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The development of massive sequencing has provided a relatively inexpensive method to obtain the transcriptome of a species. Taking advantage of this technique, we used a previously obtained transcriptome of P. acuta to identify 18 genes related to different pathways of interest in ecotoxicology and then examined how exposure to phthalates changed the transcription of these genes. The processes of interest include DNA repair, the stress response, detoxification, apoptosis, immunity, energy reserves, and lipid transportation. There is a growing interest in combining ecologically relevant endpoints with biochemical and molecular parameters to seek a more integrative analysis. In this sense, increasing the number of described genes will allow for the design of standard arrays that could be used in combination with toxicity tests. In this way, initiatives such as the Adverse Outcome Pathway wiki24 will increase its relevance in assessing old and new compounds and provide putative mechanisms of action to explain the differences to the animals’ specific physiology. Furthermore, increasing knowledge at the molecular level in P. acuta supports its use as a representative of freshwater gastropods in toxicity analysis. There is a lack of model freshwater mollusks, which is one of the animal groups whose pollution response is currently less known.The 18 newly identified genes evaluated in this work show homology with those previously described in other species, as expected, mainly with the freshwater snail Biomphalaria glabrata, which belongs to the Planorbidae family. rad21 and rad50 are both involved in DNA repair: rad21 is an essential gene encoding a DNA double-strand break repair protein21, and rad50 is a member of the protein complex MRN (including Mre11, RAD50, and Nbs1) that functions in DNA double-strand break repair to recognize and process DNA ends as well as a signal for cell cycle arrest25. There is very little information about these genes in mollusks, with only one report in Crassostrea gigas for rad5026. The relevance of these genes is that their detection can be combined with other methodologies, such as the comet assay, to perform an integrated study to determine whether a compound is genotoxic and whether the organism has the ability to compensate for the damage.The Cat and SOD Mn genes allow us to evaluate the status of oxidative stress. Oxidative stress analysis is usually focused on biochemical parameters, such as enzyme activity. However, it should also include a transcriptional activity study because it can provide additional information about the mid- and long-term responses. Protein turnover can also be relevant in the response, especially in chronic exposure to toxicants. Detoxification mechanisms are also important to assess the response to toxicants. GST activity is one of the most used methods to assess detoxification27, but it does not differentiate between the members involved. The situation is similar regarding cytochrome P450s, which show high diversity with many roles in the cell28. Our identification of the Cyp72a15 gene increases the number of cytochromes 450 s described in P. acuta. Evaluating changes in these genes can help to elucidate how the organism can process the toxicants.The sHSP17.9 and HSC70-4 genes extend the battery of genes available to assess the stress response of P. acuta. sHSP17.9 is difficult to match with other species’ genes because while they all have an alpha-crystallin domain, there is no other sequence that presently allows for homology to be established. Additional functional studies will help to search for homology. It is worth mentioning that HIF1α offers a new aspect of stress related to hypoxia29. The stress response mainly focuses on the canonical heat shock proteins, so other mechanisms involved in specific stresses, such as hypoxia, are usually neglected. With the identification of HIF1a in P. acuta, researchers can evaluate the effect of a toxicant on oxygen intake in this species.The remaining identified genes allow for the analysis of pathways that can also be altered by toxicants, like apoptosis (AIF3), the immune system (ApA), energy reserves (PYGL), and lipid transport (ORP8). To our knowledge, in this study these genes have been analyzed for the first time concerning pollution in freshwater mollusks. The last three genes, DNMT1, KATB6, and HDAC1, are involved in epigenetic mechanisms. There is increasing evidence that epigenetic regulation is one of the long-term effects of toxicants. However, the genes involved in this process in invertebrates are still poorly represented in toxicity analysis. The description of these three genes opens the possibility of analyzing their role in the epigenetic response and its relevance in the transgenerational effects that have started to be described with different toxicants30,31,32.Plastics in the environment are a growing problem. During the degradation process, the polymers themselves and the compounds used as additives, including phthalates, are released. Hence, the presence of phthalates is increasing in the environment5,33,34. We analyzed three phthalates in this work, namely BBP, DEP, and DEHP; they showed a differential impact in P. acuta. DEP and DEHP, did not alter any of the mRNA levels. Researchers have described previously that both phthalates can alter the physiology of invertebrates16,35,36,37,38, including mollusks39,40,41. Other phthalates can also alter development and growth, which could be related to the endocrine-disrupting activity described for those chemicals. The molecular mechanisms involved are still under investigation, but some data are available. In the clam Venerupis philippinarum, DEHP alters the immune response40. In H. diversicolor, DBP affects oxidative stress, lipid and energy metabolism, and osmoregulation17. In other invertebrates, including Chironomus riparius42, Drosophila melanogaster43, and Caenorhabditis elegans15, phthalates alter endocrine pathways. The changes affect the ecdysone response as well as the expression of insulin-like peptide. Other pathways are also affected by phthalates, such as oxidative stress and detoxification routes44 and the stress response14. Finally, in C. elegans, exposure to environmentally relevant concentrations of diethylhexyl phthalate produces genomic instability by altering the expression of genes involved in DNA repair during meiosis37. It is clear then that phthalates can have a broad spectrum of actions in the cell, with a significant alteration of metabolism but primarily affecting oxidative stress and the endocrine system.The previous studies performed in mollusks have revealed alterations in several physiological processes; the analyzed molecular mechanisms mainly involved oxidative stress and immunity17,41. A recent review of the impact of phthalates on aquatic animals summarizes the effects observed, suggesting that activation of the detoxification system (cytochrome P450s) and endocrine system receptors of aquatic animals cause oxidative stress, metabolic disorders, endocrine disorders, and immunosuppression8. It would activate a cascade response that could cause genotoxicity and cell apoptosis, resulting in the disruption of growth and development. Considering this, the absence of a response observed in P. acuta exposed to DEP and DEHP is striking. The differences observed can be assigned to the type of analysis (molecular vs. physiological), the exposure time (1 week vs. a few hours or days), the concentration used (μg/L vs. mg/L), and evidently, the species used. Additional research will help elucidate the differential response in P. acuta compared with other organisms. However, it is essential to highlight that the obtained results suggest that P. acuta can manage the environmentally relevant doses of DEP and DEHP used in this work. This species may be less sensitive to these phthalates, but this eventually will require further research, including the use of other methodological approaches, to confirm it.In contrast to DEP and DEHP, BBP showed a marked effect: it increased the mRNA levels of almost all the analyzed genes. It is essential to consider that most studies on invertebrates that involve transcriptional activity analysis use arthropods and short exposure times14,44,45,46. Limited data are available on mollusks and, usually, they are marine representatives40,47. To our knowledge, this is the first study on a freshwater snail that shows that BBP can produce a substantial effect on cell metabolism. Several of the altered pathways can explain, in some way, the effects observed in other organisms, like DNA repair by the alteration of rad21 and rad50, which are related to DNA damage, or the alteration of the genes involved in histone and DNA modification (KAT6B, HDAC1, and DNMT1), which are related to epigenetic regulation. Apoptosis, which phthalates can also alter, also seems to be modulated in P. acuta by altering the AIF3 and the casp3 genes. Furthermore, the three phases of the detoxification could be acting since the genes tested (three cytochrome P450s, three GSTs, and MRP-1) were upregulated.Genes involved in oxidative stress and the stress response were also altered, as shown by the changes in the mRNA levels of Cat, SODs, stress proteins, and the hypoxia-related transcription factor genes. These changes support the alteration of oxidative stress, the stress response, and detoxification, backing previous analysis and adding new insight about the mechanisms involved in modulating these processes. In this sense, the absence of changes in GSTm1 supports a differential role for each GST family member in the response to toxicants. The altered acetylcholinesterase mRNA level also suggests effects in the nervous system, requiring additional research to elucidate the damage to the central nervous system. Finally, the alteration of PYGL, ApA, and ORP8, involved in energy metabolism, immunity, and lipid transport, respectively, shows that P. acuta responds to BBP in a way that has been observed in other organisms. In summary, the present gene profile obtained in response to BBP in P. acuta supports the proposed mechanisms and cellular processes in studies with other animals8. Immunity, oxidative stress, the stress response, detoxification, apoptosis, epigenetic modulation, DNA repair, lipid metabolism, and energy metabolism are modulated. The nervous system could also be affected. Of note, some genes showed differences in transcription based on the phthalate concentration. These findings suggest there are subtle differences, and additional kinetic analysis is required to elucidate early and late activated genes and the relevance of the damage for the population’s future.The obtained results are in line with previous studies in other organisms, which have confirmed that BBP can induce different types of damage such as apoptosis48, genotoxicity49, oxidative stress50, stress response activation45, or endocrine disruption14. Although there are studies in invertebrates showing the impact on development and other physiological processes39,51, most of them did not focus on the putative mode of action, with only a few of them trying to delve into the response mechanisms. Here we have shown that BBP can extensively affect the cell transcriptional activity in P. acuta. These results could be considered to reflect specific alterations on these pathways. This scenario would mean that BBP is the most active phthalate in P. acuta, with a broad spectrum of action and a potential effect on many pathways. However, the more probable picture is something that has been recently proposed: alterations in the oxidative stress response and the endocrine system cause a cascade of responses that affect different pathways and ultimately block growth and development8. It is relevant to keep in mind that BBP is a known endocrine disruptor47. A recent study in Daphnia magna provides some insight. Specifically, RNA-Seq revealed that genes involved in signal transduction, cell communication, and embryonic development were significantly down-regulated, while those related to biosynthesis, metabolism, cell homeostasis, and redox homeostasis were remarkably upregulated upon BBP exposure46. Although the organism and the stage analyzed are different from our study, those results support the idea that BBP can simultaneously alter multiple pathways, and it fits better with the regulatory role of the endocrine system and the extensive affection by oxidative stress.As stated before, the results obtained in this work show that DEP and DEHP had no apparent effect to P. acuta after 1 week exposure to environmentally relevant concentrations. However, BBP showed a strong effect. The difference in response could be due to several reasons that need to be explored in future work. One possibility is the structure of each compound. In this sense, BBP has two benzene rings while DEP and DEHP have only one. This factor could determine the biological activity of these compounds. Another possibility is that DEP and DEHP have effects earlier than the time studied, and the cell returned to the basal state, being able to process and remove the compounds. Finally, it cannot be dismissed that DEP and DEHP are not toxic to P. acuta, at least at environmentally relevant concentrations. In any case, BBP alters the metabolism of this species and produces a broad impact on different pathways. Additional research should be done in P. acuta and other freshwater species to determine the impact on organisms based on the freshwater ecosystem food web. More

Volcanic ash soilWe used commercially available Kanuma soil as volcanic ash soil (fine-grained pumice, Akagi Engei Co., Ltd.) for growth experiment 1. Kanuma soil is a fully weathered pyroclastic fall from the eruption of Mt. Akagi 44,000 years ago19. The soil contains 30.8% aluminum (allophane and imogolite) and 1.4% iron (ferrihydrite)20. For growth experiment 2, we used three natural volcanic ash soil types—immature soil of pumice (Kanuma soil, C horizon), as well as mature soils of andosol (A–B horizon) and topsoil (the surface of andosol, P to A horizon)—collected from a riverbed in Kanuma City (36°35′ N, 139°44′ E; 200 m a.s.l.), central Japan, where the vegetation is a cypress forest. This place is managed by the Kanuma Civil Engineering Office. The topsoil was collected at a depth of approximately 0–10 cm from the soil surface after removing the fallen leaves on the soil surface. The andosol layer, typically distributed at a depth of approximately 10–75 cm, was collected from a depth of approximately 10–30 cm. Below the andosol layer, the Akadama soil layer is distributed; further below, the pumice Kanuma soil is distributed. The pumice was collected approximately 50 cm under the Akadama layer.Temporal information on soil formation was confirmed by direct radiocarbon dating of the soil samples. After removing soil carbonate with 1.0 M HCl, the total organic fraction was analyzed using an accelerator mass spectrometer (0.5MV compact AMS system, NEC) at the laboratory of radiocarbon dating, University of Tokyo. Conventional radiocarbon age after correction of isotopic fractionation with δ13C values was calibrated to a calendar date with the calibration dataset IntCal1321.The elemental analysis of total phosphorus, nitrogen, and carbon in the soil samples was performed by Createrra Inc. (http://www.createrra.co.jp/english/top.html).Plant speciesOn the volcanic ash soil of Mt. Fuji, Japan’s highest volcano, vegetation in primary succession generally changes from herbaceous plants such as Fallopia japonica (Houtt.) Ronse Decr. var. japonica to nitrogen-fixing alder plants, and finally to non-nitrogen fixing Betula ermanii Cham22,23. Hence, we used three species—F. japonica, the alder species Alnus inokumae Murai et Kusaka, and B. ermanii—owned by and grown in our research institute, Nikko Botanical Garden, for the growth experiments. Experimental research on these plants, including the collection of plant material, comply with the relevant institutional, national, and international guidelines and legislation.Litter incubation experimentSamples (1 g) of F. japonica litter leaves—collected upon leaf fall on an autumn day, dried at 80 °C for at least 48 h, and then crushed—were placed in cultivating tubes (n = 5). Then, 5 g of wet soil from the Nikko Botanical Garden (36°45′ N, 139°35′ E; 647 m a.s.l.) in Nikko, central Japan, was added to 500 mL of water and stirred (solution I). As inoculation, 0.1 mL of the supernatant of solution I was added to the tubes24. Considering that the amounts of phosphorus and nitrogen in the solution I were approximately 0.003 mg/L and 0.3 mg/L, respectively, they were determined to have not affected the initial value (t = 0). Next, 2 mL of water was added to the tubes, which were then kept at 30 °C. The tubes were left open to maintain an aerobic environment. The efflux of phosphorus and nitrogen from the leaves was measured every week for ten weeks. For these measurements, 5 mL of water was added and the tube was centrifuged for 10 min (solution II). The supernatant of solution II was then used for phosphorus and nitrogen measurements, and the residue was continuously kept at 30 °C.Growth experimentsGrowth experiments were conducted in an open-type greenhouse in Nikko Botanical Garden. The greenhouse is only vinyl on the ceiling and good ventilation to keep the temperature constant. The mean monthly highest and lowest temperatures and the monthly precipitation observed in the botanical garden during the cultivation period are provided in Table 1. In the growth experiments, irrigation with tap water was provided to the plants and litter leaves in the morning and evening. The phosphorus and nitrogen concentration of the tap water were approximately 0.03 mg/L and 0.25 mg/L respectively.Table 1 Nikko botanical garden weather data (May–October 2019).Full size tableGrowth experiment 1: Comparative experiment on the growth of plant species with and without litterThe seedlings used for the experiment were from the species F. japonica, A. inokumae, and B. ermanii. A similar seedling size was used for each plant species. Seedlings of A. inokumae coexist with N-fixing actinomycetes.Six plants per species were collected before cultivation (t = 0) and dried in an oven at 80 °C for at least 48 h to measure the dry weight. There were four experimental groups for each species: a control (Con), a nitrogen addition (N: 10 mM NH4NO3), a phosphorus addition (P: 10 mM NaH2PO4), and a nitrogen and phosphorus addition (NP: 10 mM NH4NO3 + 10 mM NaH2PO4). Once a week, 50 mL of each nutrients was added to a 0.25-L garden pot. To verify whether the addition of litter (denoted by +) improved plant growth, litter leaves of F. japonica were placed on the soils. To verify if nutrients leached from litter sustained plant growth, we also combined nutrient and litter additions (Con+, N+, P+, NP+). When nutrients were added to the soil once a week, litter bag was removed before fertilizer application and returned after that.To reproduce how litter is deposited and supplies nutrients on volcanic ash soil in primary succession, F. japonica litter was collected in Nikko in the autumn of 2018 and dried at 80 °C or 2 days or more (the same litter was used in incubation). Approximately 9 g of litter leaves was packed in a tea mesh bag25 to prevent it from flying in the wind and placed on the soil surface of the garden pots. As indicated by the equation below, the amount of litter added to the 8 × 8 cm (0.0064 m2) garden pot used in this experiment amounts to approximately three years of litter production when converted to the amount of leaf litter in a 15-year-old alder forest, i.e., about 430 g/m2 per year26.$$frac{9,g}{{430frac{g}{{ m^{2} }} yr times 0.0064 m^{2} }} cong 3.3 yr$$Six seedlings per group of A. inokumae and B. ermanii were cultivated for approximately 2 months (June 7–August 22, 2019) and 12 seedlings per group of F. japonica were cultivated for about 1 month (September 10–October 15, 2019). The experiment was stopped after 1 month for F. japonica as it grew rapidly in 2 nutrient conditions (NP, NP+) and the roots overflowed from the garden pot. At the end of the experiment, growth was evaluated by measuring dry weight after drying seedlings at 80 °C for at least 48 h. Subsequently, the total phosphorus and nitrogen content of the dried seedlings were also measured (chemical analysis).The mass of phosphorus leached from litter during the cultivation period was calculated from the difference in the phosphorus contents of the litter before and after cultivation.Growth experiment 2: Comparative experiment on plant growth with old organic matterEight F. japonica seedlings were cultivated in three different soil-types (pumice, andosol, and topsoil, as mentioned above) under three experimental conditions (Con, N, P, same nutrition as growth experiment 1) from May 29 to July 12, 2019. These plants were then harvested and oven-dried at 80 °C for at least 48 h to measure dry weight. Subsequently, the total phosphorus and nitrogen content of the seedlings were also measured (chemical analysis).Chemical analysisPhosphorusWe used the dry destruction method to pretreat total phosphorus measurements in plant tissue27. A sample of the plant (0.05 g) was burned at 550 °C for 1 h. The plant ash was dissolved in 10 mL of 2 M H2SO4 and shaken for over 16 h; then, the solution was filtered. The filtrate was diluted at a 1:10 ratio with tris(hydroxymethyl)aminomethane (pH 8.0).The soil for available phosphorus were pretreated by Truog’ s method28. The soil (0.05 g) was dissolved in 10 mL of 0.002 M H2SO4, shaken for 30 min, and the solution was filtered. The filtrate was diluted at a 1:10 ratio with water.The amount of phosphorus in the sample solution was measured by the molybdenum blue colorimetric method29.NitrogenThe total nitrogen in plant tissue was measured using an elemental analyzer (EA; Vario Macro cube, Elementar, Germany). A few milligrams of the dried plant sample were placed in a tin capsule for EA combustion. EA carried out sample combustion and N2 separation/detection from the combusted gases and provided us with nitrogen contents.The soil sample preparation for available nitrogen measurements was based on the incubation methodology30. Half of the sampled soils were analyzed fresh, and the other half incubated for four weeks at 30 °C before analysis. 2 M KCl (20 mL) was added to 2 g of the soil sample; the solution was shaken for 1 h and filtered. The filtrate was collected, and the volume of nitrogen was measured by indophenol blue absorptiometry after reducing all to ammonia using Pack Test WAK-TNi (Kyoritsu Chemical-Check Lab., Corp, Tokyo, Japan). Available nitrogen was taken as the difference in the concentration of inorganic nitrogen (NO3-N, NO2-N and NH4-N) between incubated and fresh soil.Statistical analysisAll statistical analyses were performed with EZR31 (Saitama Medical Center, Jichi Medical University, Saitama, Japan), which is a graphical user interface for R (The R Foundation for Statistical Computing, Vienna, Austria). More precisely, it is a modified version of R commander designed to add statistical functions frequently used in biostatistics. The figure’s values are mean ± SE. Intergroup differences for nutrition conditions in soil, and soil-types were evaluated using non-parametric Kruskal–Wallis with post-hoc Steel–Dwass tests. In addition, comparisons between with or without litter were evaluated using two-tailed Mann–Whitney U-test. p values are * p  More

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Persian Gulf water and sediment samples along the oil pollution continuumWater and sediment samples were collected along the circulation current of the Persian Gulf from Hormuz Island [HW (SAMN12878178) and HS (SAMN12878113)), Asaluyeh area (AW (SAMN12878179) and AS (SAMN12878114)), and Khark Island (KhW (SAMN12878180) and KhS (SAMN12878115)] (Fig. 1). Physicochemical characteristics and Ionic content of the collected samples are presented in the Supplementary Table S1. The GC-FID analyses showed high TPH and polyaromatic hydrocarbon (PAH) concentrations in the Khark sediment (KhS) (Supplementary Table S2). The GC-SimDis analysis showed that C25–C38 HCs were dominant in the KhS (~ 60%), followed by  > C40 HCs (~ 14%) (Supplementary Fig. S1). Chrysene, fluoranthene, naphthalene, benzo(a)anthracene and phenanthrene were respectively the most abundant PAHs in KhS. This pollution could originate from oil spillage due to Island airstrikes during the imposed war (1980–1988), sub-sea pipeline failures, and discharge of oily wastewater or ballast water of oil tankers (ongoing for ~ 50 years)12. The TPH of other water and sediment samples was below the detection limit of our method ( 2%) representatives were enriched in KhS (Fig. 2B). The co-presence of the orders Methanosarcinals, Alteromanadales, and Thermotogae (Petrotogales) in the KhS hints at potential oil reservoir seepage around the sampling site since these taxa are expected to be present in oil reservoirs38. The main HC pollutants in the Asalouyeh are low molecular weight aromatic compounds that mainly influence the prokaryotic population in the water column and rarely precipitate into sediments hence the similarity of AS to HS microbial composition as they both experience low pollution rates.Apart from oil-degrading Proteobacteria (e.g. Alteromonadales, Rhodobacterales, and Oceanospirillales), a diversity of sulfur/ammonia-oxidizing chemolithoautotrophic Proteobacteria were present in these sediments although at lower abundances e.g., (Acidithiobacillales (KhS 1.8%), Chromatiales (HS 1.5, AS 1.1, KhS 0.85%), Ectothiorhodospirales (HS 3.75, AS 2.3, KhS 1.7%), Halothiobacillales (KhS 2.6%), Thiotrichales (HS 1.5, AS 1.1, KhS 0.3%), Thiohalorhabdales (HS 0.7, AS 1.2, KhS 0.5%), Thiomicrospirales (KhS 1.5%)) (Fig. 2B).Sulfate-reducing bacteria (SRB) in HS comprised up to 16.2% of the community (Desulfobacterales, NB1-j, Myxococcales, Syntrophobacterales, and Thermodesulfovibrionia). Similar groups along with Desulfarculales, comprised the SRB functional guild of the AS (~ 18.9%). In comparison, Desulfuromonadales and Desulfobacterales were the SRB representatives in KhS with a total abundance of only ~ 3.3%. The lower phylogenetic diversity and community contribution of SRBs in KhS hint at the potential susceptibility of some SRBs to oil pollution or that HC degraders might outcompete them (e.g., Deferribacterales). Additionally, KhS was gravel-sized sediment (particles ≥ 4 mm diameter), whereas HS and AS samples were silt and sand-sized sediments39. The higher oxygen penetration in gravel particles of KhS hampers anaerobic metabolism of sulfate/nitrate-reducing bacteria hence their lower relative abundance in this sample (Fig. 2B).Whereas in water samples, sulfur/ammonia-oxidizing chemolithoautotrophs such as Thiomicrospirales and sulfate/nitrate-reducing bacteria such as Desulfobacterales, NB1-j, Deferribacterales, Anaerolineales, Nitrosococcales, Nitrosopumilales, and Pirellulales were present in very small quantities (lower than 0.5% in each sample).Chronic exposure to oil pollution shapes similar prokaryotic communities as oil spill eventsWe analyzed the prokaryotic community composition of 41 oil-polluted marine water metagenomes (different depths in the water column) from Norway (Trondheimsfjord), Deepwater Horizon (Gulf of Mexico), the northern part of the Gulf of Mexico (dead zone) and Coal Oil Point of Santa Barbara; together with 65 oil exposed marine sediment metagenomes (beach sand, surface sediments and deep-sea sediments) originating from DWH Sediment (Barataria Bay), Municipal Pensacola Beach (USA) and a hydrothermal vent in Guaymas Basin (Gulf of California) in comparison with the PG water and sediment samples (in total 112 datasets) (Supplementary Table S3). This extensive analysis allowed us to get a comparative overview of the impact of chronic oil pollution on the prokaryotic community composition.Hydrocarbonoclastic bacteria affiliated to Oceanospirillales, Cellvibrionales (Porticoccaceae family), and Alteromonadales40 comprised a significant proportion of the prokaryotic community in samples with higher aliphatic compounds pollution e.g. DWHW.BD3 (sampled six days after the incubation of unpolluted water with Macondo oil), DWHW.he1, and DWHW.he2 (oil-polluted water samples incubated with hexadecane), DWHW.BM1, DWHW.BM2, DWHW.OV1 and DWHW.OV2 (sampled immediately after the oil spill in the Gulf of Mexico) (Fig. 3). Samples treated with Macondo oil, hexadecane, naphthalene, phenanthrene, and those taken immediately after the oil spill in the Gulf of Mexico had a significantly lower proportion of SAR11 due to the dominance of bloom formers and potential susceptibility of SAR11 to oil pollutants (Fig. 3).Figure 3The abundance of unassembled 16S rDNA reads from unassembled metagenomes of different oil-polluted water samples (41). Row names are microbial taxa at the order level. For taxa with lower frequency, the higher taxonomic level is shown (47 taxa in total). The right-hand dendrogram represents the clustering of rows based on the Pearson correlation. Columns are the name of water samples. Samples are clustered based on Pearson correlation and the color scale on the top left represents the row Z-score. Figure was plotted using “circlize” and “ComplexHeatmap” packages in R.Full size imageFlavobacteriales and Rhodobacterales were present in relatively high abundance in almost all oil-polluted water samples except for those with recent pollution. Samples named NTW5, NTW6, NTW11, NTW12, which were incubated with MC252 oil for 32–64 days, represented similar prokaryotic composition dominating taxa that are reportedly involved in degrading recalcitrant compounds like PAHs in the middle-to-late stages of the oil degradation process (Alteromonadales, Cellvibrionales, Flavobacteriales, and Rhodobacterales). Whereas at the earlier contamination stages, samples represented a different community composition with a higher relative abundance of Oceanospirillales (e.g., NTW8, NTW9, NTW15, NTW16, and NTW17 sampled after 0–8 days incubation) (Fig. 3).The non-metric multidimensional analysis of the prokaryotic community of 106 oil-polluted water and sediment samples, together with the PG samples, is represented in Fig. 4. Water and sediment samples expectedly represented distinct community compositions. The AW sample was placed near samples treated with phenanthrene and naphthalene in the NMDS plot showing the impact of aromatic compounds on its microbial community. The KhW sample was located near NTW13 in the plot, both of which had experienced recent oil pollution.Figure 4Non-metric multidimensional scaling (NMDS) of the Persian Gulf water and sediment metagenomes along with oil-polluted marine water and sediment metagenomes based on Bray–Curtis dissimilarity of the abundance of 16S rDNA reads in unassembled metagenomes at the order level. Samples with different geographical locations are shown in different colors. PG water and sediment samples are shown in red. Water and sediment samples are displayed by triangle and square shapes, respectively. Figure was plotted using “vegan” library in R.Full size imageThe orders Oceanospirillales, Alteromonadales, and Pseudomonadales were present in relatively high abundances in all oil-polluted water samples except for HW (PG input water) and samples collected from the northern Gulf of Mexico dead zone (GOMDZ) (Fig. 3). Persian Gulf was located in the proximity of the developing oxygen minimum zone (OMZ) of the Arabian Sea that is slowly expanding towards the Gulf of Oman41. Potential water exchange with OMZ areas could be the cause of higher similarity to the GOMDZ microbial community42.Our results suggest that water samples with similar contaminants and exposure time to oil pollution enrich for similar phylogenetic diversity in their prokaryotic communities (Fig. 3). Marine prokaryotes represent vertical stratification with discrete community composition across the depth profile. According to our analyses, the prokaryotic communities of the oil-polluted areas are consistently dominated by similar taxa regardless of sampling depth or geographical location. We speculate that the high nutrient input due to crude oil intrusion into the water presumably disturbs this stratification and HC degrading microorganisms are recruited to the polluted sites where their populations flourish.The inherent heterogeneity of the sediment prokaryotic communities is retained even after exposure to oil pollution, reflected in their higher alpha diversity (Supplementary Fig. S3). However, similar taxa dominate the community in response to oil pollution (Fig. 5).Figure 5The abundance of unassembled 16S rDNA reads from unassembled metagenomes of different oil-polluted sediment samples (65). Row names are microbial taxa at the order level. For taxa with lower frequency, the higher taxonomic level is shown (77 taxa in total). The right-hand dendrogram represents the clustering of rows based on the Pearson correlation. Columns are the name of sediment samples. Samples are clustered based on Pearson correlation and the color scale on the top left represents the row Z-score. Figure was plotted using “circlize” and “ComplexHeatmap” packages in R.Full size imageIn sediment samples, Deltaproteobacteria had the highest abundance, followed by Gammaproteobacteria representatives. Ectothiorhodospirales, Rhizobiales, Desulfobacterales, Myxococcales, and Betaproteobacteriales representatives were present in almost all samples at relatively high quantities (Fig. 5). Sulfate/nitrate-reducing bacteria were major HC degraders in sediment, showing substrate specificity for anaerobic HC degradation43. Desulfobacterales and Myxococcales were ubiquitous sulfate-reducers, present in almost all oil-polluted sediment samples44. Sulfate-reducing Deltaproteobacteria play a key role in anaerobic PAH degradation, especially in sediments containing recalcitrant HC types45. Members of Rhizobiales are involved in nitrogen fixation, which accelerates the HC removal process in the sediment samples46, and therefore their abundance increase in response to oil pollution (Fig. 5).Prokaryotes involved in nitrogen/sulfur cycling of sediments are defined by factors such as trace element composition, temperature, pressure, and more importantly, depth and oxygen availability. In oil-polluted sediment samples, the simultaneous reduction of available oxygen with an accumulation of recalcitrant HCs along the depth profile complicates the organic matter removal. However, anaerobic sulfate-reducing HC degrading bacteria will cope with this complexity47. Prokaryotic communities of HS and AS samples represented similar phylogenetic diversity (Figs. 4, 5). Their prokaryotic community involved in the nitrogen and sulfur cycling resembles the community of DWHS samples. The KhS sample had a similar prokaryotic community to deeper sediment samples collected from 30 to 40 cm depth (USFS3, USFS11, and USFS12) which could be due to our sampling method using a grab sampling device.Our results show that the polluted sediments’ sampling depth (surface or subsurface) defines the dominant microbial populations. Hydrocarbon degrading microbes had the ubiquitous distribution in almost all oil-polluted water and sediment samples including Oceanospirillales, Cellvibrionales, Alteromonadales, Flavobacteriales, Pseudomonadales, and Rhodobacterales. Mentioned orders along with Ectothiorhodospirales, Rhizobiales, Desulfobacterales, Myxococcales, and Betaproteobacteriales and also representatives of Deltaproteobacteria phylum dominated in sediment samples. However, their order of frequency varies depending on the type of oil pollution present at the sampling location and the exposure time.Genome-resolved metabolic analysis of the Persian Gulf’s prokaryotic community along the pollution continuumA total of 82 metagenome-assembled genomes (MAGs) were reconstructed from six sequenced metagenomes of the PG (completeness ≥ 40% and contamination ≤ 5%). Amongst them, eight MAGs belonged to domain Archaea and 74 to domain bacteria. According to GTDB-tk assigned taxonomy (release89) (https://data.gtdb.ecogenomic.org/releases/release89/), reconstructed MAGs were affiliated to Gammaproteobacteria (36.6%), Alphaproteobacteria (12.2%), Flavobacteriaceae (9.7%), Thermoplasmatota (5%) together with some representatives of other phyla (MAG stats in Supplementary Table S4).A collection of reported enzymes involved in the degradation of different aromatic and aliphatic HCs under both aerobic and anaerobic conditions was surveyed in the annotated MAGs of this study43,48,49,50. The KEGG orthologous accession numbers (KOs) of genes involved in HC degradation were collected, and the distribution of KEGG orthologues detected at least in one MAG (n = 76 genes) is represented in Fig. 6.Figure 6Hydrocarbon degrading enzymes present in recovered MAGs from the PG water and sediment metagenomes. Row names represent the taxonomy of recovered MAGs and their completeness is provided as a bar plot on the right side. The color indicates the MAG origin. The size of dots indicates the presence or absence of each enzyme in each recovered MAG. Columns indicate the type of hydrocarbon and in the parenthesis is the name of the enzyme hydrolyzing this compound followed by its corresponding KEGG orthologous accession number. Figure was plotted using “reshape2” and “ggplot2” packages in R.Full size imageA combination of different enzymes runs the oil degradation process. Mono- or dioxygenases are the main enzymes triggering the HC degradation process under aerobic conditions. Under anaerobic conditions, degradation is mainly started by the addition of fumarate or in some cases, by carboxylation of the substrate. Therefore, bacteria containing these genes will potentially initiate the degradation process that will be continued by other heterotrophs. Enzymes such as decarboxylase, hydroxylase, dehydrogenase, hydratase, and isomerases act on the products of initiating enzymes mentioned above through a series of oxidation/reduction reactions.Various microorganisms cooperate to cleave HCs into simpler compounds that could enter common metabolic pathways. Mono- or dioxygenases which are involved in the degradation of alkane (alkane 1-monooxygenase, alkB/alkM), cyclododecane (cyclododecanone monooxygenase, cddA), Biphenyl (Biphenyl 2, 3-dioxygenase subunit alpha/beta, bphA1/A2, Biphenyl-2, 3-diol 1, 2-dioxygenase, bphC), phenol (phenol 2-monooxygenase, pheA), toluene (benzene 1, 2-dioxygenase subunit alpha/beta todC1/C2, hydroxylase component of toluene-4-monooxygenase, todE), xylene (toluate/benzoate 1,2-dioxygenase subunit alpha/beta/electron transport component, xylX/Y/Z, hydroxylase component of xylene monooxygenase, xylM) and naphthalene/phenanthrene (catechol 1,2 dioxygenase, catA, a shared enzyme between naphthalene/phenanthrene /phenol degradation) were detected in recovered MAGs of the PG.The key enzymes including Alkylsuccinate synthase (I)/(II) (assA1/A2), benzylsuccinate synthase (BssA)/benzoyl-CoA reductase (BcrA), ethylbenzene dehydrogenase (EbdA), and 6-oxo-cyclohex-1-ene-carbonyl-CoA hydrolase (BamA) that are responsible for initiating the degradation of alkane, toluene, ethylbenzene and benzoate exclusively under anaerobic conditions were not detected in reconstructed MAGs of this study. Consequently, recovered MAGs of this study are not initiating anaerobic degradation via known pathways while they have the necessary genes to continue the degradation process started by other microorganisms.The MAG KhS_63 affiliated to Immundisolibacter contained various types of mono- or dioxygenases and had the potential to degrade a diverse range of HCs such as alkane, cyclododecane, toluene, and xylene (Fig. 6). Members of this genus have been reported to degrade high molecular weight PAHs51.Lutimaribacter representatives have been isolated from seawater and reported to be capable of degrading cyclohexylacetate52. We also detected enzymes responsible for alkane, cycloalkane (even monooxygenase enzymes), and naphthalene degradation under aerobic conditions and alkane, ethylbenzene, toluene, and naphthalene degradation under anaerobic conditions in KhS_39 affiliated to this genus (Fig. 6).The MAGs KhS_15 and KhS_26 affiliated to Roseovarius had the enzymes for degrading alkane (alkane monooxygenase, aldehyde dehydrogenase), cycloalkane, naphthalene, and phenanthrene under aerobic and toluene and naphthalene under anaerobic condition. PAHs degradation has been reported for other representatives of this taxa as well53.The MAGs KhS_11 (a representative of Rhodobacteraceae) and KhS_53 (Marinobacter) had alkB/alkM, KhS_27 (GCA-2701845), KhS_29 (UBA5862) and KhS_40 (from Porticoccaceae family) had cddA, KhS_13 and KhS_21 (UBA5335) and KhS_38 (Oleibacter) had both alkB/alkM and xylM genes. They were among microbes that were initiating the degradation of alkane, cycloalkane and xylene compounds. Other MAGs recovered from Khark sediment were involved in the continuation of the degradation pathway. For example, KhS_1 was affiliated to the genus Halomonas and had different enzymes to degrade intermediate compounds. Halomonas representatives have been frequently isolated from oil-polluted environments54. The phylum Krumholzibacteria has been first introduced in 2019 and reported to contain heterotrophic nitrite reducers55. Two MAGs, KhS_5 and KhS_10, were affiliated to this phylum and contained enzymes involved in the anaerobic degradation of toluene, phenol, and naphthalene (Fig. 6).The MAGs KhS_12 and KhW_31 affiliated to the genus Flexistipes, in Deferribacterales order, were reconstructed from both KhW and KhS samples. Deferribacterales are reported to be present in the medium to high-temperature oil reservoirs with HC degradation activity and also in high-temperature oil-degrading consortia56. The type strain of this species was isolated from environments with a minimum salinity of 3% and a temperature of 45–50 °C57. The presence of this genus in KhS could be due to natural oil seepage from the seabed as PG reservoirs mainly have medium to high temperature and high salinity. Enzymes involved in the degradation of alkane, phenol, toluene and naphthalene under anaerobic conditions were present in MAGs KhS_12 and KhW_31.As mentioned earlier, Flavobacteriales are potent marine indigenous HC degraders that bloom in response to oil pollution58. Flavobacteriales affiliated MAGs (KhW_2, KhW_3, AW_21, and AW_33) were recovered from KhW and AW and mostly contained enzymes that participate in the degradation of aromatic compounds under anaerobic conditions. KhW_2 and KhW_3 also had both alkB/M (alkane monooxygenase) and xylM enzyme, which initiates the alkane and xylene bioremediation in Khark water. Among other recovered MAGs from KhW sample, KhW_18 (UBA724), KhW_24 (clade SAR86), KhW_43 (UBA3478) had alkB/M, and xylM, KhW_24 (clade SAR86) had alkB/M and cddA, and KhW_28 (from Rhodobacteraceae family) had alkB/M and pheA genes in their genome to initiate the degradation process (Fig. 6).Marinobacter (KhW_15) was another MAG reconstructed from KhW sample. This genus is one of the main cultivable genera that play a crucial role in the bioremediation of a wide range of oil derivatives in polluted marine ecosystems54.Marine Group II (MGII) and Poseidonia representatives of Thermoplasmatota that have been reported to be nitrate-reducing Archaea59, were recovered from AW sample (AW_40, AW_45) and contained several enzymes contributing in alkane (alkane monooxygenase, aldehyde dehydrogenase) and naphthalene/phenanthrene/phenol/xylene degradation (decarboxylase) under aerobic conditions. The HC degradation potential of representatives of this phylum has been previously reported60.In the Asalouyeh water sample, MAGs AW_25 (UBA4421) and AW_38 (UBA8337) had cddA, AW_21 (UBA8444) had catA, AW_11 (Poseidonia) and AW_17 (from Rhizobiales order) had both alkB/M and xylM, and AW_4 (UBA8337) had catA and pheA genes and had potential to trigger the breakdown of their corresponding oil derivatives.Other recovered genomes had the potential to metabolize the product of initiating enzymes. For instance, AW_23 contained enzymes involved in the degradation of naphthalene, phenol and cyclododecane and was affiliated to the genus Alteromonas (Fig. 6).Three recovered MAGs of HW affiliated to Pseudomonadales (HW_23), Poseidoniales (HW_24), and Flavobacteriales (HW_30) contained some initiating enzymes to degrade cyclododecane/biphenyl/toluene, alkane/xylene, and alkane/xylene/naphthalene/phenanthrene, respectively. A representative of Heimdallarchaeia that are mainly recovered from sediment samples was reconstructed from the Hormuz water sample (HW_28). It had a completeness of 81% and contained enzymes involved in anaerobic degradation of alkanes. This archaeon could potentially be an input from the neighboring OMZ as this phyla include representatives adopted to microoxic niches61. Containing genes with the potential to initiate the oil derivative degradation in the input water with no oil exposure reiterates the intrinsic ability of marine microbiota for HC degradations and oil bioremediation.While 16S rRNA provides an overview of the community, MAGs provide the possibility to inspect the metabolic capability of the microbiota. We decided to provide both in this manuscript as we believe they are complementary. Having the full picture provided by the combination of these analyses allows for a better understanding of the community structure and their metabolic capabilities. This is even more evident for sediment samples as they are highly diverse, and reconstructing MAGs from sediment metagenomes is still a bottlenecks. In this case, we rely more on the 16S rRNA to provide an overall view of the community composition.This said, we see similar taxonomic distribution in the MAGs and 16S rRNA e.g., the prevalence of Flavobacteriales and Rhodobacterales in KhW and KhS, Synechococcales, and Desulfobacteriales and Flavobacteriales in HW, HS and AW samples, respectively.Additionally, some rare microbiota representatives were recovered among reconstructed MAGs. For example, the Immundisolibacterales showed an abundance of only 0.8% in the KhS sample based on 16S rRNA but the recovered KhS_63 MAG was affiliated to this taxon. Notably, this MAG contained many genes involved in hydrocarbon degradation having the highest potential in hydrocarbon degradation. More