Response of bacterial and fungal communities to high petroleum pollution in different soils

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.

Impact of mixed-species forest plantations on soil mycobiota community structure and diversity in the Congolese coastal plains

Mixed tree plantations containing nitrogen (N2)-fixing species have the potential to enhance C sequestration, soil biodiversity and forest productivity. Here, we investigated the impact of Acacia mangium and Eucalyptus urophilla x E. grandis mixed plantations in the Congolese coastal plains on soil mycobiota community structure and diversity by ITS metabarcoding sequencing and bioinformatic analysis. Higher Faith's phylogenetic diversity and Evenness' was found in Eucalyptus monoculture relative to stands containing Acacia. Differences in beta diversity were found among Eucalyptus and Acacia monoculture, and mixed-species stands highlight the effects of plant species on fungal community structure. Ascomycota, Basidiomycota and Rozellomycota phyla were predominant in all stands, with both Dikarya (Ascomycota and Basidiomycota) accounting for more than 70% in all stands. Correlation analysis revealed that sulfur (S) was the most correlated soil attribute with the three predominant phyla but also with Mucoromycota and Calcarisporiellomycota phyla, although mostly negatively correlated (4 out of 5). Phosphorus was mostly positively correlated to soil attributes (3 out of 4) and nitrogen was correlated twice, positively and negatively. Distance-based redundancy analysis revealed a positive correlation of nitrogen (p-value = 0.0019, contribution = 22%) and phosphorus (p-value = 0.0017, contribution = 19%) with soil mycobiota. A high prevalence of generalists (28% to 38%) than specialists (9% to 24%) were found among the different sites. In stands containing Acacia (pure and mixed species) the soil mycobiota harbor the prevalence of generalist strategies with the potential to withstand environmental stresses and utilize a higher number of resources against specialists in Eucalyptus stands. Stronger positive correlation between soil attributes and main fungal taxa, higher generalists' strategies and lower Faith's phylogenetic diversity and Evenness were reported in stands containing Acacia. This highlights the potential of mixed-species in preserving community stability following environmental disturbances and increasing the number of resources confirming their important ecological role in boosting the resilience of the forest ecosystems to climate and land-use (plant species as shown by PCA analysis) changes.

Bacillus subtilis Strain YJ-15, Isolated from the Rhizosphere of Wheat Grown under Saline Conditions, Increases Soil Fertility and Modifies Microbial Community Structure

Soil salinization during wheat cultivation considerably diminishes soil fertility and impedes wheat growth, primarily due to rhizosphere microbial community changes. Our study investigates the application of Bacillus subtilis YJ-15, a strain isolated from the rhizosphere of wheat cultivated in salinized soil, as a soil remediation agent. This strain has demonstrated significant salt tolerance, disease suppression capabilities, and growth-promoting attributes in previous studies. The wheat rhizosphere was examined to assess the impact of Bacillus subtilis YJ-15 on microbial community composition and soil fertility. Fertility of soil in saline soil was significantly increased by inoculating wheat with YJ-15. The microbial community structure within the wheat rhizosphere inoculated with Bacillus subtilis YJ-15 was analyzed through sequencing on the Illumina MiSeq platform. Phyla Proteobacteria and Acidobacteria were identified as the dominant bacteria. Basidiomycota, Mortierellomycota, and Ascomycota dominated the fungal phyla. Among the bacterial genera, Pseudomonas, Arthrobacter, and Bacillus were predominant. The predominant fungal genera included Alternaria, Cephalotrichum, Mortierella, and Chaetomium. A significant increase in Gaiella and Haliangium levels was observed in the YJ group compared to the control group. Additionally, the fungal genera Epicoccum, Sporidiobolus, and Lecythophora have significantly increased in YJ abundance. One of the potential benefits of Bacillus subtilis YJ-15 in the cultivation of wheat on salinized land is its ability to enhance the rhizosphere microbial community structure and improve soil fertility.

Interaction effects of pH and land cover on soil microbial diversity are climate-dependent

Factors regulating the diversity and composition of soil microbial communities include soil properties, land cover and climate. How these factors interact at large scale remains poorly investigated. Here, we used an extensive dataset including 715 locations from 24 European countries to investigate the interactive effects of climatic region, land cover and pH on soil bacteria and fungi. We found that differences in microbial diversity and community composition between land cover types depended on the climatic region. In Atlantic, Boreal and Continental regions, microbial richness was higher in croplands and grasslands than woodlands while richness in Mediterranean areas did not vary significantly among land cover types. These differences were further related to soil pH, as a driver of bacterial and fungal richness in most climatic regions, but the interaction of pH with land cover depended on the region. Microbial community composition differed the most between croplands and woodlands in all regions, mainly due to differences in pH. In the Mediterranean region, bacterial communities in woodlands and grasslands were the most similar, whereas in other regions, grassland and cropland-associated bacteria showed more similarity. Overall, we showed that key factors interact in shaping soil microbial communities in a climate-dependent way at large scale.

Soil Microbiome in Conditions of Oil Pollution of Subarctic Ecosystems

The present study aimed to investigate the recovery of soil quality and the bacterial and fungal communities following various recultivation methods in areas contaminated with oil. Oil spills are known to have severe impacts on ecosystems; thus, the restoration of contaminated soils has become a significant challenge nowadays. The study was conducted in the forest-tundra zone of the European North-East, where 39 soil samples from five oil-contaminated sites and reference sites were subjected to metagenomic analyses. The contaminated sites were treated with different biopreparations, and the recovery of soil quality and microbial communities were analyzed. The analysis of bacteria and fungi communities was carried out using 16S rDNA and ITS metabarcoding. It was found that 68% of bacterial OTUs and 64% of fungal OTUs were unique to the reference plot and not registered in any of the recultivated plots. However, the species diversity of recultivated sites was similar, with 50-80% of bacterial OTUs and 44-60% of fungal OTUs being common to all sites. New data obtained through soil metabarcoding confirm our earlier conclusions about the effectiveness of using biopreparations with indigenous oil-oxidizing micro-organisms also with mineral fertilizers, and herbaceous plant seeds for soil remediation. It is possible that the characteristics of microbial communities will be informative in the bioindication of soils reclaimed after oil pollution.

Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil

Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.

Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater

Wastewater treatment processes can eliminate many pollutants, yet remainder pollutants contain organic compounds and microorganisms released into ecosystems. These remainder pollutants have the potential to adversely impact downstream ecosystem processes, but their presence is currently not being monitored. This study was set out with the aim of investigating the effectiveness and sensitivity of non-target screening of chemical compounds, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding techniques for detecting treated wastewater in receiving waters. We aimed at assessing the impact of introducing 33 % treated wastewater into a triplicated large-scale mesocosm setup during a 10-day exposure period. Discharge of treated wastewater significantly altered the chemical signature as well as the microeukaryotic and prokaryotic diversity of the mesocosms. Non-target screening, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding detected these changes with significant covariation of the detected pattern between methods. The 18S V9 rRNA gene metabarcoding exhibited superior sensitivity immediately following the introduction of treated wastewater and remained one of the top-performing methods throughout the study. Full-length 16S rRNA gene metabarcoding demonstrated sensitivity only in the initial hour, but became insignificant thereafter. The non-target screening approach was effective throughout the experiment and in contrast to the metabarcoding methods the signal to noise ratio remained similar during the experiment resulting in an increasing relative strength of this method. Based on our findings, we conclude that all methods employed for monitoring environmental disturbances from various sources are suitable. The distinguishing factor of these methods is their ability to detect unknown pollutants and organisms, which sets them apart from previously utilized approaches and allows for a more comprehensive perspective. Given their diverse strengths, particularly in terms of temporal resolution, these methods are best suited as complementary approaches.

Microbiome engineering for bioremediation of emerging pollutants

Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.

Potential Utilization of Bacterial Consortium of Symbionts Marine Sponges in Removing Polyaromatic Hydrocarbons and Heavy Metals, Review

Toxic materials in waste generally contain several components of the global trending pollutant category, especially PAHs and heavy metals. Bioremediation technology for waste management that utilizes microorganisms (bacteria) has not been fully capable of breaking down these toxic materials into simple and environmentally friendly chemical products. This review paper examines the potential application of a consortium of marine sponge symbionts with high performance and efficiency in removing PAHs and heavy metal contaminants. The method was carried out through a review of several related research articles by the author and published by other researchers. The results of the study conclude that the development of global trending pollutant (GTP) bioremediation technology could be carried out to increase the efficiency of remediation. Several types of marine sponge symbiont bacteria, hydrocarbonoclastic (R-1), metalloclastic (R-2), and metallo-hydro-carbonoclastic (R-3), have the potential to be applied to improve waste removal performance. A consortium of crystalline bacterial preparations is required to mobilize into GTP-exposed sites rapidly. Bacterial symbionts of marine sponges can be traced mainly to sea sponges, whose body surface is covered with mucus.

Fungal assisted bio-treatment of environmental pollutants with comprehensive emphasis on noxious heavy metals: Recent updates

In the present time of speedy developments and industrialization, heavy metals are being uncovered in aquatic environment and soil via refining, electroplating, processing, mining, metallurgical activities, dyeing and other several metallic and metal based industrial and synthetic activities. Heavy metals like lead (Pb), mercury (Hg), cadmium (Cd), arsenic (As), Zinc (Zn), Cobalt (Co), Iron (Fe), and many other are considered as seriously noxious and toxic for the aquatic environment, human, and other aquatic lives and have damaging influences. Such heavy metals, which are very tough to be degraded, can be managed by reducing their potential through various processes like removal, precipitation, oxidation-reduction, bio-sorption, recovery, bioaccumulation, bio-mineralization etc. Microbes are known as talented bio-agents for the heavy metals detoxification process and fungi are one of the cherished bio-sources that show noteworthy aptitude of heavy metal sorption and metal tolerance. Thus, the main objective of the authors was to come with a comprehensive review having methodological insights on the novel and recent results in the field of mycoremediation of heavy metals. This review significantly assesses the potential talent of fungi in heavy metal detoxification and thus, in environmental restoration. Many reported works, methodologies and mechanistic sights have been evaluated to explore the fungal-assisted heavy metal remediation. Herein, a compact and effectual discussion on the recent mycoremediation studies of organic pollutants like dyes, petroleum, pesticides, insecticides, herbicides, and pharmaceutical wastes have also been presented.

The Analysis of the Mycobiota in Plastic Polluted Soil Reveals a Reduction in Metabolic Ability

Plastic pollution is a growing environmental issue that results in its accumulation and persistence in soil for many decades, with possible effects on soil quality and ecosystem services. Microorganisms, and especially fungi, are a keystone of soil biodiversity and soil metabolic capacity. The aim of this research was to study soil fungal biodiversity and soil microbial metabolic profiles in three different sites in northern Italy, where macro- and microplastic concentration in soil was measured. The metabolic analyses of soil microorganisms were performed by Biolog EcoPlates, while the ITS1 fragment of the 18S ribosomal cDNA was used as a target for the metabarcoding of fungal communities. The results showed an intense and significant decrease in soil microbial metabolic ability in the site with the highest concentration of microplastics. Moreover, the soil fungal community composition was significantly different in the most pristine site when compared with the other two sites. The metabarcoding of soil samples revealed a general dominance of Mortierellomycota followed by Ascomycota in all sampled soils. Moreover, a dominance of fungi involved in the degradation of plant residues was observed in all three sites. In conclusion, this study lays the foundation for further research into the effect of plastics on soil microbial communities and their activities.

Bioremediation potential of native microorganisms of the southern chernozem

In the course of the conducted studies, main groups of soil microorganisms in the southern chernozem were identified. The resistance of isolates to the action of oil in the concentration range of 15–25%, the possibility of using it as a carbon source, the ability of soil microbiota to biodegradate oil in contaminated soil and the resistance of bacteria to low temperatures, high NaCl concentrations, acid and alkali resistance were established. 15 genera (31 species) of heterotrophic bacteria were isolated from uncontaminated soil samples of the southern chernozem subtype. Our assessment of the abundance dynamics of microorganisms isolated from laboratory contaminated soils showed that as a result of oil exposure, there was a significant decrease in the numbers of microorganisms: by the 180th day of our experiment, 10 bacteria species belonging to 3 genera were isolated, namely: Bacillus, Micrococcus and Serratia. Among the isolated bacteria, resistance to the action of the pollutant at a concentration of 25% was established for B. coagulans, B. mojavensis, B. megaterium, M. luteus, as well as for the museum strain of B. pumilus CM. By cultivating the studied bacterial strains on a carbon-free medium M9 with 15 and 20% oil added, their ability to use petroleum hydrocarbons as the only carbon source was established; however, when the concentration increased to 25%, only M. luteus, B. mojavensis and B. pumilus KM retained this ability. The presence of hydrocarbon-oxidizing bacteria in soil samples contributed to the 42% decrease in the oil mass concentration in 180 days. The most significant decrease in the concentration of petroleum products occurred in the period from the 10th to the 30th day and amounted to 25%, which is probably due to the increase in the numbers of heterotrophic bacteria. The ability to grow at a temperature of +4°C was established for representatives of the genus Bacillus, including the museum strain of B. pumillus CM, 4 strains of bacilli remained viable in an acidic environment (pH 5), 7 strains of bacilli and M. luteus and S. plymuthica remained viable in an alkaline environment (pH 9). The studied bacterial strains were growing on a GRM-agar with a NaCl concentration of 7%, the ability to grow at a NaCl concentration of 15% was preserved only by the museum strain of B. pumillus KM. The obtained results open the prospects for the use of hydrocarbon-oxidizing bacteria with a high adaptive potential as potential oil destructors capable of biodegradation at low temperatures, in conditions of high salinity and in a wide range of pH of the medium.

Phytomanagement of a Lead-Polluted Shooting Range Using an Aromatic Plant Species and Its Effects on the Rhizosphere Bacterial Diversity and Essential Oil Production

This field study aimed to assess the baseline conditions of a long-term shooting range in Argentina polluted with 428 mg kg^-1 lead (Pb) to evaluate the establishment and development of Helianthus petiolaris plants and address the efficacy of the phytomanagement strategy through: (i) element accumulation in plant tissues; (ii) rhizosphere bacterial diversity changes by Illumina Miseq™, and (iii) floral water and essential oil yield, composition, and element concentration by GC-MS and ICP. After one life cycle growing in the polluted sites, in the roots of Helianthus petiolaris plants, Pb concentration was between 195 and 304 mg kg^-1 Pb. Only a limited fraction of the Pb was translocated to the aerial parts. The predominance of the genus Serratia in the rhizosphere of Helianthus petiolaris plants cultivated in the polluted sites and the decrease in the essential oil yield were some effects significantly associated with soil Pb concentration. No detectable Pb concentration was found in the floral water and essential oil obtained. Extractable Pb concentration in the soil reduced between 28% and 45% after the harvest.

Environmental DNA-based profiling of benthic bacterial and eukaryote communities along a crude oil spill gradient in a coral reef in the Persian Gulf

Coral reef ecosystems in the Persian Gulf are frequently exposed to crude oil spills. We investigated benthic bacterial and eukaryote community structures at such coral reef sites subjected to different degrees of polycyclic aromatic hydrocarbon (PAH) pollution using environmental DNA (eDNA) metabarcoding. Both bacterial and eukaryote communities responded with pronounced shifts to crude oil pollution and distinguished control sites, moderately and heavily impacted sites with significant confidentiality. The observed community patterns were predominantly driven by Alphaproteobacteria and metazoans. Among these, we identified individual genera that were previously linked to oil spill stress, but also taxa, for which a link to hydrocarbon still remains to be established. Considering the lack of an early-warning system for the environmental status of coral reef ecosystems exposed to frequent crude-oil spills, our results encourage further research towards the development of an eDNA-based biomonitoring tool that exploits benthic bacterial and eukaryote communities as bioindicators.

Study on the Changes in Immobilized Petroleum-Degrading Bacteria Beads in a Continuous Bioreactor Related to Physicochemical Performance, Degradation Ability, and Microbial Community

Continuous bioreactors for petroleum degradation and the effect factors of these bioreactors have rarely been mentioned in studies. In addition, indigenous bacteria living in seawater could influence the performance of continuous bioreactors with respect to petroleum degradation in practice. In this paper, a bioreactor fitted with immobilized petroleum-degrading bacteria beads was designed for further research. The results indicated that the diesel degradation rate of the bioreactor could remain above 50% over 27 days, while degradation performance decreased with bioremediation time. Intriguingly, the diameters of immobilized petroleum-degrading bacteria beads were reduced by 32.49% after 45 days remediation compared with the initial size of the immobilized petroleum-degrading bacteria beads. Change in immobilized petroleum-degrading bacteria beads was considered to correlate remarkably with reduced degradation efficiency. Therefore, this paper will be helpful for further study and improvement of bioreactors in the practical context of oil-spill accident recovery.

A Metagenomic and Gene Expression Analysis in Wheat (T. durum) and Maize (Z. mays) Biofertilized with PGPM and Biochar

Commodity crops, such as wheat and maize, are extremely dependent on chemical fertilizers, a practice contributing greatly to the increase in the contaminants in soil and water. Promising solutions are biofertilizers, i.e., microbial biostimulants that when supplemented with soil stimulate plant growth and production. Moreover, the biofertilizers can be fortified when (i) provided as multifunctional consortia and (ii) combined with biochar with a high cargo capacity. The aim of this work was to determine the molecular effects on the soil microbiome of different biofertilizers and delivery systems, highlight their physiological effects and merge the data with statistical analyses. The measurements of the physiological parameters (i.e., shoot and root biomass), transcriptomic response of genes involved in essential pathways, and characterization of the rhizosphere population were analyzed. The results demonstrated that wheat and maize supplemented with different combinations of selected microbial consortia and biochar have a positive effect on plant growth in terms of shoot and root biomass; the treatments also had a beneficial influence on the biodiversity of the indigenous rhizo-microbial community, reinforcing the connection between microbes and plants without further spreading contaminants. There was also evidence at the transcriptional level of crosstalk between microbiota and plants.

Ecological risk assessment of priority PAHs pollutants in crude oil contaminated soil and its impacts on soil biological properties

Polycyclic aromatic hydrocarbons (PAHs) are one of the major toxic constituents of crude oil and therefore, an understanding on PAHs associated risks and their relationship with soil biological parameters are necessary for adopting effective risk-based and site specific remediation strategies in the contaminated soil. Here, risks evaluation of eight detected PAHs in terms of toxic equivalent concentration (TEQ_C), benzo(a)pyrene equivalent (BaPeq), contamination factor (CF), pollution load index (PLI), hazard quotient (HQ), hazard index (HI), toxic unit for individual PAHs (TU) and PAHs mixture (TU_m) have been evaluated. Besides, the effect of PAHs contamination on soil biological properties has also been investigated and correlated with PAHs concentrations. The TEQc of eight PAHs was recorded in the range of 0.06-5.0 mg kg^-1 soil_, whereas the BaPeq value was 25.3 mg kg^-1 soil which exceed the permissible limit. Similarly, CF (85.5-1668.2), PLI (322.8), HQ (311.7-8340.9), HI (26,443.8), TU (227.9-3821.6) and TU_m(7916.2) also exceed the permissible values for non-toxic conditions indicating carcinogenic risk for humans. Besides, activities of soil dehydrogenase, urease, alkaline-phosphatase, catalase, amylase and cellulase were decreased by 1.5-2.3 folds in the contaminated soil than control. The results of Pearson's correlation matrix also established negative impact of PAHs on the soil's biological properties.

Interactions between bacteria and eukaryotic microorganisms and their response to soil properties and heavy metal exchangeability nearby a coal-fired power plant

Persistent heavy metal (HM) contaminated soil provides special habitat for microorganisms, HM stress and complex abiotic factors bring great uncertainty for the development of bacteria and eukaryotic microbes. Despite numerous studies about HMs' effect on soil microorganisms, the key factors affecting microbial communities in severe HM contaminated soil and their interactions are still not definite. In this study, the effect of HM fractions and soil properties on the interaction between bacterial communities and eukaryotic microorganisms was studied by high-throughput Illumina sequencing and simplified continuous extraction of HM in severe HM contaminated soil. Based on amplification and sequencing of the 18S rRNA gene, this study revealed that protists and algae were the most predominant eukaryotic microorganisms, and the dominant phyla were SAR, Opisthokonta and Archaeplastida in HM seriously polluted soil. These results also showed that exchangeable As was negatively correlated with bacterial Shannon and Simpson indexes, while exchangeable Zn was positively correlated with Shannon and Simpson indexes of eukaryotic microbes. Moreover, the structural equation model illustrated that pH, moisture content, available potassium and phosphorus, and exchangeable Cd, As and Zn were the dominant factors shaping bacterial communities, while total organic carbon and exchangeable Zn made the predominant contributions to variations in eukaryotic microbes. In addition, eukaryotic microbes were intensely affected by the bacterial communities, with a standardized regression weight of 0.53, which exceeded the influence of other abiotic factors. It was suggested that community-level adaptions through cooperative interactions under serious HM stress in soil.

Altering Microbiomes with Hydroxyapatite Nanoparticles: A Metagenomic Analysis

Hydroxyapatite (HAp), the most abundant biological material among mammals, has been recently demonstrated to possess moderate antibacterial properties. Metagenomics provides a series of tools for analyzing the simultaneous interaction of materials with larger communities of microbes, which may aid in optimizing the antibacterial activity of a material such as HAp. Here, a microbiome intrinsic to the sample of sandy soil collected from the base of an African Natal plum (Carissa macrocarpa) shrub surrounding the children's sandbox at the Arrowhead Park in Irvine, California was challenged with HAp nanoparticles and analyzed with next-generation sequencing for hypervariable 16S ribosomal DNA base pair homologies. HAp nanoparticles overwhelmingly reduced the presence of Gram-negative phyla, classes, orders, families, genera and species, and consequently elevated the relative presence of their Gram-positive counterparts. Thermodynamic, electrostatic and chemical bonding arguments were combined in a model proposed to explain this selective affinity. The ability of amphiphilic surface protrusions of lipoteichoic acid in Gram-positive bacteria and mycolic acid in mycobacteria to increase the dispersibility of the bacterial cells and assist in their resistance to capture by the solid phase is highlighted. Within the Gram-negative group, the variability of the distal, O-antigen portion of the membrane lipopolysaccharide was shown to be excessive and the variability of its proximal, lipid A portion insufficient to explain the selectivity based on chemical sequence arguments. Instead, flagella-driven motility proves to be a factor favoring the evasion of binding to HAp. HAp displayed a preference toward binding to less pathogenic bacteria than those causative of disease in humans, while taxa having a positive agricultural effect were largely captured by HAp, indicating an evolutionary advantage this may have given it as a biological material. The capacity to selectively sequester Gram-negative microorganisms and correspondingly alter the composition of the microbiome may open up a new avenue in environmental and biomedical applications of HAp.

Marginal lands and fungi - linking the type of soil contamination with fungal community composition

Fungi can be found in almost all ecosystems. Some of them can even survive in harsh, anthropogenically transformed environments, such as post-industrial soils. In order to verify how the soil fungal diversity may be changed by pollution, two soil samples from each of the 28 post-industrial sites were collected. Each soil sample was characterized in terms of concentration of heavy metals and petroleum derivatives. To identify soil fungal communities, fungal internal transcribed spacer 2 (ITS2) amplicon was sequenced for each sample using Illumina MiSeq platform. There were significant differences in the community structure and taxonomic diversity among the analysed samples. The highest taxon richness and evenness were observed in the non-polluted sites, and lower numbers of taxa were identified in multi-polluted soils. The presence of monocyclic aromatic hydrocarbons, gasoline and mineral oil was determined as the factors driving the differences in the mycobiome. Furthermore, in the culture-based selection experiment, two main groups of fungi growing on polluted media were identified - generalists able to live in the presence of pollution, and specialists adapted to the usage of BTEX as a sole source of energy. Our selection experiment proved that it is long-term soil contamination that shapes the community, rather than temporary addition of pollutant.

The crude oil biodegradation activity of Candida strains isolated from oil-reservoirs soils in Saudi Arabia

Crude oil (petroleum) is a naturally occurring complex composed of hydrocarbon deposits and other organic materials. Bioremediation of crude oil-polluted sites is restricted by the biodiversity of indigenous microflora. They possess complementary substrates required for degrading the different hydrocarbons. In the current study, four yeast strains were isolated from different oil reservoirs in Riyadh, Saudi Arabia. The oil-biodegradation ability of these isolates showed variable oxidation effects on multiple hydrocarbons. The scanning electron microscopy (SEM) images showed morphological changes in Candida isolates compared to the original structures. The drop-collapse and oil emulsification assays showed that yeast strains affected the physical properties of tested hydrocarbons. The content of biosurfactants produced by isolated strains was quantified in the presence of different hydrocarbons to confirm the oil displacement activity. The recovery assays included acid precipitation, solvent extraction, ammonium sulfate, and zinc sulfate precipitation methods. All these methods revealed that the amount of biosurfactants correlates to the type of tested hydrocarbons, where the highest amount was produced in crude oil contaminated samples. In conclusion, the study highlights the importance of Candida isolated from contaminated soils for bioremediation of petroleum oil pollution. That raises the need for further analyses on the microbes/hydrocarbon degradation dynamics.

Improved Production of α-Amylase by Aspergillus terreus in Presence of Oxygen-Vector

n-Dodecane has been investigated as an oxygen-vector for improving α-amylase biosynthesis using the strain Aspergillus terreus. In aerobic microbial cultivation, continuous supply of oxygen is required especially due to its low solubility in the growth medium, in particular at high viscosity, but the limitations of oxygen mass transfer in these systems can be overcome by the addition of water-insoluble compounds which possess a strong affinity for oxygen, namely oxygen-vectors. The use of n-dodecane (as an oxygen-vector) in the fermentation medium of A. terreus can significantly improve the bioprocess performance and enhance α-amylase production. Using 5% n-dodecane at 35 °C, an increase of 1.8–2 times in the enzymatic activity was recorded. In the oxygen-vector’s absence, the highest amount of biomass was obtained at 35 °C, while in the presence of 5% vol. n-dodecane, the amount of fungal biomass increased by approximately 70%, with a shift in optimum temperature to 40 °C, generating also an enzymatic activity increase of 2.30 times. Moreover, the oxygen-vector’s addition in the fermentation broth influenced the fungal morphological development in the form of larger pellets with a more compact structure compared to the system without n-dodecane, with a positive effect on the fermentation performance (higher α-amylase activity production).

Investigation of Global Trends of Pollutants in Marine Ecosystems around Barrang Caddi Island, Spermonde Archipelago Cluster: An Ecological Approach

High-quality marine ecosystems are free from global trending pollutants' (GTP) contaminants. Accuracy and caution are needed during the exploitation of marine resources during marine tourism to prevent future ecological hazards that cause chain effects on aquatic ecosystems and humans. This article identifies exposure to GTP: microplastic (MP); polycyclic aromatic hydrocarbons (PAH); pesticide residue (PR); heavy metal (HM); and medical waste (MW), in marine ecosystems in the marine tourism area (MTA) area and Barrang Caddi Island (BCI) waters. A combination of qualitative and quantitative analysis methods were used with analytical instruments and mathematical formulas. The search results show the average total abundance of MPs in seawater (5.47 units/m3) and fish samples (7.03 units/m3), as well as in the sediment and sponge samples (8.18 units/m3) and (8.32 units/m3). Based on an analysis of the polymer structure, it was identified that the dominant light group was MPs: polyethylene (PE); polypropylene (PP); polystyrene (PS); followed by polyamide-nylon (PA); and polycarbonate (PC). Several PAH pollutants were identified in the samples. In particular, naphthalene (NL) types were the most common pollutants in all of the samples, followed by pyrene (PN), and azulene (AZ). Pb+2 and Cu+2 pollutants around BCI were successfully calculated, showing average concentrations in seawater of 0.164 ± 0.0002 mg/L and 0.293 ± 0.0007 mg/L, respectively, while in fish, the concentrations were 1.811 ± 0.0002 µg/g and 4.372 ± 0.0003 µg/g, respectively. Based on these findings, the BCI area is not recommended as a marine tourism destination.

Paenibacillus sp. Strain OL15 Immobilized in Agar as a Potential Bioremediator for Waste Lubricating Oil-Contaminated Soils and Insights into Soil Bacterial Communities Affected by Inoculations of the Strain and Environmental Factors

Waste lubricating oil is a widespread common soil pollutant. In this study, the waste lubricating oil degraders were isolated from the oil-contaminated soil. The bacterial strains OL6, OL15, and OL8, which tolerated a high concentration (10%) of waste lubricating oil, presented the degradation efficiency values (measured in culture broth) of 15.6 ± 0.6%, 15.5 ± 1%, and 14.8 ± 1%, respectively, and belonged to the genera Enterobacter, Paenibacillus, and Klebsiella, respectively. To maintain long survival, immobilization of a promising bioremediator, Paenibacillus sp. strain OL15, in agar exhibited the significantly highest number of surviving cells at the end of a 30-day incubation period, as compared to those in alginate and free cells. Remarkably, after being introduced into the soil contaminated with 10% waste lubricating oil, the strain OL15 immobilized in agar conferred the highest degradation percentage up to 45 ± 3%. Due to its merit as a promising soil pollutant degrader, we investigated the effect of an introduction of the strain OL15 on the alterations of a bacterial community in the oil-contaminated soil environments using 16S rRNA amplicon sequencing. The result revealed that the Proteobacteria, Acidobacteriota, Firmicutes, and Actinobacteriota were predominant phyla. The introduction of the strain affected the soil bacterial community structures by increasing total bacterial diversity and richness. The proportions of the genera Pseudomonas, Vibrio, Herbaspirillum, Pseudoalteromonas, Massilia, Duganella, Bacillus, Gordonia, and Sulfurospirillum were altered in response to the strain establishment. Soil pH, EC, OM, total N, P, Mg, Fe, and Zn were the major factors influencing the bacterial community compositions in the oil-contaminated soils.

Di- and Mono-Rhamnolipids Produced by the Pseudomonas putida PP021 Isolate Significantly Enhance the Degree of Recovery of Heavy Oil from the Romashkino Oil Field (Tatarstan, Russia)

Around the globe, only 30–50% of the amount of oil estimated to be in reservoirs (“original oil in place”) can be obtained using primary and secondary oil recovery methods. Enhanced oil recovery methods are required in the oil processing industry, and the use of microbially produced amphiphilic molecules (biosurfactants) is considered a promising efficient and environmentally friendly method. In the present study, biosurfactants produced by the Pseudomonas putida PP021 isolate were extracted and characterized, and their potential to enhance oil recovery was demonstrated. It was found that the cell-free biosurfactant-containing supernatant decreased the air–water interface tension from 74 to 28 mN m−1. Using TLC and FTIR methods, the biosurfactants produced by the isolate were classified as mono- and di-rhamnolipid mixtures. In the isolates’ genome, the genes rhlB and rhlC, encoding enzymes involved in the synthesis of mono- and di-rhamnolipids, respectively, were revealed. Both genes were expressed when the strain was cultivated on glycerol nitrate medium. As follows from the sand-packed column and core flooding simulations, biosurfactants produced by P. putida PP021 significantly enhance the degree of recovery, resulting in additional 27% and 21%, respectively.

Role of Different Material Amendments in Shaping the Content of Heavy Metals in Maize (Zea mays L.) on Soil Polluted with Petrol

Petroleum substances are among the xenobiotics that most often contaminate the natural environment. They have a strong effect on soil, water, and other components of the environment. The aim of this pot experiment has been to determine the effect of different soil material amendments (compost, 3%; bentonite, 2% relative to the soil mass or calcium oxide, in amounts corresponding to one full hydrolytic acidity) on the content of heavy metals in aerial parts of maize (Zea mays L.) grown on soil polluted with petrol (0, 2.5, 5, and 10 cm3 kg−1 of soil). The content of all heavy metals, except copper, in the aerial biomass of maize was positively correlated, but biomass yield negatively correlated, with the increasing doses of petrol. The highest increase in the content of heavy metals was noted for chromium and manganese. Materials used for phytostabilisation (compost, bentonite, and calcium oxide) had a significant effect on the content of heavy metals and biomass yield of maize. They contributed to the modified accumulation of elements, especially chromium, copper, and cobalt in the aerial biomass of maize. In comparison with the control series (without material amendments), the application of calcium oxide proved to be most effective. It had the most evident influence on the chemical composition of maize, limiting the accumulation of lead, zinc, manganese, and iron and increasing biomass yield.

A critical review on microbial degradation of petroleum-based plastics: quantitatively effects of chemical addition in cultivation media on biodegradation efficiency

Petroleum-based plastics (PBP) with different properties have been developed to suit various needs of modern lives. Nevertheless, these well-developed properties also present the double-edged sword effect that significantly threatens the sustainability of the environment. This work focuses on the impact of microbial cultivating conditions (the elementary compositions and temperature) to provide insightful information for the process optimization of microbial degradation. The major elementary compositions in cultivation media and temperature from the literature were radically reviewed and assessed using the constructed supervised machine learning algorithm. Fifty-two literatures were collected as a training dataset to investigate the impact of major chemical elements and cultivation temperature upon PBP biodegradation. Among six singular parameters (NH₄⁺, K⁺, PO₄^3-, Mg²⁺, Ca²⁺, and temperature) and thirty corresponding binary parameters, four singular (NH₄⁺, K⁺, PO₄^3-, and Mg²⁺) and six binary parameters (NH₄⁺/K⁺, NH₄⁺/PO₄^3-, NH₄⁺/Ca²⁺, K⁺/PO₄^3-, PO₄^3-/Mg²⁺, Mg²⁺/Temp) were identified as statistically significant towards microbial degradation through analysis of variance (ANOVA). The binary effect (PO₄^3-/Mg²⁺) is found to be the most statistically significant towards the microbial degradation of PBP. The concentration range, which locates at 0.1-0.6 g/L for Mg²⁺ and 0-2.8 g/L for PO₄^3-, was identified to contribute to the maximum PBP biodegradation. Among all the investigated elements, Mg²⁺ is the only element that is statistically and significantly associated with the variations of cultivation temperature. The optimal preparation conditions within ± 20% uncertainties based upon the range of collected literature reports are recommended. Five representative cultivation elementary compositions (NH₄⁺, K⁺, PO₄^3-, Mg²⁺, and Ca²⁺) and temperature were reviewed from fifty two different literature reports to investigate their impacts on the microbial degradation of PBP using supervised machine learning algorithm. The optimal cultivation conditions based upon collected literature reports to achieve biodegradation over 80% were identified.

Microbiological Study in Petrol-Spiked Soil

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition-with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IFG); index of petrol effect on soil microorganisms and enzymes (IFP); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon-Weaver's index of bacterial taxa diversity (H); and Shannon-Weaver's index of hydrocarbon degradation (IDH). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes.