Microbial bioremediation of oil contaminated seawater: A survey of patent deposits and the characterization of the top genera applied

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.

In situ devices can culture the microbial dark matter of corals

Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.

The Impact of Highly Weathered Oil from the Most Extensive Oil Spill in Tropical Oceans (Brazil) on the Microbiome of the Coral Mussismilia harttii

In 2019, the largest oil spill ever recorded in tropical oceans in terms of extent occurred in Brazil. The oil from the spill was collected directly from the environment and used in an exposure experiment with the endangered reef-building coral Mussismilia harttii. The treatments of the experiment were control (without oil), 1% oil, 2.5% oil, and direct contact of coral with oil. The most abundant hydrocarbon in the seawater of the experiment was phenatrene, which is toxic to corals. However, overall, the concentration of PAHs was not very high. The analysis of the maximum photosynthetic capacity of Symbiodiniaceae dinoflagellates showed a small impact of oil on corals, mainly on the contact treatment. However, coral microbiomes were affected in all oil treatments, with the contact treatment showing the most pronounced impact. A greater number and abundance of stress-indicating and potentially pathogenic bacteria were found in all oil treatments. Finally, this highly weathered oil that had lain in the ocean for a long time was carrying potentially coral-pathogenic bacteria within the Vibrionaceae family and was able to transmit some of these bacteria to corals. Bacteria within Vibrionaceae are the main causes of disease in different species of corals and other marine organisms.

Use of surfactants in biodegradation of hydrophobic compounds: A review

Industrial development has led to immense emission and accumulation of hydrophobic organic compounds (HOC) in the environment. Primarily, they include petroleum hydrocarbons, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs). The extensive use of hydrophobic pesticides in agriculture led to the contamination of soil, air and water. Many of the hydrophobic substances are dangerous for the biota due to their high toxicity and carcinogenic and mutagenic activity. In addition to their widespread use, the possible adverse effects are also determined by their resistance to decomposition, including the biological one, which defines their long-term persistence in soil, water and other media. The impact of HOC on ecosystems poses a potential threat not only to the environment but also to human health. Numerous studies were devoted to the remediation of soils polluted with HOC. The approaches to remediation can be conditionally divided into mechanical, chemical and bio-methods, with the former two being widely used in the past. Bioremediation methods proved more efficient and, as a rule, more cost-effective and environmentally friendly. In recent years, the good efficiency of solubilizing agents in bioremediation processes has been demonstrated. Various surfactants have become widely popular due to their ability to increase desorption, water solubility and microbial bioavailability of HOC. In this brief review, state-of-the-art literature data on the biodegradation of hydrophobic organic compounds using surfactants were considered.

Role of Exopolysaccharides of Pseudomonas in Heavy Metal Removal and Other Remediation Strategies

Pseudomonas biofilms have been studied intensively for several decades and research outcomes have been successfully implemented in various medical and agricultural applications. Research on biofilm synthesis and composition has also overlapped with the objectives of environmental sciences, since biofilm components show exceptional physicochemical properties applicable to remediation techniques. Especially, exopolysaccharides (ExPs) have been at the center of scientific interest, indicating their potential in solving the environmental issues of heavy metal land and water contamination via sorptive interactions and flocculation. Since exposure to heavy metal via contaminated water or soil poses an imminent risk to the environment and human health, ExPs provide an interesting and viable solution to this issue, alongside other effective and green remedial techniques (e.g., phytostabilization, implementation of biosolids, and biosorption using agricultural wastes) aiming to restore contaminated sites to their natural, pollution-free state, or to ameliorate the negative impact of heavy metals on the environment. Thus, we discuss the plausible role and performance of Pseudomonas ExPs in remediation techniques, aiming to provide the relevant available and comprehensive information on ExPs’ biosynthesis and their usage in heavy metal remediation or other environmental applications, such as wastewater treatment via bioflocculation and soil remediation.

Conotoxin Patenting Trends in Academia and Industry

Sea snails of the genus Conus produce toxins that have been the subjects of numerous studies, projects, publications, and patents over the years. Since Conus toxins were discovered in the 1960s, their biological activity has been thought to have high pharmaceutical potential that could be explored beyond the limits of academic laboratories. We reviewed 224 patent documents related to conotoxins and conopeptides globally to determine the course that innovation and development has taken over the years, their primary applications, the technological trends over the last six years, and the leaders in the field, since the only previous patent review was performed in 2015 and focused in USA valid patents. In addition, we explored which countries/territories protect their inventions and patents and the most relevant collaborations among assignees. We also evaluated whether academia or pharmaceutical companies are the future of conotoxin research. We concluded that the 224 conotoxin patents reviewed in this study have more academic value than industrial value, which was noted by the number of active patents that have not yet been licensed and the contributions to medical research, especially as tools to study neuropathic pain, inflammation, immunology, drug design, receptor binding sites, cancer, neurotransmission, epilepsy, peptide biosynthesis, and depression. The aim of this review is to provide an overview of the current state of conotoxin patents, their main applications, and success based on the number of licensing and products in the market.

Hydrocarbons Biodegradation by Rhodococcus: Assimilation of Hexadecane in Different Aggregate States

The aim of our study was to reveal the peculiarities of the adaptation of rhodococci to hydrophobic hydrocarbon degradation at low temperatures when the substrate was in solid states. The ability of actinobacteria Rhodococcus erythropolis (strains X5 and S67) to degrade hexadecane at 10 °C (solid hydrophobic substrate) and 26 °C (liquid hydrophobic substrate) is described. Despite the solid state of the hydrophobic substrate at 10 °C, bacteria demonstrate a high level of its degradation (30–40%) within 18 days. For the first time, we show that specialized cellular structures are formed during the degradation of solid hexadecane by Rhodococcus at low temperatures: intracellular multimembrane structures and surface vesicles connected to the cell by fibers. The formation of specialized cellular structures when Rhodococcus bacteria are grown on solid hexadecane is an important adaptive trait, thereby contributing to the enlargement of a contact area between membrane-bound enzymes and a hydrophobic substrate.

Remediation of petroleum hydrocarbons-contaminated soil: Analysis based on Chinese patents

Increasing soil petroleum hydrocarbons (PHs) pollution have caused world-wide concerns. The removal of PHs from soils mainly involves physical, chemical, biological processes and their combinations. To date, most reviews in this field based on research articles, but limited papers focused on the integration of remediation technologies from the perspective of patents. In this study, 20-years Chinese patents related to the remediation of soil PHs were comprehensively analyzed. It showed an increasing number of patent applications and the patents' quantity were positively correlated with Chinese GDP over the years, suggesting the more the economy developed the more environmental problems and corresponding solutions emerged. In addition, chemical technologies were mostly used in a combination to achieve faster and better effects, while the physical technologies were often used alone due to high costs. In all PHs remediation techniques, bacteria-based bioremediation was the most used from 2000 to 2019. Bacillus spp. and Pseudomonas spp. were the most used bacteria for PHs treatment because these taxa were widely harboring functions such as biosurfactant production and hydrocarbon degradation. The future research on joint technologies combining microbial and physicochemical ones for better remediation effect and application are highly encouraged.

Bioremediation of Petroleum Hydrocarbons in Seawater: Prospects of Using Lyophilized Native Hydrocarbon-Degrading Bacteria

This work aimed to develop a bioremediation product of lyophilized native bacteria to respond to marine oil spills. Three oil-degrading bacterial strains (two strains of Rhodococcus erythropolis and one Pseudomonas sp.), isolated from the NW Portuguese coast, were selected for lyophilization after biomass growth optimization (tested with alternative carbon sources). Results indicated that the bacterial strains remained viable after the lyophilization process, without losing their biodegradation potential. The biomass/petroleum ratio was optimized, and the bioremediation efficiency of the lyophilized bacterial consortium was tested in microcosms with natural seawater and petroleum. An acceleration of the natural oil degradation process was observed, with an increased abundance of oil-degraders after 24 h, an emulsion of the oil/water layer after 7 days, and an increased removal of total petroleum hydrocarbons (47%) after 15 days. This study provides an insight into the formulation and optimization of lyophilized bacterial agents for application in autochthonous oil bioremediation.

Port Sediments: Problem or Resource? A Review Concerning the Treatment and Decontamination of Port Sediments by Fungi and Bacteria

Contamination of marine sediments by organic and/or inorganic compounds represents one of the most critical problems in marine environments. This issue affects not only biodiversity but also ecosystems, with negative impacts on sea water quality. The scientific community and the European Commission have recently discussed marine environment and ecosystem protection and restoration by sustainable green technologies among the main objectives of their scientific programmes. One of the primary goals of sustainable restoration and remediation of contaminated marine sediments is research regarding new biotechnologies employable in the decontamination of marine sediments, to consider sediments as a resource in many fields such as industry. In this context, microorganisms—in particular, fungi and bacteria—play a central and crucial role as the best tools of sustainable and green remediation processes. This review, carried out in the framework of the Interreg IT-FR Maritime GEREMIA Project, collects and shows the bioremediation and mycoremediation studies carried out on marine sediments contaminated with ecotoxic metals and organic pollutants. This work evidences the potentialities and limiting factors of these biotechnologies and outlines the possible future scenarios of the bioremediation of marine sediments, and also highlights the opportunities of an integrated approach that involves fungi and bacteria together.

Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites

BACKGROUND

Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities.

RESULTS

The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome.

CONCLUSIONS

Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs. Video abstract.

Optimization of an Autochthonous Bacterial Consortium Obtained from Beach Sediments for Bioremediation of Petroleum Hydrocarbons

Oil spill pollution remains a serious concern in marine environments and the development of effective oil bioremediation techniques are vital. This work is aimed at developing an autochthonous hydrocarbon-degrading consortium with bacterial strains with high potential for hydrocarbons degradation, optimizing first the growth conditions for the consortium, and then testing its hydrocarbon-degrading performance in microcosm bioremediation experiments. Bacterial strains, previously isolated from a sediment and cryopreserved in a georeferenced microbial bank, belonged to the genera Pseudomonas, Rhodococcus and Acinetobacter. Microcosms were assembled with natural seawater and petroleum, for testing: natural attenuation (NA); biostimulation (BS) (nutrients addition); bioaugmentation with inoculum pre-grown in petroleum (BA/P) and bioaugmentation with inoculum pre-grown in acetate (BA/A). After 15 days, a clear blending of petroleum with seawater was observed in BS, BA/P and BA/A but not in NA. Acetate was the best substrate for consortium growth. BA/A showed the highest hydrocarbons degradation (66%). All bacterial strains added as inoculum were recovered at the end of the experiment. This study provides an insight into the capacity of autochthonous communities to degrade hydrocarbons and on the use of alternative carbon sources for bacterial biomass growth for the development of bioremediation products to respond to oil spills.

Petroleum Contaminated Seawater Detoxification in Microcosm by Halotolerant Consortium Isolated from Persian Gulf

Bioremediation of a petroleum contaminated seawater from Persian Gulf was investigated and efficiency of natural attenuation by native halotolerant bacterial consortium, biostimulation by addition of macro nutrients (nitrogen and phosphorus) and surfactant and bioaugmentation by application of halotolerant hydrocarbon degrading strains were evaluated. Biodegradation rates in defined conditions were studied for 30 days. Four pure isolates including Bacillus sp. PG-1, Pseudomonas aeruginosa PG-2, Paenibacillus lautus PG-3, and Pseudomonas putida PG-4 were used to preparation of bacterial consortium. Results indicated that the bioaugmentation yielded the best TPH removal efficiency of 56.24%, followed by biostimulation with surfactant addition (removal of 31.52%). The most bacterial density was also observed for bioaugmentation bioreactor. Toxicity of reaction medium was evaluated by oxygen consumption rate inhibition, dehydrogenase activity inhibition and growth rate inhibition methods in which, the least toxicity rates of 27%, 25% and 31% were observed for bioaugmentation based bioreactor, respectively. Simultaneous bioaugmentation and biostimulation can efficiently reduce the crude oil content in the surface of seawater using halotolerant strains.

Bioremediation and biomass production of microalgae cultivation in river watercontaminated with pharmaceutical effluent

This work evaluated the potential of microalgae of Chlorella sp., SL7A, Chlorococcum sp., SL7B and Neochloris sp.,SK57 cultivated in river water contaminated with pharmaceutical effluent for biomass and lipid production. It has been observed that fast growing algae in this medium is Neochloris sp.SK57. Maximum biomass and lipid yield was obtained from Neochloris sp. SK57 (0.52 g/l) and Chlorococcum sp. SL7B (0.129 g/l)along with drycell weight of lipid was 28%.The increased in biomass and lipid in this media is could due to assimilation of organic nutrients and stress due to other components present in the river water. Fatty acid profile of algal biomass showed that saturated fatty acids production is enhanced in oils of Neochloris sp. SK57, and its suitability in food and fuel applications. Water quality of the river water was monitored before and after algal cultivation. Results showed that quality of river water was improved after algal cultivation.

Changes in microbial community in the presence of oil and chemical dispersant and their effects on the corrosion of API 5L steel coupons in a marine-simulated microcosm

The influence of crude oil and chemical dispersant was evaluated over planktonic bacteria and biofilms grown on API 5L steel surfaces in microcosm systems. Three conditions were simulated, an untreated marine environment and a marine environment with the presence of crude oil and a containing crude oil and chemical dispersant. The results of coupon corrosion rates indicated that in the oil microcosm, there was a high corrosion rate when compared with the other two systems. Analysis of bacterial communities by 16S rRNA gene sequencing described a clear difference between the different treatments. In plankton communities, the Bacilli and Gammaproteobacteria classes were the most present in numbers of operational taxonomic unit (OTUs). The Vibrionales, Oceanospirillales, and Alteromonadales orders were predominant in the treatment with crude oil, whereas in the microcosm containing oil and chemical dispersant, mainly members of Bacillales order were detected. In the communities analyzed from biofilms attached to the coupons, the most preponderant class was Alphaproteobacteria, followed by Gammaproteobacteria. In the control microcosm, there was a prevalence of the orders Rhodobacterales, Aeromonadales, and Alteromonadales, whereas in the dispersed oil and oil systems, the members of the order Rhodobacterales were present in a larger number of OTUs. These results demonstrate how the presence of a chemical dispersant and oil influence the corrosion rate and bacterial community structures present in the water column and biofilms grown on API 5L steel surfaces in a marine environment. KEY POINTS: • Evaluation of the effects of oil and chemical surfactants on the corrosion of API 5L. • Changes in microbial communities do not present corrosive biofilm on API 5L coupons.

Coronaviruses: A patent dataset report for research and development (R&D) analysis

This work shows a patent database for Coronaviruses that provides an overview of the patenting activity and trends in focused antiviral therapy with the use of triazole based compounds, glycoprotein, and protease inhibitors as possible treatment. The patent data was obtained from Orbit Intelligence Software using a patent family structure to get a big database that could be used for built patent landscape report (PLR), market analysis, technical and competitive intelligence, and monitoring and survey of a new ideas for the treatment of coronavirus diseases. The raw data is reported in four databases, which were classified according to different items: legal status (alive, dead), 1^st application year (after 2015, 2011-2015, 2006-2010, 2001-2005), and Top 5 International Patents Classifications (IPC). The main players, the investment trend, markets, geographical distribution, technology overview, technologies distribution, and patent citation are showed by this analysed data report.

Systematic degradation mechanism and pathways analysis of the immobilized bacteria: Permeability and biodegradation, kinetic and molecular simulation

In order to effectively improve the degradation rate of diesel, a systematic analysis of the degradation mechanism used by immobilized bacteria is necessary. In the present study, diesel degradation mechanisms were assessed by analyzing permeability, biodegradation, adsorption kinetics, and molecular simulation. We found that bacteria immobilized on cinnamon shells and peanut shells degraded relatively high amounts of diesel (69.94% and 64.41%, respectively). The primary degradation pathways used by immobilized bacteria included surface adsorption, internal uptake, and biodegradation. Surface adsorption was dominant in the early stage of degradation, whereas biodegradation was dominant in later stages. The diesel adsorption rate of the immobilized bacteria was in agreement with the pseudo second-order kinetic model. The immobilized bacteria and diesel interacted through hydrogen bonds.

Host-associated microbiomes drive structure and function of marine ecosystems

The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host–microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.

The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. This Perspective article outlines research priorities to strengthen our current knowledge of host-microbiome interactions, to help predict responses to anthropogenic stressors and to inform future management strategies.