Responses of Mycobacterium sp. LB501T to the low bioavailability of solid anthracene

Transport of marine tracer phage particles in soil

Marine phages have been applied to trace ground- and surface water flows. Yet, information on their transport in soil and related particle intactness is limited. Here we compared the breakthrough of two lytic marine tracer phages (Pseudoalteromonas phages PSA-HM1 and PSA-HS2) with the commonly used Escherichia virus T4 in soil- and sand-filled laboratory percolation columns. All three phages showed high mass recoveries in the effluents and a higher transport velocity than non-reactive tracer Br^-. Comparison of effluent gene copy numbers (CN) to physically-determined phage particle counts or infectious phage counts showed that PSA-HM1 and PSA-HS2 retained high phage particle intactness (I_p > 81%), in contrast to T4 (I_p < 36%). Our data suggest that marine phages may be applied in soil to mimic the transport of (bio-) colloids or anthropogenic nanoparticles of similar traits. Quantitative PCR (qPCR) thereby allows for highly sensitive quantification and thus for the detection of even highly diluted marine tracer phages in environmental samples.

Unraveling the complex regulatory networks in biofilm formation in bacteria and relevance of biofilms in environmental remediation

Biofilms are assemblages of bacteria embedded within a matrix of extracellular polymeric substances (EPS) attached to a substratum. The process of biofilm formation is a complex phenomenon regulated by the intracellular and intercellular signaling systems. Various secondary messenger molecules such as cyclic dimeric guanosine 3',5'-monophosphate (c-di-GMP), cyclic adenosine 3',5'-monophosphate (cAMP), and cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) are involved in complex signaling networks to regulate biofilm development in several bacteria. Moreover, the cell to cell communication system known as Quorum Sensing (QS) also regulates biofilm formation via diverse mechanisms in various bacterial species. Bacteria often switch to the biofilm lifestyle in the presence of toxic pollutants to improve their survivability. Bacteria within a biofilm possess several advantages with regard to the degradation of harmful pollutants, such as increased protection within the biofilm to resist the toxic pollutants, synthesis of extracellular polymeric substances (EPS) that helps in the sequestration of pollutants, elevated catabolic gene expression within the biofilm microenvironment, higher cell density possessing a large pool of genetic resources, adhesion ability to a wide range of substrata, and metabolic heterogeneity. Therefore, a comprehensive account of the various factors regulating biofilm development would provide valuable insights to modulate biofilm formation for improved bioremediation practices. This review summarizes the complex regulatory networks that influence biofilm development in bacteria, with a major focus on the applications of bacterial biofilms for environmental restoration.

Overview of Approaches to Improve Rhizoremediation of Petroleum Hydrocarbon-Contaminated Soils

Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.

Revealing of Non-Cultivable Bacteria Associated with the Mycelium of Fungi in the Kerosene-Degrading Community Isolated from the Contaminated Jet Fuel

Fuel (especially kerosene) biodamage is a challenge for global industry. In aviation, where kerosene is a widely used type of fuel, its biodeterioration leads to significant damage. Six isolates of micromycetes from the TS-1 aviation kerosene samples were obtained. Their ability to grow on the fuel was studied, and the difference between biodegradation ability was shown. Micromycetes belonged to the Talaromyces, Penicillium, and Aspergillus genera. It was impossible to obtain bacterial isolates associated with their mycelium. However, 16S rRNA metabarcoding and microscopic observations revealed the presence of bacteria in the micromycete isolates. It seems to be that kerosene-degrading fungi were associated with uncultured bacteria. Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were abundant in the fungal cultures isolated from the TS-1 jet fuel samples. Most genera among these phyla are known as hydrocarbon degraders. Only bacteria-containing micromycete isolates were able to grow on the kerosene. Most likely, kerosene degradation mechanisms are based on synergism of bacteria and fungi.

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.

Biofilms of Halobacterium salinarum as a tool for phenanthrene bioremediation

The use of hyperhalophilic microorganisms is emerging as a sustainable alternative to clean hydrocarbon-polluted hypersaline water bodies. In line with this practice, this work reports on the ability of the archaeon Halobacterium salinarum to develop biofilms on a solid surface conditioned by the presence of phenanthrene crystals, which results in the removal of the contaminating compound. The cell surface hydrophobicity does not change during the removal process and this organism is shown to constitutively produce a surfactant molecule with specific action on aromatic hydrocarbons, both indicating that phenanthrene removal might proceed through a non-contact mechanism. A new approach is presented to follow the process in situ through epifluorescence microscopy by monitoring phenanthrene auto-fluorescence.

Biofilm formation as a microbial strategy to assimilate particulate substrates

In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man-made organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle-degrading biofilms are widespread and have been observed in aquatic and terrestrial natural ecosystems, in polluted and man-driven environments and in the digestive tracts of animals. They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non-dissolved organic carbon, and considers the advantage provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.

DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

Enhanced conversion of sterols to steroid synthons by augmenting the peptidoglycan synthesis gene pbpB in Mycobacterium neoaurum

Some species of mycobacteria have been modified to transform sterols to valuable steroid synthons. The unique cell wall of mycobacteria has been recognized as an important organelle to absorb sterols. Some cell wall inhibitors (e.g., vancomycin and glycine) have been validated to enhance sterol conversion by interfering with transpeptidation in peptidoglycan biosynthesis. Therefore, two transpeptidase genes, pbpA and pbpB, were selected to rationally modify the cell wall to simulate the enhancement effect of vancomycin and glycine on sterol conversion in a 22-hydroxy-23,24-bisnorchol-4-ene-3-one (4-HBC) producing strain (WIII). Unexpectedly, the pbpA or pbpB gene augmentation was conducive to the utilization of sterols. The pbpB augmentation strain WIII-pbpB was further investigated for its better performance. Compared to WIII, the morphology of WIII-pbpB was markedly changed from oval to spindle, indicating alterations of the cell wall. Biochemical analysis indicated that the altered cell wall properties of WIII-pbpB might contribute to the positive effect on sterol utilization. The productivity of 4-HBC was enhanced by 28% in the WIII-pbpB strain compared to that of WIII. These results demonstrated that the modification of peptidoglycan synthesis can improve the conversion of sterols to steroid synthons in mycobacteria.

Variation in cell surface characteristics and extracellular polymeric substances during the biodegradation of monocyclic and heterocyclic aromatic hydrocarbons in single and multi-substrate systems

The variation in surface characteristics and the composition of extracellular polymeric substances (EPS) of bacterial cells during biodegradation of single and multi-aromatic hydrocarbons was investigated in the present study. The maximum cell surface hydrophobicity (CSH) of 80.1% was observed during the degradation of toluene. Bacterial cells acquired more negative surface charge with an increase in CSH and vice versa. Proteins constituted the major fraction of EPS during biodegradation of benzene and toluene with protein/carbohydrate ratio varying between 2.19 and 3.1. Carbohydrates constituted the major fraction of EPS in the presence of pyridine. A significant variation in cell surface characteristics was observed in multi-substrate systems involving heterocyclic and monocyclic aromatic hydrocarbons. An increase in EPS production (62.89 mg/g) did not facilitate enhanced degradation of hydrophobic substrates in multi-substrate system involving benzothiophene, benzofuran, benzene and toluene. Under toxic conditions, especially at higher concentration of target pollutants, a significant increase in concentration of polysaccharides was observed compared to proteins.

Molecular and eco-physiological characterization of arsenic (As)-transforming Achromobacter sp. KAs 3-5T from As-contaminated groundwater of West Bengal, India

Molecular and eco-physiological characterization of arsenic (As)-transforming and hydrocarbon-utilizing Achromobacter type strain KAs 3-5^T has been investigated in order to gain an insight into As-geomicrobiology in the contaminated groundwater. The bacterium is isolated from As-rich groundwater of West Bengal, India. Comparative 16S rRNA gene sequence phylogenetic analysis confirmed that the strain KAs 3-5^T is closely related to Achromobacter mucicolens LMG 26685^T (99.17%) and Achromobacter animicus LMG 26690^T (99.17%), thus affiliated to the genus Achromobacter. Strain KAs 3-5^T is nonflagellated, mesophilic, facultative anaerobe, having a broad metabolic repertoire of using various sugars, sugar-/fatty acids, hydrocarbons as principal carbon substrates, and O₂, NO₃^-, NO₂^-, and Fe³⁺ as terminal electron acceptors. Growth with hydrocarbons led to cellular aggregation and adherence of the cells to the hydrocarbon particles confirmed through electron microscopic observations. The strain KAs 3-5^T showed high As resistance (MIC of 5 mM for As³⁺, 25 mM for As⁵⁺) and reductive transformation of As⁵⁺ under aerobic conditions while utilizing both sugars and hydrocarbons. Molecular taxonomy specified a high genomic GC content (65.5 mol %), ubiquinone 8 (UQ-8) as respiratory quinone, spermidine as predominant polyamine in the bacterium. The differential presence of C_12:0, C_14:0 2-OH, C_18:1 ω7c, and C _14:0 iso 3-OH/ C_16:1 iso fatty acids, phosphatidylglycerol (PG), phosphatidylcholine (PC), two unknown phospholipid (PL1, PL2) as polar lipids, low DNA-DNA relatedness (33.0-41.0%) with the Achromobacter members, and unique metabolic capacities clearly indicated the distinct genomic and physiological properties of strain KAs 3-5^T among known species of the genus Achromobacter. These findings lead to improve our understanding on metabolic flexibility of bacteria residing in As-contaminated groundwater and As-bacteria interactions within oligotrophic aquifer system.

Membrane Fatty Acid Composition and Cell Surface Hydrophobicity of Marine Hydrocarbonoclastic Alcanivorax borkumensis SK2 Grown on Diesel, Biodiesel and Rapeseed Oil as Carbon Sources

The marine hydrocarbonoclastic bacterium Alcanivorax borkumensis is well known for its ability to successfully degrade various mixtures of n-alkanes occurring in marine oil spills. For effective growth on these compounds, the bacteria possess the unique capability not only to incorporate but also to modify fatty intermediates derived from the alkane degradation pathway. High efficiency of both these processes provides better competitiveness for a single bacteria species among hydrocarbon degraders. To examine the efficiency of A. borkumensis to cope with different sources of fatty acid intermediates, we studied the growth rates and membrane fatty acid patterns of this bacterium cultivated on diesel, biodiesel and rapeseed oil as carbon and energy source. Obtained results revealed significant differences in both parameters depending on growth substrate. Highest growth rates were observed with biodiesel, while growth rates on rapeseed oil and diesel were lower than on the standard reference compound (hexadecane). The most remarkable observation is that cells grown on rapeseed oil, biodiesel, and diesel showed significant amounts of the two polyunsaturated fatty acids linoleic acid and linolenic acid in their membrane. By direct incorporation of these external fatty acids, the bacteria save energy allowing them to degrade those pollutants in a more efficient way. Such fast adaptation may increase resilience of A. borkumensis and allow them to strive and maintain populations in more complex hydrocarbon degrading microbial communities.

Biodegradation of marine oil spills in the Arctic with a Greenland perspective

New economic developments in the Arctic, such as shipping and oil exploitation, bring along unprecedented risks of marine oil spills. Microorganisms have played a central role in degrading and reducing the impact of the spilled oil during past oil disasters. However, in the Arctic, and in particular in its pristine areas, the self-cleaning capacity and biodegradation potential of the natural microbial communities have yet to be uncovered. This review compiles and investigates the current knowledge with respect to environmental parameters and biochemical constraints that control oil biodegradation in the Arctic. Hereby, seawaters off Greenland are considered as a case study. Key factors for biodegradation include the bioavailability of hydrocarbons, the presence of hydrocarbon-degrading bacteria and the availability of nutrients. We show how these key factors may be influenced by the physical oceanographic conditions in seawaters off Greenland and other environmental parameters including low temperature, sea ice, sunlight regime, suspended sediment plumes and phytoplankton blooms that characterize the Arctic. Based on the acquired insights, a first qualitative assessment of the biodegradation potential in seawaters off Greenland is presented. In addition to the most apparent Arctic characteristics, such as low temperature and sea ice, the impact of typical Arctic features such as the oligotrophic environment, poor microbial adaptation to hydrocarbon degradation, mixing of stratified water masses, and massive phytoplankton blooms and suspended sediment plumes merit to be topics of future investigation.

Immediate response mechanisms of Gram-negative solvent-tolerant bacteria to cope with environmental stress: cis-trans isomerization of unsaturated fatty acids and outer membrane vesicle secretion

Bacteria have evolved an array of adaptive mechanisms enabling them to survive and grow in the presence of different environmental stresses. These mechanisms include either modifications of the membrane or changes in the overall energy status, cell morphology, and cell surface properties. Long-term adaptations are dependent on transcriptional regulation, the induction of anabolic pathways, and cell growth. However, to survive sudden environmental changes, bacterial short-term responses are essential to keep the cells alive after the occurrence of an environmental stress factor such as heat shock or the presence of toxic organic solvents. Thus far, two main short-term responses are known. On the one hand, a fast isomerization of cis into trans unsaturated fatty leads to a quick rigidification of the cell membrane, a mechanism known in some genera of Gram-negative bacteria. On the other hand, a fast, effective, and ubiquitously present countermeasure is the release of outer membrane vesicles (OMVs) from the cell surface leading to a rapid increase in cell surface hydrophobicity and finally to the formation of cell aggregates and biofilms. These immediate response mechanisms just allow the bacteria to stay physiologically active and to employ long-term responses to assure viability upon changing environmental conditions. Here, we provide insight into the two aforementioned rapid adaptive mechanisms affecting ultimately the cell envelope of Gram-negative bacteria.

Sorption, transport and biodegradation - An insight into bioavailability of persistent organic pollutants in soil

Contamination of soils with persistent organic pollutants (POPs), such as organochlorine pesticide, polybrominated diphenyl ethers, halohydrocarbon, polycyclic aromatic hydrocarbons (PAHs) is of increasing concern. Microbial degradation is potential mechanism for the removal of POPs, but it is often restricted by low bioavailability of POPs. Thus, it is important to enhance bioavailability of POPs in soil bioremediation. A series of reviews on bioavailability of POPs has been published in the past few years. However, bioavailability of POPs in relation to soil organic matter, minerals and soil microbes has been little studied. To fully understand POPs bioavailability in soil, research on interactions of POPs with soil components and microbial responses in bioavailability limitation conditions are needed. This review focuses on bioavailability mechanisms of POPs in terms of sorption, transport and microbial adaptation, which is particularly novel. In consideration of the significance of bioavailability, further studies should investigate the influence of various bioremediation strategies on POPs bioavailability.

Osmotic stress in colony and planktonic cells of Pseudomonas putida mt-2 revealed significant differences in adaptive response mechanisms

Planktonic cells and those grown on surfaces (or as colony biofilm) are known to show significant differences regarding growth behavior, cell physiology, gene expression and stress tolerance. In order to compare stress behavior of different growth forms, shake cultures for planktonic growth and agar plate cultivation for colony growth, were carried out with the well investigated model organism, Pseudomonas putida mt-2. Cells were exposed to sodium chloride to cause osmotic stress as one main environmental stressor bacteria have to cope with when growing in soil. Planktonic cells were more tolerant with a complete inhibition of growth at 0.7 M NaCl, compared to 0.5 M for agar-grown cells. Cell surface hydrophobicity, measured as water contact angles, was significantly higher for agar-grown cells (92°) than for planktonic cells (40°), and increased in the presence of NaCl. Agar-grown cells also showed a significantly higher degree of saturation of membrane fatty acids that increased in the presence of NaCl. These results demonstrate that planktonic and colony grown bacteria show different responses when confronted with osmotic stress suggesting that the tolerance and adaptive mechanisms are dependent on the environmental conditions as well as the initial physiological state.

Enhanced biodegradation of PAHs in historically contaminated soil by M. gilvum inoculated biochar

The inoculation of rice straw biochar with PAH-degrading Mycobacterium gilvum (1.27 × 10¹¹ ± 1.24 × 10¹⁰ cell g^-1), and the subsequent amendment of this composite material to PAHs contaminated (677 mg kg^-1) coke plant soil, was conducted in order to investigate if would enhance PAHs biodegradation in soils. The microbe-biochar composite showed superior degradation capacity for phenanthrene, fluoranthene and pyrene. Phenanthrene loss in the microbe-biochar composite, free cell alone and biochar alone treatments was, respectively, 62.6 ± 3.2%, 47.3 ± 4.1% and non-significant (P > 0.05); whereas for fluoranthene loss it was 52.1 ± 2.3%; non-significant (P > 0.05) and non-significant (P > 0.05); and for pyrene loss it was 62.1 ± 0.9%; 19.7 ± 6.5% and 13.5 ± 2.8%. It was hypothesized that the improved remediation was underpinned by i) biochar enhanced mass transfer of PAHs from the soil to the carbonaceous biochar "sink", and ii) the subsequent degradation of the PAHs by the immobilized M. gilvum. To test this mechanism, a surfactant (Brij 30; 20 mg g^-1 soil), was added to impede PAHs mass transfer to biochar and sorption. The surfactant increased solution phase PAH concentrations and significantly (P < 0.05) reduced PAH degradation in the biochar immobilized M. gilvum treatments; indicating the enhanced degradation occurred between the immobilized M. gilvum and biochar sorbed PAHs.

Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation

Background

Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects.

Results

A metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential.

Conclusion

In this work we have focused on the biogeographical distribution of hydrocarbon degrading and biosurfactant producing genes. Our principle results can be seen as an important step forward in the application of bioremediation techniques, by considering the biostimulation, optimization or manipulation of a starting microbial consortia from the areas with higher degradation and biosurfactant producing genetic diversity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-1077-4) contains supplementary material, which is available to authorized users.

Methanogenic Biocathode Microbial Community Development and the Role of Bacteria

The cathode microbial community of a methanogenic bioelectrochemical system (BES) is key to the efficient conversion of carbon dioxide (CO₂) to methane (CH₄) with application to biogas upgrading. The objective of this study was to compare the performance and microbial community composition of a biocathode inoculated with a mixed methanogenic (MM) culture to a biocathode inoculated with an enriched hydrogenotrophic methanogenic (EHM) culture, developed from the MM culture following pre-enrichment with H₂ and CO₂ as the only externally supplied electron donor and carbon source, respectively. Using an adjacent Ag/AgCl reference electrode, biocathode potential was poised at -0.8 V (versus SHE) using a potentiostat, with the bioanode acting as the counter electrode. When normalized to cathode biofilm biomass, the methane production in the MM- and EHM-biocathode was 0.153 ± 0.010 and 0.586 ± 0.029 mmol CH₄/mg biomass-day, respectively. This study showed that H₂/CO₂ pre-enriched inoculum enhanced biocathode CH₄ production, although the archaeal communities in both biocathodes converged primarily (86-100%) on a phylotype closely related to Methanobrevibacter arboriphilus. The bacterial community of the MM-biocathode was similar to that of the MM inoculum but was enriched in Spirochaetes and other nonexoelectrogenic, fermentative Bacteria. In contrast, the EHM-biocathode bacterial community was enriched in Proteobacteria, exoelectrogens, and putative producers of electron shuttle mediators. Similar biomass levels were detected in the MM- and EHM-biocathodes. Thus, although the archaeal communities were similar in the two biocathodes, the difference in bacterial community composition was likely responsible for the 3.8-fold larger CH₄ production rate observed in the EHM-biocathode. Roles for abundant OTUs identified in the biofilm and inoculum cultures were highlighted on the basis of previous reports.

Soil properties and microbial ecology of a paddy field after repeated applications of domestic and industrial sewage sludges

The effects of repeated application of two types of sewage sludge, domestic and industrial (petrochemical, PSS) sludges, into paddy fields over a 5-year period on the soil properties and microbial ecology were studied and compared with conventional NPK fertilizer application. Soil organic matter and total nitrogen contents were significantly higher in the two sludge treatments than that in fertilized plots after 5 years. Soil concentrations of potentially toxic metals were low after 5 years of both sludge treatments, but the polycyclic aromatic hydrocarbons (PAHs) showed differences between the two sludge types. Concentrations of high-molecular-weight PAHs were significantly higher (p < 0.05) in the petrochemical sludge treatment than the domestic sludge treatment or the fertilizer control, although the total concentrations of 16 types of PAH in the petrochemical sludge treatment were only slightly higher than in the domestic sludge treatment and the control. The biological toxicity of soil dimethyl sulfoxide extracts from the petrochemical sludge treatment was also significantly higher (p < 0.05) than those from the fertilizer control and the domestic sludge treatment when evaluated using Photobacterium phosphoreum T3. Both types of sewage sludge increased soil microbial activity, but only the petrochemical sludge led to enrichment with specific PAH degraders such as Mycobacterium, Nocardioides, and Sphingomonas.

Soil-Bacterium Compatibility Model as a Decision-Making Tool for Soil Bioremediation

Bioremediation of organic pollutant contaminated soil involving bioaugmentation with dedicated bacteria specialized in degrading the pollutant is suggested as a green and economically sound alternative to physico-chemical treatment. However, intrinsic soil characteristics impact the success of bioaugmentation. The feasibility of using partial least-squares regression (PLSR) to predict the success of bioaugmentation in contaminated soil based on the intrinsic physico-chemical soil characteristics and, hence, to improve the success of bioaugmentation, was examined. As a proof of principle, PLSR was used to build soil-bacterium compatibility models to predict the bioaugmentation success of the phenanthrene-degrading Novosphingobium sp. LH128. The survival and biodegradation activity of strain LH128 were measured in 20 soils and correlated with the soil characteristics. PLSR was able to predict the strain's survival using 12 variables or less while the PAH-degrading activity of strain LH128 in soils that show survival was predicted using 9 variables. A three-step approach using the developed soil-bacterium compatibility models is proposed as a decision making tool and first estimation to select compatible soils and organisms and increase the chance of success of bioaugmentation.

Hydrocarbonoclastic Alcanivorax Isolates Exhibit Different Physiological and Expression Responses to n-dodecane

Autochthonous microorganisms inhabiting hydrocarbon polluted marine environments play a fundamental role in natural attenuation and constitute promising resources for bioremediation approaches. Alcanivorax spp. members are ubiquitous in contaminated surface waters and are the first to flourish on a wide range of alkanes after an oil-spill. Following oil contamination, a transient community of different Alcanivorax spp. develop, but whether they use a similar physiological, cellular and transcriptomic response to hydrocarbon substrates is unknown. In order to identify which cellular mechanisms are implicated in alkane degradation, we investigated the response of two isolates belonging to different Alcanivorax species, A. dieselolei KS 293 and A. borkumensis SK2 growing on n-dodecane (C12) or on pyruvate. Both strains were equally able to grow on C12 but they activated different strategies to exploit it as carbon and energy source. The membrane morphology and hydrophobicity of SK2 changed remarkably, from neat and hydrophilic on pyruvate to indented and hydrophobic on C12, while no changes were observed in KS 293. In addition, SK2 accumulated a massive amount of intracellular grains when growing on pyruvate, which might constitute a carbon reservoir. Furthermore, SK2 significantly decreased medium surface tension with respect to KS 293 when growing on C12, as a putative result of higher production of biosurfactants. The transcriptomic responses of the two isolates were also highly different. KS 293 changes were relatively balanced when growing on C12 with respect to pyruvate, giving almost the same amount of upregulated (28%), downregulated (37%) and equally regulated (36%) genes, while SK2 transcription was upregulated for most of the genes (81%) when growing on pyruvate when compared to C12. While both strains, having similar genomic background in genes related to hydrocarbon metabolism, retained the same capability to grow on C12, they nevertheless presented very different physiological, cellular and transcriptomic landscapes.

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.

The Role of Hydrophobicity and Surface Receptors at Hyphae of Lyophyllum sp. Strain Karsten in the Interaction with Burkholderia terrae BS001 - Implications for Interactions in Soil

The soil bacterium Burkholderia terrae strain BS001 can interact with varying soil fungi, using mechanisms that range from the utilization of carbon/energy sources such as glycerol to the ability to reach novel territories in soil via co-migration with growing fungal mycelia. Here, we investigate the intrinsic properties of the B. terrae BS001 interaction with the basidiomycetous soil fungus Lyophyllum sp. strain Karsten. In some experiments, the ascomycetous Trichoderma asperellum 302 was also used. The hyphae of Lyophyllum sp. strain Karsten were largely hydrophilic on water-containing media versus hydrophobic when aerial, as evidenced by contact angle analyses (CA). Co-migration of B. terrae strain BS001 cells with the hyphae of the two fungi occurred preferentially along the - presumably hydrophilic - soil-dwelling hyphae, whereas aerial hyphae did not allow efficient migration, due to reduced thickness of their surrounding mucous films. Moreover, the cell numbers over the length of the hyphae in soil showed an uneven distribution, i.e., the CFU numbers increased from minima at the inoculation point to maximal numbers in the middle of the extended hyphae, then decreasing toward the terminal side. Microscopic analyses of the strain BS001 associations with the Lyophyllum sp. strain Karsten hyphae in the microcosms confirmed the presence of B. terrae BS001 cells on the mucous matter that was present at the hyphal surfaces of the fungi used. Cell agglomerates were found to accumulate at defined sites on the hyphal surfaces, which were coined ‘fungal-interactive’ hot spots. Evidence was further obtained for the contention that receptors for a physical bacterium-fungus interaction occur at the Lyophyllum sp. strain Karsten hyphal surface, in which the specific glycosphingolipid ceramide monohexoside (CMH) plays an important role. Thus, bacterial adherence may be mediated by heterogeneously distributed fungal-specific receptors, implying the CMH moieties. This study sheds light on the physical aspects of the B. terrae BS001 – Lyophyllum sp. strain Karsten interaction, highlighting heterogeneity along the hyphae with respect to hydrophobicity and the presence of potential anchoring sites.

Rhodococcus erythropolis cells adapt their fatty acid composition during biofilm formation on metallic and non-metallic surfaces

Several parameters are involved in bacterial adhesion and biofilm formation including surface type, medium composition and cellular surface hydrophobicty. When the cells are placed inside tubes, parameters such as oxygen availability should also influence cell adhesion. To understand which cellular lipids are involved in the molecular events of biofilm formation in Rhodococcus erythropolis, cell adhesion was promoted on different metallic and non-metallic surfaces immersed in culture media. These cells were able to modulate the fatty acid composition of the cell membrane in response to both the surface to which they adhered and the growth medium used. To assess the response of the cells to both surfaces and operational conditions, biofilms were also promoted inside a reactor built with five different types of tubes and with medium recirculation. The biofilm biomass could be directly related not to the hydrophobicity of the tubes used but to the oxygen permeability of the tubes. Besides this, cell age influenced the adhesion of the R. erythropolis cells to the tubes. Principal component analysis showed that the lipid composition of the cells could separate cells attached to metallic from those on non-metallic surfaces in the plane formed by PC1 and PC2, and influence biofilm biomass.

Insight into the Modulation of Dissolved Organic Matter on Microbial Remediation of PAH-Contaminated Soils

Microorganisms play a key role in degradation of polycyclic aromatic hydrocarbons (PAHs) in environments. Dissolved organic matter (DOM) can enhance microbial degradation of PAHs in soils. However, it is not clear how will the soil microbial community respond to addition of DOM during bioremediation of PAH-contaminated soils. In this study, DOMs derived from various agricultural wastes were applied to remediate the aging PAH-contaminated soils in a 90-day microcosm experiment. Results showed that the addition of DOMs offered a more efficient and persistent elimination of soil PAHs compared to the control which had no DOM addition. PAH removal effects were different among treatments with various DOMs; the addition of DOMs with high proportion of hydrophobic fraction could remove PAHs more efficiently from the soil. Low-molecular-weight (LMW) PAHs were more easily eliminated than that with high-molecular-weight (HMW). Addition of DOMs significantly increased abundance of 16S ribosomal RNA (rRNA), pdo1, nah, and C12O genes and obviously changed community compositions of nah and C12O genes in different ways in the PAH-contaminated soil. Phylogenetic analyses of clone libraries exhibited that all of nah sequences and most of C12O sequences were affiliated into Gammaproteobacteria and Betaproteobacteria. These results suggested that external stimuli produced by DOMs could enhance the microbial degradation of PAHs in soils through not only solubilizing PAHs but also altering abundance and composition of indigenous microbial degraders. Our results reinforce the understanding of role of DOMs in mediating degradation of PAHs by microorganims in soils.

Petroleum hydrocarbon degrading bacteria associated with chitosan as effective particle-stabilizers for oil emulsification

Bacteria act as an effective oil emulsifier with chitosan in sea water, together with its dramatically enhanced biodegradation.

Biodegradation of aliphatic hydrocarbons in the presence of hydroxy cucurbit[6]uril

Aliphatic hydrocarbons are one of the major environmental pollutants with reduced bioavailability. The present study focuses on the effect of hydroxy cucurbit[6]uril on the bioavailability of hydrocarbons. A bacterial consortium was used for biodegradation studies under saline and non-saline conditions. Based on denaturing gradient gel electrophoresis results it was found that the consortium under saline conditions had two different strains. The experiment was conducted in microcosms with tetradecane, hexadecane, octadecane and mixture of the mentioned hydrocarbons as the sole carbon source. The residual hydrocarbon was quantified using gas chromatography every 24h. It was found that biodegradation of tetradecane and hexadecane, as individual carbon source increased in the presence of hydroxy CB[6], probably due to the increase in their bioavailability. In case of octadecane this did not happen. Bioavailability of all three aliphatic hydrocarbons was increased when provided as a mixture to the consortium under saline conditions.

How microorganisms use hydrophobicity and what does this mean for human needs?

Cell surface hydrophobicity (CSH) plays a crucial role in the attachment to, or detachment from the surfaces. The influence of CSH on adhesion of microorganisms to biotic and abiotic surfaces in medicine as well as in bioremediation and fermentation industry has both negative and positive aspects. Hydrophobic microorganisms cause the damage of surfaces by biofilm formation; on the other hand, they can readily accumulate on organic pollutants and decompose them. Hydrophilic microorganisms also play a considerable role in removing organic wastes from the environment because of their high resistance to hydrophobic chemicals. Despite the many studies on the environmental and metabolic factors affecting CSH, the knowledge of this subject is still scanty and is in most cases limited to observing the impact of hydrophobicity on adhesion, aggregation or flocculation. The future of research seems to lie in finding a way to managing the microbial adhesion process, perhaps by steering cell hydrophobicity.

Biodegradation of pyrene by a Pseudomonas aeruginosa strain RS1 isolated from refinery sludge

High molecular weight (HMW) polynuclear aromatic hydrocarbons (PAHs) with more than three rings are inherently difficult to degrade. Degradation of HMW PAHs is primarily reported for actinomycetes, such as, Rhodococcus and Mycobacterium. This study reports pyrene degradation by a Pseudomonas aeruginosa strain isolated from tank bottom sludge in a refinery. High cell surface hydrophobicity induced during growth on pyrene facilitated its utilization as sole carbon source. Specific growth rate (μ) in the range of 0.03-0.085 h(-1) could be achieved over the concentration range 25-500 mg/L. The specific growth rate and specific pyrene utilization rate increased linearly with increase in total pyrene concentration. Although various degradation intermediates were identified in the aqueous phase, accumulation of total organic carbon (TOC) in the aqueous phase was only a small fraction of TOC equivalents of pyrene lost from the cultures. The degradation pathway appears to be similar to that reported for Mycobacterium sp. PYR-I.

Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms

Petroleum-based products are a primary energy source in the industry and daily life. During the exploration, processing, transport and storage of petroleum and petroleum products, water or soil pollution occurs regularly. Biodegradation of the hydrocarbon pollutants by indigenous microorganisms is one of the primary mechanisms of removal of petroleum compounds from the environment. However, the physical contact between microorganisms and hydrophobic hydrocarbons limits the biodegradation rate. This paper presents an updated review of the petroleum hydrocarbon uptake and transport across the outer membrane of microorganisms with the help of outer membrane proteins.

Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area

Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by real-time quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.

Trans-membrane transport of fluoranthene by Rhodococcus sp. BAP-1 and optimization of uptake process

The mechanism of transport of (14)C-fluoranthene by Rhodococcus sp. BAP-1, a Gram-positive bacterium isolated from crude oil-polluted soil, was examined. Our finding demonstrated that the mechanism for fluoranthene travel across the cell membrane in Rhodococcus sp. BAP-1 requires energy. Meanwhile, the transport of fluoranthene involves concurrent catabolism of (14)C, that leading to the generation of significant amount of (14)CO2. Combined with trans-membrane transport dynamic and response surface methodology, a significant influence of temperature, pH and salinity on cellular uptake rate was screened by Plackett-Burman design. Then, Box-Behnken design was employed to optimize and enhanced the trans-membrane transport process. The results predicted by Box-Behnken design indicated that the maximum cellular uptake rate of fluoranthene could be achieve to 0.308μmolmin(-1)mg(-1)·protein (observed) and 0.304μmolmin(-1)mg(-1)·protein (predicted) when the initial temperature, pH and salinity were set at 20°C, 9% and 1%, respectively.

Adaptation of the hydrocarbonoclastic bacterium Alcanivorax borkumensis SK2 to alkanes and toxic organic compounds: a physiological and transcriptomic approach

The marine hydrocarbonoclastic bacterium Alcanivorax borkumensis is able to degrade mixtures of n-alkanes as they occur in marine oil spills. However, investigations of growth behavior and physiology of these bacteria when cultivated with n-alkanes of different chain lengths (C6 to C30) as the substrates are still lacking. Growth rates increased with increasing alkane chain length up to a maximum between C12 and C19, with no evident difference between even- and odd-numbered chain lengths, before decreasing with chain lengths greater than C19. Surface hydrophobicity of alkane-grown cells, assessed by determination of the water contact angles, showed a similar pattern, with maximum values associated with growth rates on alkanes with chain lengths between C11 and C19 and significantly lower values for cells grown on pyruvate. A. borkumensis was found to incorporate and modify the fatty acid intermediates generated by the corresponding n-alkane degradation pathway. Cells grown on distinct n-alkanes proved that A. borkumensis is able to not only incorporate but also modify fatty acid intermediates derived from the alkane degradation pathway. Comparing cells grown on pyruvate with those cultivated on hexadecane in terms of their tolerance toward two groups of toxic organic compounds, chlorophenols and alkanols, representing intensely studied organic compounds, revealed similar tolerances toward chlorophenols, whereas the toxicities of different n-alkanols were significantly reduced when hexadecane was used as a carbon source. As one adaptive mechanism of A. borkumensis to these toxic organic solvents, the activity of cis-trans isomerization of unsaturated fatty acids was proven. These findings could be verified by a detailed transcriptomic comparison between cultures grown on hexadecane and pyruvate and including solvent stress caused by the addition of 1-octanol as the most toxic intermediate of n-alkane degradation.

Deciphering the traits associated with PAH degradation by a novel Serratia marcesencs L-11 strain

Polycyclic aromatic hydrocarbons (PAHs) are wide spread industrial pollutants that are released into the environment from burning of coal, distillation of wood, operation of gas works, oil refineries, vehicular emission, and combustion process. In this study a lipolytic bacterium was isolated from mixed stover compost of Saccharum munja and Brassica campestris. This strain was identified by both classical and 16S ribosomal DNA sequencing method and designated as Serratia marcesencs L-11. HPLC-based quantitation revealed 39- 100% degradation of PAH compounds within seven days. Further its ability to produce catechol 1, 2-dioxygenase (1.118 μM mL(-1) h(-1)) and biosurfactants (0.88 g L(-1)) during growth in PAH containing medium may be responsible for its PAH-degradation potential. This novel bacterium with an ability to produce lipases, biosurfactant and ring cleavage enzyme can prove to be useful for in-situ degradation of PAH compounds.

Characterization of acetonitrile-tolerant marine bacterium Exiguobacterium sp. SBH81 and its tolerance mechanism

A Gram-positive marine bacterium, Exiguobacterium sp. SBH81, was isolated as a hydrophilic organic-solvent tolerant bacterium, and exhibited high tolerance to various types of toxic hydrophilic organic solvents, including acetonitrile, at relatively high concentrations (up to 6% [v/v]) under the growing conditions. Investigation of its tolerance mechanisms illustrated that it does not rely on solvent inactivation processes or modification of cell surface characteristics, but rather, increase of the cell size lowers solvent partitioning into cells and the extrusion of solvents through the efflux system. A test using efflux pump inhibitors suggested that secondary transporters, i.e. resistance nodulation cell division (RND) and the multidrug and toxic compound extrusion (MATE) family, are involved in acetonitrile tolerance in this strain. In addition, its acetonitrile tolerance ability could be stably and significantly enhanced by repetitive growth in the presence of toxic acetonitrile. The marked acetonitrile tolerance of Exiguobacterium sp. SBH81 indicates its potential use as a host for biotechnological fermentation processes as well as bioremediation.

Activity and viability of polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LB126 in a DC-electrical field typical for electrobioremediation measures

There has been growing interest in employing electro‐bioremediation, a hybrid technology of bioremediation and electrokinetics for the treatment of contaminated soil. Knowledge however on the effect of weak electrokinetic conditions on the activity and viability of pollutant‐degrading microorganisms is scarce. Here we present data about the influence of direct current (DC) on the membrane integrity, adenosine triphosphate (ATP) pools, physico‐chemical cell surface properties, degradation kinetics and culturability of fluorene‐degrading Sphingomonas sp. LB126. Flow cytometry was applied to quantify the uptake of propidium iodide (PI) and the membrane potential‐related fluorescence intensities (MPRFI) of individual cells within a population. Adenosine tri‐phosphate contents and fluorene biodegradation rates of bulk cultures were determined and expressed on a per cell basis. The cells' surface hydrophobicity and electric charge were assessed by contact angle and zeta potential measurements respectively. Relative to the control, DC‐exposed cells exhibited up to 60% elevated intracellular ATP levels and yet remained unaffected on all other levels of cellular integrity and functionality tested. Our data suggest that direct current (X = 1 V cm⁻¹; J = 10.2 mA cm⁻²) as typically used for electrobioremediation measures has no negative effect on the activity of the polycyclic aromatic hydrocarbon (PAH)‐degrading soil microorganism, thereby filling a serious gap of the current knowledge of the electrobioremediation methodology.