spatial distances and environmental conditions. 239 Phyla, 508 Classes, 810 Orders, 1417 Families, 2048 Genera, 511 Species of microbial communities were obtained from 16 samples in three regions. The physicochemical properties of the soil, microorganisms' community structure has been changed by Petroleum hydrocarbon (PHA). Alpha diversity results showed that the soil contained high bacterial diversity, especially in Qingyang's loess soil. The bacterial abundance was in the order of loess soil > black soil > sandy soil. Beta diversity revealed that spatial distance limitation and random variation of repeated samples may be the main factors leading to soil heterogeneity and microbial community structure differences. The dominant bacteria phyla with broad petroleum hydrocarbon degradation ability such as Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were identified. Pseudomonas, Bacillus, Nocardioides, Oceanobacillus, Sphingomonas, Alkanindiges and Streptomyces were identified as functional microbial for the PHA degradation. The microbial communities manifested the co-exclusion under different geological conditions, and played the key role in the soil PHA degradation through amino acid metabolism, energy metabolism and carbohydrate metabolism. The correlation results of amos structural equation showed that the diversity and abundance of soil microorganisms in different regions were controlled by soil PHA content and environmental factors. Altitude, annual average temperature and annual rainfall were positively correlated with microbial diversity. Annual rainfall and soil physical and chemical factors exhibited the most significant influence on it. Microbial diversity indirectly affected the PHA content in different type soil. We believe that reshape the structure and diversity of microbial communities in soil could be changed and reshaped by different geological conditions, pollutants and soil type. This study can provide helps for understanding the ecological effect of geomicrobiology formation under the driving force of geographic environment and other factors.

Metagenomic insights into the microbial community structure and resistomes of a tropical agricultural soil persistently inundated with pesticide and animal manure use

Persistent use of pesticides and animal manure in agricultural soils inadvertently introduced heavy metals and antibiotic/antibiotic resistance genes (ARGs) into the soil with deleterious consequences. The microbiome and heavy metal and antibiotic resistome of a pesticide and animal manure inundated agricultural soil (SL6) obtained from a vegetable farm at Otte, Eiyenkorin, Kwara State, Nigeria, was deciphered via shotgun metagenomics and functional annotation of putative ORFs (open reading frames). Structural metagenomics of SL6 microbiome revealed 29 phyla, 49 classes, 94 orders, 183 families, 366 genera, 424 species, and 260 strains with the preponderance of the phyla Proteobacteria (40%) and Actinobacteria (36%), classes Actinobacteria (36%), Alphaproteobacteria (18%), and Gammaproteobacteria (17%), and genera Kocuria (16%), Sphingobacterium (11%), and Brevundimonas (10%), respectively. Heavy metal resistance genes annotation conducted using Biocide and Metal Resistance Gene Database (BacMet) revealed the detection of genes responsible for the uptake, transport, detoxification, efflux, and regulation of copper, cadmium, zinc, nickel, chromium, cobalt, selenium, tungsten, mercury, and several others. ARG annotation using the Antibiotic Resistance Gene-annotation (ARG-ANNOT) revealed ARGs for 11 antibiotic classes with the preponderance of β-lactamases, mobilized colistin resistance determinant (mcr-1), macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside resistance genes, among others. The persistent use of pesticide and animal manure is strongly believed to play a major role in the proliferation of heavy metal and antibiotic resistance genes in the soil. This study revealed that agricultural soils inundated with pesticide and animal manure use are potential hotspots for ARG spread and may accentuate the spread of multidrug resistant clinical pathogens.

Effects of biochar on catalysis treatment of 4-nonylphenol in estuarine sediment and associated microbial community structure

The effect of pyrolysis temperature on the generation of polycyclic aromatic hydrocarbons (PAHs) in sewage sludge biochar (SSB) and the removal of hazardous chemicals from esturine sediments by SSB and sodium percarbonate (SPC), exemplified by 4-nonylphenol (4-NP) were studied. SSB synthesized at 500 °C (SSB500) achieved the highest 4-NP degradation efficiency of 73%, at pH₀ 9.0 in 12 h of reaction time. The enhanced 4-NP degradation was attributed to the SSB500 activation activation of SPC that produced sufficient •OH and CO₃^-• due to electron-transfer interaction on the Fe-Mn redox pairs. The microbial community diversity and composition of the treated sediment were compared using high-throughput sequencing. Results showed SSB/SPC treatment increased the microbial diversity and richness in the sediments. Proteobacteria were the keystone phylum, while Thioalkalispira genera were responsible for 4-NP degradation in the SSB/SPC treatment. Over all, results revealed the change in the bacterial community during the environmental applications of SSB, which provided essential information for better understanding of the monitoring and improvement of sustainable sediment ecosystems.

Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil

The effects of cadmium (Cd) contamination on the microbial community structure, soil physicochemistry and heavy metal resistome of a tropical agricultural soil were evaluated in field-moist soil microcosms. A Cd-contaminated agricultural soil (SL5) and an untreated control (SL4) were compared over a period of 5 weeks. Analysis of the physicochemical properties and heavy metals content of the two microcosms revealed a statistically significant decrease in value of the soil physicochemical parameters (P < 0.05) and concentration of heavy metals (Cd, Pb, Cr, Zn, Fe, Cu, Se) content of the agricultural soil in SL5 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the predominance of the phyla, classes, genera and species of Proteobacteria (37.38%), Actinobacteria (35.02%), Prevotella (6.93%), and Conexibacter woesei (8.93%) in SL4, and Proteobacteria (50.50%), Alphaproteobacteria (22.28%), Methylobacterium (9.14%), and Methylobacterium radiotolerans (12,80%) in SL5, respectively. Statistically significant (P < 0.05) difference between the metagenomes was observed at genus and species delineations. Functional annotation of the two metagenomes revealed diverse heavy metal resistome for the uptake, transport, efflux and detoxification of various heavy metals. It also revealed the exclusive detection in SL5 metagenome of members of RND (resistance nodulation division) protein czcCBA efflux system (czcA, czrA, czrB), CDF (cation diffusion facilitator) transporters (czcD), and genes for enzymes that protect the microbial cells against cadmium stress (sodA, sodB, ahpC). The results obtained in this study showed that Cd contamination significantly affects the soil microbial community structure and function, modifies the heavy metal resistome, alters the soil physicochemistry and results in massive loss of some autochthonous members of the community not adapted to the Cd stress.

Bioreactor performance using biochar and its effect on aerobic granulation

The effects that rice husk (biochar-rh), rice bran (biochar-rb) and walnut shell (biochar-ws) biochar had on aerobic granulation and reactor performance during the treatment of petroleum wastewater have been investigated. The different biochars reduced aerobic granulation time by 15 days compared with the control and also increased resistance to shock loading. The average COD and TN removal increased by 3.2%-5.1% and 10%-13%, respectively. Bacteria having functional metabolisms associated with the treatment of petroleum wastewaters were enriched in granular sludge that contained biochars. The reactor containing biochar-rb was the most stable and removed the most nutrients. The reactor containing biochar-rh had the largest initial granule size. This study provides insights into how the physicochemical properties of different biochars influence aerobic granular sludge systems.

Biodegradability enhancement of hydrolyzed polyacrylamide wastewater by a combined Fenton-SBR treatment process

An efficient way to solve the environmental pollution deriving from hydrolyzed polyacrylamide (HPAM)-containing drilling wastewater is urgent. This work adopted a novel method coupling Fenton oxidation with sequencing batch reactor (SBR) to treat gas-field drilling wastewater successively. This Fenton-SBR process reduced COD, HPAM, NH₄⁺-N and total phosphorus (TP) concentrations of drilling wastewater by 98.35%, 87.58%, 94.50% and 93.52%, respectively. While simulated HPAM wastewater with similar HPAM concentration to Fenton-oxidized drilling wastewater was treated only by biological process, and the COD and HPAM removal efficiencies reached 78.26% and 62.95%. The result indicates that the biodegradability of the drilling wastewater was enhanced after Fenton oxidation. Moreover, the analysis on microbial community structure indicates the dominant bacteria in treated drilling wastewater were different from that in treated simulated-wastewater. It can be considered the Fenton-SBR process possesses potential to be applied to treating the drilling wastewater.

Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi

Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called "Terra dei Fuochi". The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.