Bioaugmentation as a soil bioremediation approach

SIP-metagenomics reveals key drivers of rhizospheric Benzo[a]pyrene bioremediation via bioaugmentation with indigenous soil microbes

Rhizoremediation and bioaugmentation have proven effective in promoting benzo[a]pyrene (BaP) degradation in contaminated soils. However, the mechanism underlying bioaugmented rhizospheric BaP degradation with native microbes is poorly understood. In this study, an indigenous BaP degrader (Stenotrophomonas BaP-1) isolated from petroleum-contaminated soil was introduced into ryegrass rhizosphere to investigate the relationship between indigenous degraders and rhizospheric BaP degradation. Stable isotope probing and 16S rRNA gene amplicon sequencing subsequently revealed 15 BaP degraders, 8 of which were directly associated with BaP degradation including Bradyrhizobium and Streptomyces. Bioaugmentation with strain BaP-1 significantly enhanced rhizospheric BaP degradation and shaped the microbial community structure. A correlation of BaP degraders, BaP degradation efficiency, and functional genes identified active degraders and genes encoding polycyclic aromatic hydrocarbon-ring hydroxylating dioxygenase (PAH-RHD) genes as the primary drivers of rhizospheric BaP degradation. Furthermore, strain BaP-1 was shown to not only engage in BaP metabolism but also to increase the abundance of other BaP degraders and PAH-RHD genes, resulting in enhanced rhizospheric BaP degradation. Metagenomic and correlation analyses indicated a significant positive relationship between glyoxylate and dicarboxylate metabolism and BaP degradation, suggesting a role for these pathways in rhizospheric BaP biodegradation. By identifying BaP degraders and characterizing their metabolic characteristics within intricate microbial communities, our study offers valuable insights into the mechanisms of bioaugmented rhizoremediation with indigenous bacteria for high-molecular-weight PAHs in petroleum-contaminated soils.

Engineering multi-degrading bacterial communities to bioremediate soils contaminated with pesticides residues

Parallel to the important use of pesticides in conventional agriculture there is a growing interest for green technologies to clear contaminated soil from pesticides and their degradation products. Bioaugmentation i. e. the inoculation of degrading micro-organisms in polluted soil, is a promising method still in needs of further developments. Specifically, improvements in the understanding of how degrading microorganisms must overcome abiotic filters and interact with the autochthonous microbial communities are needed in order to efficiently design bioremediation strategies. Here we designed a protocol aiming at studying the degradation of two herbicides, glyphosate (GLY) and isoproturon (IPU), via experimental modifications of two source bacterial communities. We used statistical methods stemming from genomic prediction to link community composition to herbicides degradation potentials. Our approach proved to be efficient with correlation estimates over 0.8 - between model predictions and measured pesticide degradation values. Multi-degrading bacterial communities were obtained by coalescing bacterial communities with high GLY or IPU degradation ability based on their community-level properties. Finally, we evaluated the efficiency of constructed multi-degrading communities to remove pesticide contamination in a different soil. While results are less clear in the case of GLY, we showed an efficient transfer of degrading capacities towards the receiving soil even at relatively low inoculation levels in the case of IPU. Altogether, we developed an innovative protocol for building multi-degrading simplified bacterial communities with the help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil.

Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes

At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.

A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater

Biodegradation of pollutants is a sustainable and cost-effective solution to groundwater pollution. Here, we investigate microbial populations involved in biodegradation of poly-contaminants in a pipeline for heavily contaminated groundwater. Groundwater moves from a polluted park to a treatment plant, where an aerated bioreactor effectively removes the contaminants. While the biomass does not settle in the reactor, sediment is collected afterwards and used to seed the new polluted groundwater via a backwash cycle. The pipeline has successfully operated since 1999, but the biological components in the reactor and the contaminated park groundwater have never been described. We sampled seven points along the pipeline, representing the entire remediation process, and characterized the changing microbial communities using genome-resolved metagenomic analysis. We assembled 297 medium- and high-quality metagenome-assembled genome sequences representing on average 46.3% of the total DNA per sample. We found that the communities cluster into two distinct groups, separating the anaerobic communities in the park groundwater from the aerobic communities inside the plant. In the park, the community is dominated by members of the genus Sulfuricurvum, while the plant is dominated by generalists from the order Burkholderiales. Known aromatic compound biodegradation pathways are four times more abundant in the plant-side communities compared to the park-side. Our findings provide a genome-resolved portrait of the microbial community in a highly effective groundwater treatment system that has treated groundwater with a complex contamination profile for two decades.

Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review

Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.

Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation

Microbiomes are typically characterized by high species diversity but it is poorly understood how such system-level complexity can be generated and propagated. Here, we used soil microcosms as a model to study development of bacterial communities as a function of their starting complexity and environmental boundary conditions. Despite inherent stochastic variation in manipulating species-rich communities, both laboratory-mixed medium complexity (21 soil bacterial isolates in equal proportions) and high-diversity natural top-soil communities followed highly reproducible succession paths, maintaining 16S rRNA gene amplicon signatures prominent for known soil communities in general. Development trajectories and compositional states were different for communities propagated in soil microcosms than in liquid suspension. Compositional states were maintained over multiple renewed growth cycles but could be diverged by short-term pollutant exposure. The different but robust trajectories demonstrated that deterministic taxa-inherent characteristics underlie reproducible development and self-organized complexity of soil microbiomes within their environmental boundary conditions. Our findings also have direct implications for potential strategies to achieve controlled restoration of desertified land.

IMPORTANCE There is now a great awareness of the high diversity of most environmental (“free-living”) and host-associated microbiomes, but exactly how diverse microbial communities form and maintain is still highly debated. A variety of theories have been put forward, but testing them has been problematic because most studies have been based on synthetic communities that fail to accurately mimic the natural composition (i.e., the species used are typically not found together in the same environment), the diversity (usually too low to be representative), or the environmental system itself (using designs with single carbon sources or solely mixed liquid cultures). In this study, we show how species-diverse soil bacterial communities can reproducibly be generated, propagated, and maintained, either from individual isolates (21 soil bacterial strains) or from natural microbial mixtures washed from top-soil. The high replicate consistency we achieve both in terms of species compositions and developmental trajectories demonstrates the strong inherent deterministic factors driving community formation from their species composition. Generating complex soil microbiomes may provide ways for restoration of damaged soils that are prevalent on our planet.

Microbial associations for bioremediation. What does "microbial consortia" mean?

Microbial associations arise as useful tools in several biotechnological processes. Among them, bioremediation of contaminated environments usually takes advantage of these microbial associations. Despite being frequently used, these associations are indicated using a variety of expressions, showing a lack of consensus by specialists in the field. The main idea of this work is to analyze the variety of microbial associations referred to as "microbial consortia" (MC) in the context of pollutants biodegradation and bioremediation. To do that, we summarize the origin of the term pointing out the features that an MC is expected to meet, according to the opinion of several authors. An analysis of related bibliography was done seeking criteria to rationalize and classify MC in the context of bioremediation. We identify that the microbe's origin and the level of human intervention are usually considered as a category to classify them as natural microbial consortia (NMC), artificial microbial consortia (AMC), and synthetic microbial consortia (SMC). In this sense, NMC are those associations composed by microorganisms obtained from a single source while AMC members come from different sources. SMC are a class of AMC in which microbial composition is defined to accomplish a certain specific task. We propose that the effective or potential existence of the interaction among MC members in the source material should be considered as a category in the classification as well, in combination with the origin of the source and level of intervention. Cross-kingdom MC and new developments were also considered. Finally, the existence of grey zones in the limits between each proposed microbial consortia category is addressed. KEY POINTS: • Microbial consortia for bioremediation can be obtained through different methods. • The use of the term "microbial consortia" is unclear in the specialized literature. • We propose a simplified classification for microbial consortia for bioremediation.

Isolation of a Novel Endophytic Bacillus Strain Capable of Transforming Pentachlorophenol and Structure Determination of Pentachlorophenol Phosphate Using Single-Crystal X-ray Diffraction

A novel approach for the remediation of upland soils contaminated with pentachlorophenol (C₆HCl₅O; PCP) (1), a fungicide, wood perservative, and herbicide, through the exploitation of plant-endophytic bacteria may overcome the existing issues in bioaugmentaion and phytoremidiation. In this study, we isolated the endophytic Bacillus sp. strain PCP15 and determined its metabolite of PCP (1). This strain degraded 8.03 μmol L^-1 PCP (1) within 24 h and generated the novel metabolite PCP phosphate (3). The PCP15 strain showed nearly complete growth inhibition of 20 μmol L^-1 PCP (1). In contrast, PCP15 showed resistance to PCP phosphate (3), indicating that the phosphorylation of PCP, which has never previously been reported in organisms, contributed to the detoxification of PCP (1) in bacterial cells. Our results show the potential for practical application of this strain in hybrid remediation of PCP (1)-contaminated soils and reveal a novel PCP (1) detoxification mechanism in organisms.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation

Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.

Evaluation of response of dynamics change in bioaugmentation process in diesel-polluted seawater via high-throughput sequencing: Degradation characteristic, community structure, functional genes

Identification of microorganisms that contribute to the whole microbial community is important. In this study, dynamic changes in bioaugmentation process in diesel-polluted seawater collected from two different sites were assessed via simulation experiments. Ultraviolet spectrophotometry and analysis using the molecular operating environment software revealed that the degradation rate of diesel due to bioaugmentation was higher than 70 % after 45 days because of the formation of hydrogen bonds among biosurfactants and diesel components. Community structure and functional genes were analysed via high-throughput sequencing. Results showed that community diversity recovered during bioaugmentation. Principal coordinate analysis showed that the difference in microbial community between the two sites was considerably smaller than that when diesel was added and bioaugmentation was conducted. After bioaugmentation, the main families playing key roles in degradation that became dominant were Alcanivoracaceae, Rhodobiaceae, and Rhodospirillaceae. Moreover, the abundance of functional genes remarkably increased at two different sites.

Crude oil pollution and biodegradation at the Persian Gulf: A comprehensive and review study

The Persian Gulf consider as the fundamental biological marine condition between the seas. There is a different assortment of marine life forms including corals, wipes, and fish in this marine condition. Mangrove timberlands are found all through this sea-going biological system. Sullying of the Persian Gulf to oil-based goods is the principle of danger to this marine condition and this contamination can effectively affect this differing marine condition. Numerous specialists examined the result of oil contamination on Persian Gulf marine creatures including corals sponges, bivalves, and fishes. These analysts affirmed this oil contamination on the Persian Gulf significantly diminished biodiversity. Diverse microorganisms fit to consume oil-based commodities detailed by various scientists from the Persian Gulf and their capacity to the debasement of unrefined petroleum has been examined. There has additionally been little exploration of cyanobacteria, yeast, and unrefined petroleum debasing organisms in this sea-going environment. Biosurfactants are amphipathic molecules that upgrade the disintegration of oil and increment their bioavailability to corrupt microscopic organisms. Additionally, biosurfactant-producing bacteria were discovered from the Persian Gulf, and the capability to degradation of crude oil in microscale was evaluated. The current review article aims to collect the finding of various researches performed in the Persian Gulf on oil pollution and crude-oil biodegradation. It is expected that by applying biological methods in combination with mechanical and chemical methods, the hazard consequences of crude-oil contamination on this important aquatic ecosystem at the world will be mitigated and a step towards preserving this diverse marine environment.

Impact of Plant Growth Promoting Bacteria on Salicornia ramosissima Ecophysiology and Heavy Metal Phytoremediation Capacity in Estuarine Soils

Salicornia ramosissima is a C₃ halophyte that grows naturally in South Western Spain salt marshes, under soil salinity and heavy metal pollution (mostly Cu, Zn, As, and Pb) caused by both natural and anthropogenic pressure. However, very few works have reported the phytoremediation potential of S. ramosissima. In this work, we studied a microbe-assisted phytoremediation strategy under greenhouse conditions. We inoculated plant growth promoting (PGP) and heavy metal resistant bacteria in pots with S. ramosissima and natural non-polluted and polluted sediments collected from Spanish estuaries. Then, we analyzed plant ecophysiological and metal phytoaccumulation response. Our data suggested that inoculation in polluted sediments improved S. ramosissima plant growth in terms of relative growth rate (RGR) (32%) and number of new branches (61%). S. ramosissima photosynthetic fitness was affected by heavy metal presence in soil, but bacteria inoculation improved the photochemical apparatus integrity and functionality, as reflected by increments in net photosynthetic rate (21%), functionality of PSII (F_m and F_v/F_m) and electron transport rate, according to OJIP derived parameters. Beneficial effect of bacteria in polluted sediments was also observed by augmentation of intrinsic water use efficiency (28%) and slightly water content (2%) in inoculated S. ramosissima. Finally, our results demonstrated that S. ramosissima was able to accumulate great concentrations of heavy metals, mostly at root level, up to 200 mg Kg^–1 arsenic, 0.50 mg Kg^–1 cadmium, 400 mg Kg^–1 copper, 25 mg Kg^–1 nickel, 300 mg Kg^–1 lead, and 300 mg Kg^–1 zinc. Bioaugmentation incremented S. ramosissima heavy metal phytoremediation potential due to plant biomass increment, which enabled a greater accumulation capacity. Thus, our results suggest the potential use of heavy metal resistant PGPB to ameliorate the capacity of S. ramosissima as candidate for phytoremediation of salty polluted ecosystems.

Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil

Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria.

Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments

Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.

The effect of bioaugmentation of petroleum-contaminated soil with Rhodococcus erythropolis strains on removal of petroleum from soil

The aim of the study was to assess the impact of inoculation of petroleum-contaminated soil with the hydrocarbon-degrading bacterial strains Rhodococcus erythropolis CD 130 and CD 167 or their consortium on the removal of hydrocarbons from the soil. Additionally, changes in the activity and structure of soil autochthonous bacterial communities were studied. At the end of the experiment, the fastest hydrocarbon removal was seen in the soil treated with the CD 167 strain (38.40%) and was statistically higher compared to the removal of total petroleum hydrocarbons (TPH) observed in soils inoculated with strain CD 130 (29.8%) or bacterial consortium CD 130 + CD 167 (29.72%). The rifampicin-resistant CD 130 and CD 167 strains, introduced as single strains or a consortium, survived in the soil for 42 days. The introduction of gram-positive strains of R. erythropolis primarily caused an increase in the biomass of branched phospholipid fatty acids (PLFAs), characteristic for gram-positive bacteria. Nevertheless, changes in the concentrations of gram-positive and gram-negative PLFA markers were periodic, and at the end of the experiment, significant changes were observed only in the case of the soil bioaugmented with the CD 167 strain. After the bioaugmentation, higher values of substrate-induced respiration (SIR) were observed in all the inoculated soils compared to the non-inoculated control. Nonetheless, after 91 days of incubation, a significant decrease in soil respiration was observed in the soil treated with single CD 130 or CD 167 strains or with their consortium. The number of transcripts of the CYP153 gene obtained on days 91 and 182 reflected the results of the hydrocarbon loss. The level of expression of the alkH gene in experimental soil was estimated and found to be higher than the level of expression of the CYP153 gene but did not coincide with the loss of hydrocarbons. The introduction of strains CD 130, CD 167, or CD 130 + CD 167 caused temporary changes in the composition of the soil autochthonous bacterial community, but it seems that these changes were needed for the enhanced removal of hydrocarbons from this soil.

Effect of Bacillus cereus on the ecotoxicity of metal-based fungicide spiked soils: Earthworm bioassay

Soil microorganisms exhibit varying levels of metal tolerance across a diverse range of environmental conditions. The use of metal-based fungicides such as mancozeb and copper oxychloride could potentially result in increased levels of manganese, zinc and copper which may adversely affect soil mesofauna. Under standardized earthworm bioassay conditions (temperature, pH, soil type and water content), we investigated the effect of Bacillus cereus on mancozeb and copper oxychloride ecotoxicity towards Eisenia andrei. A metal-tolerant Bacillus cereus strain previously isolated from a gold mining site was introduced into fungicide spiked soils. Earthworms were exposed to bacterial inoculated and non-inoculated substrates of mancozeb (8, 44, 800 and 1250 mg kg^-1) and copper oxychloride (200, 450, 675 and 1000 mg kg^-1). Experimental trials assessed avoidance-behavior, growth and reproduction utilizing standardized protocols (ISO and OECD). In the avoidance-behavior, E. andrei showed significant (p< 0.05) preference for inoculated substrates. Further, significant (p< 0.05) increases in biomass, survival, cocoons, juveniles and lower soil and tissue Mn, Cu and Zn contents were recorded at 8 and 44 mg kg^-1 mancozeb and copper oxychloride 200 and 450 mg kg^-1 inoculated soils compared to non-inoculated. However, at 800 and 1250 mg kg^-1 mancozeb and 675 and 1000 mg kg^-1 copper oxychloride concentrations, reproductive success in both inoculated and non-inoculated treatments was negatively (p< 0.05) affected. In conclusion, Bacillus cereus decreased the ecotoxicity of metal-based fungicides towards Eisenia andrei at 8 and 44 mg kg^-1 mancozeb and 200 and 450 mg kg^-1 copper oxychloride concentrations. The outcome observed with the inoculated substrates at elevated fungicides concentrations maybe as a result of the environmental conditions (pH and temperature).

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.

PGPR Reduce Root Respiration and Oxidative Stress Enhancing Spartina maritima Root Growth and Heavy Metal Rhizoaccumulation

The present study aims to unravel ecophysiological mechanisms underlying plant-microbe interactions under natural abiotic stress conditions, specifically heavy metal pollution. Effect of plant growth promoting rhizobacteria (PGPR) bioaugmentation on Spartina maritima in vivo root respiration and oxidative stress was investigated. This autochthonous plant is a heavy metal hyperaccumulator cordgrass growing in one of the most polluted estuaries in the world. The association with native PGPR is being studied with a view to their biotechnological potential in environmental decontamination. As a novelty, the oxygen-isotope fractionation technique was used to study the in vivo activities of cytochrome oxidase (COX) and alternative oxidase (AOX) pathways. Inoculated plants showed decreased antioxidant enzymatic activities and in vivo root respiration rates. The reduction in respiratory carbon consumption and the stress alleviation may explain the increments observed in S. maritima root biomass and metal rhizoaccumulation after inoculation. For the first time, plant carbon balance and PGPR are interrelated to explain the effect of rhizobacteria under abiotic stress.

Hydrocarbon Degradation and Bacterial Community Responses During Remediation of Sediment Artificially Contaminated with Heavy Oil

　Natural biodegradation of heavy oil in the marine environment can be accelerated by the addition of nutrients or seeding of pre-selected microorganisms. In this study, a microcosm experiment was conducted to investigate the effects of inorganic nutrient supplementation (biostimulation) and bacterial consortium amendment (bioaugmentation) on the natural degradative processes of artificially contaminated sediment. Our results revealed that the addition of nutrients had greater effect on remediation than the addition of bacterial cells. Supplementation of inorganic nutrients promoted and sustained the growth of oil-degrading and heterotrophic bacteria throughout the experimental period. Highest reduction in the total petroleum hydrocarbons, and of their components, n-alkanes, polycylic aromatic hydrocarbons (PAHs) and alkyl PAHs, were obtained in the biostimulated microcosms. Changes in the bacterial community were monitored by the PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) method targeting the 16S rDNA gene. Results revealed different responses of the bacterial community to the addition of heavy oil and remediation agents. Shifts in the bacterial communities in the seawater were more dynamic than in the sediment. Results of this study showed that addition of remediation agents significantly enhanced the natural biodegradation of heavy oil in a sediment-seawater microcosm trial.

Development of bioreactors for comparative study of natural attenuation, biostimulation, and bioaugmentation of petroleum-hydrocarbon contaminated soil

Bioremediation of soil and groundwater sites contaminated by petroleum hydrocarbons is known as a technically viable, cost-effective, and environmentally sustainable technology. The purpose of this study is to investigate laboratory-scale bioremediation of petroleum-hydrocarbon contaminated soil through development of eight bioreactors, two bioreactors for each bioremediation mode. The modes were: (1) natural attenuation (NA); (2) biostimulation (BS) with oxygen and nutrients; (3) bioaugmentation (BA) with hydrocarbon degrading isolates; (4) a combination of biostimulation and bioaugmentation (BS-BA). Total petroleum hydrocarbons (TPH) mass balance over the bioreactors showed about 2% of initial 20,000mgkg-soil^-1 TPH was removed by advection due to synthetic groundwater which was flowing through the soil, and the rest of decrease in TPH was caused by biodegradation. The BS-BA mode showed the highest TPH biodegradation percentage (89.7±0.3%) compared to the NA (51.4±0.6%), BS (81.9±0.3%) and BA (62.9±0.5%) modes. Furthermore, an increase in microbial population was another evidence of TPH biodegradation by microorganism. Reaction rate data from each bioremediation mode were fitted with a first-order reaction rate model. The Monod kinetic constants including maximum specific growth rate of microorganisms (μ_max) and substrate concentration at half-velocity constant (K_s) were estimated for each bioremediation modes.

Assessment of three approaches of bioremediation (Natural Attenuation, Landfarming and Bioagumentation - Assistited Landfarming) for a petroleum hydrocarbons contaminated soil

Contamination with total petroleum hydrocarbons (TPH) subsequent to refining activities, is currently one of the major environmental problems. Among the biological remediation approaches, landfarming and in situ bioremediation strategies are of great interest. Purpose of this study was to verify the feasibility of a remediation process wholly based on biological degradation applied to contaminated soils from a decommissioned refinery. This study evaluated through a pot experiment three bioremediation strategies: a) Natural Attenuation (NA), b) Landfarming (L), c) Bioaugmentation-assisted Landfarming (LB) for the treatment of a contaminated soil with petroleum hydrocarbons (TPHs). After a 90-days trial, Bioagumentation - assistited Landfarming approach produced the best results and the greatest evident effect was shown with the most polluted samples reaching a reduction of about 86% of total petroleum hydrocarbons (TPH), followed by Landfarming (70%), and Natural Attenuation (57%). The results of this study demonstrated that the combined use of bioremediation strategies was the most advantageous option for the treatment of contaminated soil with petroleum hydrocarbons, as compared to natural attenuation, bioaugmentation or landfarming applied alone. Besides, our results indicate that incubation with an autochthonous bacterial consortium may be a promising method for bioremediation of TPH-contaminated soils.

Bioaugmentation: an effective commercial technology for the removal of phenols from wastewater

Phenol represents a huge problem in industrial wastewater effluents and needs to be removed due to its toxic and carcinogenic nature. The removal of phenol from the wastewater is often both expensive and time consuming; there is therefore a requirement for a more effective, sustainable solution for the removal of phenol from wastewaters. Bioaugmentation or the addition of phenol degrading microorganisms to contaminated effluents is one such sustainable approach being considered. Here, we describe how bioaugmentation has been applied for the biological treatment of phenol in industrial wastewaters.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

A composite microbial agent containing bacterial and fungal species: Optimization of the preparation process, analysis of characteristics, and use in the purification for volatile organic compounds

Proper preservation of microbial activity over long periods poses a considerable challenge for pollutant biopurification. A composite microbial agent, mainly composed of bacteria and fungi isolated by the current research team, was constructed in this study and its performance in the removal of mixed waste gases (containing α-pinene, n-butyl acetate and o-xylene) was investigated. According to the removal efficiency in the first 24h and the response to starvation, the optimal ratio of selected carriers (activated carbon, wheat bran and sawdust) was found to be 1:2:1. In some cases of storages, the removal capability of the microbial agent was more than twice that of the suspension. Microbial analysis showed that the inoculated bacterial and fungal strains dominated the agent preparation and utilization. These results indicated that the agent has potential for use in biopurification of mixed waste gas, favoring the reduction of environmental passives and longer retention of microbial activity.

From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects

Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.

Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation

Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.

Biodegradation of 2,4-dinitroanisole (DNAN) by Nocardioides sp. JS1661 in water, soil and bioreactors

2,4-Dinitroanisole (DNAN), a low sensitivity replacement for TNT, is a key component of a new class of melt cast formulations designed for use in insensitive munitions. It is therefore essential that its fate and transport in the environment be assessed before its large scale implementation. Several recent studies have described reductive biotransformation pathways leading to dead-end products. Recently a Nocardioides strain, JS1661 was isolated based on its ability to mineralize DNAN via the 2,4-dinitrophenol (DNP) pathway. However, its potential for degrading DNAN under environmentally relevant conditions was not examined. Therefore we evaluated the aerobic biodegradation of DNAN by JS1661 in non-sterile soil, aqueous media and in a fluidized bed bioreactor over a wide range of DNAN concentrations. DNAN was completely degraded under all tested conditions with little or no accumulation of DNP and almost stoichiometric release of nitrite. Furthermore, when DNAN was used as the sole carbon and nitrogen source, the accumulation of nitrite was dramatically reduced. The results of the study revealed the robustness of the strain over a range of loading rates in various physical environments suggesting that it could provide the basis for waste treatment, bioremediation and bioaugmentation applications.

Influence of 3-Chloroaniline on the Biofilm Lifestyle of Comamonas testosteroni and Its Implications on Bioaugmentation

Bioaugmentation has been frequently proposed in wastewater and soil treatment to remove toxic aromatic compounds. The performance of bioaugmentation is affected by a number of biological and environmental factors, including the interaction between the target pollutant and the augmented bacterial cells. In this study, using Comamonas testosteroni and 3-chloroaniline (3-CA) as the model organism and target pollutant, we explored the influence of toxic aromatic pollutants on the biofilm lifestyle of bacteria capable of degrading aromatic compounds toward a better understanding of cell-pollutant interaction in bioaugmentation. Our results showed that the exposure to 3-CA greatly reduced the retention of C. testosteroni cells in packed-bed bioreactors (from 22% to 15% after three pore volumes), which could be attributed to the altered bacterial motility and cell surface hydrophobicity. To further understand the molecular mechanisms, we employed an integrated genomic and transcriptomic analysis to examine the influence of 3-CA on the expression of genes important to the biofilm lifestyle of C. testosteroni We found that exposure to 3-CA reduced the intracellular c-di-GMP level by downregulating the expression of genes encoding c-di-GMP synthases and induced massive cell dispersal from the biofilms. Our findings provide novel environmental implications on bioaugmentation, particularly in biofilm reactors, for the treatment of wastewater containing recalcitrant industrial pollutants.

IMPORTANCE

Bioaugmentation is a bioremediation approach that often has been described in the literature but has almost never been successfully applied in practice. Many biological and environmental factors influence the overall performance of bioaugmentation. Among these, the interaction between the target pollutant and the augmented bacterial cells is one of the most important factors. In this study, we revealed the influence of toxic aromatic pollutants on the biofilm lifestyle of bacteria capable of degrading aromatic compounds toward a better understanding of cell-pollutant interaction in bioaugmentation. Our findings provide novel environmental implications on bioaugmentation for the treatment of wastewater containing recalcitrant industrial pollutants; in particular, the exposure to toxic pollutants may reduce the retention of augmented organisms in biofilm reactors by reducing the c-di-GMP level, and approaches to elevating or maintaining a high c-di-GMP level may be promising to establish and maintain sustainable bioaugmentation activity.

Plasmid-Mediated Tolerance Toward Environmental Pollutants

The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.

Changes of benthic bacteria and meiofauna assemblages during bio-treatments of anthracene-contaminated sediments from Bizerta lagoon (Tunisia)

Sediments from Bizerta lagoon were used in an experimental microcosm setup involving three scenarios for the bioremediation of anthracene-polluted sediments, namely bioaugmentation, biostimulation, and a combination of both bioaugmentation and biostimulation. In order to investigate the effect of the biotreatments on the benthic biosphere, 16S rRNA gene-based T-RFLP bacterial community structure and the abundance and diversity of the meiofauna were determined throughout the experiment period. Addition of fresh anthracene drastically reduced the benthic bacterial and meiofaunal abundances. The treatment combining biostimulation and bioaugmentation was most efficient in eliminating anthracene, resulting in a less toxic sedimentary environment, which restored meiofaunal abundance and diversity. Furthermore, canonical correspondence analysis showed that the biostimulation treatment promoted a bacterial community favorable to the development of nematodes while the treatment combining biostimulation and bioaugmentation resulted in a bacterial community that advantaged the development of the other meiofauna taxa (copepods, oligochaetes, polychaetes, and other) restoring thus the meiofaunal structure. The results highlight the importance to take into account the bacteria/meiofauna interactions during the implementation of bioremediation treatment.

Remediation of nitrate-contaminated water by solid-phase denitrification process-a review

The paper presents a compilation of various autotrophic and heterotrophic ways of solid-phase denitrification. It covers a complete understanding of various pathways followed during denitrification process. The paper gives a brief review on various governing factors on which the process depends. It focuses mainly on the solid-phase denitrification process, its applicability, efficiency, and disadvantages associated. It presents a critical review on various methodologies associated with denitrification process reported in past years. A comparative study has also been carried out to have a better understanding of advantages and disadvantages of a particular method. We summarize the various organic and inorganic substances and various techniques that have been used for enhancing denitrification process and suggest possible gaps in the research areas whi'ch are worthy of future research.

Bioaugmentation of soil contaminated with high-level crude oil through inoculation with mixed cultures including Acremonium sp

Heavy contamination of soil with crude oil has caused significant negative environmental impacts and presents substantial hazards to human health. To explore a highly efficient bioaugmentation strategy for these contaminations, experiments were conducted over 180 days in soil heavily contaminated with crude oil (50,000 mg kg(-1)), with four treatments comprised of Bacillus subtilis inoculation with no further inoculation (I), or reinoculation after 100 days with either B. subtilis (II), Acremonium sp.(III), or a mixture of both organisms (IV). The removal values of total petroleum hydrocarbons were 60.1 ± 2.0, 60.05 ± 3.0, 71.3 ± 5.2 and 74.2 ± 2.7 % for treatment (I-IV), respectively. Treatments (III-IV) significantly enhanced the soil bioremediation compared with treatments (I-II) (p < 0.05). Furthermore, significantly (p < 0.05) greater rates of degradation for petroleum hydrocarbon fractions were observed in treatments (III-IV) compared to treatments (I-II), and this was especially the case with the degradative rates for polycyclic aromatic hydrocarbons and crude oil heavy fractions. Dehydrogenase activity in treatment (III-IV) containing Acremonium sp. showed a constant increase until the end of experiments. Therefore reinoculation with pure fungus or fungal-bacterial consortium should be considered as an effective strategy in bioaugmentation for soil heavily contaminated with crude oil.

Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery

The term water stress refers to the effects of low water availability on microbial growth and physiology. Water availability has been proposed as a major constraint for the use of microorganisms in contaminated sites with the purpose of bioremediation. Sphingomonas wittichii RW1 is a bacterium capable of degrading the xenobiotic compounds dibenzofuran and dibenzo-p-dioxin, and has potential to be used for targeted bioremediation. The aim of the current work was to identify genes implicated in water stress in RW1 by means of transposon mutagenesis and mutant growth experiments. Conditions of low water potential were mimicked by adding NaCl to the growth media. Three different mutant selection or separation method were tested which, however recovered different mutants. Recovered transposon mutants with poorer growth under salt-induced water stress carried insertions in genes involved in proline and glutamate biosynthesis, and further in a gene putatively involved in aromatic compound catabolism. Transposon mutants growing poorer on medium with lowered water potential also included ones that had insertions in genes involved in more general functions such as transcriptional regulation, elongation factor, cell division protein, RNA polymerase β or an aconitase.

Bioremediation treatment of hydrocarbon-contaminated Arctic soils: influencing parameters

The Arctic environment is very vulnerable and sensitive to hydrocarbon pollutants. Soil bioremediation is attracting interest as a promising and cost-effective clean-up and soil decontamination technology in the Arctic regions. However, remoteness, lack of appropriate infrastructure, the harsh climatic conditions in the Arctic and some physical and chemical properties of Arctic soils may reduce the performance and limit the application of this technology. Therefore, understanding the weaknesses and bottlenecks in the treatment plans, identifying their associated hazards, and providing precautionary measures are essential to improve the overall efficiency and performance of a bioremediation strategy. The aim of this paper is to review the bioremediation techniques and strategies using microorganisms for treatment of hydrocarbon-contaminated Arctic soils. It takes account of Arctic operational conditions and discusses the factors influencing the performance of a bioremediation treatment plan. Preliminary hazard analysis is used as a technique to identify and assess the hazards that threaten the reliability and maintainability of a bioremediation treatment technology. Some key parameters with regard to the feasibility of the suggested preventive/corrective measures are described as well.

Simultaneous efficient removal of high-strength ammonia nitrogen and chemical oxygen demand from landfill leachate by using an extremely high ammonia nitrogen-resistant strain

Bioaugmentation is a promising technology for pollutant elimination from stressed environments, and it would provide an efficient way to solve challenges in traditional biotreatment of wastewater with high strength of ammonia nitrogen (NH4(+)-N). A high NH4(+)-N-resistant bacteria strain, identified as Bacillus cereus (Jlu BC), was domesticated and isolated from the bacteria consortium in landfill leachate. Jlu BC could survive in 100 g/L NH4(+)-N environment, which indicated its extremely high NH4(+)-N tolerance than the stains found before. Jlu BC was employed in the bioaugmented system to remove high strength of NH4(+)-N from landfill leachate, and to increase the removal efficiency, response surface methodology (RSM) was used for optimizing bioaugmentation degradation conditions. At the optimum condition (initial pH 7.33, 4.14 days, initial chemical oxygen demand [COD] concentration [18,000 mg/L], 3.5 mL inoculated domesticated bacteria strain, 0.3 mg/mL phosphorus supplement, 30 °C, and 170 rpm), 94.74 ± 3.8% removal rate of NH4(+)-N was obtained, and the experiment data corresponded well with the predicted removal rate of the RSM models (95.50%). Furthermore, COD removal rate of 81.94 ± 1.4% was obtained simultaneously. The results presented are promising, and the screened strain would be of great practical importance in mature landfill leachate and other NH4(+)-N enrichment wastewater pollution control.

Degradation of three benzonitrile herbicides by Aminobacter MSH1 versus soil microbial communities: pathways and kinetics

BACKGROUND

The herbicide dichlobenil was banned in the European Union after its metabolite 2,6-dichlorobenzamide (BAM) was encountered in groundwater. Owing to structural similarities, bromoxynil and ioxynil might be converted to persistent metabolites in a similar manner. To examine this, we used an indigenous soil bacterium Aminobacter sp. MSH1 which is capable of mineralizing dichlobenil via BAM and 2,6-dichlorobenzoic acid (2,6-DCBA).

RESULTS

Strain MSH1 converted bromoxynil and ioxynil to the corresponding aromatic metabolites, 3,5-dibromo-4-hydroxybenzoic acid (BrAC) and 3,5-diiodo-4-hydroxybenzoic acid (IAC) following Michaelis-Menten kinetics (adjusted R(2) between 0.907 and 0.999). However, in contrast to 2,6-DCBA, degradation of these metabolites was not detected in the pure-culture studies, suggesting that they might pose an environmental risk if similar partial degradation occurred in soil. By contrast, experiments with natural soils indicated 20-30% mineralization of ioxynil and bromoxynil within the first week.

CONCLUSION

The degradation pathway of the three benzonitriles is initially driven by similar enzymes, after which more specific enzymes are responsible for further degradation. Ioxynil and bromoxynil mineralization in soil is not dependent on previous benzonitrile exposure. The accumulation of dead-end metabolites, as seen for dichlobenil, is not a major problem.

Evaluation of the biodegradation of Alaska North Slope oil in microcosms using the biodegradation model BIOB

We present the details of a numerical model, BIOB that is capable of simulating the biodegradation of oil entrapped in the sediment. The model uses Monod kinetics to simulate the growth of bacteria in the presence of nutrients and the subsequent consumption of hydrocarbons. The model was used to simulate experimental results of Exxon Valdez oil biodegradation in laboratory columns (Venosa et al., 2010). In that study, samples were collected from three different islands: Eleanor Island (EL107), Knight Island (KN114A), and Smith Island (SM006B), and placed in laboratory microcosms for a duration of 168 days to investigate oil bioremediation through natural attenuation and nutrient amendment. The kinetic parameters of the BIOB model were estimated by fitting to the experimental data using a parameter estimation tool based on Genetic Algorithms (GA). The parameter values of EL107 and KN114A were similar whereas those of SM006B were different from the two other sites; in particular biomass growth at SM006B was four times slower than at the other two islands. Grain size analysis from each site revealed that the specific surface area per unit mass of sediment was considerably lower at SM006B, which suggest that the surface area of sediments is a key control parameter for microbial growth in sediments. Comparison of the BIOB results with exponential decay curves fitted to the data indicated that BIOB provided better fit for KN114A and SM006B in nutrient amended treatments, and for EL107 and KN114A in natural attenuation. In particular, BIOB was able to capture the initial slow biodegradation due to the lag phase in microbial growth. Sensitivity analyses revealed that oil biodegradation at all three locations were sensitive to nutrient concentration whereas SM006B was sensitive to initial biomass concentration due to its slow growth rate. Analyses were also performed to compare the half-lives of individual compounds with that of the overall polycyclic aromatic hydrocarbons (PAHs).

Fungal hyphae stimulate bacterial degradation of 2,6-dichlorobenzamide (BAM)

Introduction of specific degrading microorganisms into polluted soil or aquifers is a promising remediation technology provided that the organisms survive and spread in the environment. We suggest that consortia, rather than single strains, may be better suited to overcome these challenges. Here we introduced a fungal-bacterial consortium consisting of Mortierella sp. LEJ702 and the 2,6-dichlorobenzamide (BAM)-degrading Aminobacter sp. MSH1 into small sand columns. A more rapid mineralisation of BAM was obtained by the consortium compared to MSH1 alone especially at lower moisture contents. Results from quantitative real-time polymerase chain reaction (qPCR) demonstrated better spreading of Aminobacter when Mortierella was present suggesting that fungal hyphae may stimulate bacterial dispersal. Extraction and analysis of BAM indicated that translocation of the compound was also affected by the fungal hyphae in the sand. This suggests that fungal-bacterial consortia are promising for successful bioremediation of pesticide contamination.

Potential of the microbial community present in an unimpacted beach sediment to remediate petroleum hydrocarbons

The potential of the microbial communities present in the intertidal zone of an unimpacted beach (a beach that did not suffer any significant oil spill) to degrade hydrocarbons was investigated. For that, laboratory-based microcosms (50-ml flasks) were set up with sandy beach sediment spiked with crude oil and incubated with local seawater for 15 days in the dark. Three bioremediation treatments were tested (biostimulation (BS), autochthonous bioaugmentation (AB), and combined treatment of biostimulation + bioaugmentation (BS + AB)) and the results were compared with natural attenuation (NA). Visual inspection showed clearly an oil solubility increase (confirmed by a higher hydrocarbons concentration in supernatant solutions) for all tested treatments when compared to NA. Significant degradation of the oil, shown by different profiles of petroleum hydrocarbons, was also observed for the different treatments particularly for BS + AB. Therefore, the microbial community of this unimpacted beach sediment could respond to an oil spill, degrading hydrocarbons. But to increase the natural attenuation pace, obtained results indicated that BS + AB is an appropriate approach for the bioremediation of beaches recently impacted by an oil spill. The autochthonous microbial cultures can be obtained "before" or "after" the contamination of the target site, being inoculated into the site right after it contamination.

Enhancement of the diesel oil degradation ability of a marine bacterial strain by immobilization on a novel compound carrier material

A novel floatable and biodegradable carrier material was made by coating puffed foxtail millet (PFM) with a calcium alginate (CA)-chitosan compound membrane. A diesel oil-degrading marine bacterial strain, Acinetobacter sp. F9, was immobilized on the carrier material. The number of viable F9 cells immobilized on the carrier material reached approximately 5×10(9) CFU/g. This formulation could be stored at -20°C and 4°C for 10 weeks without a significant decrease in the number of viable immobilized cells. SEM results showed that the coating membrane was porous and that F9 cells were immobilized on the walls of the pores. The immobilized F9 cells were able to remove more than 90% of the diesel oil by the second day, while free F9 cells did not remove 90% of the diesel oil until the seventh day. GC-MS analysis indicated that the immobilized F9 cells could remove diesel oil more completely than free cells. The immobilization of the F9 cells enhanced their ability to biodegrade diesel oil.

Bioaugmentation for treating transient or continuous p-nitrophenol shock loads in an aerobic sequencing batch reactor

Bioaugmentation with an enriched microbial population was applied in an aerobic sequencing batch reactor (SBR) receiving transient or continuous shock loads of p-nitrophenol (PNP). The effect of the amount of biomass added for bioaugmentation was assessed by using two different dosages (2% or 5% w/w of the total biomass in the seeded SBR). In both cases, total PNP removal was achieved during the transient PNP shock load occurring after bioaugmentation. However, after a long PNP starvation period the only experiment still showing total PNP removal during a second PNP shock load was the one where a dosage of 5% w/w was applied. The results suggested that the dosage is a key factor for the implementation of a successful bioaugmentation strategy. In addition, the performance of a bioaugmented SBR receiving a continuous PNP shock load was enhanced when compared to a non-bioaugmented SBR.