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Abstract A distinctive feature of the Deepwater Horizon (DwH) oil spill was the formation of significant quantities of marine oil snow (MOS), for which the mechanism(s) underlying its formation remain unresolved. Here, we show that Alteromonas strain TK-46(2), Pseudoalteromonas strain TK-105 and Cycloclasticus TK-8 – organisms that became enriched in sea surface oil slicks during the spill – contributed to the formation of MOS and/or dispersion of the oil. In roller-bottle incubations, Alteromonas cells and their produced EPS yielded MOS, whereas Pseudoalteromonas and Cycloclasticus did not. Interestingly, the Cycloclasticus strain was able to degrade n -alkanes concomitantly with aromatics within the complex oil mixture, which is atypical for members of this genus. Our findings, for the first time, provide direct evidence on the hydrocarbon-degrading capabilities for these bacteria enriched during the DwH spill, and that bacterial cells of certain species and their produced EPS played a direct role in MOS formation. Highlights • Alteromonas cells and its EPS contributed to MOS formation during Gulf spill. • The chemical nature of bacterial cell surfaces and EPS contribute to MOS formation. • Cycloclasticus likely contributed to degradation of n -alkanes during the spill. • Certain bacterial species and their produced EPS played a role in MOS formation. [ABSTRACT FROM AUTHOR]

Microplastics (<5 mm) have often been studied under in-vitro conditions where plastics have been investigated in isolation. However, in the natural environment microplastics readily form agglomerates conferring the particles with properties different to their pristine counterparts. Here, we examined the interaction of exopolymers with polystyrene nanoplastics and microplastics. Formation of plastic agglomerates was examined using simulated sea surface conditions. Flow cytometry coupled with microscopy revealed that nano- and microplastic particle spheres form agglomerates in seawater with a mucilagenous material and an associated microbial community. To characterise this material, differential staining methods revealed it to be glycoprotein in composition. Exposing increasing concentrations of a marine bacterial glycoprotein EPS to nano- or microplastics revealed that these types of polymers contribute to the formation and abundance of plastic agglomerates. This work highlights the importance of EPS on the fate of plastic and future research should take this into account when evaluating the impact of plastics. [ABSTRACT FROM AUTHOR]

As oil reserves in established basins become depleted, exploration and production moves towards relatively unexploited areas, such as deep waters off the continental shelf. The Faroe-Shetland Channel (FSC, NE Atlantic) and adjacent areas have been subject to increased focus by the oil industry. In addition to extreme depths, metocean conditions in this region characterise an environment with high waves and strong winds, strong currents, complex circulation patterns, sharp density gradients, and large small- and mesoscale variability. These conditions pose operational challenges to oil spill response and question the suitability of current oil spill modelling frameworks (oil spill models and their forcing data) to adequately simulate the behaviour of a potential oil spill in the area. This article reviews the state of knowledge relevant to deepwater oil spill modelling for the FSC area and identifies knowledge gaps and research priorities. Our analysis should be relevant to other areas of complex oceanography. [ABSTRACT FROM AUTHOR]

This work evaluated the performance of a microalgae treatment process for settled municipal wastewater in a laboratory setting under static culturing conditions, as an alternative to traditional, energy intensive secondary and tertiary wastewater treatment systems. Primary tank settled wastewater (PSW) was first enriched with small quantities of glucose (< 300 mg L − 1 ) as an organic carbon source to facilitate the bioremediation by the mixotrophic microalga Chlorella vulgaris . Characterisation of the wastewater revealed significant reductions in NH 3 -N (from 28.9 to 0.1 mg L − 1 ) and PO 4 -P (from 3.2 to 0.1 mg L − 1 ) in just 2 days. Additionally, the exogenous glucose appeared completely removed from the wastewater after the first day. These achieved levels of treatment in respect of both the NH 3 -N and PO 4 -P were much higher than those recorded without C. vulgaris treatment with or without glucose enrichment. This would mean that the microalgae were chiefly responsible for removing the inorganic nitrogen and phosphorus, while the naturally occurring heterotrophic organisms had consumed the carbonaceous matter. The reliability of this process was evaluated across a further three independent batches of PSW with varying compositions of these inorganics and chemical oxygen demand using alternative organic (glycerol) and inorganic (CO 2 ) carbon sources. The efficiency of the microalgae treatment process at reducing NH 3 -N and PO 4 -P was consistent in PSW enriched with organic carbon, resulting in > 90% reduction of the inorganic compounds in each batch. The results demonstrate that microalgal culturing processes to treat PSW in bioreactors without aeration are a key area to develop as an alternative biological treatment option. [ABSTRACT FROM AUTHOR]

Members of the Marinobacter genus play an important role in hydrocarbon degradation in the ocean – a topic of special significance in light of the recent Deepwater Horizon oil spill of 2010. The Marinobacter group has thus far lacked a genus level phylogenetic probe that would allow in situ identification of representative members. Here, we developed two new 16S rRNA-targeted oligonucleotide probes (Mrb-0625-a and Mrb-0625-b) to enumerate Marinobacter species by fluorescence in situ hybridization (FISH). In silico analysis of this probe set demonstrated 80% coverage of the Marinobacter genus. A competitor probe was developed to block hybridization by Mrb-0625-a to six Halomonas species with which it shared a one base pair mismatch. The probe set was optimized using pure cultures, and then used in an enrichment experiment with a deep sea oil plume water sample collected from the Deepwater Horizon oil spill. Marinobacter cells rapidly increased as a significant fraction of total microbial abundance in all incubations of original contaminated seawater as well as those amended with n -hexadecane, suggesting this group may be among the first microbial responders to oil pollution in the marine environment. The new probe set will provide a reliable tool for quantifying Marinobacter in the marine environment, particularly at contaminated sites where these organisms can play an important role in the biodegradation of oil pollutants. [ABSTRACT FROM AUTHOR]

Recently, studies have begun to identify oil-degrading bacteria and host-taxon specific bacterial assemblages associated with the coral holobiont, including deep-sea cold-water corals, which are thought to provide metabolic functions and additional carbon sources to their coral hosts. Here, we describe the identification of Marinobacter on the soft tissue of Lophelia pertusa coral polyps by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). L. pertusa samples from three reef sites in the northeast Atlantic (Logachev, Mingulay and Pisces) were collected at depth by vacuum seal to eliminate contamination issues. After decalcification, histological processing and sagittal sectioning of the soft coral polyp tissues, the 16S rRNA-targeted oligonucleotide HRP-labelled probe Mrb-0625-a, and Cyanine 3 (Cy3)-labelled tyramides, were used to identify members of the hydrocarbon-degrading genus Marinobacter. Mrb-0625-a-hybridized bacterial cell signals were detected in different anatomical sites of all polyps collected from each of the three reef sites, suggesting a close, possibly intimate, association between them, but the purpose of which remains unknown. We posit that Marinobacter , and possibly other hydrocarbon-degrading bacteria associated with Lophelia , may confer the coral with the ability to cope with toxic levels of hydrocarbons in regions of natural oil seepage and where there is an active oil and gas industry presence. • Identification of the oil-degrader Marinobacter associated with Lophelia pertusa. • Use of a bespoke vacuum seal sampler at depth to collect coral polyps. • CARD-FISH was coupled with histological methods to analyse the coral polyps. • Marinobacter detected in different anatomical sites of polyps from three reef sites. • Marinobacter may confer Lophelia with the ability to cope with toxic hydrocarbons. [ABSTRACT FROM AUTHOR]

One of the defining features of the Deepwater Horizon oil spill was the rapid formation and persistence of a hydrocarbon plume in deep water. Here we use 16S rRNA gene clone libraries and pyrosequencing of 16S rRNA gene fragments to outline the temporal dynamics of the bacterial community in the water column near the Macondo wellhead. Our timeline starts with the pre-spill (March 2010) status of the water column bacterial community, continues through the bacterial enrichments dominating the hydrocarbon plume after the blowout (DWH Oceanospirillales , Cycloclasticus , Colwellia in late May 2010), and leads towards post-spill bacterial communities with molecular signatures related to degradation of phytoplankton pulses (September and October 2010; July 2011) in the water column near the Macondo wellhead. We document a dramatic transition as the complex bacterial community before the oil spill was temporarily overwhelmed by a few specialized bacterial groups responding to the massive influx of hydrocarbons in May 2010. In September and October 2010, this bacterial bloom had been replaced by a diversified bacterial community which resembled its predecessor prior to the spill. Notably, the post-plume 16S rRNA gene clone libraries and pyrosequencing datasets illustrated the continued presence of oil-degrading bacteria in the water column near the Macondo wellhead which we posit to represent an inherent signature of hydrocarbon catabolic potential to the Gulf of Mexico. The pyroseqencing results detected and tracked minority bacterial populations that were not visible in the conventional 16S rRNA gene clone libraries and allowed us to identify natural reservoirs of the Deepwater Horizon Oceanospirillales within and outside of the Gulf of Mexico. [ABSTRACT FROM AUTHOR]

Marine plastic debris is well characterized in terms of its ability to negatively impact terrestrial and marine environments, endanger coastal wildlife, and interfere with navigation, tourism and commercial fisheries. However, the impacts of potentially harmful microorganisms and pathogens colonising plastic litter are not well understood. The hard surface of plastics provides an ideal environment for opportunistic microbial colonisers to form biofilms and might offer a protective niche capable of supporting a diversity of different microorganisms, known as the “Plastisphere”. This biotope could act as an important vector for the persistence and spread of pathogens, faecal indicator organisms (FIOs) and harmful algal bloom species (HABs) across beach and bathing environments. This review will focus on the existent knowledge and research gaps, and identify the possible consequences of plastic-associated microbes on human health, the spread of infectious diseases and bathing water quality. [ABSTRACT FROM AUTHOR]

We studied long-term (64.5 weeks) biodegradation of diesel fuel, diesel/biodiesel blends (B10-B90) and biodiesel fuels in urban soil microcosms containing indigenous microorganisms, or indigenous microorganisms augmented with a hydrocarbon-degrading bacterial community. Mineralization extent (mmol of CO 2 per day) of B10-B30 blends was smaller compared with diesel fuel at both short- (28 days) and long-term (109 days), and increased with biodiesel content. Priming with hydrocarbon degraders accelerated mineralization in the short-term (by up to 140%), with highest influence using blends with lower biodiesel content, but did not significantly influence kinetics and mineralization extent in the long-term. Although the biodiesel fraction was degraded completely within 64.5 weeks, 3–12% of the total aromatic and aliphatic hydrocarbons remained in the microcosms. Barcoded 16S rRNA gene MiSeq sequencing analysis revealed a significant effect of blend type on the community structure, with a marked enrichment of Sphingobacteriia and Actinobacteria classes. However, no significant influence was determined in the long-term, suggesting that the inoculated bacterial community may not have survived. Our findings show that biodiesel is preferentially degraded in urban soil and suggest that the value of bioaugmentation for bioremediating biodiesel fuels with hydrocarbon-degrading bacteria is limited to short-term exposures to lower (B10-B30) blends. Unlabelled Image • Long-term (64.5 weeks) biodegradation of diesel/biodiesel in urban soil was studied. • 3–12% of the total aromatic and aliphatic hydrocarbons remained in the microcosms. • Effect of bioaugmentation was evaluated. • MiSeq sequencing analysis revealed a significant effect of blend type. • No significant influence of bioaugmentation was determined in the long-term. [ABSTRACT FROM AUTHOR]

Abstract Some studies have described the isolation and 16S rRNA gene sequence-based identification of hydrocarbon-degrading bacteria living associated with marine eukaryotic phytoplankton, and thus far the direct visual observation of these bacteria on micro-algal cell surfaces ('phycosphere') has not yet been reported. Here, we developed two new 16S rRNA-targeted oligonucleotide probes, PCY223 and ALGAR209, to respectively detect and enumerate the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). To enhance the hybridization specificity with the ALGAR209 probe, a competitor probe was developed. These probes were tested and optimized using pure cultures, and then used in enrichment experiments with laboratory cultures of micro-algae exposed to phenanthrene, and with coastal water enriched with crude oil. Microscopic analysis revealed these bacteria are found in culture with the micro-algal cells, some of which were found attached to algal cells, and whose abundance increased after phenanthrene or crude oil enrichment. These new probes are a valuable tool for identifying and studying the ecology of P. algicola and A. aromaticivorans in laboratory and field samples of micro-algae, as well as opening new fields of research that could harness their ability to enhance the bioremediation of contaminated sites. Highlights • Two new 16S rRNA-targeted probes for CARD-FISH were developed to detect and enumerate P. algicola and A. aromaticivorans. • We show the direct visual association/attachment of these obligate hydrocarbonoclastic bacteria with micro-algae. • These probes will provide a valuable tool for identifying and examining these bacteria in lab and field samples. [ABSTRACT FROM AUTHOR]

Thraustochytrids were first discovered in 1934, and since the 1960's they have been increasingly studied for their beneficial and deleterious effects. This review aims to provide an enhanced understanding of these protists with a particular emphasis on their taxonomy, ecology and biotechnology applications. Over the years, thraustochytrid taxonomy has improved with the development of modern molecular techniques and new biochemical markers, resulting in the isolation and description of new strains. In the present work, the taxonomic history of thraustochytrids is reviewed, while providing an up-to-date classification of these organisms. It also describes the various biomarkers that may be taken into consideration to support taxonomic characterization of the thraustochytrids, together with a review of traditional and modern techniques for their isolation and molecular identification. The originality of this review lies in linking taxonomy and ecology of the thraustochytrids and their biotechnological applications as producers of docosahexaenoic acid (DHA), carotenoids, exopolysaccharides and other compounds of interest. The paper provides a summary of these aspects while also highlighting some of the most important recent studies in this field, which include the diversity of polyunsaturated fatty acid metabolism in thraustochytrids, some novel strategies for biomass production and recovery of compounds of interest. Furthermore, a detailed overview is provided of the direct and current applications of thraustochytrid-derived compounds in the food, fuel, cosmetic, pharmaceutical, and aquaculture industries and of some of the commercial products available. This review is intended to be a source of information and references on the thraustochytrids for both experts and those who are new to this field. [ABSTRACT FROM AUTHOR]

Abstract: Variable inorganic nutrient concentrations were used to generate silicate (Si) or nitrogen (N) limited conditions in cultures of the marine diatom Skeletonema costatum. Dissolved organic matter (DOM) harvested in the nutrient limited phase of these cultures was added to a natural bacterial community. Enhanced bacterial abundance and bacterial production were observed, in comparison to un-supplemented controls, when Si-limited (Si-DOM) rather than N-limited (N-DOM) diatom derived DOM or inorganic nutrients was added. This indicates that the bacterial population was limited by organic rather than inorganic resources but only Si-DOM had sufficient lability to alleviate this. Within the bacterial assemblage, a notable increase in the proportion of γ-Proteobacteria was evident on receipt of only Si-DOM. Assessment of the composition of the added DOM suggested that the observed dynamics were related to organic matter composition rather than molecular size as, within the Si- and N-DOM, the proportions of low and high molecular weight compounds were similar, but the polysaccharide and protein signatures were different. [ABSTRACT FROM AUTHOR]

This study evaluated the performance of microalgae under static cultivation for primary settled municipal wastewater (PSW) treatment as a low energy treatment process. The availability of a suitable carbon substrate was determined to be the main limiting factor affecting the algal treatment performance. To overcome the material cost of applying commercial sources of organic carbon, we evaluated pot ale – a carbohydrate-rich by-product from the production of malt whiskey – as a carbon substrate to promote microalgae growth and the removal of nitrogen (NH 3 –N) and phosphate (PO 4 –P) in PSW. For this, the mixotrophic microalgal species Chlorella vulgaris was used in batch experiments of PSW enriched with pot ale. Characterisation of the wastewater in the microalgae treatments compared with the control treatments (WWC) and wastewater with pot ale (WWPA) highlighted that C. vulgaris was a key organism in the algal-bacterial consortium responsible in inorganic N and P removal. We also observed a high variability in the characteristics of PSW across independent batches enriched with pot ale, which resulted in variability in the N and P removal efficiency by the alga, from 99% to 58% at reducing NH 3 –N, and from 94% to 58% at reducing PO 4 –P. As an extension of these batch-wise operated treatments, we investigated removal of NH 3 –N and PO 4 –P under semi-continuous operation with pot ale enrichment and found this to be a viable system for potential further development. This work highlights the use of pot ale enrichment with microalgae as a promising application for enhancing the efficiency of inorganic nutrient removal from PSW. [Display omitted] • Pot ale enrichment with microalgae significantly enhances the inorganic nutrient (N & P) removal. • C. vulgaris played a key role in inorganic N and P removal from PSW. • Availability of the carbon substrate is a major factor affecting PSW treatment by micro-algae. • Removal of N and P under semi-continuous operation with pot ale is a viable option for development. [ABSTRACT FROM AUTHOR]

Heavy metal/metalloids (HMs) and polycyclic aromatic hydrocarbons (PAHs) in soil have caused serious environmental problems, compromised agriculture quality, and have detrimental effects on all forms of life including humans. There is a need to develop appropriate and effective remediation methods to resolve combined contaminated problems. Although conventional technologies exist to tackle contaminated soils, application of biochar as an effective renewable adsorbent for enhanced bioremediation is considered by many scientific researchers as a promising strategy to mitigate HM/PAH co-contaminated soils. This review aims to: (i) provide an overview of biochar preparation and its application, and (ii) critically discuss and examine the prospects of (bio)engineered biochar for enhancing HMs/PAHs co-remediation efficacy by reducing their mobility and bioavailability. The adsorption effectiveness of a biochar largely depends on the type of biomass material, carbonisation method and pyrolysis conditions. Biochar induced soil immobilise and remove metal ions via various mechanisms including electrostatic attractions, ion exchange, complexation and precipitation. PAHs remediation mechanisms are achieved via pore filling, hydrophobic effect, electrostatic attraction, hydrogen bond and partitioning. During last decade, biochar engineering (modification) via biological and chemical approaches to enhance contaminant removal efficiency has garnered greater interests. Hence, the development and application of (bio)engineered biochars in risk management, contaminant management associated with HM/PAH co-contaminated soil. In terms of (bio)engineered biochar, we review the prospects of amalgamating biochar with hydrogel, digestate and bioaugmentation to produce biochar composites. Unlabelled Image • Microbial-enhanced biochar to tackle complex chemical mixtures in soil • Biochar engineered with hydrogel, digestate and microbes for wider bioremediation options • Bioengineered biochar reviving bioremediation and sustainability • Field scale application and verification needs [ABSTRACT FROM AUTHOR]

Biochar has been proposed as a suitable biostimulant for the remediation of hydrocarbon contamination, and also has the potential to act as a carrier for hydrocarbonoclastic microorganisms which could bioaugment endogenous microbial communities. However, the evidence regarding the biostimulatory effects of biochars on hydrocarbon bioremediation is somewhat equivocal, possibly due to variability of the physicochemical properties of biochar and soil across studies. Here, we use standard biochars with defined properties produced from softwood pellets (SWP) and rice husk (RH) at pyrolysis temperatures of 550 °C or 700 °C to test the effects of biochar amendment on microbial community composition and hydrocarbon degradation in soil microcosms contaminated with diesel oil. Combining this approach for the first time with specific analysis of microbial community composition using amplicon sequence variants (ASVs), we find that oil contamination causes extreme short-term loss of soil microbial diversity, and highly-specific selection of a limited set of genera defined by 13 ASVs. Biochar ameliorates the short-term loss of diversity, and in the longer term (9 weeks), changes community composition in a type-specific manner. The majority of the 13 selected ASVs are further enriched on biochar particles, although SWP biochars perform better than RH biochar in enrichment of putative hydrocarbonoclastic Aquabacterium spp. However, complete degradation of normal (n) alkanes from the aliphatic hydrocarbon fraction is prevented in the presence of biochar amendment, possibly due to their adsorption onto the char surface. Furthermore, we show that putative hydrocarbon degraders released from diesel-amended soil can subsequently be enriched to high levels on SWP biochar particles in growth medium supplemented with diesel oil as the sole carbon source; these include selected ASVs representing the genera Rhodococcus , Aquabacterium , and Cavicella. This work suggests that use of biochar pre-enriched with endogenous, conditionally-rare hydrocarbon degrading bacteria is a promising strategy for bioaugmentation of diesel-contaminated soils. Unlabelled Image • Biochar was evaluated for the biostimulation of hydrocarbon contaminated soils. • Amplicon sequence variants (ASVs) reveal specific soil microbial responses to oil. • Oil amplifies 13 ASVs - putative hydrocarbon degraders - to high relative abundance. • Standard biochars reduce soil diversity loss and are enriched in oil-selected ASVs. • Biochar enriched with endogenous microbes is a promising approach to bioremediation. [ABSTRACT FROM AUTHOR]

Improving the ecological status of water sources is a growing focus for many developed and developing nations, in particular with reducing nitrogen and phosphorus in wastewater effluent. In recent years, mixotrophic micro-algae have received increased interest in implementing them as part of wastewater treatment. This is based on their ability to utilise organic and inorganic carbon, as well as inorganic nitrogen (N) and phosphorous (P) in wastewater for their growth, with the desired results of a reduction in the concentration of these substances in the water. The aim of this review is to provide a critical account of micro-algae as an important step in wastewater treatment for enhancing the reduction of N, P and the chemical oxygen demand (COD) in wastewater, whilst utilising a fraction of the energy demand of conventional biological treatment systems. Here, we begin with an overview of the various steps in the treatment process, followed by a review of the cellular and metabolic mechanisms that micro-algae use to reduce N, P and COD of wastewater with identification of when the process may potentially be most effective. We also describe the various abiotic and biotic factors influencing micro-algae wastewater treatment, together with a review of bioreactor configuration and design. Furthermore, a detailed overview is provided of the current state-of-the-art in the use of micro-algae in wastewater treatment. Wastewater treatment dates back to the 1800s when the first municipal water treatment plant was built in Scotland, and since then the process has become established throughout the world for treatment of municipal and other sewage. In addition to any preceding physical and mechanical treatment operations, the process fundamentally relies on the biological breakdown of organic matter and pollutants, driven by bacterial consortia. In recent years, mixotrophic micro-algae have received increased interest in implementing them as part of wastewater treatment. This is based on their ability to utilise organic and inorganic carbon, as well as inorganic nitrogen (N) and phosphorous (P) in wastewater for their growth, with the desired results of a reduction in the concentration of these substances in the water. The aim of this review is to provide a critical account of micro-algae as an important step in wastewater treatment for enhancing the reduction of N, P and the chemical oxygen demand (COD) in wastewater, whilst utilising a fraction of the energy demand of conventional biological treatment systems. Here, we begin with an overview of the various steps in the treatment process, followed by a review of the cellular and metabolic mechanisms that micro-algae use to reduce N, P and COD of wastewater with identification of when the process may potentially be most effective. We also describe the various abiotic and biotic factors influencing micro-algae wastewater treatment, together with a review of bioreactor configuration and design. Furthermore, a detailed overview is provided of the current state-of-the-art in the use of micro-algae in wastewater treatment. This review is intended to be a source of information and references for both experts and those who are new to this field, with the hope also that it will garner significant interest towards integrating micro-algae for the enhanced and cost-effective treatment of wastewater. Unlabelled Image • A critical overview of the role of micro-algae cultivation for wastewater treatment. • Efficient reduction of N, P, and COD by micro-algae in wastewater treatment discussed. • The energy demand of conventional biological treatment systems compared to micro-algae cultivation. • Economic challenges of microalgal cultivation in wastewater treatment reviewed. • Various abiotic and biotic factors influencing micro-algae discussed. [ABSTRACT FROM AUTHOR]