Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils

Prokaryotic, Microeukaryotic, and Fungal Composition in a Long-Term Polychlorinated Biphenyl-Contaminated Brownfield

Polychlorinated biphenyls (PCBs) are recognized as persistent organic pollutants and accumulate in organisms, soils, waters, and sediments, causing major health and ecological perturbations. Literature reported PCB bio-transformation by fungi and bacteria in vitro, but data about the in situ impact of those compounds on microbial communities remained scarce while being useful to guide biotransformation assays. The present work investigated for the first time microbial diversity from the three-domains-of-life in a long-term contaminated brownfield (a former factory land). Soil samples were ranked according to their PCB concentrations, and a significant increase in abundance was shown according to increased concentrations. Microbial communities structure showed a segregation from the least to the most PCB-polluted samples. Among the identified microorganisms, Bacteria belonging to Gammaproteobacteria class, as well as Fungi affiliated to Saccharomycetes class or Pleurotaceae family, including some species known to transform some PCBs were abundantly retrieved in the highly polluted soil samples.

Mechanism of polycyclic aromatic hydrocarbons degradation in the rhizosphere of Phragmites australis: Organic acid co-metabolism, iron-driven, and microbial response

Microbial co-metabolism is crucial for the efficient biodegradation of polycyclic aromatic hydrocarbons (PAHs); however, their intrinsic mechanisms remain unclear. To explore the co-metabolic degradation of PAHs, root organic acids (ROAs) (phenolic ROAs: caffeic acid [CA] and ferulic acid [FA]; non-phenolic ROAs: oxalic acid [OA]) were exogenously added as co-metabolic substrates under high (HFe) and low (LFe) iron levels in this study. The results demonstrated that more than 90% of PAHs were eliminated from the rhizosphere of Phragmites australis. OA can promote the enrichment of unrelated degrading bacteria and non-specific dioxygenases. FA with a monohydroxy structure can activate hydroxylase; however, it relies on phytosiderophores released by plants (such as OA) to adapt to stress. Therefore, non-specific co-metabolism occurred in these units. The best performance for PAH removal was observed in the HFe-CA unit because: (a) HFe concentrations enriched the Fe-reducing and denitrifying bacteria and promoted the rate-limiting degradation for PAHs as the enzyme cofactor; (b) CA with a dihydroxyl structure enriched the related degrading bacteria, stimulated specific dioxygenase, and activated Fe to concentrate around the rhizosphere simultaneously to perform the specific co-metabolism. Understanding the co-metabolic degradation of PAHs will help improve the efficacy of rhizosphere-mediated remediation.

Exploring the PAHs dissipation and indigenous bacteria response in soil amended with two different microbial inoculants

This study investigated the bioremediation of PAHs in soil by two different microbial inoculants prepared with Paracoccus aminovorans HPD-2 and the carrier humic acid (HA) or montmorillonite (Mont). After incubation for 42 d, the greatest removal of PAHs, 42.8 % or 41.6 %, was observed in microcosms with 0.2 % HA inoculant or 2 % Mont inoculant. The PAH removal efficiency in these treatments was significantly greater than that in soil amended only with planktonic HPD-2. Bacterial community analysis showed that the survival of Paracoccus aminovorans was enhanced in the treatments with Mont inoculant compared with the treatments with HA inoculant or with HPD-2 alone. Moreover, the diversity of PAH-degrading bacterial genera was greater in the treatments containing Mont inoculant than in the treatments containing HA inoculant. These results indicate that the organic material HA and inorganic material Mont promote PAH removal in different ways. Specifically, HA promotes PAHs bioavailability to accelerate the degradation of PAHs in soil, whereas Mont protects PAH-degrading microorganisms to promote pollutant removal. Overall, the findings suggest that HA and Mont are promising materials for microbial immobilization for the bioremediation of PAH-contaminated soil.

Current and emerging trends in bioaugmentation of organic contaminated soils: A review

Organic contaminated soils constitute an important environmental problem, whereas field applicability of existing physical-chemical methods has encountered numerous obstacles, such as high chemical cost, large energy consumption, secondary pollution, and soil degradation. Bioaugmentation is an environmentally friendly and potentially economic technology that efficiently removes toxic pollutants from organic contaminated soils by microorganisms or their enzymes and bioremediation additives. This review attempted to explore the recent advances in bioaugmentation of organic contaminated soils and provided a comprehensive summary of various bioaugmentation methods, including bacterial, fungus, enzymes and bioremediation additives. The practical application of bioaugmentation is frequently limited by soil environmental conditions, microbial relationships, enzyme durability and remediation cycles. To tackle these problems, the future of bioaugmentation can be processed from sustainability of broad-spectrum bioremediation carriers, microbial/enzyme agents targeting combined contaminants, desorption of environmentally friendly additives and small molecular biological stimulants. Findings of this research are expected to provide new references for bioaugmentation methods that are practically feasible and economically potential.

Effects of Corn Straw and Citric Acid on Removal of PAHs in Contaminated Soil Related to Changing of Bacterial Community and Functional Gene Expression

Root exudates can stimulate microbial degradation in rhizosphere, but it is unclear whether the rhizodegradation of polycyclic aromatic hydrocarbons (PAHs) occurs in corn straw-amended soil. Either citric acid or corn straw was added into PAHs-contaminated soil to investigate their effect on the removal of PAHs. Either corn straw (Y) or combined application of corn straw and citric acid (YN100) significantly (p < 0.05) enhanced the removal of soil PAHs by 8.43% and 18.62%, respectively. Both Y and YN100 treatments obviously increased the abundance of PAHs degraders and the potential hosts of PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes. Interestingly, the copies of PAH-RHDα Gram-negative bacteria genes under YN100 treatment was significantly (p < 0.05) higher than those under Y treatment. The present results indicated that combined application of corn straw and citric acid could efficiently enhance the removal of PAHs in soil, mainly via increasing the relative abundances of PAH-degrading bacteria and the expression of PAH-RHDα genes in contaminated soil.

Efficient Microcystis removal and sulfonamide-resistance gene propagation mitigation by constructed wetlands and functional genes analysis

Increasingly prevalent Microcystis blooms and the propagation of the associated resistance genes represent global environmental problems. Constructed wetlands (CWs) are a cost-effective technology used for wastewater treatment. In this study, the herb Alisma orientale and three industrial byproducts, namely, blast furnace slag, biochar, and sawdust, were selected to construct mini-CW units. Their potential to remediate toxic Microcystis and their influences on the behaviors of antibiotic-resistant genes (ARGs, sul1, sul2, and intl1) were analyzed. Approximately 98.46% of Microcystis cells were removed by the sawdust-based CW in just 2 d, wherein <0.37 μg/L residual microcystin (MC)-LR was detected, with a removal efficiency of >96.47%, which is potentially caused by the higher relative abundance of MC-degrading gene mlrA on the substrate. Lower target ARG accumulations in the sawdust-based CW may be attributed to the lower intl1 relative abundance and microbial function mobile element content, which could influence horizontal gene transfer. In three sequential batches for the treatment of eutrophic lake water, six sawdust-based CW units were assembled into CW microcosms. The efficiency of removal of Microcystis and MC-LR by planted CW microcosms ranged between 92.00% and 95.88% and between 86.48% and 94.82%, respectively; this was significantly (P < 0.05) higher than that by unplanted ones. Less accumulation of target ARGs was also observed in planted CWs. Planting considerably improved nitrogen removal, possibly owing to the enrichment of genes involved in the KEGG nitrogen metabolism pathway in the substrate through metagenomic analysis.

Mitigation of petroleum-hydrocarbon-contaminated hazardous soils using organic amendments: A review

The term "Total petroleum hydrocarbons" (TPH) is used to describe a complex mixture of petroleum-based hydrocarbons primarily derived from crude oil. Those compounds are considered as persistent organic pollutants in the terrestrial environment. A wide array of organic amendments is increasingly used for the remediation of TPH-contaminated soils. Organic amendments not only supply a source of carbon and nutrients but also add exogenous beneficial microorganisms to enhance the TPH degradation rate, thereby improving the soil health. Two fundamental approaches can be contemplated within the context of remediation of TPH-contaminated soils using organic amendments: (i) enhanced TPH sorption to the exogenous organic matter (immobilization) as it reduces the bioavailability of the contaminants, and (ii) increasing the solubility of the contaminants by supplying desorbing agents (mobilization) for enhancing the subsequent biodegradation. Net immobilization and mobilization of TPH have both been observed following the application of organic amendments to contaminated soils. This review examines the mechanisms for the enhanced remediation of TPH-contaminated soils by organic amendments and discusses the influencing factors in relation to sequestration, bioavailability, and subsequent biodegradation of TPH in soils. The uncertainty of mechanisms for various organic amendments in TPH remediation processes remains a critical area of future research.

Functional potential of sewage sludge digestate microbes to degrade aliphatic hydrocarbons during bioremediation of a petroleum hydrocarbons contaminated soil

Sewage sludge digestate is a valuable organic waste which can be used as fertilizer in soil bioremediation. Sewage sludge digestate is not only a good source of nutrients but is also rich in bacteria carrying alkB genes, which are involved in aliphatic hydrocarbons metabolism. Increase of alkB genes ratio in polluted soils has been observed to improve bioremediation efficiency. In this study, for the first time, the genetic potential of indigenous microorganisms of digestate to degrade petroleum products was assessed. The objectives were to study petroleum hydrocarbons (PHCs) removal together with shifts in soil taxa and changes in the concentration of alkB genes after digestate application. Initial alkB genes concentration in contaminated soils and digestate was 1.5% and 4.5%, respectively. During soil incubation with digestate, alkB genes percentage increased up to 11.5% and after the addition of bacteria immobilized onto biochar this value increased up to 60%. Application of digestate positively affected soil respiration and bacterial density, which was concomitant with enhanced PHCs degradation. Incubation of soil amended with digestate resulted in 74% PHCs decrease in 2 months, while extra addition of bacteria immobilized onto biochar increased this value up to 95%. The use of digestate affected the microbial community profiles by increasing initial bacterial density and diversity, including taxa containing recognized PHCs degraders. This study reveals the great potential of digestate as a soil amendment which additionally improves the abundance of alkB genes in petroleum contaminated soils.

Diversity and structure of phenanthrene degrading bacterial communities associated with fungal bioremediation in petroleum contaminated soil

Fungal bioremediation is a promising technique for the cleanup of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). However, due to limited understanding of the composition and dynamics of the native PAH-degrading microorganisms in contaminated sites, its application has been difficult. In the present study, DNA stable-isotope probing was performed to identify indigenous phenanthrene (PHE)-degrading bacteria and determine their diversity during the fungal bioremediation process. The results showed a total of 14 operational taxonomic units (OTUs) enriched in the heavy DNA fractions, which were related to seven genera (Sphingomonas, Sphingobacterium, Acidovorax, Massilia, Flavobacterium, Cupriavidus, Aeromicrobium, and unclassified Chitinophagaceae). Along with enhanced efficiency of PHE removal, the number and diversity of indigenous PHE-degrading bacteria in soil bioaugmented with fungi were significantly increased. Furthermore, based on the results of linear model analysis, we found that PHE degraders affiliated with the genus Sphingomonas were significantly enriched during fungal bioremediation. Moreover, fungal bioaugmentation promoted indigenous functional Proteobacteria involved in PAH degradation through co-metabolism, suggesting that PAH biodegradation was attributable to cooperative metabolism by fungi and indigenous bacteria. Our findings provide new insights into the diversity of PHE-degrading communities and support a more comprehensive view of the fungal bioremediation process.

The linkage between methane production activity and prokaryotic community structure in the soil within a shale gas field in China

Soil methane generation mainly driven by soil prokaryotic microbes can be coupled with the degradation of petroleum hydrocarbons (PHCs); however, the relationship between prokaryotic community structure and methane production activity in soil with the potential risk of PHC contamination is seldom reported. In this study, 3 soil samples (CS-1 to CS-3) in the area nearby an exploratory gas well and 5 soil samples (DC-1 to DC-5) in a drill cutting dump area were obtained from the Fuling shale gas field (Chongqing City, China). Then, the prokaryotic community structure was examined by Illumina Miseq sequencing, and the linkage between soil methane production rate (MPR) and prokaryotic community composition was analyzed. The results indicated that 2 samples (DC-4 and DC-5) collected from the drill cutting dump area had significantly higher MPR than the other samples, and a significant and positive relationship (r = 0.44, P < 0.05) was found between soil MPR and soil organic matter (OM) content. The prokaryotic community composition in the sample (DC-5) with the highest MPR was different from those in the other samples, and soil OM and MPR were the major factors significantly correlated with the prokaryotic community structure in this soil. The samples (DC-4 and DC-5) with higher MPR had a higher relative abundance of Archaea and different archaeal community structures from the other samples, and the MPR was the sole factor significantly correlated with the archaeal genus composition in this soil. Therefore, both the prokaryotic and archaeal community structures are essential in the determination of soil MPR, and the bacterial genus of Saccharibacteria and the archaeal genus of Methanolobus might be the key contributors for methane generation in this soil from the shale gas field.

Modified clays alter diversity and respiration profile of microorganisms in long-term hydrocarbon and metal co-contaminated soil

Clays and surfactant‐modified clays (organoclays) are becoming popular as pollutant sorbents due to their high reactivity and low‐cost availability. However, the lack of field testing and data on ecotoxicity limits their application. Considering such aspects, this study assessed the impact of clay amendments to polycyclic aromatic hydrocarbons (PAHs)/cadmium (Cd)‐contaminated soil on microbial respiration profiles (active vs. inactive cells) using redox staining and the relative abundance and diversity of bacteria and archaea. These clay products are bentonite, cationic surfactant‐modified bentonite and palmitic acid‐grafted surfactant‐modified bentonite). After 70 days, the addition of bentonite and its modified forms altered microbial community structure mainly among dominant groups (Actinobacteria, Proteobacteria, Firmicutes and Chloroflexi) with effects varying depending on material loading to soil. Among amendments, fatty acid (palmitic acid) tailored cationic surfactant‐modified bentonite proved to be microbial growth supportive and significantly increased the number of respiration‐active microbial cells by 5% at a low dose of material (e.g. 1%). Even at high dose (5%), the similarity index using operational taxonomic units (OTUs) also indicates that this modified organoclay‐mixed soil provided only slightly different environment than control soil, and therefore, it could offer more biocompatibility than its counterpart organoclay at similar dose (e.g. cationic surfactant‐modified bentonite). This study promotes designing ‘eco‐safe’ clay‐based sorbents for environmental remediation.

Effect of digestate application on microbial respiration and bacterial communities' diversity during bioremediation of weathered petroleum hydrocarbons contaminated soils

Digestate is an organic by-product of biogas production via anaerobic digestion processes and has a great potential as soil fertilizer due to concentrated nutrients. In this study, we examined digestate as a potential nutrient and microbial seeding for bioremediation of weathered (aged) petroleum hydrocarbon contaminated soils. We analysed 6 different treatments in microcosm using two industrial soils having different textures: a clay rich soil and a sandy soil. After 30 days of incubation, the highest total petroleum hydrocarbons (TPH) removal was observed in microcosms containing digestate together with bulking agent (17.8% and 12.7% higher than control in clay rich soil and sandy soil, respectively) or digestate together with immobilized bacteria (13.4% and 9% higher than control in clay rich soil and sandy soil, respectively). After digestate application microbial respiration was enhanced in sandy soil and inhibited in clay rich soil due to aggregates formation. After bulking agent addition to clay rich soil aggregates size was reduced and oxygen uptake was improved. Application of digestate to soil resulted in the development of distinct microbial groups in amended and non-amended soils. Genera containing species able to degrade TPH like Acinetobacter and Mycobacterium were abundant in digestate and in soil amended with digestate. Quantification of alkB genes, encoding alkane monoxygenase, revealed high concentration of these genes in digestate bacterial community. After application of digestate, the level of alkB genes significantly increased in soils and remained high until the end of the treatment. The study revealed great potential of digestate as a nutrient and bacteria source for soil bioremediation.

Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient

The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.

Influence of bacterial community composition and soil factors on the fate of phenanthrene and benzo[a]pyrene in three contrasting farmland soils

The fate of polycyclic aromatic hydrocarbons (PAHs) determines their potential risk in soil, which may be directly affected by abiotic conditions and indirectly through the changes in decomposer communities. In comparison, the indirect effects on the fate remain largely elusive. In this study, the fate of phenanthrene and benzo[a]pyrene and the corresponding bacterial changes were investigated in three contaminated farmland soils using a ¹⁴C tracer method and Miseq sequencing. The results showed that most benzo[a]pyrene was consistently extractable with dichloromethane (DCM) after the 60-day incubation (60.4%-78.2%), while phenanthrene was mainly mineralized to CO₂ during the 30-day incubation (40.4%-58.7%). Soils from Guangzhou (GZ) showed a different distribution pattern of ¹⁴C-PAHs exemplified by low mineralization and disparate bound residue formation. The PAH fate in the Shenyang (SY) and Nanjing (NJ) soils were similar to each other than to that in the GZ soil. The fate in the GZ soil seemed to be linked to the distinct edaphic properties, such as organic matter content, however soil microbial community could have influenced the distribution pattern of PAHs. This potential role of microorganisms was reflected by the unique changes in the copy numbers of Gram positive RHD_α gene, and by the distinct shifts in bacterial community composition during the incubation. A quite different shift in bacterial communities was found in the GZ microcosms which may influence PAH mineralization and non-extractable residue (NER) formation.

Removal of Chloroxylenol Disinfectant by an Activated Sludge Microbial Community

Chloroxylenol (CHL) is an antimicrobial ingredient that is frequently used in antiseptics/disinfectants for skin (e.g. hand soap) and non-living surfaces. CHL is an alternative to triclosan and triclocarban, the use of which has recently been banned in some countries. Accordingly, the more widespread use of CHL may significantly increase its occurrence and level in aquatic environments in the near future, eventually resulting in potential ecological risks. Wastewater treatment plants (WWTPs) may be a point source of CHL in natural environments due to extensive discharge through urban waste stream disposal. While the satisfactory removal of CHL in WWTPs is critical for maintaining healthy aquatic ecosystems, the extent of CHL removal and whether CHL causes system upset/failure in WWTPs currently remain unknown. In the present study, we conducted bioreactor operation and batch experiments to investigate the fate and effects of CHL and elucidate the mechanisms underlying degradation at various levels from environmentally relevant to high levels (0.5–5 mg L⁻¹). Bioreactors partially removed CHL (44–87%) via a largely biological route. Microbial association networks constructed using 16S rRNA gene sequencing data revealed selective enrichment and a correlation between Sphingobium and CHL, implying its involvement in the biological breakdown of CHL through dehalogenation and ring hydroxylation pathways. The present results provide insights into the behavior and effects of CHL in activated sludge communities and important information for the sustainable management of CHL that may be an emerging issue in the urban water cycle.

Influencing mechanisms of hematite on benzo(a)pyrene degradation by the PAH-degrading bacterium Paracoccus sp. Strain HPD-2: insight from benzo(a)pyrene bioaccessibility and bacteria activity

Iron oxides are reactive inorganic soil components that play an important role in the fate and transport of organic pollutants. Here, hematite was selected to investigate its effect on the biodegradation of benzo[a]pyrene (BaP) by Paracoccus sp. strain HPD-2. Approximately 60% of the total BaP was degraded in the absence of hematite after 7 days but only 30.8 and 20.8% of that was degraded after the addition of 10 and 20 mg  mL^-1 hematite, respectively, indicating that the addition of hematite could significantly inhibit the biodegradation of BaP (P < 0.05). The hematite also lowered bacterium activity by coating the cells and by generating reactive oxygen species that destroyed the cells. Two-photon confocal laser scanning microscope images showed that the addition of hematite substantially decreased the amount of BaP combined with the bacterium, and this also enabled us to observe directly the migration and regression of BaP in the interaction between HPD-2 and hematite. Higher death ratio of HPD-2 might lower the BaP access to live cells because dead cells have a higher adsorption affinity for BaP than live cells. These observations enhance our understanding of the mechanisms by which metal oxides, organic pollutants and degrading-bacteria interact during the biodegradation process.

Effect of the nitrification inhibitor (3, 4-dimethylpyrazole phosphate) on the activities and abundances of ammonia-oxidizers and denitrifiers in a phenanthrene polluted and waterlogged soil

Through a 60-day microcosm incubation, the effect of 3, 4-dimethylpyrazole phosphate (DMPP) on the activities and abundances of ammonia-oxidizers and denitrifiers in phenanthrene-polluted soil was investigated. Five treatments were conducted for clean soil (CK), phenanthrene added (P), phenanthrene and DMPP added (PD), phenanthrene and urea added (PU), and phenanthrene, urea, and DMPP added (PUD) soils. The results indicate that the potential nitrification rate (PNR) in the P treatment was significantly higher than that in the PD treatment only on day 7, whereas the PNR in the PU treatment was significantly higher than that in the PUD treatment on each sampling day. The abundance of soil ammonia-oxidizing bacteria (AOB) in the PU treatment was significantly higher than that in the PUD treatment on each sampling day. Moreover, the abundance of AOB but rather than the ammonia-oxidizing archaea (AOA) had significantly positive correlation with soil PNR (P < 0.05). DMPP showed no obvious effect on the soil denitrification enzyme activity (DEA), which could have inhibited the abundances of denitrification-related narG, nirS, and nirK genes. The results of this study should provide a deeper understanding of the interaction between soil polycyclic aromatic hydrocarbons (PAH) contamination, ammonia oxidization, and denitrification, and offer valuable information for assessing the potential contribution of denitrification for soil PAH elimination.

Mild acid and alkali treated clay minerals enhance bioremediation of polycyclic aromatic hydrocarbons in long-term contaminated soil: A 14C-tracer study

Bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soils requires a higher microbial viability and an increased PAH bioavailability. The clay/modified clay-modulated bacterial degradation could deliver a more efficient removal of PAHs in soils depending on the bioavailability of the compounds. In this study, we modified clay minerals (smectite and palygorskite) with mild acid (HCl) and alkali (NaOH) treatments (0.5-3 M), which increased the surface area and pore volume of the products, and removed the impurities without collapsing the crystalline structure of clay minerals. In soil incubation studies, supplements with the clay products increased bacterial growth in the order: 0.5 M HCl ≥ unmodified ≥ 0.5 M NaOH ≥ 3 M NaOH ≥ 3 M HCl for smectite, and 0.5 M HCl ≥ 3 M NaOH ≥ 0.5 M NaOH ≥ 3 M HCl ≥ unmodified for palygorskite. A¹⁴C-tracing study showed that the mild acid/alkali-treated clay products increased the PAH biodegradation (5-8%) in the order of 0.5 M HCl ≥ unmodified > 3 M NaOH ≥ 0.5 M NaOH for smectite, and 0.5 M HCl > 0.5 M NaOH ≥ unmodified ≥ 3 M NaOH for palygorskite. The biodegradation was correlated (r = 0.81) with the bioavailable fraction of PAHs and microbial growth as affected particularly by the 0.5 M HCl and 0.5 M NaOH-treated clay minerals. These results could be pivotal in developing a clay-modulated bioremediation technology for cleaning up PAH-contaminated soils and sediments in the field.

Biodegradation of Phenanthrene in Polycyclic Aromatic Hydrocarbon-Contaminated Wastewater Revealed by Coupling Cultivation-Dependent and -Independent Approaches

The indigenous microorganisms responsible for degrading phenanthrene (PHE) in polycyclic aromatic hydrocarbons (PAHs)-contaminated wastewater were identified by DNA-based stable isotope probing (DNA-SIP). In addition to the well-known PHE degraders Acinetobacter and Sphingobium, Kouleothrix and Sandaracinobacter were found, for the first time, to be directly responsible for indigenous PHE biodegradation. Additionally, a novel PHE degrader, Acinetobacter tandoii sp. LJ-5, was identified by DNA-SIP and direct cultivation. This is the first report and reference to A. tandoii involved in the bioremediation of PAHs-contaminated water. A PAH-RHD_α gene involved in PHE metabolism was detected in the heavy fraction of ¹³C treatment, but the amplification of PAH-RHD_α gene failed in A. tandoii LJ-5. Instead, the strain contained catechol 1,2-dioxygenase and the alpha/beta subunits of protocatechuate 3,4-dioxygenase, indicating use of the β-ketoadipate pathway to degrade PHE and related aromatic compounds. These findings add to our current knowledge on microorganisms degrading PHE by combining cultivation-dependent and cultivation-independent approaches and provide deeper insight into the diversity of indigenous PHE-degrading communities.

A preliminary report of indigenous fungal isolates from contaminated municipal solid waste site in India

Municipal solid waste (MSW) containing harmful substances is a major concern in waste management and can cause adverse effects on diversity of fungi in soil. The main objective was to evaluate the fungal diversity inhabiting in the soil nearby MSW disposal site. The fungal strains were isolated in potato dextrose agar (PDA), media at temperatures 28 ± 1 °C by using standard serial dilution pour plate method, and appeared fungal colonies identified based on morphological characteristics. The overall most fungal diversity was found in soil sample collected from S5, followed by S4, S3, S1, and least in S2 site. A total of 24 fungal isolates recovered from the different MSW sites and Aspergillus sp., Fusarium sp., and Curvularia sp. genus has isolated from all the samples. In addition, the metal tolerance index performed because it needs to classify the fungus for their best use as potential agent for environmental protection. The metal tolerance outcomes revealed that both metals (cadmium and chromium) has appeared as the highest growth inhibitor for most strains and even fungal colonies did not propagate very well on the surface of media. Therefore, these findings suggest that the pre-adapted indigenous fungal isolates have proven remarkable tolerance ability to both metals. Furthermore, these highly metal-tolerant fungal strains are recommended for detail research or can use in pilot-scale bioremediation application to treat contaminated site.

Benzo(a)pyrene degradation and microbial community responses in composted soil

Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation.

WHOP, a Genomic Region Associated With Woody Hosts in the Pseudomonas syringae Complex Contributes to the Virulence and Fitness of Pseudomonas savastanoi pv. savastanoi in Olive Plants

Bacteria from the Pseudomonas syringae complex belonging to phylogroups 1 and 3 (PG1 and PG3, respectively) isolated from woody hosts share a genomic region herein referred to as WHOP (from woody host and Pseudomonas spp.), which is absent in strains infecting herbaceous organs. In this work, we show that this region is also encoded in P. syringae pv. actinidifoliorum (PG1) and six additional members of PG3, namely, Pseudomonas savastanoi pv. retacarpa, three P. syringae pathovars, Pseudomonas meliae, and Pseudomonas amygdali. Partial conservation of the WHOP occurs in only a few PG2 strains. In P. savastanoi pv. savastanoi NCPPB 3335, the WHOP region is organized into four operons and three independently transcribed genes. While the antABC and catBCA operons mediate the catabolism of anthranilate and catechol, respectively, the ipoABC operon confers oxygenase activity to aromatic compounds. The deletion of antABC, catBCA, or ipoABC in NCPPB 3335 caused reduced virulence in woody olive plants without affecting knot formation in nonwoody plants; catBCA, dhoAB, and PSA3335_3206 (encoding a putative aerotaxis receptor) were also required for the full fitness of this strain exclusively in woody olive plants. Overall, this study sheds light on the evolution and adaptation of bacteria from the P. syringae complex to woody hosts and highlights the enzymatic activities encoded within the WHOP region that are essential for this process.

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China

Agricultural soils in oilfields have high risk for polycyclic aromatic hydrocarbon (PAH) pollution. In this study, from the Jianghan Oilfield (Hubei Province, China) with a history of >50 years, 7 soil samples (OS-1 to OS-7) were collected. Subsequently, the bacterial, archaeal, and fungal community structures were investigated by Illumina MiSeq sequencing, and the relationship between microbial community structure and soil PAH content was analyzed. The results indicated that bacterial and archaeal Chao 1 indices showed a significantly negative relationship with soil PAH content, and only the bacterial Shannon index had a significantly negative relationship with soil PAH content. Moreover, the community structure of bacteria (r ² = 0.9001, p = 0.013) showed a stronger correlation with PAH content than that of fungi (r ² = 0.7357, p = 0.045), and no significant relationship was found between archaeal community structure (r ² = 0.4553, p = 0.262) and soil PAH content. In addition, the relative greater abundances of some bacterial genus belonging to Actinobacteria (Mycobacterium and Micromonospora) and Proteobacteria (Pseudomonas, Lysobacter, Idiomarina, Oxalobacteraceae, and Massilia), fungal genus belonging to Ascomycota (Sordariales and Pleosporales), and archaeal phylum (Euryarchaeota) were detected in the soil samples (OS-3 and OS-5) with greater PAH content. In summary, soil PAHs showed an obvious influence and selectivity on the soil microbiota. Furthermore, compared with fungi and archaea, bacteria was more sensitive to soil PAH pollution, and the diversity indices and community structure of bacteria both might be suitable indicators for assessment of soil PAH stress on the soil ecosystem.

Production of Biomass Crops Using Biowastes on Low-Fertility Soil: 1. Influence of Biowastes on Plant and Soil Quality

Land application of biosolids to low-fertility soil can improve soil quality by increasing concentrations of macronutrients and trace elements. Mixing biosolids with sawdust could reduce the risks of contaminant accumulation posed by rebuilding soils using biosolids alone. We aimed to determine the effects of biosolids and biosolids-sawdust on the plant quality and chemical composition of sorghum, rapeseed, and ryegrass. Plants were grown in a greenhouse over a 5-mo period in a low-fertility soil amended with biosolids (1250 kg N ha), biosolids-sawdust (0.5:1), or urea (200 kg N ha). Biosolids application increased the biomass of sorghum, rapeseed, and ryegrass up to 14.0, 11.9, and 4.1 t ha eq, respectively. Mixing sawdust with biosolids resulted in a growth response similar to biosolids treatments in rapeseed but nullified the effect of biosolids in sorghum. Urea fertilization provided insufficient nutrients to promote rapeseed growth and seed production, whereas seed yields after biosolids application were 2.5 t ha. Biosolids and biosolids-sawdust application enhanced plant quality by increasing element concentrations, especially Zn, and potentially toxic elements (Cd, Cr, Ni) did not exceed food safety standards. An application of 50 t ha of biosolids, equivalent to 1250 kg N ha, did not exceed current soil limits of Cu, Zn, and Cd and hence was effective in rebuilding soil without accumulating contaminants. The effect of mixing sawdust with biosolids varies with plant species but can further enhance plant nutrient quality in biomass and seeds, especially P, Cu, Zn, Mn, Fe, S, and Na.

Wheat straw biochar amendments on the removal of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil

Soil amendments of wheat straw biochar (BC), lignocellulosic substrate (LS), BC+LS, and BC+LS+BR (surfactant Brij30) were investigated for the first time in order to remedy polycyclic aromatic hydrocarbons (PAHs)-polluted soil using pilot scale microcosm incubation. We hypothesized that the removal of PAHs could be inhibited due to the adsorption and immobilization of biochar and the inhibition depends on the molecular-weight of PAHs. The removal rates of phenanthrene (PHE) and Benzo[a]pyrene (BaP) ranked as C=BC>LS=LS+BC=LS+BC+BR and C=BC=LS+BC+BR>LS=LS+BC. Wheat straw biochar inhibited the removal of PHE and accelerated BaP removal. The activity of Dehydrogenase (DH) was depressed by the addition of the biochar while the activity of polyphenol oxidase (PPO) was stimulated. Lignocellulose and surfactant are favourable to sustain soil microbiological activity and the removal of PAHs although the diversity of bacterial community was not significantly changed. The findings implied that the components of PAHs are necessary to consider when the amendments are implemented by associated biochar in PAH-polluted soil.

Biodegradation of sulfonamide antibiotics in sludge

Sulfonamide antibiotics are widely used in human and veterinary medicine. This study assessed the degradation of three sulfonamides (100 mg kg(-1) each of sulfamethoxazole, sulfadimethoxine and sulfamethazine) and changes in the microbial communities of sewage sludge. Sulfamethoxazole degradation was enhanced by spent mushroom compost (SMC), SMC extract, and extract-containing microcapsules in the sludge. The degradation of sulfonamides in sludge and SMC mixtures occurred in the order of sulfamethoxazole > sulfadimethoxine > sulfamethazine. Bioreactor experiments revealed that the sulfonamides removal rates in sludge with SMC were greater than those in sludge alone. The sulfonamides removal rates were enhanced by the addition of SMC for six time additions. The sulfonamides concentrations were 200 and 500 mg kg(-1) for the first to third additions and the fourth to sixth additions, respectively. With the high correlations between TOC and the proportions of sulfonamides remaining in sludge, sulfonamides may be mineralized to a greater extent with SMC in sludge than in sludge alone. Four bacterial genera were identified from the different settings and stages of the bioreactor experiments. Acinetobacter and Pseudomonas were major bacterial communities that were responsible for sulfonamide degradation in sludge.

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters

Industrial wasteland soils with aged PAH and heavy metal contaminations are environments where pollutant toxicity has been maintained for decades. Although the communities may be well adapted to the presence of stressors, knowledge about microbial diversity in such soils is scarce. Soil microbial community dynamics can be driven by the presence of plants, but the impact of plant development on selection or diversification of microorganisms in these soils has not been established yet. To test these hypotheses, aged-contaminated soil samples from a field trial were collected. Plots planted with alfalfa were compared to bare soil plots, and bacterial and fungal diversity and abundance were assessed after 2 and 6 years. Using pyrosequencing of 16S rRNA gene and ITS amplicons, we showed that the bacterial community was dominated by Proteobacteria, Actinobacteria, and Bacteroidetes and was characterized by low Acidobacteria abundance, while the fungal community was mainly represented by members of the Ascomycota. The short-term toxic impact of pollutants usually reduces the microbial diversity, yet in our samples bacterial and fungal species richness and diversity was high suggesting that the community structure and diversity adapted to the contaminated soil over decades. The presence of plants induced higher bacterial and fungal diversity than in bare soil. It also increased the relative abundance of bacterial members of the Actinomycetales, Rhizobiales, and Xanthomonadales orders and of most fungal orders. Multivariate analysis showed correlations between microbial community structure and heavy metal and PAH concentrations over time, but also with edaphic parameters (C/N, pH, phosphorus, and nitrogen concentrations).

Environmental microbiology as a mosaic of explored ecosystems and issues

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.