Ecological response of nitrification to oil spills and its impact on the nitrogen cycle

Nitrogen utilization efficiency assessment during bioremediation of petroleum-contaminated loess soils: insights from metagenomic analysis

Nitrogen addition is commonly used to remediate total petroleum hydrocarbons (TPH) in petroleum-contaminated soils. However, acceptable exogenous nitrogen dosages and their utilization efficiency for the degradation of hydrocarbons in oil-polluted soils are not well understood. This study compared the hydrocarbon bioremediation capacity by applying different doses of NH4Cl as a stimulant in soils contaminated with TPH at 8553 and 17090 mg/kg. The results showed acceptable exogenous nitrogen levels ranging from 60 to 360 mg N/kg soil, and the optimal nitrogen dosage for TPH remediation was 136 mg N/kg in soils with different TPH concentrations. The nitrogen availability efficiency (NAE) and nitrogen polarization factor availability (NPFA) in the 136 mg N/kg addition treatments were 6.69 and 20.47 mg/mg in 8533 mg/kg TPH-polluted soil, and 6.03 and 31.11 mg/mg in 17090 mg/kg TPH-polluted soil, respectively. Metagenomic analysis revealed that the application of 136 mg/kg nitrogen facilitated ammonia oxidation and nitrite reduction to nitric oxide, and induced soil microorganisms to undergo regulatory or adaptive changes in energy supply and metabolic state, which could aid in restoring the ecological functions of petroleum-contaminated soils. These findings underscore that 136 mg/kg of nitrogen dosage application is optimal for remediation of petroleum-contaminated soils irrespective of the TPH concentrations. This exogenous nitrogen application dosage for TPH remediation aligns with the nitrogen requirements for crop growth in agriculture.

Metagenomic analysis reveals the microbial response to petroleum contamination in oilfield soils

The response of the microbes to total petroleum hydrocarbons (TPHs) in three types of oilfield soils was researched using metagenomic analysis. The ranges of TPH concentrations in the grassland, abandoned well, working well soils were 1.16 × 102-3.50 × 102 mg/kg, 1.14 × 103-1.62 × 104 mg/kg, and 5.57 × 103-3.33 × 104 mg/kg, respectively. The highest concentration of n-alkanes and 16 PAHs were found in the working well soil of Shengli (SL) oilfield compared with those in Nanyang (NY) and Yanchang (YC) oilfields. The abandoned well soils showed a greater extent of petroleum biodegradation than the grassland and working well soils. Α-diversity indexes based on metagenomic taxonomy showed higher microbial diversity in grassland soils, whereas petroleum-degrading microbes Actinobacteria and Proteobacteria were more abundant in working and abandoned well soils. RDA demonstrated that low moisture content (MOI) in YC oilfield inhibited the accumulation of the petroleum-degrading microbes. Synergistic networks of functional genes and Spearman's correlation analysis showed that heavy petroleum contamination (over 2.10 × 104 mg/kg) negatively correlated with the abundance of the nitrogen fixation genes nifHK, however, in grassland soils, low petroleum content facilitated the accumulation of nitrogen fixation genes. A positive correlation was observed between the abundance of petroleum-degrading genes and denitrification genes (bphAa vs. nirD, todC vs. nirS, and nahB vs. nosZ), whereas a negative correlation was observed between alkB (alkane- degrading genes) and amo (ammonia oxidation), hao (nitrification). The ecotoxicity of petroleum contamination, coupled with petroleum hydrocarbons (PH) degradation competing with nitrifiers for ammonia inhibited ammonia oxidation and nitrification, whereas PH metabolism promoted the denitrification process. Moreover, positive correlations were observed between the abundance of amo gene and MOI, as well as between the abundance of the dissimilatory nitrate reduction gene nirA and clay content. Thus, improving the soil physicochemical properties is a promising approach for decreasing nitrogen loss and alleviating petroleum contamination in oilfield soils.

Soil amendments promoting nitrifying bacteria recovery faster than the denitrifying bacteria at post soil fumigation

Chloropicrin (CP) is a soil fumigant that not only reduces disease-causing pathogenic microbes but regrettably also those that benefit soil quality and crop health. However, we have few knowledge on rapidly restoring populations of beneficial microbes suppressed by CP fumigation. Here we used genetic sequencing technology to monitor changes in the recovery of soil bacteria in response to ammonium sulfate added to the soil following CP fumigation. The results showed that regardless of the N fertilizer addition rate, the accumulated NH4+-N in CP fumigated soil was rapidly consumed within 42 d. The rapid reduction in NH4+-N coincided with the observed recovery nitrogen-cycling microorganisms, especially the nitrification bacteria AOA and AOB that contributed to the formation of NH4+-N. Additionally, we further observed that the resilience index of nitrifying bacteria (AOB and AOA) was greater than the resilience index of denitrifying bacteria that contain the denitrification genes nirS, nirK and nosZ (0.12 to 0.55 vs. -0.27 to 0.073). These results revealed that N fertilizer stimulated the recovery of nitrifying bacteria more than denitrifying bacteria. Our research suggests that ammonium sulfate applied to CP fumigated soil could be used commercially to improve soil health as a result of an increase in beneficial microbes.

Mitigation of hydrocarbon toxicity using bacterial consortium in microcosm environment for agrarian fecundity

Petroleum contamination in the soil has been well emphasized as a toxic and hazardous soil pollution contributing to a significant portion of soil infertility worldwide. In the present study, bacterial consortium CHM1 composed of 5 strains belonging to genera Klebsiella, Pantoea, and Enterobacter was evaluated for hydrocarbon degradation ability in the soil environment, as well as their performance in remediating ecotoxicity and phytotoxicity. Initially, the degradation efficiency (1.98%/day) in the soil environment was evaluated. Scanning Electron Microscopy combined with Energy Dispersive X-ray spectroscopy revealed an increase in nitrogen content by 24.98% and a decrease in carbon content by 22.76% implying an improvement in soil fertility. The Fourier Transform InfraRed spectroscopy and Gas Chromatographic analysis revealed significant depletion of aromatic, cyclic, long aliphatic, and complex acid and ester content of the test soil. Moreover, the quantitative PCR analysis exhibited the non-competitive coexistence of each component of the CHM1 consortium. Different enzymatic assays revealed elevated dehydrogenase and superoxide dismutase activity in the degradation system due to the introduction of CHM1 in the soil microcosm. Vibrio fischeri-assisted ecotoxicity analysis had established the potential of CHM1 to efficiently minimize the ecotoxicity of hydrocarbon contamination. The phytotoxicity analysis was performed using four different plant models viz. Chickpeas (Cicer arientinum), Coriander (Coriandrum sativum), Fenugreek (Trigonella foenum-graecum), and Spinach (Spinacia oleracea) exhibiting CHM1 amendment helped to restore plant germination and growth in hydrocarbon-contaminated soil system efficiently. The promising results from this study indicated the possible application of the bacterial consortium in hydrocarbon-contaminated land management and soil restoration for cultivation or other plantation purposes.

Dichlorodiphenyltrichloroethane inhibits soil ammonia oxidation by altering ammonia-oxidizing archaeal and bacterial communities

Dichlorodiphenyltrichloroethane (DDT), a persistent organic pollutant, has known effects on natural microbes. However, its effects on soil ammonia-oxidizing microbes, significant contributors to soil ammoxidation, remain unexplored. To address this, we conducted a 30-day microcosm experiment to systematically study the effects of DDT contamination on soil ammonia oxidation and the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings revealed that DDT inhibited soil ammonia oxidation in the early stage (0-6 days), but it gradually recovered after 16 days. The copy numbers of amoA gene of AOA decreased in all DDT-treated groups from 2 to 10 days, while that of AOB decreased from 2 to 6 days but increased from 6 to 10 days. DDT influenced the diversity and community composition of AOA but had no significant effect on AOB. Further, the dominant AOA communities comprised uncultured_ammonia-oxidizing_crenarchaeote and Nitrososphaera sp. JG1: while the abundance of the latter significantly and negatively correlated with NH 4+-N (P ≤ 0.001), DDT (0.001 < P ≤ 0.01), and DDD (0.01 < P ≤ 0.05) and positively correlated with NO3--N (P ≤ 0.001), that of the former significantly and positively correlated with DDT (P ≤ 0.001), DDD (P ≤ 0.001), and NH 4+-N (0.01 < P ≤ 0.05) and negatively correlated with NO3--N (P ≤ 0.001). Among AOB, the dominant group was the unclassified Nitrosomonadales in Proteobacteria, which showed significant negative correlation with NH 4+-N (0.01 < P ≤ 0.05) and significant positive correlation with NO3--N (0.001 < P ≤ 0.01). Notably, among AOB, only Nitrosospira sp. III7 exhibited significant negative correlations with DDE (0.001 < P ≤ 0.01), DDT (0.01 < P ≤ 0.05), and DDD (0.01 < P ≤ 0.05). These results indicate that DDT and its metabolites affect soil AOA and AOB, consequently affecting soil ammonia oxidation.

Shrimp laccase degrades polycyclic aromatic hydrocarbons from an oil spill disaster in Brazil: A tool for marine environmental bioremediation

Our work aims to purify, characterize and evaluate a laccase from by-products of the shrimp farming industry (Litopenaeus vannamei) for the degradation of Polycyclic Aromatic Hydrocarbons (PAHs) from 2019 oil spill in Brazilian coast. The enzyme was purified by affinity chromatography and characterized as thermostable, with activity above 90 °C and at alkaline pH. In addition, the laccase was also tolerant to copper, lead, cadmium, zinc, arsenic, hexane and methanol, with significant enzymatic activation in acetone and 10 mM mercury. Concerning PAHs' degradation, the enzyme degraded 42.40 % of the total compounds, degrading >50 % of fluorene, C4-naphthalenes, C3-naphthalenes, C2-naphthalenes, anthracene, acenaphthene, 1-methylnaphthalene and 2-methylnaphthalene. Thus, this laccase demonstrated important characteristics for bioremediation of marine environments contaminated by crude oil spills, representing a viable and ecological alternative for these purposes.

Aerobic biodegradation of quinoline under denitrifying conditions in membrane-aerated biofilm reactor

Aerobic denitrification is being investigated as a novel biological nitrogen removal process, yet the knowledge on aerobic denitrification is limited to pure culture isolations and its occurrence in bioreactors remains unclear. This study investigated the feasibility and capacity of applying aerobic denitrification in membrane aerated biofilm reactor (MABR) for biological treatment of quinoline-laden wastewater. Stable and efficient removals of quinoline (91.5 ± 5.2%) and nitrate (NO₃^-) (86.5 ± 9.3%) were obtained under different operational conditions. Enhanced formation and function of extracellular polymeric substances (EPS) were observed at increasing quinoline loadings. MABR biofilm was highly enriched with aerobic quinoline-degrading bacteria, with a predominance of Rhodococcus (26.9 ± 3.7%) and secondary abundance of Pseudomonas (1.7 ± 1.2%) and Comamonas (0.94 ± 0.9%). Metagenomic analysis indicated that Rhodococcus contributed significantly to both aromatic degradation (24.5 ± 21.3%) and NO₃^- reduction (4.5 ± 3.9%), indicating its key role in aerobic denitrifying quinoline biodegradation. At increasing quinoline loadings, abundances of aerobic quinoline degradation gene oxoO and denitrifying genes of napA, nirS and nirK increased; there was a significant positive correlation of oxoO with nirS and nirK (p < 0.05). Aerobic quinoline degradation was likely initiated by hydroxylation, encoded by oxoO, followed by stepwise oxidations through 5,6-dihydroxy-1H-2-oxoquinoline or 8-hydroxycoumarin pathway. The results advance our understanding of quinoline degradation during biological nitrogen removal, and highlight the potential implementation of aerobic denitrification driven quinoline biodegradation in MABR for simultaneous removal of nitrogen and recalcitrant organic carbon from coking, coal gasification and pharmaceutical wastewaters.

Coupling of Anammox Activity and PAH Biodegradation: Current Insights and Future Directions

Anaerobic ammonium oxidation (anammox) has shown success in past years for the treatment of municipal and industrial wastewater containing inorganic nutrients (i.e., nitrogen). However, the increase in polycyclic aromatic hydrocarbon (PAH)-contaminated matrices calls for new strategies for efficient and environmentally sustainable remediation. Therefore, the present review examined the literature on the connection between the anammox process and PAHs using VOSviewer to shed light on the mechanisms involved during PAH biodegradation and the key factors affecting anammox bacteria. The scientific literature thoroughly discussed here shows that PAHs can be involved in nitrogen removal by acting as electron donors, and their presence does not adversely affect the anammox bacteria. Anammox activity can be improved by regulating the operating parameters (e.g., organic load, dissolved oxygen, carbon-to-nitrogen ratio) and external supplementation (i.e., calcium nitrate) that promote changes in the microbial community (e.g., Candidatus Jettenia), favoring PAH degradation. The onset of a synergistic dissimilatory nitrate reduction to ammonium and partial denitrification can be beneficial for PAH and nitrogen removal.

Impacts of dispersants on microbial communities and ecological systems

Accidental oil spills can result in catastrophic ecological insults and therefore require rapid intervention to mitigate the potential impacts to aquatic ecosystems. One of the largest oil spills, known as the Deepwater Horizon oil spill, occurred in the Spring of 2010 near the coast of Louisiana (USA) due to an explosion during oil drilling activities. Millions of gallons of oil were released into the Gulf of Mexico, impacting thousands of ocean miles and coastal areas linked to the gulf. Among the actions taken during the remediation efforts was the unprecedented large use of Corexit dispersants, including at the subsurface to prevent oil from reaching the surface. While there is evidence that dispersants can accelerate the biodegradation of oil, reports on their potential toxicity to aquatic biota and to microbial functions have also been documented. In this review, we will examine the most recent literature on the impact of dispersants on microbial communities implicated in oil degradation and overall ecological networks. The primary focus will be on studies using Corexit but other dispersants will be discussed if data are available. We will share the literature gaps identified and discuss future work that is needed to reconcile some of the discrepancies found on the effectiveness of dispersants on oil degradation and their potential toxicity. KEY POINTS: • Chemical dispersants have been applied as a chemical response measure for oil spills. • The effects of chemical dispersants on microbial communities have been the subject of substantial research. • This work seeks to review recent work on the impact of chemical dispersants on oil biodegradation, microbial communities, and ecosystems.

Assessment of seasonal variation in distribution, source identification, and risk of polycyclic aromatic hydrocarbon (PAH)-contaminated sediment of Ikpoba River, South-South Nigeria

The study aims to assess the seasonal variation in distribution, source identification, and risk of 20 polycyclic aromatic hydrocarbons (20 PAHs) in the sediment of the Ikpoba River, south-south Nigeria. The PAHs were extracted in an ultrasonic bath with a mixture of n-hexane and dichloromethane (1:1 v/v). The extract was cleaned by silica-alumina gel mixed with anhydrous Na₂SO₄ in a chromatography column, eluted by n-hexane, and analysed by gas chromatography-mass spectrometry. The range of the average PAHs in mg.kg-dw was 0.15 (Nap)-0.54 (Acy) and 0.13 (D.al.P)-0.99 (Acy) in wet and dry periods correspondingly, indicating an increase in concentration from wet to dry period. However, the rings of the average concentration of the PAHs show 6 and 3 rings to be the highest values during the wet and dry seasons, respectively. Based on the human health risk analysis, the hazard quotient (HQ) and hazard index (HI), and carcinogenic risk indices showed low non-carcinogenic and carcinogenic risk for both seasons. The ecological risk analysis showed the mean effect range median quotient (mERMQ) recorded a medium-low effect on the biota of the locations, except in AS3 during the wet season and also in WS8 and WS9 during the dry season. The minimum value of the toxic equivalent quotient (TEQ) was > 0.2 mg/kg, which indicated a recommendation for the clean-up of the Ikpoba River. The isomer ratio and the principal component analysis (PCA) revealed the sources of the PAHs to be majorly combustion, followed by pyrolytic and petrogenic sources for both seasons.

Use of Taguchi design for optimization of diesel-oil biodegradation using consortium of Pseudomonas stutzeri, Cellulosimicrobium cellulans, Acinetobacter baumannii and Pseudomonas balearica isolated from tarball in Terengganu Beach, Malaysia

A consortium of bacteria capable of decomposing oily hydrocarbons was isolated from tarballs on the beaches of Terengganu, Malaysia, and classified as Pseudomonas stutzeri, Cellulosimicrobium cellulans, Acinetobacter baumannii and Pseudomonas balearica. The Taguchi design was used to optimize the biodegradation of diesel using these bacteria as a consortium. The highest biodegradation of diesel-oil in the experimental tests was 93.6%, and the individual n-alkanes decomposed 87.6-97.6% over 30 days. Optimal settings were inoculum size of 2.5 mL (1.248 OD_600nm); 12% (v/v) the initial diesel-oil in a minimal salt medium of pH 7.0, 30.0 gL^-1 NaCl and 2.0 gL^-1 NH₄NO₃ concentration, incubated at 42 °C temperature and 150 rpm agitation speed. Parameters significantly improved diesel-oil removal by consortium as shown by the model determination coefficient (R² = 90.89%; P < 0.001) with a synergistic effect of agitation speed significantly contributing 81.03%. Taguchi design determined the optimal settings for the parameters under study, which significantly improved diesel-oil removal by consortium. This can be used to design a novel bioremediation strategy that can achieve optimal decontamination of oil pollution in a shorter time.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40201-022-00812-3.

The microbial communities (bacteria, algae, zooplankton, and fungi) improved biofloc technology including the nitrogen-related material cycle in Litopenaeus vannamei farms

Microbes are essential in biofloc technology for controlling nitrogen levels in water. The composition and function of microorganisms with biofloc systems were reported; however, data on microorganisms other than bacteria, such as algae (which are essential in the nitrogen cycle) and zooplankton (which are bacterial and algal predators), remain limited. The microbial communities (including bacteria, algae, zooplankton, and fungi) were investigated in shrimp farms using biofloc technology. Using Illumina MiSeq sequencing, the V4 region of 18S rRNA and the V3-V4 region of 16S rRNA were utilized for the analysis of the eukaryotic and prokaryotic microbial communities. As a result, it was found that the biofloc in the shrimp farm consisted of 48.73%-73.04% eukaryotic organisms and 26.96%-51.27% prokaryotic organisms. In these shrimp farms, prokaryotic microbial communities had higher specie richness and diversity than eukaryotic microbial communities. However, the eukaryotic microbial communities were more abundant than their prokaryotic counterparts, while algae and zooplankton dominated them. It was discovered that the structures of the microbial communities in the shrimp farms seemed to depend on the effects of predation by zooplankton and other related organisms. The results provided the nitrogen cycle in biofloc systems by the algal and bacterial groups in microbial communities.

Characterization of two novel strains of Pseudomonas aeruginosa on biodegradation of crude oil and its enzyme activities

Crude oil contaminant is one of the major problem to environment and its removal process considered as most challenging tool currently across the world. In this degradation study, crude oil hydrocarbons are degraded on various pH optimization conditions (pH 2, 4,6,7,8 and 10) by using two biosurfactant producing bacterial strains Pseudomonas aeruginosa PP3 and Pseudomonas aeruginosa PP4. During crude oil biodegradation, degradative enzymes alkane hydroxylase and alcohol dehydrogenase were examined and found to be higher in PP4 than PP3. Biodegradation efficiency (BE) of crude oil by both PP3 and PP4 were analysed by gas chromatography mass spectroscopy (GCMS). Based on strain PP3, the highest BE was observed in pH 2 and pH 4 were found to be 62% and 69% than pH 6, 7, 8 and 10 (47%, 47%, 49% and 45%). It reveals that PP3 was survived effectively in acidic condition and utilized the crude oil hydrocarbons. In contrast, the highest BE of PP4 was observed in pH 7 (78%) than pH4 (68%) and pH's 2, 6, 8 and 10 (52%, 52%, 43% and 53%) respectively. FTIR spectra results revealed that the presence of different functional group of hydrocarbons (OH, -CH₃, CO, C-H) in crude oil. GCMS results confirmed that both strains PP3 and PP4 were survived in acidic condition and utilized the crude oil hydrocarbons as sole carbon sources. This is the first observation on biodegradation of crude oil by the novel strains of Pseudomonas aeruginosa in acidic condition with higher BE. Overall, the extracellular enzymes and surface active compounds (biosurfactant) produced by bacterial strains were played a key role in crude oil biodegradation process.

Microbial bioremediation of produced water under different redox conditions in marine sediments

The discharge of produced water from offshore oil platforms is an emerging concern due to its potential adverse effects on marine ecosystems. In this study, we investigated the feasibility and capability of using marine sediments for the bioremediation of produced water. We utilized a combination of porewater and solid phase analysis in a series of sediment batch incubations amended with produced water and synthetic produced water to determine the biodegradation of hydrocarbons under different redox conditions. Significant removal of benzene, toluene, ethylbenzene and xylene (BTEX) compounds was observed under different redox conditions, with biodegradation efficiencies of 93-97% in oxic incubations and 45-93% in anoxic incubations with nitrate, iron oxide or sulfate as the electron acceptor. Higher biodegradation rates of BTEX were obtained by incubations dominated by nitrate reduction (104-149 nmolC/cm³/d) and oxygen respiration (52-57 nmolC/cm³/d), followed by sulfate reduction (14-76 nmolC/cm³/d) and iron reduction (29-39 nmolC/cm³/d). Chemical fingerprint analysis showed that hydrocarbons were biodegraded to smaller alcohols/acids under oxic conditions compared to anoxic conditions with nitrate, indicating that the presence of oxygen facilitated a more complete biodegradation process. Toxicity of treated produced water to the marine copepod Acartia tonsa was reduced by half after sediment incubations with oxygen and nitrate. Our study emphasizes the possibility to use marine sediment as a biofilter for treating produced water at sea without extending the oil and gas platform or implementing a large-scale construction.

Polyethylene microplastics interfere with the nutrient cycle in water-plant-sediment systems

Increasing microplastic (MP) pollution and its effects on aquatic systems have become a global issue; however, the impact of MPs on biogeochemical cycles is poorly understood. A simulation study was performed to analyse the influence of polyethylene (PE) microplastics on the morphological, physiological, and stoichiometric (C, N, P) characteristics of submerged plants, and to investigate their effects on the nutrient cycle and microbial community in freshwater sediment. The results showed that PE-MPs treatments significantly decreased leaf nitrogen and carbon contents. Exposure to 1% PE-MPs suppressed the plant height, total biomass, root activity, and relative growth rate of Vallisneria natans. Decrease in dissolved oxygen (DO) concentrations (19.93-40.26%) were observed in the 1% PE-MPs treatment group compared to that in the control between 1 and 6 days. The activities of enzymes (ammonia monooxygenase and nitrate reductase) related to the nitrogen cycle were significantly altered by the addition of PE-MPs. We found that PE-MPs acted as obstacle disruptors, resulting in a reduction in the release of nitrogen and phosphorus from the sediment to the overlying water. This is because PE-MPs significantly alter the composition and metabolic properties of the microbial communities in sediments, the plant growth, and the nutrient cycle. These findings helped evaluate the impacts of PE-MPs on the water-plant-sediment system and on the biogeochemical cycles of the freshwater ecosystems.

Biological Process of Alkane Degradation by Gordonia sihwaniensis

With the development of the petroleum industry, oil pollution has become widespread. It is harmful to the digestive, immune, reproductive, and nervous systems of fishes, wild animals, and humans, causing severe threats to ecological safety and human health. Gordonia has increasingly attracted attention in the treatment of alkane pollution for its outstanding performance against hydrophobic refractory substances. However, the lack of knowledge about alkane uptake and degradation restricts the application of gordonia. In this paper, we studied the strain lys1-3 of Gordonia sihwaniensis isolated from coal chemical wastewater, which showed good alkane degradation performance by lys1-3. It is found that stimulated by an alkane, lys1-3 secreted biosurfactants, which emulsified large alkane particles to smaller particles. By active transport, unmodified alkane was transferred into cells and produced a large amount of acid, which was secreted out of the cells.

Identification of suspended particulate matters as the hotspot of polycyclic aromatic hydrocarbon degradation-related bacteria and genes in the Pearl River Estuary using metagenomic approaches

Bacterial degradation is unequivocally considered as an important way for the cleanup of polycyclic aromatic hydrocarbon (PAHs) in the aquatic environment. However, the diversity and distribution of PAH-degrading bacterial communities and PAH degradation-related genes (PAHDGs) in ambient environment need to be investigated. In this study, bacteria in the water of the Pearl River Estuary (PRE) were initially separated as the particle-attached bacteria (PAB) and free-living bacteria (FLB), and were further characterized using metagenomic approaches. Proteobacteria (80.1 %) was identified as the most abundant PAH-degrading phylum in the PRE water, followed by Bacteroidetes, Actinobacteria, and Firmicutes. A substantial difference in the community structure was observed between PAH-degrading PAB and FLB. Both of PAH-degrading bacteria and PAHDGs were enriched on the suspended particulate matters (SPMs), with the range of enrichment factor (EF) from 7.84 × 10⁴ to 6.64 × 10⁶ (PAH-degrading bacteria) and from 1.14 × 10³ to 1.76 × 10⁵ (PAHDGs). The levels of PAH-degrading bacteria 16 S rRNA genes and PAHDGs on the SPMs were both significantly correlated with those in the aqueous phase (AP) in the PRE water (p < 0.05), indicating a dynamic distribution of PAH-degrading bacteria between these two phases. The total PAH concentrations on the SPMs of the PRE water were also significantly correlated with the total PAHDG levels in the PAB (p < 0.05). Our results suggested that the SPMs could be the important compartment for the elimination of PAHs from the aquatic environment.

Temporal changes of microbial community structure and nitrogen cycling processes during the aerobic degradation of phenanthrene

Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g^-1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%-194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.

Influence of nutrient status on the response of the diatom Phaeodactylum tricornutum to oil and dispersant

Phytoplankton play a central role in our ecosystems, they are responsible for nearly 50 percent of the global primary productivity and major drivers of macro-elemental cycles in the ocean. Phytoplankton are constantly subjected to stressors, some natural such as nutrient limitation and some manmade such as oil spills. With increasing oil exploration activities in coastal zones in the Gulf of Mexico and elsewhere, an oil spill during nutrient-limited conditions for phytoplankton growth is highly likely. We performed a multifactorial study exposing the diatom Phaeodactylum tricornutum (UTEX 646) to oil and/or dispersants under nitrogen and silica limitation as well as co-limitation of both nutrients. Our study found that treatments with nitrogen limitation (-N and–N-Si) showed overall lower growth and chlorophyll a, lower photosynthetic antennae size, lower maximum photosynthetic efficiency, lower protein in exopolymeric substance (EPS), but higher connectivity between photosystems compared to non-nitrogen limited treatments (-Si and +N+Si) in almost all the conditions with oil and/or dispersants. However, certain combinations of nutrient limitation and oil and/or dispersant differed from this trend indicating strong interactive effects. When analyzed for significant interactive effects, the–N treatment impact on cellular growth in oil and oil plus dispersant conditions; and oil and oil plus dispersant conditions on cellular growth in–N-Si and–N treatments were found to be significant. Overall, we demonstrate that nitrogen limitation can affect the oil resistant trait of P. tricornutum, and oil with and without dispersants can have interactive effects with nutrient limitation on this diatom.

A metagenomic view of how different carbon sources enhance the aniline and simultaneous nitrogen removal capacities in the aniline degradation system

To cross nitrogen removal barrier, carbon sources (sodium succinate (Z1), sodium acetate (Z2) and glucose (Z3)) were applied in aniline degradation reactor to enrich heterotrophic nitrifiers and denitrifiers. The aniline was degraded almost completely and the nitrogen removal performance was improved in three systems. The total nitrogen (TN) removal efficiency of Z2 was the highest. The dominant bacteria were phylum Proteobacteria, class BetaProteobacteria, and genus Thauera (Z1, Z3), Leptothrix (Z2). Different aniline degrading bacteria, heterotrophic nitrifiers and denitrifiers were enriched, and Z2 had more high-abundance communities. Three systems followed the meta-cleavage pathway for the aniline degradation according to the genes annotation. Particularly, the contribution of each genus to nitrogen metabolism and aromatic compounds degradation in the Z2 was more evenly distributed, rather than relying mainly on the contribution of Thauera in Z1 and Z3 so that more functional genes related nitrogen metabolism and aniline degradation were more abundant in Z2.

Succession pattern and phylotype analysis of microphytobenthic communities in a simulated oil spill seagrass mesocosm experiment

Microphytobenthic communities play a significant role in nutrient modulation, sediment stabilization, and primary production in seagrass beds, which provide various ecosystem services. We hypothesized that microphytobenthic communities in sediments of chronically oil-exposed seagrass beds will exhibit increased resiliency to stressors associated with oil exposure as opposed to seagrass beds never exposed to oil spills. We prepared 14-liter seawater mesocosms, each containing a submersed macrophyte Ruppia maritima collected from the Chandeleur Islands, Louisiana, and Estero Bay, Florida. Mesocosms were initially exposed to 50% water-accommodated oil fractions (WAF) and subsequently diluted by 50% with daily artificial seawater exchanges over 8 days to simulate tidal dilution. High-throughput amplicon sequencing based on 23S rRNA gene targeting cyanobacteria and chloroplasts of eukaryotic microphytobenthos was conducted to assess the impact of oiling on microphytobenthic communities with additional assessment via microscopy. High-throughput sequencing in combination with traditional microscopic analysis provided a robust examination in which both methods roughly complemented each other. Distinct succession patterns were detected in benthic algal communities of chronically oil-exposed (Louisiana) versus unexposed (Florida) seagrass bed sediments. The impact of oiling in microphytobenthos across all samples showed that benthic diatoms dominated all algal communities with sample percentages ranging from 42 to 97%, followed by cyanobacteria (2 to 50%). It is noteworthy that drastic changes in microphytobenthic community structure in terms of the larger taxonomic level were not observed, rather change occurred at the phylotype level. These results were also confirmed by microscopy. Similarity percentages (SIMPER) analysis identified seven phylotypes (Cyanobacteria, Bacillariophyceae, and Mediophyceae) in the Louisiana samples and one phylotype (Bacillariophyceae) in the Florida samples that increased in relative sequence abundance after oil exposure. The detailed phylotype analysis identifying sentinel microphytobenthic indicators provides a base for future research on benthic microalgae response to ecosystem disturbance.

Statistical Optimisation of Diesel Biodegradation at Low Temperatures by an Antarctic Marine Bacterial Consortium Isolated from Non-Contaminated Seawater

Hydrocarbon pollution is widespread around the globe and, even in the remoteness of Antarctica, the impacts of hydrocarbons from anthropogenic sources are still apparent. Antarctica’s chronically cold temperatures and other extreme environmental conditions reduce the rates of biological processes, including the biodegradation of pollutants. However, the native Antarctic microbial diversity provides a reservoir of cold-adapted microorganisms, some of which have the potential for biodegradation. This study evaluated the diesel hydrocarbon-degrading ability of a psychrotolerant marine bacterial consortium obtained from the coast of the north-west Antarctic Peninsula. The consortium’s growth conditions were optimised using one-factor-at-a-time (OFAT) and statistical response surface methodology (RSM), which identified optimal growth conditions of pH 8.0, 10 °C, 25 ppt NaCl and 1.5 g/L NH₄NO₃. The predicted model was highly significant and confirmed that the parameters’ salinity, temperature, nitrogen concentration and initial diesel concentration significantly influenced diesel biodegradation. Using the optimised values generated by RSM, a mass reduction of 12.23 mg/mL from the initial 30.518 mg/mL (4% (w/v)) concentration of diesel was achieved within a 6 d incubation period. This study provides further evidence for the presence of native hydrocarbon-degrading bacteria in non-contaminated Antarctic seawater.

Responses of ammonia-oxidizing microorganisms to biochar and compost amendments of heavy metals-polluted soil

Heavy metal pollution affects soil ecological function. Biochar and compost can effectively remediate heavy metals and increase soil nutrients. The effects and mechanisms of biochar and compost amendments on soil nitrogen cycle function in heavy-metal contaminated soils are not fully understood. This study examined how biochar, compost, and their integrated use affected ammonia-oxidizing microorganisms in heavy metal polluted soil. Quantitative PCR was used to determine the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Ammonia monooxygenase (AMO) activity was evaluated by the enzyme-linked immunosorbent assay. Results showed that compost rather than biochar improved nitrogen conversion in soil. Biochar, compost, or their integrated application significantly reduced the effective Zn and Cd speciation. Adding compost obviously increased As and Cu effective speciation, bacterial 16S rRNA abundance, and AMO activity. AOB, stimulated by compost addition, was significantly more abundant than AOA throughout remediation. Correlation analysis showed that AOB abundance positively correlated with NO₃^--N (r = 0.830, P < 0.01), and that AMO activity had significant correlation with EC (r = -0.908, P < 0.01) and water-soluble carbon (r = -0.868, P < 0.01). Those seem to be the most vital factors affecting AOB community and their function in heavy metal-polluted soil remediated by biochar and compost.

Immediate social and economic impacts of a major oil spill on Brazilian coastal fishing communities

In August 2019, a major oil spill hit nine Brazilian coastal states, affecting marine ecosystems and fishing communities. In this study, we assess the immediate social and economic impacts of this oil spill on fishing communities of the northeast coast. We conducted semi-structured interviews and focal meetings with 381 fishers and shellfish gatherers to understand the perceived socioeconomic impacts on different types of fishing. We also obtained information on fish consumption after the oil spill, which we compared with data prior to the oil spill from the same communities. Sales decreased by more than 50% for all types of fishing, strongly impacting local income generation. These communities, which are already social-ecologically vulnerable, have had their subsistence, food security and cultural maintenance strongly compromised. We argue that there is a clear need for coordinated state interventions to mitigation the impacts, considering it's environmental, social, economic, human health and political dimensions.

Biosurfactant electrospun nanofibers exhibit minimal side effects on the structure and function of the liver tissue in male rat model

Oil spills can result in significant damage to marine estuaries, rivers, lakes, wetlands, and shorelines. Electrospun nanofibers containing biosurfactant (ENFs) can be used to clean oil spills up and protect the environmental biology. Present work aimed to study the side-effects of prepared nanofibers on animal models. Screening of the prepared ECNFs on animals showed that three of them (PVA-5, PEO-1, and PEO-5) are safe to hepatic tissues and liver functions. Furthermore, oxidative stress did not change after using these nanofibers. The PVA-1 nanofibers, however, were found to cause major pathological changes in the liver tissue. In addition, PVA-1 nanofibers were proved to alter the total white blood count and the neutrophil percentages significantly in comparison to the control. In conclusion, PVA-5, PEO-1, and PEO-5 are safe to hepatic tissues and liver functions.

Integrated Omics Elucidate the Mechanisms Driving the Rapid Biodegradation of Deepwater Horizon Oil in Intertidal Sediments Undergoing Oxic-Anoxic Cycles

Crude oil buried in intertidal sands may be exposed to alternating oxic and anoxic conditions but the effect of this tidally induced biogeochemical oscillation remains poorly understood, limiting the effectiveness of remediation and managing efforts after oil spills. Here, we used a combination of metatranscriptomics and genome-resolved metagenomics to study microbial activities in oil-contaminated sediments during oxic-anoxic cycles in laboratory chambers that closely emulated in situ conditions. Approximately 5-fold higher reductions in the total petroleum hydrocarbons were observed in the oxic as compared to the anoxic phases with a relatively constant ratio between aerobic and anaerobic oil decomposition rates even after prolonged anoxic conditions. Metatranscriptomics analysis indicated that the oxic phases promoted oil biodegradation in subsequent anoxic phases by microbially mediated reoxidation of alternative electron acceptors like sulfide and by providing degradation-limiting nitrogen through biological nitrogen fixation. Most population genomes reconstructed from the mesocosm samples represented uncultured taxa and were present typically as members of the rare biosphere in metagenomic data from uncontaminated field samples, implying that the intertidal communities are adapted to changes in redox conditions. Collectively, these results have important implications for enhancing oil spill remediation efforts in beach sands and coastal sediments and underscore the role of uncultured taxa in such efforts.

Effects of Zeolite and Biochar Addition on Ammonia-Oxidizing Bacteria and Ammonia-Oxidizing Archaea Communities during Agricultural Waste Composting

The effects of zeolite and biochar addition on ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities during agricultural waste composting were determined in this study. Four treatments were conducted as follows: Treatment A as the control with no additive, Treatment B with 5% of zeolite, Treatment C with 5% of biochar, and Treatment D with 5% of zeolite and 5% biochar, respectively. The AOB and AOA amoA gene abundance as well as the ammonia monooxygenase (AMO) activity were estimated by quantitative PCR and enzyme-linked immunosorbent assay, respectively. The relationship between gene abundance and AMO enzyme activity was determined by regression analysis. Results indicated that the AOB was more abundant than that of AOA throughout the composting process. Addition of biochar and its integrated application with zeolite promoted the AOB community abundance and AMO enzyme activity. Significant positive relationships were obtained between AMO enzyme activity and AOB community abundance (r2 = 0.792; P < 0.01) and AOA community abundance (r2 = 0.772; P < 0.01), indicating that both bacteria and archaea played significant roles in microbial ammonia oxidation during composting. Using biochar and zeolite might promote the nitrification activity by altering the sample properties during agricultural waste composting.

Bacterial Community Legacy Effects Following the Agia Zoni II Oil-Spill, Greece

In September 2017 the Agia Zoni II sank in the Saronic Gulf, Greece, releasing approximately 500 tonnes of heavy fuel oil, contaminating the Salamina and Athens coastlines. Effects of the spill, and remediation efforts, on sediment microbial communities were quantified over the following 7 months. Five days post-spill, the concentration of measured hydrocarbons within surface sediments of contaminated beaches was 1,093-3,773 μg g-1 dry sediment (91% alkanes and 9% polycyclic aromatic hydrocarbons), but measured hydrocarbons decreased rapidly after extensive clean-up operations. Bacterial genera known to contain oil-degrading species increased in abundance, including Alcanivorax, Cycloclasticus, Oleibacter, Oleiphilus, and Thalassolituus, and the species Marinobacter hydrocarbonoclasticus from approximately 0.02 to >32% (collectively) of the total bacterial community. Abundance of genera with known hydrocarbon-degraders then decreased 1 month after clean-up. However, a legacy effect was observed within the bacterial community, whereby Alcanivorax and Cycloclasticus persisted for several months after the oil spill in formerly contaminated sites. This study is the first to evaluate the effect of the Agia Zoni II oil-spill on microbial communities in an oligotrophic sea, where in situ oil-spill studies are rare. The results aid the advancement of post-spill monitoring models, which can predict the capability of environments to naturally attenuate oil.

Tracking functional bacterial biomarkers in response to a gradient of contaminant exposure within a river continuum

Within all aquatic environments, aside from the physical dispersal of dissolved and/or particulate phase contaminants, alteration from both biological and chemical processes are shown to change the chemistry of the parent compounds. Often these alterations can lead to secondary influences because of cooperative microbial processes (i.e. coupled respiratory pathways and/or energy and biodegradation cycles), complicating our understanding of the biological impact that these mobile compounds impose on ecosystem health. The McMurray Formation (MF) (the formation constituting the minable bituminous oil sands) is a natural, ongoing source of hydrocarbon-bound sediments to river ecosystems in the region (via terrestrial and aquatic erosion), providing a natural "mesocosm" to track and characterize the effects of these compounds on regional aquatic primary productivity. Here we characterize the natural, in-situ microbial response to increasing hydrocarbon exposure along a river continuum in the downstream direction. Using the Steepbank River (STB), suspended and bed sediment samples were collected at 3 sites from upstream to downstream, as the water flows into and through the MF. Samples were then analyzed for the active, in-situ gene expression of the microbial communities. Results from both suspended and bed sediments show clear and significant shifts in the microbial metabolic processes within each respective compartment, in response to the elevated polycyclic aromatic compound (PAC) concentrations. Specific genes likely responsible for hydrocarbon breakdown (Alkane Monooxygenase, Benzoyl-CoA Reductase etc.) experience elevated expression levels, while certain energy metabolism genes (nitrogen, sulfur, methane) reveal fundamental shifts in their pathway specificity, indicating an adaptation response in their basic energy metabolism. Expression from suspended sediments reveal subtle yet delayed metabolic response further downstream compared to bed sediments, indicative of the erosion and transport dynamics within a lotic system. These results provide insight into the use of novel clusters of gene biomarkers to track the active, in-situ microbial response of both emerging and legacy contaminants. Such information will be important in determining the best management strategies for the monitoring and assessment of aquatic health in both natural and contaminated ecosystems.

The Effects of Crude Oil and Dispersant on the Larval Sponge Holobiont

Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function.

Accidental oil spills from shipping and during extraction can threaten marine biota, particularly coral reef species which are already under pressure from anthropogenic disturbances. Marine sponges are an important structural and functional component of coral reef ecosystems; however, despite their ecological importance, little is known about how sponges and their microbial symbionts respond to petroleum products. Here, we use a systems biology-based approach to assess the effects of water-accommodated fractions (WAF) of crude oil, chemically enhanced water-accommodated fractions of crude oil (CWAF), and dispersant (Corexit EC9500A) on the survival, metamorphosis, gene expression, and microbial symbiosis of the abundant reef sponge Rhopaloeides odorabile in larval laboratory-based assays. Larval survival was unaffected by the 100% WAF treatment (107 μg liter⁻¹ polycyclic aromatic hydrocarbon [PAH]), whereas significant decreases in metamorphosis were observed at 13% WAF (13.9 μg liter⁻¹ PAH). The CWAF and dispersant treatments were more toxic, with decreases in metamorphosis identified at 0.8% (0.58 μg liter⁻¹ PAH) and 1.6% (38 mg liter⁻¹ Corexit EC9500A), respectively. In addition to the negative impact on larval settlement, significant changes in host gene expression and disruptions to the microbiome were evident, with microbial shifts detected at the lowest treatment level (1.6% WAF; 1.7 μg liter⁻¹ PAH), including a significant reduction in the relative abundance of a previously described thaumarchaeal symbiont. The responsiveness of the R. odorabile microbial community to the lowest level of hydrocarbon treatment highlights the utility of the sponge microbiome as a sensitive marker for exposure to crude oils and dispersants.

IMPORTANCE Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function.

Sorption and removal of crude oil spills from seawater using peat-derived biochar: An optimization study

Bio-based sorbents are preferred over chemical-based methods for the clean-up of crude oil spills in marine environments because bio-based sorbents are more environmentally friendly. This study evaluates the use of peat-derived biochar (PB) as a bio-sorbent for the sorption and removal of crude oil spills from synthetic seawater. Experiments were designed to determine the effect of four operating factors (PB/crude oil contact time, PB dosage, oil dosage, and temperature) on two performance indicators (crude oil sorption capacity of PB, S, and oil removal efficiency, R%). Regression models containing linear, quadratic, and two-way interaction terms were developed to predict S and R% from the four factors. Response surface methodology (RSM) was employed to identify the optimum conditions for the sorption and removal of crude oil from seawater. The performance indicators were predicted with a high degree of accuracy, i.e. with coefficient of determination (R²) values exceeding 90%. The optimum values of S and R% were estimated to be 32.5 g of crude oil/g of sorbent and 91.2% respectively. These optimum values were attained after 70 min of PB/crude oil contact time and at a temperature of 45 °C. The spent sorbent maintained its performance after three cycles of regeneration and reuse, suggesting that the material is reusable.

Draft Genome Sequence of Nitrosomonas sp. Strain APG5, a Betaproteobacterial Ammonia-Oxidizing Bacterium Isolated from Beach Sand

Nitrosomonas sp. strain APG5 (=NCIMB 14870 = ATCC TSA-116) was isolated from dry beach sand collected from a supralittoral zone of the northwest coast of the United States. The draft genome sequence revealed that it represents a new species of the cluster 6 Nitrosomonas spp. that is closely related to Nitrosomonas ureae and Nitrosomonas oligotropha.

Nitrosomonas sp. strain APG5 (=NCIMB 14870 = ATCC TSA-116) was isolated from dry beach sand collected from a supralittoral zone of the northwest coast of the United States. The draft genome sequence revealed that it represents a new species of the cluster 6 Nitrosomonas spp. that is closely related to Nitrosomonas ureae and Nitrosomonas oligotropha.