Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil

Combined influence of the nanoplastics and polycyclic aromatic hydrocarbons exposure on microbial community in seawater environment

Nanoplastics (NPs) and polycyclic aromatic hydrocarbons (PAHs) are recognized as persistent organic pollutant (POPs) with demonstrated physiological toxicity. When present in aquatic environments, the two pollutants could combine with each other, resulting in cumulative toxicity to organisms. However, the combined impact of NPs and PAHs on microorganisms in seawater is not well understood. In this study, we conducted an exposure experiment to investigate the individual and synergistic effects of NPs and PAHs on the composition, biodiversity, co-occurrence networks of microbial communities in seawater. Exposure of individuals to PAHs led to a reduction in microbial community richness, but an increase in the relative abundance of species linked to PAHs degradation. These PAHs-degradation bacteria acting as keystone species, maintained a microbial network complexity similar to that of the control treatment. Exposure to individual NPs resulted in a reduction in the complexity of microbial networks. Furthermore, when PAHs and NPs were simultaneously present, the toxic effect of NPs hindered the presence of keystone species involved in PAHs degradation, subsequently limiting the degradation of PAHs by marine microorganisms, resulting in a decrease in community diversity and symbiotic network complexity. This situation potentially poses a heightened threat to the ecological stability of marine ecosystems. Our work strengthened the understanding of the combined impact of NPs and PAHs on microorganisms in seawater.

Predicting Hydrocarbon Primary Biodegradation in Soil and Sediment Systems Using System Parameterization and Machine Learning

Technical complexity associated with biodegradation testing, particularly for substances of unknown or variable composition, complex reaction products, or biological materials (UVCB), necessitates the advancement of non-testing methods such as quantitative structure-property relationships (QSPRs). Models for describing the biodegradation of petroleum hydrocarbons (HCs) have been previously developed. A critical limitation of available models is their inability to capture the variability in biodegradation rates associated with variable test systems and environmental conditions. Recently, the Hydrocarbon Biodegradation System Integrated Model (HC-BioSIM) was developed to characterize the biodegradation of HCs in aquatic systems with the inclusion of key test system variables. The present study further expands the HC-BioSIM methodology to soil and sediment systems using a database of 2195 half-life (i.e., degradation time [DT]50) entries for HCs in soil and sediment. Relevance and reliability criteria were defined based on similarity to standard testing guidelines for biodegradation testing and applied to all entries in the database. The HC-BioSIM soil and sediment models significantly outperformed the existing biodegradation HC half-life (BioHCWin) and virtual evaluation of chemical properties and toxicities (VEGA) quantitative Mario Negri Institute for Pharmacological Research (IRFMN) models in soil and sediment. Average errors in predicted DT50s were reduced by up to 6.3- and 8.7-fold for soil and sediment, respectively. No significant bias as a function of HC class, carbon number, or test system parameters was observed. Model diagnostics demonstrated low variability in performance and high consistency of parameter usage/importance and rule structure, supporting the generalizability and stability of the models for application to external data sets. The HC-BioSIM provides improved accuracy of Persistence categorization, with correct classification rates of 83.9%, and 90.6% for soil and sediment, respectively, demonstrating a significant improvement over the existing BioHCWin (70.7% and 58.6%) and VEGA (59.5% and 18.5%) models. Environ Toxicol Chem 2024;43:1352-1363. © 2024 Concawe. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Spatial heterogeneity plays a vital role in shaping the structure and function of estuarine carbon-fixing bacterial communities

Carbon-fixing bacterial communities are essential drivers of carbon fixation in estuarine ecosystems that critically affect the global carbon cycle. This study compared the abundances of the Calvin cycle functional genes cbbL and cbbM and Reductive tricarboxylic acid cycle gene aclB, as well as compared carbon-fixing bacterial community features in the two estuaries, predicted potential ecological functions of carbon-fixation bacteria, and analyzed their symbiosis strategies in two estuaries having different geographical distributions. Gammaproteobacteria was the dominant carbon-fixing bacterial community in the two estuaries. However, a higher number of Alphaproteobacteria were noted in the Liaohe Estuary, and a higher number of Betaproteobacteria were found in the Yalujiang Estuary. The carbon-fixing functional gene levels exhibited the order of aclB > cbbL > cbbM, and significant effects of Cu, Pb, and petroleum were observed (p < 0.05). Nitrogen-associated nutrient levels are major environmental factors that affect carbon-fixing bacterial community distribution patterns. Spatial factors significantly affected cbbL carbon-fixing functional bacterial community structure more than environmental factors. With the increase in offshore distance, the microbial-led processes of methylotrophy and nitrogen fixation gradually weakened, but a gradual strengthening of methanotrophy and nitrification was observed. Symbiotic network analysis of the microorganisms mediating these ecological processes revealed that the carbon-fixing bacterial community in these two estuaries had a non-random symbiotic pattern, and microbial communities from the same module were strongly linked among the carbon, nitrogen, and sulfur cycle. These findings could advance the understanding of carbon fixation in estuarine ecosystems.

Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth

The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.

The remediation of marine sediments containing polycyclic aromatic hydrocarbons by peroxymonosulfate activated with Sphagnum moss-derived biochar and its benthic microbial ecology

This research was to study the efficiency of Sphagnum moss-derived biochar (SMBC) in removing polycyclic aromatic hydrocarbons (PAHs) from marine sediment using a peroxymonosulfate (PMS)-based carbon-advanced oxidation process (PMS-CAOPs). Sphagnum moss-derived biochar (SMBC) was generated via a simple thermochemical process for PMS activation toward enhancing decontamination of sediments. At pH 6, the SMBC/PMS system achieved a PAH removal efficiency exceeding 78% in 12 h reaction time. Moreover, PAHs of 6-, 5-, 4-, 3-, and 2-ring structures exhibited 98%, 74%, 68%, 85%, and 91%, of removal, respectively. The SMBC activation of PMS generated both radicals (SO4•- and HO•) and nonradical (1O2), species responsible for PAHs degradation, attributed primarily to inherent iron and carbon moieties. The significant PAHs degradation efficiency showcased by the SMBC/PMS process holds promise for augmenting the performance of indigenous benthic microbial activity in sediment treatment contexts. The response of sediment microbial communities to PAH-induced stress was particularly associated with the Proteobacteria phylum, specifically the Sulfurovum genus. The findings of the present study highlight the efficacy of environmentally benign reactive radical/nonradical-based PMS-CAOP using pristine carbon materials, offering a sustainable strategy for sediment treatment.

Functional response of microbial communities in lab-controlled oil-contaminated marine sediment

Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.

Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy)

Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.

Key genes of electron transfer, the nitrogen cycle and tetracycline removal in bioelectrochemical systems

BACKGROUND

Soil microbial fuel cells (MFCs) can remove antibiotics and antibiotic resistance genes (ARGs) simultaneously, but their removal mechanism is unclear. In this study, metagenomic analysis was employed to reveal the functional genes involved in degradation, electron transfer and the nitrogen cycle in the soil MFC.

RESULTS

The results showed that the soil MFC effectively removed tetracycline in the overlapping area of the cathode and anode, which was 64% higher than that of the control. The ARGs abundance increased by 14% after tetracycline was added (54% of the amplified ARGs belonged to efflux pump genes), while the abundance decreased by 17% in the soil MFC. Five potential degraders of tetracycline were identified, especially the species Phenylobacterium zucineum, which could secrete the 4-hydroxyacetophenone monooxygenase encoded by EC 1.14.13.84 to catalyse deacylation or decarboxylation. Bacillus, Geobacter, Anaerolinea, Gemmatirosa kalamazoonesis and Steroidobacter denitrificans since ubiquinone reductase (encoded by EC 1.6.5.3), succinate dehydrogenase (EC 1.3.5.1), Coenzyme Q-cytochrome c reductase (EC 1.10.2.2), cytochrome-c oxidase (EC 1.9.3.1) and electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) served as complexes I, II, III, IV and ubiquinone, respectively, to accelerate electron transfer. Additionally, nitrogen metabolism-related gene abundance increased by 16% to support the microbial efficacy in the soil MFC, and especially EC 1.7.5.1, and coding the mutual conversion between nitrite and nitrate was obviously improved.

CONCLUSIONS

The soil MFC promoted functional bacterial growth, increased functional gene abundance (including nitrogen cycling, electron transfer, and biodegradation), and facilitated antibiotic and ARG removal. Therefore, soil MFCs have expansive prospects in the remediation of antibiotic-contaminated soil. This study provides insight into the biodegradation mechanism at the gene level in soil bioelectrochemical remediation.

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean

IMPORTANCE

Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native microbial communities to oil spills is not well understood. Here, we explored the baseline hydrocarbon-degrading communities of a subarctic Atlantic region to uncover the metabolic potential of the bacteria that inhabit the surface and subsurface water. We conducted enrichments with a 13C-labeled hydrocarbon to capture the fraction of the community actively using the hydrocarbon. We then combined this approach with metagenomics to identify the metabolic potential of this hydrocarbon-degrading community. This revealed previously undescribed uncultured bacteria with unique metabolic mechanisms involved in aerobic hydrocarbon degradation, indicating that temperature may be pivotal in structuring hydrocarbon-degrading baseline communities. Our findings highlight gaps in our understanding of the metabolic complexity of hydrocarbon degradation by native marine microbial communities.

Insights into Antarctic microbiomes: diversity patterns for terrestrial and marine habitats

Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. To explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly of thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa previously described for habitats of the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.

Variations of different PAH fractions and bacterial communities during the biological self-purification in the soil vertical profile

Wild PAH-contaminated sites struggle to provide continuous and stable monitoring, resulting in the potential risks of contaminated soil utilization could not be evaluated effectively. This work provided a 9-months laboratory simulation which was close to the natural ecological process. These results believed that PAH-degrading bacteria (PDB) preferred to degrade organic extracted PAH (PAH_OS) and fresh bound-PAH (79.36-99.97%). The formation and migration efficiency of PAH binding with HA humic acid (HA) (PAH_HA) was lower than that of PAH binding with fulvic acid (FA) and humin (HM) (PAH_FA and PAH_HM), leading to PAH_HA had more persistent retention and influenced bacterial communities in shallow soils. Besides, phylum Proteobacteria gradually dominated the bacterial community and decreased 12.05-20.48% diversity at all depths during the biological self-purification process. Although the effect of this process enhanced the abundance of 28 genes 16 s rRNA and three PAH-degrading genes (PDGs) by 5.91-2047.34 times (phe, nahAc and nidA), the top 30 genera maintained their ecological characteristics. This study provided insights into the important influencing factor and mechanism of the biological self-purification processes and discerned the linkages between bacterial communities and environmental variables in the vertical profile, which is important to the isolation and application of PDB and ecological risk assessment.

Distribution of bound-PAH residues and their correlations with the bacterial community at different depths of soil from an abandoned chemical plant site

The situ pollutant residue and microbial characteristics in contaminated environments are crucial for ecological restoration and soil utilization. This work reported the variation of polycyclic aromatic hydrocarbon (PAH) residues and the bacterial community at different depths in an aged-abandoned site. These results unveiled that over 90% of low molecular weight (LMW) and medium molecular weight (MMW), 52.84-76.88% of high molecular weight (HMW) bound-PAH (BP) residues were sequestrated in humin (HM). The stresses of PAH and soil depth enhanced the frequency of bacteria associations, especially positive associations. We enriched and cultured PAH degradation bacteria (PDB) from the sampling site mainly consisting of Pseudomonas and Acinetobacter, which were originally 0.39-0.52% abundant in the sampling site. The abundances of PDB and PAH-degradation genes (PDGs) were higher at shallower depths and increased with high PAH concentration. Simultaneously, Pearson correlation analysis and experimental verification found that the process of PAH binding with SOM limited the further increase of PDB and PDGs in PAH-contaminated sites. These findings may illustrate possible ecological risks of contaminated soils and provide guidance for the isolation and application of PDB.

Morphological and transcriptional effects of crude oil and dispersant exposure on the marine sponge Cinachyrella alloclada

Marine sponges play important roles in benthic ecosystems. More than providing shelter and food to other species, they help maintain water quality by regulating nitrogen and ammonium levels in the water, and bioaccumulate heavy metals. This system, however, is particularly sensitive to sudden environmental changes including catastrophic pollution event such as oil spills. Hundreds of oil platforms are currently actively extracting oil and gas in the Gulf of Mexico. To test the vulnerability of the benthic ecosystems to oil spills, we utilized the Caribbean reef sponge, Cinachyrella alloclada, as a novel experimental indicator. We have exposed organisms to crude oil and oil dispersant for up to 24 h and measured resultant gene expression changes. Our findings indicate that 1-hour exposure to water accommodated fractions (WAF) was enough to elicit massive shifts in gene expression in sponges and host bacterial communities (8052 differentially expressed transcripts) with the up-regulation of stress related pathways, cancer related pathways, and cell integrity pathways. Genes that were upregulated included heat shock proteins, apoptosis, oncogenes (Rab/Ras, Src, CMYC), and several E3 ubiquitin ligases. 24-hour exposure of chemically enhanced WAF (CE-WAF) had the greatest impact to benthic communities, resulting in mostly downregulation of gene expression (4248 differentially expressed transcripts). Gene deregulation from 1-hour treatments follow this decreasing trend of toxicity: WAF > CE-WAF > Dispersant, while the 24-hour treatment showed a shift to CE-WAF > Dispersant > WAF in our experiments. Thus, this study supports the development of Cinachyrella alloclada as a research model organism and bioindicator species for Florida reefs and underscores the importance of developing more efficient and safer ways to remove oil in the event of a spill catastrophe.

Spatio-temporal variation of the microbial community of the coast of Lebanon in response to petroleum hydrocarbon pollution

In this study, the coast of Lebanon was analyzed for the dynamic changes in sediment microbial communities in response to a major petroleum oil spill and tar contamination that occurred in the summer of 2021. Spatio-temporal variations in the microbial structure along the shores of Lebanon were assessed in comparison to baseline microbial structure determined in 2017. Microbial community structure and diversity were determined using Illumina MiSeq technology and DADA2 pipeline. The results show a significant diversity of microbial populations along the Lebanese shore, and a significant change in the sediment microbial structure within four years. Namely, Woeseia, Blastopirellula, and Muriicola were identified in sediment samples collected in year 2017, while a higher microbial diversity was observed in 2021 with Woeseia, Halogranum, Bacillus, and Vibrio prevailing in beach sediments. In addition, the results demonstrate a significant correlation between certain hydrocarbon degraders, such as Marinobacter and Vibrio, and measured hydrocarbon concentrations.

Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes

BACKGROUND

Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identified genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratified, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems.

RESULTS

Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean.

CONCLUSIONS

Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our findings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles. Video Abstract.

Sulfide causes histological damage, oxidative stress, metabolic disorders and gut microbiota dysbiosis in juvenile sea cucumber Apostichopus japonicus Selenka

Sulfide is a common harmful substance in sediments, with an especially high risk for deposit feeder organisms. The sea cucumber Apostichopus japonicus is a typical benthic feeder, and its intestine is the first line of defense and serves as a crucial barrier function. In this study, histological, physiological, gut microbiota, and metabolomic analyses were performed to explore the toxic response in the intestine of juvenile A. japonicus exposed to 0, 0.8, and 1.6 mg/L sulfide stress for 96 h. The results revealed sulfide-induced intestinal inflammatory symptoms and oxidative stress. Moreover, gut bacterial composition was observed after sulfide exposure, with an increase in Proteobacteria and a decrease in Cyanobacteria and Planctomycetes. Specifically, sulfide increased a set of sulfide-removing bacteria and opportunistic pathogens while decreasing several putative beneficial substance-producing bacteria. The metabolomic analysis indicated that sulfide also disturbed metabolic homeostasis, especially lipid and energy metabolism, in intestine. Interestingly, several intestinal bacteria were further identified to be significantly correlated with metabolic changes; for example, the decreased abundance levels of Bacillus, Corynebacterium, and Psychromonas were positively correlated with important energy metabolites, including maleic acid, farnesyl pyrophosphate, thiamine, butynoic acid, and deoxycholic acid. Thus, our research provides new insights into the mechanisms associated with the intestinal metabolic and microbiota response involved in sulfide stress adaptation strategies of juvenile A. japonicus.

Biodegradation of polystyrene (PS) by marine bacteria in mangrove ecosystem

Plastics pollution poses a new threat to marine ecosystems. Mangrove locating at estuary worldwide is probably the most heavily polluted area trapping various plastics transported from terrestrial and nearby marine aquaculture. Expanded polystyrene (EPS) is one of most common plastic debris therein and even in the plastic garbage. Here we showed the bacterial diversity of the polystyrene-degrading microbial community from EPS waste sites from a subtropical mangrove area. After enrichment with EPS, the degradation consortia were obtained. They shared a similar community structure dominated by bacteria of Sphingomonadaceae, Rhodanobacteraceae, Rhizobiaceae, Dermacoccaceae, Rhodocyclaceae, Hyphomicrobiaceae, and Methyloligellaceae. Diverse bacteria standing for the first member of the genera of Novosphingobium, Gordonia, Stappia, Mesobacillus, Alcanivorax, Flexivirga, Cytobacillus, Thioclava, and Thalassospira showed PS degradation capability as a pure culture. Further, PS biodegradation of Gordonia sp. and Novosphingobium sp. was quantified by weight loss, in addition to obvious morphological and structural changes of the PS films observed by SEM, ATR-FTIR, and contact angle analysis. The formation of new oxygen-containing functional groups implied the degradation pathway of oxidation. Although the degradation rates ranged from 2.7% to 7.7% after one month in lab and possibly lower in situ, their role in EPS removal is unneglectable.

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by microbial consortium from paddy rice soil

Polycyclic aromatic hydrocarbons (PAHs) are among the most widely spread pollutants in the environment including the agricultural soil. PAH degradation by indigenous bacteria is an effective and economical means to remove these pollutants from the environment. Here, we report a bacterial consortium (Pdy-1) isolated from paddy rice soil in northern Japan able to degrade polycyclic aromatic hydrocarbons (PAHs) at high rates. Pdy-1 was incubated with a mixture of PAH compounds (fluorene, phenanthrene, and pyrene) in Bushnell Haas Medium at a final concentration of 100 mg/L each. PDY-1 degraded 100% of fluorene, 95% of phenanthrene, and 52% of pyrene in 5 days. Phenanthrene and pyrene were completely degraded at 10 d and 15 d, respectively. Cloning of the 16S rRNA gene revealed that the consortium was composed of 40% Achromobacter and 7% each of Castelaniella, Rhodanobacter, and Hypomicrobium. Comamonas, Ferrovibrio, Terrimonas, Bordetella, Rhizobium, and Pseudonocardia were also detected. PCR-DGGE showed the dynamics of the consortium during the incubation period. Real-time PCR revealed that PAH degrading genes such as the gram-positive ring dihydroxylating genes (PAH-RDH) and pyrene dioxygenase (nidA) were most abundant at day 5 when the rapid biodegradation of the PAHs was observed. This study improves our understanding on dynamics and characteristics of an effective PAH-degrading bacterial consortium from paddy rice soil.

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

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

Impact of Petroleum Contamination on the Structure of Saline Soil Bacterial Communities

Petroleum contamination may lead to variations in soil microbial community structure and activities. The bioremediation of petroleum-contaminated soil typically depends on the characteristics and activities of oil-degrading microorganisms, which can be introduced or be part of the native soil microbiota. Thus, analyzing the structure of the microbial community and internal relationships in the bioremediation process is critical. Our study characterized the physical and chemical properties, microbial community structure, and microbial diversity of surface soil collected near an oilfield. The total carbon (TC), total organic carbon (TOC), and microbial diversity in oil-contaminated soil was found higher than in uncontaminated samples. Proteobacteria abundance was inhibited with oil pollution, while Actinomycetes abundance was enhanced. Some indigenous hydrocarbon-degrading bactera were enriched by oil pollution, such as Bacillus, Actinomarinales norank, Balneolaceae uncultured, Marinobacter, and Pseudomonas. Furthermore, Rokubacteria, Nitrospirae, and Entotheonellaeota were significant differences in the contaminated group. There were 16 genera with significant differences in the polluted group, such as Woeseia, Pelagibius, Pontibacillus, IS_44, Aliifodinibius, while Halothiobacillus, Algoriphagus, Novosphingobium, etc. had significant differences in the uncontaminated group. Redundancy analysis demonstrated that the responses of the microorganisms to the evaluated environmental factors were different, and TC was the most important driver of microbial community variation. Moreover, TOC was the largest contributor to operational taxonomic unit (OTU) and Chao index variations. Our results provide a theoretical basis for the enhancement of microbial activity in oil-contaminated soil, which might improve bioremediation efficacy.

A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils

The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.

Microbial Communities of Seawater and Coastal Soil of Russian Arctic Region and Their Potential for Bioremediation from Hydrocarbon Pollutants

The development of Arctic regions leads to pollution of marine and coastal environments with oil and petroleum products. The purpose of this work was to determine the diversity of microbial communities in seawater, as well as in littoral and coastal soil, and the potential ability of their members to degrade hydrocarbons degradation and to isolate oil-degrading bacteria. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, the dominance of bacteria in polar communities was shown, the proportion of archaea did not exceed 2% (of the total number of sequences in the libraries). Archaea inhabiting the seawater belonged to the genera Nitrosopumilus and Nitrosoarchaeum and to the Nitrososphaeraceae family. In the polluted samples, members of the Gammaproteobacteria, Alphaproteobacteria, and Actinomycetes classes predominated; bacteria of the classes Bacteroidia, Clostridia, Acidimicrobiia, Planctomycetia, and Deltaproteobacteria were less represented. Using the iVikodak program and KEGG database, the potential functional characteristics of the studied prokaryotic communities were predicted. Bacteria were potentially involved in nitrogen and sulfur cycles, in degradation of benzoate, terephthalate, fatty acids, and alkanes. A total of 19 strains of bacteria of the genera Pseudomonas, Aeromonas, Oceanisphaera, Shewanella, Paeniglutamicibacter, and Rhodococcus were isolated from the studied samples. Among them were psychrotolerant and psychrophilic bacteria growing in seawater and utilizing crude oil, diesel fuel, and motor oils. The data obtained suggest that the studied microbial communities could participate in the removal of hydrocarbons from arctic seawater and coastal soils and suggested the possibility of the application of the isolates for the bioaugmentation of oil-contaminated polar environments.

Hydrocarbon bioremediation on Arctic shorelines: Historic perspective and roadway to the future

Climate change has become one of the greatest concerns of the past few decades. In particular, global warming is a growing threat to the Canadian high Arctic and other polar regions. By the middle of this century, an increase in the annual mean temperature of 1.8 °C-2.7 °C for the Canadian North is predicted. Rising temperatures lead to a significant decrease of the sea ice area covered in the Northwest Passage. As a consequence, a surge of maritime activity in that region increases the risk of hydrocarbon pollution due to accidental fuel spills. In this review, we focus on bioremediation approaches on Arctic shorelines. We summarize historical experimental spill studies conducted at Svalbard, Baffin Island, and the Kerguelen Archipelago, and review contemporary studies that used modern omics techniques in various environments. We discuss how omics approaches can facilitate our understanding of Arctic shoreline bioremediation and identify promising research areas that should be further explored. We conclude that specific environmental conditions strongly alter bioremediation outcomes in Arctic environments and future studies must therefore focus on correlating these diverse parameters with the efficacy of hydrocarbon biodegradation.

Mixed bacterial consortium can hamper the efficient degradation of crude oil hydrocarbons

Crude oil degradation efficiency can be improved because of co-metabolism that exists when bacterial consortium is applied. However, because of possible vulnerability to environmental conditions and/or antagonistic interactions among members of the consortium, the degradation efficiency can be hampered. In this laboratory-based study, the biodegradation potentials of pure bacterial isolates namely Pseudomonas aeruginosa strain W15 (MW320658), Providencia vermicola strain W8 (MW320661) and Serratia marcescens strain W13 (MW320662) earlier isolated from crude oil-contaminated site and their consortium were evaluated using 3% crude oil-supplemented Bushnell Haas media. The efficiency was evaluated based on the viable cell count, biosurfactant analyses, percentage hydrocarbon degradation using gravimetric analysis and gas chromatography-mass spectrophotometry (GC-MS) analysis. There was decline in the population of W13 and predominance of W15 in the consortium as the incubation period progressed. Accelerated biodegradation of the crude oil hydrocarbons through co-metabolism was not achieved with the consortium; neither was there any improved resilience nor resistance to environmental changes of strain W13. The GC-MS analyses showed that the highest degradation was produced by W15 (48.23%) compared to W8 (46.04%), W13 (45.24%) and the Consortium (28.51%). The biodegradation of the crude oil hydrocarbons by W15, W8, W13 axenic cultures and their consortium treatments demonstrated that the bacterial constituent in a consortium can influence the synergistic effect that improves bioremediation. Future research that focuses on evaluating possible improvement in bioremediation through maintenance of diversity by continuous bioaugmentation using vulnerable but efficient degraders in a consortium is necessary to further understand the application of consortia for bioremediation improvement.

From Surface Water to the Deep Sea: A Review on Factors Affecting the Biodegradation of Spilled Oil in Marine Environment

Over the past century, the demand for petroleum products has increased rapidly, leading to higher oil extraction, processing and transportation, which result in numerous oil spills in coastal-marine environments. As the spilled oil can negatively affect the coastal-marine ecosystems, its transport and fates captured a significant interest of the scientific community and regulatory agencies. Typically, the environment has natural mechanisms (e.g., photooxidation, biodegradation, evaporation) to weather/degrade and remove the spilled oil from the environment. Among various oil weathering mechanisms, biodegradation by naturally occurring bacterial populations removes a majority of spilled oil, thus the focus on bioremediation has increased significantly. Helping in the marginal recognition of this promising technique for oil-spill degradation, this paper reviews recently published articles that will help broaden the understanding of the factors affecting biodegradation of spilled oil in coastal-marine environments. The goal of this review is to examine the effects of various environmental variables that contribute to oil degradation in the coastal-marine environments, as well as the factors that influence these processes. Physico-chemical parameters such as temperature, oxygen level, pressure, shoreline energy, salinity, and pH are taken into account. In general, increase in temperature, exposure to sunlight (photooxidation), dissolved oxygen (DO), nutrients (nitrogen, phosphorous and potassium), shoreline energy (physical advection—waves) and diverse hydrocarbon-degrading microorganisms consortium were found to increase spilled oil degradation in marine environments. In contrast, higher initial oil concentration and seawater pressure can lower oil degradation rates. There is limited information on the influences of seawater pH and salinity on oil degradation, thus warranting additional research. This comprehensive review can be used as a guide for bioremediation modeling and mitigating future oil spill pollution in the marine environment by utilizing the bacteria adapted to certain conditions.

Understanding the Implications of Predicted Function for Assessment of Rapid Bioremediation in a Farmland-Oilfield Mixed Area

Farmland-oilfield mixed areas are fragile ecosystems that require dynamic remediation to counteract the undesirable impact of energy development. Practicable assessment methods are pivotal to a fast and accurate evaluation of the in situ bioremediation process. Petroleum pollutants impose component-dependent effects on autochthonous microbiota before and after remediation. Here, the predicted functional response of soil microbiomes to petroleum pollutants was analyzed in a historically polluted farmland-oilfield mixed area from the perspective of developing a set of feasible biomarkers for immediate post-bioremediation evaluation. An array of microbial, genetic, systematic, and phenotypic biomarkers was proposed. Our results showed that the biomarkers could proxy the stage of the bioremediation multidimensionally. We argue that functional diversity should be considered together with microbial community dynamic to evaluate the restoration status of the microbial communities in petroleum-contaminated farmland-oilfield mixed environments.

Dissolved organic matter production from herder application and in-situ burning of crude oil at high latitudes: Bioavailable molecular composition patterns and microbial community diversity effects

Chemical herders and in-situ burning (ISB) are designed to mitigate the effects that oil spills may have on the high latitude marine environment. Little information exists on the water solubilization of petroleum residues stemming from chemically herded ISB and whether these bioavailable compounds have measurable impacts on marine biota. In this experiment, we investigated the effects of Siltech OP40 and crude oil ISB on a) petroleum-derived dissolved organic matter (DOM_HC) composition and b) seawater microbial community diversity over 28 days at 4 °C in aquarium-scale mesocosms. Ultra-high resolution mass spectrometry and fluorescence spectroscopy revealed increases in aromaticity over time, with ISB and ISB+OP40 samples having higher % aromatic classes in the initial incubation periods. ISB+OP40 contained a nearly 12-fold increase in the number of DOM_HC formulae relative to those before ISB. 16S rRNA gene sequencing identified differences in microbial alpha diversity between seawater, ISB, OP40, and ISB+OP40. Microbial betadiversity shifts were observed that correlated strongly with aromatic/condensed relative abundance and incubation time. Proteobacteria, specifically from the genera Marinomonas and Perlucidibaca experienced -22 and +24 log₂-fold changes in ISB+OP40 vs. seawater, respectively. These findings provide an important opportunity to advance our understanding of chemical herders and ISB in the high latitude marine environment.

Bacterial community profile of the crude oil-contaminated saline soil in the Yellow River Delta Natural Reserve, China

Crude oil contamination greatly influence soil bacterial community. Proliferative microbes in the crude oil-contaminated soil are closely related to the living conditions. Oil wells in the Yellow River Delta Natural Reserve (YRDNR) region is an ideal site for investigating the bacterial community of crude oil-contaminated saline soil. In the present study, 18 soil samples were collected from the depths of 0-20 cm and 20-40 cm around the oil wells in the YRDNR. The bacterial community profile was analyzed through high-throughput sequencing to trace the oil-degrading aerobic and anaerobic bacteria. The results indicated that C₁₅-C₂₈ and C₂₉-C₃₈ were the main fractions of total petroleum hydrocarbon (TPH) in the sampled soil. These TPH fractions had a significant negative effect on bacterial biodiversity (Shannon, Simpson, and Chao1 indices), which led to the proliferation of hydrocarbon-degrading bacteria. A comprehensive analysis between the environmental factors and soil microbial community structure showed that Streptococcus, Bacillus, Sphingomonas, and Arthrobacter were the aerobic hydrocarbon-degrading bacteria; unidentified Rhodobacteraceae and Porticoccus were considered to be the possible facultative anaerobic bacteria with hydrocarbon biodegradation ability; Acidithiobacillus, SAR324 clade, and Nitrosarchaeum were predicted to be the anaerobic hydrocarbon-degrading bacteria in the sub-surface soil. Furthermore, large amount of carbon sources derived from TPH was found to cause depletion of bioavailable nitrogen in the soil. The bacteria associated with nitrogen transformation, such as Solirubrobacter, Candidatus Udaeobacter, Lysinibacillus, Bradyrhizobium, Sphingomonas, Mycobacterium, and Acidithiobacillus, were highly abundant; these bacteria may possess the ability to increase nitrogen availability in the crude oil-contaminated soil. The bacterial community functions were significantly different between the surface and the sub-surface soil, and the dissolved oxygen concentration in soil was considered to be potential influencing factor. Our results could provide useful information for the bioremediation of crude oil-contaminated saline soil.

Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0

Mangroves provide a variety of ecosystem services and contribute greatly to the global biogeochemical cycle. Microorganisms play important roles in biogeochemical cycles and maintain the dynamic balance of mangroves. However, the roles of bacteria in the biogeochemical cycles of mangroves and their ecological distribution and functions remain largely uncharacterized. This study thus sought to analyze and compare the ecological distributions and potential roles of bacteria in typical mangroves using 16S rRNA gene amplicon sequencing and GeoChip. Interestingly, the bacterial community compositions were largely similar in the studied mangroves, including Shenzhen, Yunxiao, Zhanjiang, Hainan, Hongkong, Fangchenggang, and Beihai mangroves. Moreover, gamma-proteobacterium_uncultured and Woeseia were the most abundant microorganisms in the mangroves. Furthermore, most of the bacterial communities were significantly correlated with phosphorus levels (P < 0.05; −0.93 < R < 0.93), suggesting that this nutrient is a vital driver of bacterial community composition. Additionally, GeoChip analysis indicated that the functional genes amyA, narG, dsrA, and ppx were highly abundant in the studied mangroves, suggesting that carbon degradation, denitrification, sulfite reduction, and polyphosphate degradation are crucial processes in typical mangroves. Moreover, several genera were found to synergistically participate in biogeochemical cycles in mangroves. For instance, Neisseria, Ruegeria, Rhodococcus, Desulfotomaculum, and Gordonia were synergistically involved in the carbon, nitrogen, and sulfur cycles, whereas Neisseria and Treponema were synergistically involved in the nitrogen cycle and the sulfur cycle. Taken together, our findings provide novel insights into the ecological roles of bacteria in the biogeochemical cycles of mangroves.

IMPORTANCE Bacteria have important functions in biogeochemical cycles, but studies on their function in an important ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved in biogeochemical cycles in seven representative mangroves of southern China. Furthermore, various functional genes from bacteria involved in biogeochemical cycles were identified by GeoChip 5.0. The functional genes associated with the carbon cycle (particularly carbon degradation) were the most abundant, suggesting that carbon degradation is the most active process in mangroves. Additionally, some high-abundance bacterial populations were found to synergistically mediate key biogeochemical cycles in the mangroves, including Neisseria, Pseudomonas, Treponema, Desulfotomaculum, and Nitrosospira. In a word, our study gives novel insights into the function of bacteria in biogeochemical cycles in mangroves.

Optimization of the Biodegradation of Aliphatic, Aromatic, and UCM Hydrocarbons from Light Crude Oil in Marine Sediment Using Response Surface Methodology (RSM)

This study describes the optimization of the biodegradation of total aliphatic (tAHCs), total aromatic (tPAHs), and unresolved complex mixture (UCM) hydrocarbons from light crude oil in marine sediment. The response surface methodology (RSM), with a Box-Behnken design, was used to optimize the hydrocarbon fraction degradation, reported as degradation efficiency (E (%)), using four independent variables (inoculum, dispersant, light oil concentration, and carbon/nitrogen ratio), all at three levels. Analysis of variance (ANOVA) showed R² values of 0.976, 0.974, and 0.975 for tAHCs, tPAHs, and UCM, respectively. All fractions exhibited a statistically significant effect (P < 0.05) in the second-order quadratic regression model for degradation. According to the models, the optimal degradation prediction was: 81.03% for tAHCs, 85.96% for tPAHs, and 92.86% for UCM. This work highlights the possibility of carrying out efficient biodegradation, of more than 80%, through an optimization process using different light oil concentrations, opening up possibilities of multiple response optimization.

Biodegradation of water-accommodated aromatic oil compounds in Arctic seawater at 0 °C

Oil spills in Arctic marine environments are expected to increase concurrently with the expansion of shipping routes and petroleum exploitation into previously inaccessible ice-dominated regions. Most research on oil biodegradation focusses on the bulk oil, but the fate of the water-accommodated fraction (WAF), mainly composed of toxic aromatic compounds, is largely underexplored. To evaluate the bacterial degradation capacity of such dissolved aromatics in Greenlandic seawater, microcosms consisting of 0 °C seawater polluted with WAF were investigated over a 3-month period. With a half-life (t_1/2) of 26 days, m-xylene was the fastest degraded compound, as measured by gas chromatography - mass spectrometry. Substantial slower degradation was observed for ethylbenzene, naphthalenes, phenanthrene, acenaphthylene, acenaphthene and fluorenes with t_1/2 of 40-105 days. Colwellia, identified by 16S rRNA gene sequencing, was the main potential degrader of m-xylene. This genus occupied up to 47 % of the bacterial community until day 10 in the microcosms. Cycloclasticus and Zhongshania aliphaticivorans, potentially utilizing one-to three-ringed aromatics, replaced Colwellia between day 10 and 96 and occupied up to 6 % and 23 % of the community, respectively. Although most of the WAF can ultimately be eliminated in microcosms, our results suggest that the restoration of an oil-impacted Arctic environment may be slow as most analysed compounds had t_1/2 of over 2-3 months and the detrimental effects of a spill towards the marine ecosystem likely persist during this time.

The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain

Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.

Draft Genome Sequence of the Planctobacterium marinum Type Strain K7

Planctobacterium marinum strain K7 is a Gram-negative gammaproteobacterium of the Alteromonadaceae family and is the sole type strain in the genus Planctobacterium. Presented here is the draft whole-genome sequence of P. marinum strain K7.

Microbial Life on the Surface of Microplastics in Natural Waters

Major water-polluting microplastics (for example, polyethylene, polypropylene and others) have lower density than water. Therefore, they are concentrated in the neustonic layer near the water-air interface altogether with dissolved or colloidal natural organic matter, hydrophobic cells and spores of bacteria. This can cause environmental and public health problems because the floating micro- and nanoparticles of plastics could be coated with biofilm of hydrophobic and often putative pathogenic bacteria. Biofilm-coated microplastics are more attractive for consumption by aquatic animals than pure microplastics, and that increases the negative impacts of microplastics. So, impacts of even small quantities of microplastics in aquatic environments must be accounted for considering their accumulation in the micro-layer of water-air interphase and its interaction with bacterioneuston. Microorganisms attached to the surface of microplastic particles could interact with them, use them as substrates for growth, to change properties and biodegrade. The study of microbial life on the surface of microplastic particles is one of the key topics to understanding their role in the environment.

Chemical Diversity and Antimicrobial Potential of Cultivable Fungi from Deep-Sea Sediments of the Gulf of Mexico

A collection of 29 cultivable fungal strains isolated from deep-sea sediments of the Gulf of Mexico were cultivated under the “one strain, many compounds” approach to explore their chemical diversity and antimicrobial potential. From the 87 extracts tested, over 50% showed antimicrobial activity, and the most active ones were those from cultures grown at 4 °C in darkness for 60 days (resembling deep-sea temperature). PCA analysis of the LC-MS data of all the extracts confirmed that culture temperature is the primary factor in the variation of the 4462 metabolite features, accounting for 21.3% of the variation. The bioactivity-guided and conventional chemical studies of selected fungal strains allowed the identification of several active and specialized metabolites. Finally, metabolomics analysis by GNPS molecular networking and manual dereplication revealed the biosynthetic potential of these species to produce interesting chemistry. This work uncovers the chemical and biological study of marine-derived fungal strains from deep-sea sediments of the Gulf of Mexico.

Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons

Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg^-1), moderate (600 mg kg^-1), and high (1200 mg kg^-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHD_α) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg^-1 sediment day^-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg^-1 sediment day^-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.

Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms

Co-contamination with chlorinated compounds and 1,4-dioxane has been reported at many sites. Recently, there has been an increased interest in bioremediation because of the potential to degrade multiple contaminants concurrently. Towards improving bioremediation efficacy, the current study examined laboratory microcosms (inoculated separately with two soils) to determine the phylotypes and functional genes associated with the biodegradation of two common co-contaminants (cis-dichloroethene [cDCE] and 1,4-dioxane). The impact of amending microcosms with lactate on cDCE and 1,4-dioxane biodegradation was also investigated. The presence of either lactate or cDCE did not impact 1,4-dioxane biodegradation one of the two soils. Lactate appeared to improve the initiation of the biological removal of cDCE in microcosms inoculated with either soil. Stable isotope probing (SIP) was then used to determine which phylotypes were actively involved in carbon uptake from cDCE and 1,4-dioxane in both soil communities. The most enriched phylotypes for ¹³C assimilation from 1,4-dioxane included Rhodopseudomonas and Rhodanobacter. Propane monooxygenase was predicted (by PICRUSt2) to be dominant in the 1,4-dioxane amended microbial communities and propane monooxygenase gene abundance values correlated with other enriched (but less abundant) phylotypes for ¹³C-1,4-dioxane assimilation. The dominant enriched phylotypes for ¹³C assimilation from cDCE included Bacteriovorax, Pseudomonas and Sphingomonas. In the cDCE amended soil microcosms, PICRUSt2 predicted the presence of DNA encoding glutathione S-transferase (a known cDCE upregulated enzyme). Overall, the work demonstrated concurrent removal of cDCE and 1,4-dioxane by indigenous soil microbial communities and the enhancement of cDCE removal by lactate. The data generated on the phylotypes responsible for carbon uptake (as determined by SIP) could be incorporated into diagnostic molecular methods for site characterization. The results suggest concurrent biodegradation of cDCE and 1,4-dioxane should be considered for chlorinated solvent site remediation.

Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.

Exploiting Microbes in the Petroleum Field: Analyzing the Credibility of Microbial Enhanced Oil Recovery (MEOR)

Crude oil is a major energy source that is exploited globally to achieve economic growth. To meet the growing demands for oil, in an environment of stringent environmental regulations and economic and technical pressure, industries have been required to develop novel oil salvaging techniques. The remaining ~70% of the world’s conventional oil (one-third of the available total petroleum) is trapped in depleted and marginal reservoirs, and could thus be potentially recovered and used. The only means of extracting this oil is via microbial enhanced oil recovery (MEOR). This tertiary oil recovery method employs indigenous microorganisms and their metabolic products to enhance oil mobilization. Although a significant amount of research has been undertaken on MEOR, the absence of convincing evidence has contributed to the petroleum industry’s low interest, as evidenced by the issuance of 400+ patents on MEOR that have not been accepted by this sector. The majority of the world’s MEOR field trials are briefly described in this review. However, the presented research fails to provide valid verification that the microbial system has the potential to address the identified constraints. Rather than promising certainty, MEOR will persist as an unverified concept unless further research and investigations are carried out.

Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): insights on the potential of Burkholderia, Pseudomonas and Cupriavidus isolates

The contamination of the environment by crude oil and its by-products, mainly composed of aliphatic and aromatic hydrocarbons, is a widespread problem. Biodegradation by bacteria is one of the processes responsible for the removal of these pollutants. This study was conducted to determine the abilities of Burkholderia sp. B5, Cupriavidus sp. B1, Pseudomonas sp. T1, and another Cupriavidus sp. X5 to degrade binary mixtures of octane (representing aliphatic hydrocarbons) with benzene, toluene, ethylbenzene, or xylene (BTEX as aromatic hydrocarbons) at a final concentration of 100 ppm under aerobic conditions. These strains were isolated from an enriched bacterial consortium (Yabase or Y consortium) that prefer to degrade aromatic hydrocarbon over aliphatic hydrocarbons. We found that B5 degraded all BTEX compounds more rapidly than octane. In contrast, B1, T1 and X5 utilized more of octane over BTX compounds. B5 also preferred to use benzene over octane with varying concentrations of up to 200 mg/l. B5 possesses alkane hydroxylase (alkB) and catechol 2,3-dioxygenase (C23D) genes, which are responsible for the degradation of alkanes and aromatic hydrocarbons, respectively. This study strongly supports our notion that Burkholderia played a key role in the preferential degradation of aromatic hydrocarbons over aliphatic hydrocarbons in the previously characterized Y consortium. The preferential degradation of more toxic aromatic hydrocarbons over aliphatics is crucial in risk-based bioremediation.

Aerobic granular sludge systems for treating hypersaline pharmaceutical wastewater: Start-up, long-term performances and metabolic function

The complex organics, residue pharmaceuticals and high salinity in pharmaceutical wastewater pose great challenges to biological wastewater treatment. In this study, granular sludge process was used for treating pharmaceutical wastewater because of its high pollutant removal efficiency. The results suggested that granules could not form within 90-d cultivation when directly fed with target hypersaline pharmaceutical wastewater (R_P) due to suppression of EPS secretion by high concentration of inhibitory organics, while granules were successfully developed with hypersaline synthetic wastewater (R_S) and diluted pharmaceutical wastewater (R_D), respectively. Further comparison of pollutant removal performance from target pharmaceutical wastewater showed that simultaneous removal of organics (effluent bCOD<1 mg L^-1) and nitrogen (average TN removal efficiency of 70.3%) could be achieved in R_D. Nevertheless, long acclimation period (i.e., 20 d) was needed for granules when carbon source was shifted from simple sodium acetate to complex organic pollutants in pharmaceutical wastewater, with nitrite significantly accumulated in R_S. Analysis of microbial community and nitrogen metabolism pathway indicated the higher abundance of nitrite oxidoreductase than that in the R_S to alleviate nitrite accumulation in the R_D, and functional strains such as Paracoccus and Mycobacterium played critical roles for high efficiency of organic degradation, nitrification and denitrification.

Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater

Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. We demonstrate the ability of the community of degraders at the POLA to incorporate carbon from naphthalene, leading to a quick shift in microbial community composition to be dominated by the normally rare Colwellia and Cycloclasticus We show that metagenome-assembled genomes (MAGs) belonged to these naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes, even when combining genes from the entire microbial community, leading us to hypothesize that promiscuous dehydrogenases replace canonical naphthalene degradation enzymes in this site. We compared metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate genomic-based recommendations for future optimization of PAH bioremediation at the POLA, e.g., ammonium as opposed to urea, heme or hemoproteins as an iron source, and polar amino acids.IMPORTANCE Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. Polycyclic aromatic hydrocarbons are the most persistent and toxic component of crude oil. Therefore, the bacteria that can break those molecules down are of particular importance. We identified such bacteria at the Port of Los Angeles (POLA), one of the busiest ports worldwide, and characterized their metabolic capabilities. We propose chemical targets based on those analyses to stimulate the activity of these bacteria in case of an oil spill in the Port POLA.

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast

Oil spills are among the most catastrophic events to marine ecosystems and current remediation techniques are not suitable for ecological restoration. Bioremediation approaches can take advantage of the activity of microorganisms with biodegradation capacity thus helping to accelerate the recovery of contaminated environments. The use of native microorganisms can increase the bioremediation efficiency since they have higher potential to survive in the natural environment while preventing unpredictable ecological impacts associated with the introduction of non-native organisms. In order to know the geographical scale to which a native bioremediation consortium can be applied, we need to understand the spatial heterogeneity of the natural microbial communities with potential for hydrocarbon degradation. In the present study, we aim to describe the genetic diversity and the potential of native microbial communities to degrade petroleum hydrocarbons, at an early stage of bioremediation, along the NW Iberian Peninsula coast, an area particularly susceptible to oil spills. Seawater samples collected in 47 sites were exposed to crude oil for 2 weeks, in enrichment experiments. Seawater samples collected in situ, and samples collected after the enrichment with crude oil, were characterized for prokaryotic communities by using 16S rRNA gene amplicon sequencing and predictive functional profiling. Results showed a drastic decrease in richness and diversity of microbial communities after the enrichment with crude oil. Enriched microbial communities were mainly dominated by genera known to degrade hydrocarbons, namely Alcanivorax, Pseudomonas, Acinetobacter, Rhodococcus, Flavobacterium, Oleibacter, Marinobacter, and Thalassospira, without significant differences between geographic areas and locations. Predictive functional profiling of the enriched microbial consortia showed a high potential to degrade the aromatic compounds aminobenzoate, benzoate, chlorocyclohexane, chlorobenzene, ethylbenzene, naphthalene, polycyclic aromatic compounds, styrene, toluene, and xylene. Only a few genera contributed for more than 50% of this genetic potential for aromatic compounds degradation in the enriched communities, namely Alcanivorax, Thalassospira, and Pseudomonas spp. This work is a starting point for the future development of prototype consortia of hydrocarbon-degrading bacteria to mitigate oil spills in the Iberian NW coast.

Interplay of microbial communities with mineral environments in coralline algae

Coralline algae are worldwide carbonate builders, considered to be foundational species and biodiversity hotspots. Coralline habitats face increasing pressure from human activities and effects related to Global Change, yet their ecological properties and adaptive responses remain poorly understood. The relationships of the algal microbiota with the mineral bioconstructions, as well as plasticity and resilience of coralline holobionts in a changing environment, are of particular interest. In the Gulf of California, Neogoniolithon trichotomum (Rhodophyta) is the main carbonate builder in tidal pools. We performed a multi-disciplinary assessment of the N. trichotomum microstructure using XRD, SEM microscopy and SR-FTIR spectromicroscopy. In the algal perithallus, magnesium-calcite and aragonite were spatially segregated and embedded in a polysaccharide matrix (rich in sulfated polysaccharides). Mg-calcites (18-19 mol% Mg) were the main mineral components of the thallus overall, followed by iron carbonates related to dolomite (ankerite) and siderite. Minerals of late evaporitic sequences (sylvite and bischofite) were also present, suggesting potential halophilic microenvironments within the algal thalli. The diverse set of abundant halophilic, halotolerant and oligotrophic taxa, whose abundance increase in the summer, further suggests this condition. We created an integrated model, based on environmental parameters and the microbiota distribution, that identified temperature and nutrient availability (particularly nitrate and silicate) as the main parameters related to specific taxa patterns. Among these, Hahella, Granulossicoccus, Ferrimonas, Spongiibacteraceae and cyanobacterial Xenococcaceae and Nostocaceae change significantly between seasons. These bacterial components might play relevant roles in algal plasticity and adaptive responses to a changing environment. This study contributes to the understanding of the interplay of the prokaryotic microbiota with the mineral microenvironments of coralline algae. Because of their carbonates with potential resistance to dissolution in a higher pCO₂ world and their seasonally dynamic bacteria, coralline algae are relevant targets to study coastal resilience and carbonated systems responses to changing environments.

Novel magnetic loofah sponge biochar enhancing microbial responses for the remediation of polycyclic aromatic hydrocarbons-contaminated sediment

Magnetic activated carbon and magnetic biochar have been widely used for contaminants removal due to the advantages of sequestration and recovery. However, the remediation function and microbial response of conductive magnetic carbonaceous materials for treating organic contaminated sediment are poorly understood. In this study we applied novel three-dimensional mesh magnetic loofah sponge biochar (MagLsBC), made from natural agricultural product, to remediate polycyclic aromatic hydrocarbons (PAHs)-contaminated sediment. Compared to other carbon-based materials, MagLsBC achieved the high reduction of PAHs content and bioavailability in sediment by respectively 31.9 % and 38.1 % after 350 days. Microbial analysis showed that MagLsBC amended sediment had different community diversity, structure and enriched dominant species associated with the aromatic hydrocarbon metabolism. And MagLsBC amendment significantly increased the aromatic compounds degradation function, which was not observed in other treatments, and methanogenesis function. Further analysis revealed that the enhanced microbial responses in MagLsBC amended sediment were related with the high conductivity of MagLsBC. These results give the new insights into the effect of magnetic carbon materials on microbial community and organic pollutants degradation function during the long period amendment, demonstrating MagLsBC as an effective material with the biostimulation potential for the risk control of PAHs contamination.

Initial oil concentration affects hydrocarbon biodegradation rates and bacterial community composition in seawater

During oil spills in the field or for laboratory incubation studies, different oil concentrations are often encountered or applied, yet how initial oil concentration affects biodegradation rates of hydrocarbons and the development of oil degraders remains unclear. We incubated seawater for 50 d with different oil concentrations (0, 50, 100, 200, 400 and 800 ppm). n-Alkanes and polycyclic aromatic hydrocarbons (PAHs), and the bacterial community were analyzed periodically. Results show that the biodegradation rates of alkanes, derived from first order kinetics, decreased with increasing oil concentration, but percent residual was ~50% regardless of the initial concentration. In contrast, the biodegradation rates of PAHs increased with concentration, and the percent residual increased with oil concentration. Increasing oil concentration resulted in increased abundances of Rhodobacterales, Altererythrobacter, and Neptuniibacter. However, Alcanivorax abundance was barely detected in 400 and 800 ppm. Overall, oil concentration critically affected the degradation of hydrocarbons and the bacterial community.

Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico

Background

Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites.

Methods

The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation.

Results

We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.

New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era

The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.

Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes

Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with hydrocarbons is limited. In this study, taxonomic (amplicon sequencing) profiles of two environmental deep-sea sediments (>1,200 m deep) were obtained, along with taxonomic and metabolomic (mass spectrometry-based metabolomics) profiles of microbes harbored in deep-sea sediments cultured with hydrocarbons as the sole energy source. Samples were collected from the Gulf of México (GM) and cultured for 28 days using simple (toluene, benzene, hexadecane, and naphthalene) and complex (petroleum API 40) hydrocarbon mixtures as the sole energy sources. The sediment samples harbored diverse microbial communities predominantly classified into Woeseiaceae and Kiloniellaceae families, whereas Pseudomonadaceae and Enterobacteriaceae families prevailed after sediments were cultured with hydrocarbons. Chemical profiling of microbial metabolomes revealed diverse chemical groups belonging primarily to the lipids and lipid-like molecules superclass, as well as the organoheterocyclic compound superclass (ClassyFire annotation). Metabolomic data and prediction of functional profiles indicated an increase in aromatic and alkane degradation in samples cultured with hydrocarbons. Previously unreported metabolites, identified as intermediates in the degradation of hydrocarbons, were annotated as hydroxylated polyunsaturated fatty acids and carboxylated benzene derivatives. In summary, this study used mass spectrometry-based metabolomics coupled to chemoinformatics to demonstrate how microbes from deep-sea sediments could be cultured in the presence of hydrocarbons. This study also highlights how this experimental approach can be used to increase the understanding of hydrocarbon degradation by deep-sea sediment microbes.IMPORTANCE High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-sea microbes. In conclusion, this study used metabolomics and chemoinformatics to demonstrate that microbes from deep-sea sediment origin thrive in the presence of toxic and difficult-to-metabolize hydrocarbons. Notably, this study provides evidence of previously unreported metabolites and the global chemical repertoire associated with the metabolism of hydrocarbons by deep-sea microbes.

Oil leakage induces changes in microbiomes of deep-sea sediments of Campos Basin (Brazil)

The Campos Basin (100,000 km²) is located on the continental shelf of southeastern Brazil. Despite the significant oil and gas industrial activities underway in the Campos Basin, scarce information is available regarding the hydrocarbon contents and microbial communities in the deep-sea sediments. To gain new insights on these aspects, we first obtained deep-sea sediment samples with different degrees of oil exposure. We obtained samples from a seabed fissure (N = 28), surroundings (250 m to 500 m from the fissure; N = 24), and a control area (N = 4). We used shotgun metagenomics to characterize the taxonomic and metabolic diversity and analyzed biogeochemical parameters (metal and oil concentration) of all samples. The high levels of unresolved complex mixture of hydrocarbons in the fissure indicate a potentially recent petrogenic contribution in these sediments. The fissure area was found to have a higher abundance of hydrocarbonoclastic bacterial genera and hydrocarbon degradation genes. These bacteria may be used as biosensors of sediment contamination. The effects of oil contamination, mainly around the fissure, are less clear at 250 m and 500 m, suggesting that the surroundings may not have been heavily affected by the oil leakage. Our study demonstrates that metagenomics can disclose biosensors for environmental monitoring.