Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

High temperature and solar radiation in the Red Sea enhance the dissolution of crude oil from surface films

The Red Sea is a hotspot of biodiversity susceptible to oil pollution. Besides, it is one of the warmest seas on the Earth with highly transparent waters. In this study, we estimated the oil dissolution rates under natural sunlight spectra and temperature conditions using coastal oil slicks collected after the 2019 Sabiti oil spill in the Red Sea. Optical analyses revealed the significant interactive effect of sunlight and temperature in enhancing the dissolution of oil into dissolved organic matter (DOM). The highest oil dissolution rate (38.68 g C m-3 d-1) was observed in full-spectrum sunlight. Oil dissolution significantly enhanced total organic carbon (TOC) and polycyclic aromatic hydrocarbons (PAHs) in seawater. High nucleic acid (HNA) bacteria, likely the oil degraders, proliferated from 30 to 70 - 90% after 4 days. The heavier stable carbon isotopic composition of methane (δ13C-CH4) and lighter stable carbon isotopic composition of carbon dioxide (δ13C-CO2) indicate the putative role of bacterial processes in the natural degradation of crude oil. The results indicated that the combined effect of temperature and solar radiation enhanced the biological and photochemical dissolution of oil on the Red Sea surface.

Microbial response to a port fuel spill: Community dynamics and potential for bioremediation

Following a fuel leakage inside a Portuguese maritime port, we conducted parallel 30-day experiments using contaminated seawater and fuel, sampled five days after the incident. This study aimed to (i)survey the native microbial community response to the spilled fuel and (ii)evaluate the efficacy of bioremediation, both biostimulation and bioaugmentation with a lyophilized bacterial consortium (Rhodococcus erythropolis, Pseudomonas sp.), in accelerating hydrocarbon degradation. Metabarcoding analysis revealed a shift in microbial communities, with increased abundance of hydrocarbon-degraders (e.g. Alcanivorax, Thalassospira). Ninety-five hydrocarbonoclastic bacteria were isolated, including key groups from the enriched communities. The lyophilized bacteria added in bioaugmentation, enhanced the abundance of hydrocarbon-degraders over time and were recovered throughout time. Bioremediation treatments favoured biodegradation, achieving over 60 % removal of total petroleum hydrocarbons after 15 days, contrasting with natural attenuation where almost no TPH was removed. This work highlights the potential of bioremediation technologies to accelerate hydrocarbon-degrading activity, for oil spills inside ports.

Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes

Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.

Food grade plastics and Bisphenol A: Associated risks, toxicity, and bioremediation approaches

Bisphenols' widespread use in day to day life has enabled its existence in various compartments of the environment. Bisphenol A (BPA) is utilized as a monomer in manufacturing polycarbonate plastics, epoxy resins, as well as flame retardants and is also considered as an endocrine disruptor. This study focuses on determining BPA concentration in daily-use food-grade plastic containers, in addition to its toxicity evaluation in environmental samples contaminated by BPA leachates. The highest concentration of BPA was observed in black poly bags (42.78 ppm), followed by slice juice bottles and infant milk bottles. Toxicity tests revealed significant impacts on Rhizobium and Chlorella sp. as a representative species of soil and aquatic environment respectively. To biodegrade the BPA, two potential strains, Brucella sp. and Brevibacillus parabrevis, were isolated from a landfill site. Qualitative and quantitative evaluation of biodegraded BPA through U-HPLC and GC-MSMS showed various metabolites of BPA. Results indicate the native bacterial isolates as potential candidates for BPA degradation while transforming this contaminant to a less toxic and hazardous form. The study also proposes the risk associated with food-grade plastic containers and recommends to establish a sustainable way for plastic waste management.

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.

Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments

Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.

Dosage concentration and pulsing frequency affect the degradation efficiency in simulated bacterial polycyclic aromatic hydrocarbon-degrading cultures

A major source of anthropogenic polycyclic aromatic hydrocarbon (PAH) inputs into marine environments are diffuse emissions which result in low PAH concentrations in the ocean water, posing a potential threat for the affected ecosystems. However, the remediation of low-dosage PAH contaminations through microbial processes remains largely unknown. Here, we developed a process-based numerical model to simulate batch cultures receiving repeated low-dosage naphthalene pulses compared to the conventionally used one-time high-dosage. Pulsing frequency as well as dosage concentration had a large impact on the degradation efficiency. After 10 days, 99.7%, 97.2%, 86.6%, or 83.5% of the 145 mg L^-1 naphthalene was degraded when given as a one-time high-dosage or in 2, 5, or 10 repeated low-concentration dosages equally spaced throughout the experiment, respectively. If the simulation was altered, giving the system that received 10 pulses time to recover to 99.7%, pulsing patterns affected the degradation of naphthalene. When pulsing 10 days at once per day, naphthalene accumulated following each pulse and if the degradation was allowed to continue until the recovered state was reached, the incubation time was prolonged to 17 days with a generation time of 3.81 days. If a full recovery was conditional before the next pulse was added, the scenario elongated to 55 days and generation time increased to 14.15 days. This indicates that dissolution kinetics dominate biodegradation kinetics, and the biomass concentration of PAH-degrading bacteria alone is not a sufficient indicator for quantifying active biodegradation. Applying those findings to the environment, a one-time input of a high dosage is potentially degraded faster than repeated low-dosage PAH pollution and repeated low-dosage input could lead to PAH accumulation in vulnerable pristine environments. Further research on the overlooked field of chronic low-dosage PAH contamination is necessary.

Bacterial community structure and diversity along the halocline of Tyro deep-sea hypersaline anoxic basin

Purpose

Tyro is a deep hypersaline anoxic basin (DHAB) located at the seafloor of the Eastern Mediterranean sea. Tyro hosts a stratified eukaryotic microbiome moving from seawater to the brine, but no reports are available on its prokaryotic community. We provide the first snapshot of the bacterial community structure in Tyro brine, seawater-brine interface, and the overlaying deep seawater.

Methods

In this study, we combined the use of molecular analyses, i.e., DNA fingerprinting and 16S rRNA pyrosequencing for the description of the bacterial community structure and taxonomy. PiCRUST2 was used to infer information on the prokaryotes functional diversity. A culture-dependent approach was applied to enrich bacteria of interest for marine biotechnology.

Results

Bacterial communities sharply clustered moving from the seawater to the Tyro brine, in agreement with the abrupt increase of salinity values. Moreover, specific taxonomic groups inhabited the seawater-brine interface compared to the overlaying seawater and their identification revealed converging taxonomy with other DHABs in the Eastern Mediterranean sea. Functional traits inferred from the prokaryote taxonomy in the upper interface and the overlaying seawater indicated metabolic pathways for the synthesis of osmoprotectants, likely involved in bacterial adaptation to the steep increasing salinity. Metabolic traits related to methane and methylated compounds and to hydrocarbon degradation were also revealed in the upper interface of Tyro. The overall capability of the Tyro microbiome for hydrocarbon metabolism was confirmed by the isolation of hydrocarbonoclastic bacteria in the sediments.

Conclusions

Our results suggest that Tyro seawater-brine interface hosts a specific microbiome adapted to the polyextreme condition typical of DHABs with potential metabolic features that could be further explored for the characterization of the metabolic network connecting the brine with the deep seawater through the chemocline. Moreover, Tyro could be a reservoir of culturable microbes endowed with functionalities of interest for biotechnological applications like hydrocarbon bioremediation.

Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns

Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.

Comparison of Hydrocarbon-Degrading Consortia from Surface and Deep Waters of the Eastern Mediterranean Sea: Characterization and Degradation Potential

The diversity and degradation capacity of hydrocarbon-degrading consortia from surface and deep waters of the Eastern Mediterranean Sea were studied in time-series experiments. Microcosms were set up in ONR7a medium at in situ temperatures of 25 °C and 14 °C for the Surface and Deep consortia, respectively, and crude oil as the sole source of carbon. The Deep consortium was additionally investigated at 25 °C to allow the direct comparison of the degradation rates to the Surface consortium. In total, ~50% of the alkanes and ~15% of the polycyclic aromatic hydrocarbons were degraded in all treatments by Day 24. Approximately ~95% of the total biodegradation by the Deep consortium took place within 6 days regardless of temperature, whereas comparable levels of degradation were reached on Day 12 by the Surface consortium. Both consortia were dominated by well-known hydrocarbon-degrading taxa. Temperature played a significant role in shaping the Deep consortia communities with Pseudomonas and Pseudoalteromonas dominating at 25 °C and Alcanivorax at 14 °C. Overall, the Deep consortium showed a higher efficiency for hydrocarbon degradation within the first week following contamination, which is critical in the case of oil spills, and thus merits further investigation for its exploitation in bioremediation technologies tailored to the Eastern Mediterranean Sea.

Two-step functional screen on multiple proteinaceous substrates reveals temperature-robust proteases with a broad-substrate range

Abstract

To support the bio-based industry in development of environment-friendly processes and products, an optimal toolbox of biocatalysts is key. Although functional screen of (meta)genomic libraries may potentially contribute to identifying new enzymes, the discovery of new enzymes meeting industry compliance demands is still challenging. This is particularly noticeable in the case of proteases, for which the reports of metagenome-derived proteases with industrial applicability are surprisingly limited. Indeed, proteolytic clones have been typically assessed by its sole activity on casein or skim milk and limited to mild screening conditions. Here, we demonstrate the use of six industry-relevant animal and plant by-products, namely bone, feather, blood meals, gelatin, gluten, and zein, as complementary substrates in functional screens and show the utility of temperature as a screening parameter to potentially discover new broad-substrate range and robust proteases for the biorefinery industry. By targeting 340,000 clones from two libraries of pooled isolates of mesophilic and thermophilic marine bacteria and two libraries of microbial communities inhabiting marine environments, we identified proteases in four of eleven selected clones that showed activity against all substrates herein tested after prolonged incubation at 55 °C. Following sequencing, in silico analysis and recombinant expression in Escherichia coli, one functional protease, 58% identical at sequence level to previously reported homologs, was found to readily hydrolyze highly insoluble zein at temperatures up to 50 °C and pH 9–11. It is derived from a bacterial group whose ability to degrade zein was unknown. This study reports a two-step screen resulting in identification of a new marine metagenome-derived protease with zein-hydrolytic properties at common biomass processing temperatures that could be useful for the modern biorefinery industry.

Key points

• A two-step multi-substrate strategy for discovery of robust proteases.

• Feasible approach for shortening enzyme optimization to industrial demands.

• A new temperature-tolerant protease efficiently hydrolyzes insoluble zein.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11235-9.

Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria

An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.

Effect of biochar on Cd and pyrene removal and bacteria communities variations in soils with culturing ryegrass (Lolium perenne L.)

Organic contaminations and heavy metals in soils cause large harm to human and environment, which could be remedied by planting specific plants. The biochars produced by crop straws could provide substantial benefits as a soil amendment. In the present study, biochars based on wheat, corn, soybean, cotton and eggplant straws were produced. The eggplant straws based biochar (ESBC) represented higher Cd and pyrene adsorption capacity than others, which was probably owing to the higher specific surface area and total pore volume, more functional groups and excellent crystallization. And then, ESBC amendment hybrid Ryegrass (Lolium perenne L.) cultivation were investigated to remediate the Cd and pyrene co-contaminated soil. With the leaching amount of 100% (v/w, mL water/g soil) and Cd content of 16.8 mg/kg soil, dosing 3% ESBC (wt%, biochar/soil) could keep 96.2% of the Cd in the 10 cm depth soil layer where the ryegrass root could reach, and it positively help root adsorb contaminations. Compared with the single planting ryegrass, the Cd and pyrene removal efficiencies significantly increased to 22.8% and 76.9% by dosing 3% ESBC, which was mainly related with the increased plant germination of 80% and biomass of 1.29 g after 70 days culture. When the ESBC dosage increased to 5%, more free radicals were injected and the ryegrass germination and biomass decreased to 65% and 0.986 g. Furthermore, when the ESBC was added into the ryegrass culture soil, the proportion of Cd and pyrene degrading bacteria Pseudomonas and Enterobacter significantly increased to 4.46% and 3.85%, which promoted the co-contaminations removal. It is suggested that biochar amendment hybrid ryegrass cultivation would be an effective method to remediate the Cd and pyrene co-contaminated soil.

Comparative Metagenomic Screening of Aromatic Hydrocarbon Degradation and Secondary Metabolite-Producing Genes in the Red Sea, the Suez Canal, and the Mediterranean Sea

Marine and ecosystem pollution due to oil spills can be addressed by identifying the aromatic hydrocarbon (HC)-degrading microorganisms and their responsible genes for biodegradation. Moreover, screening for genes coding for secondary metabolites is invaluable for drug discovery. We report here, the first metagenomic study investigating the shotgun metagenome of the Suez Canal water sampled at Ismailia city concerning its aromatic HC degradation potential in comparison to the seawater sampled at Halayeb city at the Red Sea and Sallum city at the Mediterranean Sea. Moreover, for an in-depth understanding of marine biotechnology applications, we screened for the polyketide synthases (PKSs) and nonribosomal peptide synthetase (NRPS) domains in those three metagenomes. By mapping against functional protein databases, we found that 13, 6, and 3 gene classes from the SEED database; 2, 1, and 3 gene classes from the EgGNOG; and 5, 4, and 2 genes from the InterPro2GO database were identified to be differentially abundant among Halayeb, Ismailia, and Sallum metagenomes, respectively. Also, Halayeb metagenome in the Red Sea reported the highest number of PKS domains showing higher potential in secondary metabolite production in addition to the oil degradation potential.

Impacts of Anthropogenic Pollutants on Benthic Prokaryotic Communities in Mediterranean Touristic Ports

Ports and marinas are central nodes in transport network and play a strategic role in coastal development. They receive pollution from land-based sources, marine traffic and port infrastructures on one side and constitute a potential pollution source for the adjacent coastal areas on the other. The aim of the present study was to evaluate the effects of organic and inorganic co-contamination on the prokaryotic communities in sediments from three Mediterranean ports. The structure and composition of the bacterial and archaeal communities were assessed by targeted metagenomic analysis of the 16S rRNA gene, and the links of prokaryotic communities with environmental and pollution variables were investigated. The harbors presented pronounced site-specificity in the environmental properties and pollution status. Consistently, the structure of archaeal and bacterial communities in surface sediments exhibited a strong spatial variation among the three investigated ports. On the contrary, a wide overlap in composition of prokaryotic assemblages among sites was found, but local variation in the community composition and loss of prokaryotic diversity was highlighted in a heavily impacted port sector near a shipyard. We provided evidences that organic matter, metals and PAHs as well as temperature and salinity play a strong role in structuring benthic bacterial communities significantly contributing to the understanding of their responses to anthropogenic perturbations in marine coastal areas. Among metals, copper was recognized as strongly associated with the observed changes in bacterial assemblages. Overall, this study provides the first assessment of the effects exerted by multiple organic and inorganic contaminations on benthic prokaryotes in ports over a large spatial scale and designates bacterial community as a candidate tool for the monitoring of the sediment quality status in harbors.

Ecosystem Capacity for Microbial Biodegradation of Munitions Compounds and Phenanthrene in Three Coastal Waterways in North Carolina, United States

Munitions compounds (i.e., 2,4,6-trinitrotoluene (TNT), octahy-dro-1,3,5,7-tetranitro-1,3,5,7-tetrazocin (HMX), and hexadydro-1,3,5-trinitro-1,3,5-triazin (RDX), also called energetics) were originally believed to be recalcitrant to microbial biodegradation based on historical groundwater chemical attenuation data and laboratory culture work. More recently, it has been established that natural bacterial assemblages in coastal waters and sediment can rapidly metabolize these organic nitrogen sources and even incorporate their carbon and nitrogen into bacterial biomass. Here, we report on the capacity of natural microbial assemblages in three coastal North Carolina (United States) estuaries to metabolize energetics and phenanthrene (PHE), a proxy for terrestrial aromatic compounds. Microbial assemblages generally had the highest ecosystem capacity (mass of the compound mineralized per average estuarine residence time) for HMX (21-5463 kg) > RDX (1.4-5821 kg) ≫ PHE (0.29-660 kg) > TNT (0.25-451 kg). Increasing antecedent precipitation tended to decrease the ecosystem capacity to mineralize TNT in the Newport River Estuary, and PHE and TNT mineralization were often highest with increasing salinity. There was some evidence from the New River Estuary that increased N-demand (due to a phytoplankton bloom) is associated with increased energetic mineralization rates. Using this type of analysis to determine the ecosystem capacity to metabolize energetics can explain why these compounds are rarely detected in seawater and marine sediment, despite the known presence of unexploded ordnance or recent use in military training exercises. Overall, measuring the ecosystem capacity may help predict the effects of climate change (warming and altered precipitation patterns) and other perturbations on exotic compound fate and transport within ecosystems and provide critical information for managers and decision-makers to develop management strategies based on these changes.

Unfolding microbial community intelligence in aerobic and anaerobic biodegradation processes using metagenomics

Environmental factors and available nutrients influence microbial communities, and with that, there exists a dynamic shift in community structure and hierarchy in wastewater treatment systems. Of the various factors, the availability and gradient of oxygen selectively enrich a typical microbial community and also form the community stratification which could be established through metagenomics studies. In recent years, metagenomics with various sets of bioinformatics tools has assisted in exploration and better insight into the organization and relation of the taxonomical and functional composition and associate physiological intelligence of the microbial communities. The microbial communities, under defined conditions acquire a typical hierarchy with flexible but active network of the metabolic route, which ensures the survival needs of every member residing in that community and their abundance. This knowledge of community functional organization defines the rule in designing and improving biodegradation processes in case of both aerobic and anaerobic systems.

Low-Abundance Dietzia Inhabiting a Water-Flooding Oil Reservoir and the Application Potential for Oil Recovery

With the development of molecular ecology, increasing low-abundance microbial populations were detected in oil reservoirs. However, our knowledge about the oil recovery potential of these populations is lacking. In this study, the oil recovery potential of low-abundance Dietzia that accounts for less than 0.5% in microbial communities of a water-flooding oil reservoir was investigated. On the one hand, Dietzia sp. strain ZQ-4 was isolated from the water-flooding reservoir, and the oil recovery potential was evaluated from the perspective of metabolisms and oil-displacing test. On the other hand, the strain has alkane hydroxylase genes alkB and P450 CYP153 and can degrade hydrocarbons and produce surfactants. The core-flooding test indicated that displacing fluid with 2% ZQ-4 fermentation broth increased 18.82% oil displacement efficiency, and in situ fermentation of ZQ-4 increased 1.97% oil displacement efficiency. Furthermore, the responses of Dietzia in the reservoir accompanied by the nutrient stimulation process was investigated and showed that Dietzia in some oil production wells significantly increased in the initial phase of nutrient injection and sharply decreased along with the continuous nutrient injection. Overall, this study indicates that Dietzia sp. strain has application potential for enhancing oil recovery through an ex situ way, yet the ability of oil recovery in situ based on nutrient injection is limited.

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area

Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.

Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates

Oil reserves in deep-sea sediments are currently subject to intense exploration, with associated risks of oil spills. Previous research suggests that microbial communities from deep-sea sediment (>1000m) can degrade hydrocarbons (HCs), but have a lower degradation ability than shallow (<200m) communities, probably due to in situ temperature. This study aimed to assess the effect of marine origin on microbial HC degradation potential while separating the influence of temperature, and to characterise associated HC-degrading bacterial communities. Microbial communities from 135 and 1000 m deep sediments were selectively enriched on crude oil at in situ temperatures and both consortia were subsequently incubated for 42 days at 20°C with two HC mixtures: diesel fuel or model oil. Significant HC biodegradation occurred rapidly in the presence of both consortia, especially of low molecular weight HCs and was concomitant with microbial community changes. Further, oil degradation was higher with the shallow consortium than with the deep one. Dominant HC-degrading bacteria differed based on both spatial origin of the consortia and supplemented HC types. This study provides evidence for influence of sediment spatial origin and HC composition on the selection and activity of marine HC-degrading bacterial communities and is relevant for future bioremediationdevelopments.

Biodegradation ability of two selected microbial autochthonous consortia from a chronically polluted marine coastal area (Priolo Gargallo, Italy)

The aims of this study were: (i) the characterization of the structure of the indigenous microbial community associated with the sediments under study; (ii) the isolation and characterization of microbial consortia able to degrade the aged hydrocarbons contaminating the sediments, and (iii) the assessment of related biodegradation capability of selected consortia. Samples of surface sediments were collected in Priolo Gargallo harbour (Sicily, Italy). The samples were analysed for physical, chemical (GC-FID analysis) and microbiological characteristics (qualitative (16S rDNA clone library) and quantitative (DAPI, CFU and MPN count) analysis). The sediment samples were used for the selection of two microbial consortia (indicated as PSO and PSM) with high biodegradation capacity for crude oil (∼95%) and PAHs (∼63%) respectively. Genetic analysis showed that Alcanivorax and Cycloclasticus were the dominant genera in both the PSO and PSM consortia. Oil-polluted environments naturally develop an elevated biorecovery potential. The presence of a highly specialized microbial flora (adapted to support the contamination) and their stimulation through favourable induced conditions provides a promising recovery strategy. The chance to identify and select indigenous bacteria and/or consortia with a high biodegradation capacity is fundamental for the development and optimization of bioaugmentation strategies especially for those concerning in situ applications.

Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia

Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.

Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices

Microbial degradation has long been recognized as the key rescue mechanism in shaping the oil polluted marine environments and the role of indigenous populations or their functional genomics have never been explored from Indian marine environments, post an oil spill event. In the current study, high throughput metagenomic analysis, PLFA profiling and mass spectrophotometric analysis was performed in combination with metabolomics to capture signature variations among the microbial communities in sediment, water and laboratory enrichments. Contrary to the previous reports, the bloom of Pseudomonadales (specifically genus Acinetobacter) in oiled sediment and Methylococcales in oiled water outnumbered the relative abundance of Alcanivorax in response to hydrocarbon contamination. Overall enhancement of xenobiotic degradation was suggested by metabolomic analysis in sediment and water post the spill event and varying quantitative assemblage of enzymes were found to be involved in hydrocarbon utilization. Laboratory enrichments revealed the competitive advantage of sediment communities over the water communities although unique taxa belonging to the later were also found to be enriched under in vitro conditions. Simultaneous analysis of sediment and water in the study provided explicit evidences on existence of differential microbial community dynamics, offering insight into possibilities of formulating nature identical solutions for hydrocarbon pollution.

Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines

Amine transaminases of the class III ω-TAs are key enzymes for modification of chemical building blocks, but finding those capable of converting bulky ketones and (R) amines is still challenging. Here, by an extensive analysis of the substrate spectra of 10 class III ω-TAs, we identified a number of residues playing a role in determining the access and positioning of bulky ketones, bulky amines, and (R)- and (S) amines, as well as of environmentally relevant polyamines, particularly putrescine. The results presented can significantly expand future opportunities for designing (R)-specific class III ω-TAs to convert valuable bulky ketones and amines, as well as for deepening the knowledge into the polyamine catabolic pathways.

Amination of bulky ketones, particularly in (R) configuration, is an attractive chemical conversion; however, known ω-transaminases (ω-TAs) show insufficient levels of performance. By applying two screening methods, we discovered 10 amine transaminases from the class III ω-TA family that were 38% to 76% identical to homologues. We present examples of such enzymes preferring bulky ketones over keto acids and aldehydes with stringent (S) selectivity. We also report representatives from the class III ω-TAs capable of converting (R) and (S) amines and bulky ketones and one that can convert amines with longer alkyl substituents. The preference for bulky ketones was associated with the presence of a hairpin region proximal to the conserved Arg414 and residues conforming and close to it. The outward orientation of Arg414 additionally favored the conversion of (R) amines. This configuration was also found to favor the utilization of putrescine as an amine donor, so that class III ω-TAs with Arg414 in outward orientation may participate in vivo in the catabolism of putrescine. The positioning of the conserved Ser231 also contributes to the preference for amines with longer alkyl substituents. Optimal temperatures for activity ranged from 45 to 65°C, and a few enzymes retained ≥50% of their activity in water-soluble solvents (up to 50% [vol/vol]). Hence, our results will pave the way to design, in the future, new class III ω-TAs converting bulky ketones and (R) amines for the production of high-value products and to screen for those converting putrescine.

IMPORTANCE Amine transaminases of the class III ω-TAs are key enzymes for modification of chemical building blocks, but finding those capable of converting bulky ketones and (R) amines is still challenging. Here, by an extensive analysis of the substrate spectra of 10 class III ω-TAs, we identified a number of residues playing a role in determining the access and positioning of bulky ketones, bulky amines, and (R)- and (S) amines, as well as of environmentally relevant polyamines, particularly putrescine. The results presented can significantly expand future opportunities for designing (R)-specific class III ω-TAs to convert valuable bulky ketones and amines, as well as for deepening the knowledge into the polyamine catabolic pathways.

Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.

Flow Cytometry Has a Significant Impact on the Cellular Metabolome

The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyze the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signaling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry.

The plasticity of indigenous microbial community in a full-scale heavy oil-produced water treatment plant

Indigenous microbial communities are main and promising performers for bioremediation due to their excellent adaptability, degradation capability, and inherent plasticity. Treating heavy oil-produced water (HOPW) is a challenge owing to the high recalcitrance and heterogeneity of chemicals it contains. A full-scale HOPW treatment plant was built at a capacity of 10,000 m³/d with the indigenous microbial community. After the treatment, the outlet water reached the design standard. The microbial community structures in all treatment stages were analyzed by using Illumina MiSeq 16S rRNA gene sequencing. The composition of microbial community changed greatly with the changes in environmental conditions, especially with the only artificially regulated parameter of dissolved oxygen. In the anaerobic stage, the community converted the recalcitrant chemical oxygen demand to biological oxygen demand (BOD), and played a major role in enhancing the biodegradability of HOPW. During the aerobic stage, the community mainly mineralized BOD. These results suggest that the structures of indigenous microbial community differed in different treatment stages to accomplish the corresponding functions. Based on these findings, it is proposed that exploiting the plasticity of microbial communities for bioremediation is feasible, especially treating wastewater with varied components.

Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico

The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88; H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2; H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded to Kordiimonadales, Rhodospirillales, Desulfobacterales (Desulfococcus), Syntrophobacterales and Nitrospirales (GOUTA 19, BD2-6, LCP-6), whilst Chromatiales, Oceanospirillales (Amphritea, Alcanivorax), Methylococcales, Flavobacteriales, Alteromonadales (Shewanella, ZD0117) and Rhodobacterales were the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM.

Stereoselective accumulations of hexachlorocyclohexanes (HCHs) are correlated with Sphingomonas spp. in agricultural soils across China

The wide usage of hexachlorocyclohexanes (HCHs) as pesticides has caused soil pollution and adverse health effects through direct contact or bioaccumulation in the food chain. This study quantified major HCH isomers in farmland topsoils across China, and evaluated their correlations with microbial community structure, function, and abiotic variables (e.g., moisture, pH, and temperature). Recalcitrant β-HCH was more abundant than α-, γ-, and δ-HCHs, and α-HCH enantiomeric fractions (EF) were larger than 0.5, indicating preferential degradation of (-)-α-HCH. Sphingomonas was not only a predominant population (especially in samples collected in the south), but also a promising biomarker indicating total- and β-HCH residuals, and EF values of α-HCH. Soil moisture and temperature were among the most influential factors that structured the diversity and function of soil microbial communities. The results suggested that increasing soil moisture (in the range of 5-45%) would benefit the growth of HCH-degrading populations and the enrichment of HCH-degradation related pathways. Revealing the site-specific relationships between topsoil physical, chemical, and microbial properties will benefit the in situ bioremediation of farmlands with relatively low HCH residuals across the world.

Microbial degradation of Cold Lake Blend and Western Canadian select dilbits by freshwater enrichments

Treatability experiments were conducted to determine the biodegradation of diluted bitumen (dilbit) at 5 and 25 °C for 72 and 60 days, respectively. Microbial consortia obtained from the Kalamazoo River Enbridge Energy spill site were enriched on dilbit at both 5 (cryo) and 25 (meso) ºC. On every sampling day, triplicates were sacrificed and residual hydrocarbon concentrations (alkanes and polycyclic aromatic hydrocarbons) were determined by GCMS/MS. The composition and relative abundance of different bacterial groups were identified by 16S rRNA gene sequencing analysis. While some physicochemical differences were observed between the two dilbits, their biodegradation profiles were similar. The rates and extent of degradation were greater at 25 °C. Both consortia metabolized 99.9% of alkanes; however, the meso consortium was more effective at removing aromatics than the cryo consortium (97.5 vs 70%). Known hydrocarbon-degrading bacteria were present in both consortia (Pseudomonas, Rhodococcus, Hydrogenophaga, Parvibaculum, Arthrobacter, Acidovorax), although their relative abundances depended on the temperatures at which they were enriched. Regardless of the dilbit type, the microbial community structure significantly changed as a response to the diminishing hydrocarbon load. Our results demonstrate that dilbit can be effectively degraded by autochthonous microbial consortia from sites with recent exposure to dilbit contamination.

Complementary Methodologies To Investigate Human Gut Microbiota in Host Health, Working towards Integrative Systems Biology

In 1680, Antonie van Leeuwenhoek noted compositional differences in his oral and fecal microbiota, pioneering the study of the diversity of the human microbiome. From Leeuwenhoek's time to successful modern attempts at changing the gut microbial landscape to cure disease, there has been an exponential increase in the recognition of our resident microbes as part of ourselves. Thus, the human host and microbiome have evolved in parallel to configure a balanced system in which microbes survive in homeostasis with our innate and acquired immune systems, unless disease occurs. A growing number of studies have demonstrated a correlation between the presence/absence of microbial taxa and some of their functional molecules (i.e., genes, proteins, and metabolites) with health and disease states. Nevertheless, misleading experimental design on human subjects and the cost and lack of standardized animal models pose challenges to answering the question of whether changes in microbiome composition are cause or consequence of a certain biological state. In this review, we evaluate the state of the art of methodologies that enable the study of the gut microbiome, encouraging a change in broadly used analytic strategies by choosing effector molecules (proteins and metabolites) in combination with coding nucleic acids. We further explore microbial and effector microbial product imbalances that relate to disease and health.

Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes

In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

Bridging spatially segregated redox zones with a microbial electrochemical snorkel triggers biogeochemical cycles in oil-contaminated River Tyne (UK) sediments

Marine sediments represent an important sink for a number of anthropogenic organic contaminants, including petroleum hydrocarbons following an accidental oil spill. Degradation of these compounds largely depends on the activity of sedimentary microbial communities linked to biogeochemical cycles, in which abundant elements such as iron and sulfur are shuttled between their oxidized and reduced forms. Here we show that introduction of a small electrically conductive graphite rod ("the electrochemical snorkel") into an oil-contaminated River Tyne (UK) sediment, so as to create an electrochemical connection between the anoxic contaminated sediment and the oxygenated overlying water, has a large impact on the rate of metabolic reactions taking place in the bulk sediment. The electrochemical snorkel accelerated sulfate reduction processes driven by organic contaminant oxidation and suppressed competitive methane-producing reactions. The application of a comprehensive suite of chemical, spectroscopic, biomolecular and thermodynamic analyses suggested that the snorkel served as a scavenger of toxic sulfide via a redox interaction with the iron cycle. Taken as a whole, the results of this work highlight a new strategy for controlling biological processes, such as bioremediation, through the manipulation of the electron flows in contaminated sediments.

Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing

Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria, Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years (P < 0.001, Student’s t-test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so (P > 0.05, Student’s t-test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance.

Exploring the human microbiome from multiple perspectives: factors altering its composition and function

Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.

Morphotypes and pigment profiles of halophilic bacteria: Practical data useful for novelty, taxonomic categorization and for describing novel species or new taxa

Halophilic bacteria were isolated from oil spill samples collected from West-coast of Goa. Bacteria were isolated from oil studded soil, salt marsh and offshore samples (A, A7, CSM, CB and CM) collected along the West coastline in Goa (India) i.e. Arambol beach, Calanguate beach, Candolim beach and Colva beach on Zobell Marine agar, R2A agar, Mannitol salt agar and Blood agar at temperature 22 to 24 °C. Isolates showed growth in the presence of hydrocarbons (1% phenanthrene and 2% bitumen). Diverse profiles of pigments were observed on different nutrient medium. Color of pigments produced on agar media recorded as per standard color chart. All isolates showed different growth pattern. Isolate no 11 (GOACSMMS-11) showed three different morphological features/growth patterns on Zobell Marine Agar and R2A medium in the presence of hydrocarbons. Results obtained yield new information which gives a clear idea about morphological features and pigmented profiles of hydrocarbon resistant morphotypes in the presence different media compositions. The presented datasets will be useful for studies on bacterial species showing high sequence similarity. Hence, generated data serves as a benchmark for to distinguish between genetically similar bacteria and for further research in phenotype based microbial diversity, microbial ecology of microorganisms and microbial systematics and taxonomy in addition to genotype data.

The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation

One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical–chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae, and Alcanivoracaceae), archaea (e.g., Halobacteriaceae, Desulfurococcaceae, and Methanobacteriaceae), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web.

The Variable Influence of Dispersant on Degradation of Oil Hydrocarbons in Subarctic Deep-Sea Sediments at Low Temperatures (0-5 °C)

The microbial degradation of petroleum hydrocarbons at low temperatures was investigated in subarctic deep-sea sediments in the Faroe Shetland Channel (FSC). The effect of the marine oil dispersant, Superdispersant 25 on hydrocarbon degradation was also examined. Sediments collected at 500 and 1000 m depth were spiked with a model oil containing 20 hydrocarbons and incubated at ambient temperature (5 and 0 °C, respectively) with and without marine dispersant. Treatment of sediments with hydrocarbons resulted in the enrichment of Gammaproteobacteria, and specifically the genera Pseudoalteromonas, Pseudomonas, Halomonas, and Cobetia. Hydrocarbon degradation was faster at 5 °C (500 m) with 65–89% of each component degraded after 50 days compared to 0–47% degradation at 0 °C (1000 m), where the aromatic hydrocarbons fluoranthene, anthracene, and Dibenzothiophene showed no degradation. Dispersant significantly increased the rate of degradation at 1000 m, but had no effect at 500 m. There was no statistically significant effect of Superdispersant 25 on the bacterial community structure at either station. These results show that the indigenous bacterial community in the FSC has the capacity to mitigate some of the effects of a potential oil spill, however, the effect of dispersant is ambiguous and further research is needed to understand the implications of its use.

Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms

The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.

Degradation Network Reconstruction Guided by Metagenomic Data

Network reconstruction procedures based on meta-"omics" data are an invaluable tool for inferring total and active set of reactions mediated by different members in a microbial community. Within them, network-based methods for automatic analysis of catabolic capacities in metagenomes are currently limited. Here, we describe the complete workflow, scripts, and commands allowing the automatic reconstruction of biodegradation networks using as an input meta-sequences generated by direct DNA sequencing.

Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea

Knowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions. Geographic distance was the most influential factor in prokaryotic β-diversity compared with major environmental drivers, including temperature, sediment texture, acid-volatile sulfide, and water depth, but a large unexplained variation in community composition suggested the potential effects of unmeasured abiotic/biotic factors and stochastic processes. Moreover, prokaryotic assemblages showed a biogeographic provincialism across the zones. The predicted metabolic gene composition similarly shifted as taxonomic composition did. Acid-volatile sulfide was strongly correlated with variation in metabolic gene composition. The enrichments in the relative abundance of sulfate-reducing bacteria and genes relevant with dissimilatory sulfate reduction were observed and predicted, respectively, in the Yushan area. These results provide insights into the relative importance of geographic distance and environmental condition in driving benthic prokaryotic diversity in coastal areas and predict specific biogeochemically-relevant genes for future studies.

Metagenomics: Probing pollutant fate in natural and engineered ecosystems

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.

Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment

Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms.

Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data

The analysis of catabolic capacities of microorganisms is currently often achieved by cultivation approaches and by the analysis of genomic or metagenomic datasets. Recently, a microarray system designed from curated key aromatic catabolic gene families and key alkane degradation genes was designed. The collection of genes in the microarray can be exploited to indicate whether a given microbe or microbial community is likely to be functionally connected with certain degradative phenotypes, without previous knowledge of genome data. Herein, this microarray was applied to capture new insights into the catabolic capacities of copper-resistant actinomycete Amycolatopsis tucumanensis DSM 45259. The array data support the presumptive ability of the DSM 45259 strain to utilize single alkanes (n-decane and n-tetradecane) and aromatics such as benzoate, phthalate and phenol as sole carbon sources, which was experimentally validated by cultivation and mass spectrometry. Interestingly, while in strain DSM 45259 alkB gene encoding an alkane hydroxylase is most likely highly similar to that found in other actinomycetes, the genes encoding benzoate 1,2-dioxygenase, phthalate 4,5-dioxygenase and phenol hydroxylase were homologous to proteobacterial genes. This suggests that strain DSM 45259 contains catabolic genes distantly related to those found in other actinomycetes. Together, this study not only provided new insight into the catabolic abilities of strain DSM 45259, but also suggests that this strain contains genes uncommon within actinomycetes.

Microbial community structure shifts are associated with temperature, dispersants and nutrients in crude oil-contaminated seawaters

This study tracked structure shifts of bacterial compositions before, during and after invading by crude oil to determine the microbial response and explore how temperature, dispersants and nutrients affect the composition of microbial communities or their activities of biodegradation in artificial marine environment. During petroleum hydrocarbons exposed, the composition and functional dynamics of marine microbial communities were altered, favoring bacteria that could utilize this rich carbon source such as the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes phyla. Low temperature as a dominant factor decreased bacterial richness and catabolic diversity due to abated enzymes activities in correlation with the process of biodegradation. Dispersants exerted no negative consequences on microbial composition, however, bacterial composition by the Chloroflexi, TM6, OP8, Cyanobacteria and Gemmatimonadetes phyla increased. It seemed that more frequent fertilizer application could be equally safe to bacteria and increased significantly the abundance of bacterial strains but Actinobacteria phyla decreased.

Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

An impaired metabolic response to hydrostatic pressure explains Alcanivorax borkumensis recorded distribution in the deep marine water column

Alcanivorax borkumensis is an ubiquitous model organism for hydrocarbonoclastic bacteria, which dominates polluted surface waters. Its negligible presence in oil-contaminated deep waters (as observed during the Deepwater Horizon accident) raises the hypothesis that it may lack adaptive mechanisms to hydrostatic pressure (HP). The type strain SK2 was tested under 0.1, 5 and 10 MPa (corresponding to surface water, 500 and 1000 m depth, respectively). While 5 MPa essentially inactivated SK2, further increase to 10 MPa triggered some resistance mechanism, as indicated by higher total and intact cell numbers. Under 10 MPa, SK2 upregulated the synthetic pathway of the osmolyte ectoine, whose concentration increased from 0.45 to 4.71 fmoles cell⁻¹. Central biosynthetic pathways such as cell replication, glyoxylate and Krebs cycles, amino acids metabolism and fatty acids biosynthesis, but not β-oxidation, were upregulated or unaffected at 10 MPa, although total cell number was remarkably lower with respect to 0.1 MPa. Concomitantly, expression of more than 50% of SK2 genes was downregulated, including genes related to ATP generation, respiration and protein translation. Thus, A. borkumensis lacks proper adaptation to HP but activates resistance mechanisms. These consist in poorly efficient biosynthetic rather than energy-yielding degradation-related pathways, and suggest that HP does represent a major driver for its distribution at deep-sea.