Effects of Pinus sylvestris root growth and mycorrhizosphere development on bacterial carbon source utilization and hydrocarbon oxidation in forest and petroleum-contaminated soils

Biochar-bacteria-plant combined potential for remediation of oil-contaminated soil

Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar-bacteria-plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.

Survival and growth of saprotrophic and mycorrhizal fungi in recalcitrant amine, amide and ammonium containing media

The elimination of hazardous compounds in chemical wastes can be a complex and technically demanding task. In the search for environmental-friendly technologies, fungal mediated remediation and removal procedures are of concern. In this study, we investigated whether there are fungal species that can survive and grow on solely amine-containing compounds. One compound containing a primary amine group; 2-diethylaminoethanol, one compound with a primary amide group; 2,6-dichlorobenzamide (BAM), and a third compound containing a quaternary ammonium group; N₃-trimethyl(2-oxiranyl)methanaminium chloride, were selected. The choice of these compounds was motivated by their excessive use in large scale manufacturing of protein separation media (2-diethylaminoethanol and the quaternary amine). 2,6-dichlorobenzamide, the degradation product of the herbicide 2,6-dichlorobenzonitrile (dichlobenil), was chosen since it is an extremely recalcitrant compound. Utilising part of the large fungal diversity in Northern European forests, a screening study using 48 fungal isolates from 42 fungal species, including saprotrophic and mycorrhizal fungi, was performed to test for growth responses to the chosen compounds. The ericoid (ERM) mycorrhizal fungus Rhizoscyphus ericae showed the best overall growth on 2-diethylaminoethanol and BAM in the 1–20 g L^-1 concentration range, with a 35-fold and 4.5-fold increase in biomass, respectively. For N₃-trimethyl(2-oxiranyl)methanaminium chloride, the peak growth occurred at 1 g L^-1. In a second experiment, including three of the most promising fungi (Laccaria laccata, Hygrophorus camarophyllus and Rhizoscyphus ericae) from the screening experiment, a simulated process water containing 1.9% (w/v) 2-diethylaminoethanol and 0.8% (w/v) N_3-trimethyl(2-oxiranyl)methanaminium chloride was used. Laccaria laccata showed the best biomass increase (380%) relative to a control, while the accumulation for Rhizoscyphus ericae and Hygrophorus camarophyllus were 292% and 136% respectively, indicating that mycorrhizal fungi can use amine- and amide-containing substrates as nutrients. These results show the potential of certain fungal species to be used in alternative green wastewater treatment procedures.

Plant growth, root distribution and non-aqueous phase liquid phytoremediation at the pore-scale

The success of phytoremediation is dependent on the exposure of plants to contaminants, which is controlled by root distribution, physicochemical characteristics, and contaminant behavior in the soil environment. Whilst phytoremediation has been successful in remediating hydrocarbons and other organic contaminants, there is little understanding of the impact of non-aqueous phase liquids (NAPLs) on plant behavior, root architecture and the resulting impact of this on phytoremediation. Light NAPLs (LNAPLs) may be present in pore spaces in the capillary zone as a continuous or semi-continuous phase, or as unconnected ganglia which act as individual contaminant sources. Experimental work with ryegrass (Lolium perenne) grown under hydroponic conditions in idealised pore scale models is presented, exploring how plant growth, root distribution and development, and oil removal are affected through direct physical contact with a model LNAPL (mineral oil). In the presence of low levels of LNAPL, a significant decrease in root length was observed, whilst at higher LNAPL levels root lengths increased due to root diversion and spreading, with evidence of root redistribution in the case of LNAPL contamination across multiple adjacent pores. Changes to root morphology were also observed in the presence of LNAPL with plant roots coarse and crooked compared to long, fine and smooth roots in uncontaminated columns. Root and shoot biomass also appear to be impacted by the LNAPL although the effects are complex, affected by both root diversion and thickening. Substantial levels of LNAPL removal were observed, with roots close to LNAPL sources able to remove dissolved-phase contamination, and root growth through LNAPL sources suggest that direct uptake/degradation is possible.

Ecology of Contaminant Biotransformation in the Mycosphere: Role of Transport Processes

Fungi and bacteria often share common microhabitats. Their co-occurrence and coevolution give rise to manifold ecological interactions in the mycosphere, here defined as the microhabitats surrounding and affected by hyphae and mycelia. The extensive structure of mycelia provides ideal "logistic networks" for transport of bacteria and matter in structurally and chemically heterogeneous soil ecosystems. We describe the characteristics of the mycosphere as a unique and highly dynamic bacterial habitat and a hot spot for contaminant biotransformation. In particular, we emphasize the role of the mycosphere for (i) bacterial dispersal and colonization of subsurface interfaces and new habitats, (ii) matter transport processes and contaminant bioaccessibility, and (iii) the functional stability of microbial ecosystems when exposed to environmental fluctuations such as stress or disturbances. Adopting concepts from ecological theory, the chapter disentangles bacterial-fungal impacts on contaminant biotransformation in a systemic approach that interlinks empirical data from microbial ecosystems with simulation data from computational models. This approach provides generic information on key factors, processes, and ecological principles that drive microbial contaminant biotransformation in soil. We highlight that the transport processes create favorable habitat conditions for efficient bacterial contaminant degradation in the mycosphere. In-depth observation, understanding, and prediction of the role of mycosphere transport processes will support the use of bacterial-fungal interactions in nature-based solutions for contaminant biotransformation in natural and man-made ecosystems, respectively.

Mycelia as a focal point for horizontal gene transfer among soil bacteria

Horizontal gene transfer (HGT) is a main mechanism of bacterial evolution endowing bacteria with new genetic traits. The transfer of mobile genetic elements such as plasmids (conjugation) requires the close proximity of cells. HGT between genetically distinct bacteria largely depends on cell movement in water films, which are typically discontinuous in natural systems like soil. Using laboratory microcosms, a bacterial reporter system and flow cytometry, we here investigated if and to which degree mycelial networks facilitate contact of and HGT between spatially separated bacteria. Our study shows that the network structures of mycelia promote bacterial HGT by providing continuous liquid films in which bacterial migration and contacts are favoured. This finding was confirmed by individual-based simulations, revealing that the tendency of migrating bacteria to concentrate in the liquid film around hyphae is a key factor for improved HGT along mycelial networks. Given their ubiquity, we propose that hyphae can act as focal point for HGT and genetic adaptation in soil.

Rhizoremediation of petroleum hydrocarbon, prospects and future

Oil refineries generate several tones of oily waste which is dumped in an open pit within the vicinity of oil field.

Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists

Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their development and functioning. These bacterial-fungal interactions often result in changes to the pathogenicity or the nutritional influence of one or both partners toward plants or animals (including humans). They can also result in unique contributions to biogeochemical cycles and biotechnological processes. Thus, the interactions between bacteria and fungi are of central importance to numerous biological questions in agriculture, forestry, environmental science, food production, and medicine. Here we present a structured review of bacterial-fungal interactions, illustrated by examples sourced from many diverse scientific fields. We consider the general and specific properties of these interactions, providing a global perspective across this emerging multidisciplinary research area. We show that in many cases, parallels can be drawn between different scenarios in which bacterial-fungal interactions are important. Finally, we discuss how new avenues of investigation may enhance our ability to combat, manipulate, or exploit bacterial-fungal complexes for the economic and practical benefit of humanity as well as reshape our current understanding of bacterial and fungal ecology.

Biodegradation of naphthalene and anthracene by chemo-tactically active rhizobacteria of populus deltoides

Several naphthalene and anthracene degrading bacteria were isolated from rhizosphere of Populus deltoides, which were growing in non-contaminated soil. Among these, four isolates, i.e. Kurthia sp., Micrococcus varians, Deinococcus radiodurans and Bacillus circulans utilized chrysene, benzene, toluene and xylene, in addition to anthracene and naphthalene. Kurthia sp and B. circulans showed positive chemotactic response for naphthalene and anthracene. The mean growth rate constant (K) of isolates were found to increase with successive increase in substrate concentration (0.5 to 1.0 mg/50ml). B. circulans SBA12 and Kurthia SBA4 degraded 87.5% and 86.6% of anthracene while, Kurthia sp. SBA4, B. circulans SBA12, and M. varians SBA8 degraded 85.3 %, 95.8 % and 86.8 % of naphthalene respectively after 6 days of incubation as determined by HPLC analysis.

Enhanced biodegradation of petroleum hydrocarbons in the mycorrhizosphere of sub-boreal forest soils

Petroleum hydrocarbon (PHC) contamination is becoming more common in boreal forest soils. However, linkages between PHC biodegradation and microbial community dynamics in the mycorrhizosphere of boreal forest soils are poorly understood. Seedlings (lodgepole pine, paper birch, lingonberry) were established in reconstructed soil systems, consisting of an organic layer (mor humus, coarse woody debris, or previously oil-contaminated mor humus) overlying mineral (Ae, Bf) horizons. Light crude oil was applied to the soil surface after 4 months; systems were destructively sampled at 1 and 16 weeks following treatment. Soil concentrations of four PHC fractions were determined using acetone-hexane extraction followed by gas chromatography - flame ionization detection analysis. Genotypic profiles of root-associated bacterial communities were generated using length heterogeneity-PCR of 16S rDNA. Most plant-soil treatments showed significant loss in the smaller fraction PHCs indicating an inherent capacity for biodegradation. Concentrations of total PHCs declined significantly only in planted (pine-woody debris and birch-humus) systems (averaging 59% and 82% loss between 1 and 16 weeks respectively), reinforcing the importance of the mycorrhizosphere for enhancing microbial catabolism. Bacterial community structure was correlated more with mycorrhizosphere type and complexity than with PHC contamination. However, results suggest that communities in PHC-contaminated and pristine soils may become distinct over time.

Impact of ectomycorrhizosphere on the functional diversity of soil bacterial and fungal communities from a forest stand in relation to nutrient mobilization processes

The ectomycorrhizal symbiosis alters the physicochemical and biological conditions in the surrounding soil, thus creating a particular environment called ectomycorrhizosphere, which selects microbial communities suspected to play a role in gross production and nutrient cycling. To assess the ectomycorrhizosphere effect on the structure of microbial communities potentially involved in the mobilization of nutrients from the soil minerals in a poor-nutrient environment, we compared the functional diversity of soil and ectomycorrhizosphere bacterial communities in a forest stand. Two hundred and sixty-four bacterial strains and 107 fungal strains were isolated from the bulk soil of an oak (Quercus petraea) stand and from oak-Scleroderma citrinum ectomycorrhizosphere and ectomycorrhizae, in two soil organo-mineral horizons (0 to 3 cm and 5 to 10 cm). They were characterized using two in vitro tests related to their capacities to mobilize iron and phosphorus. We demonstrated that the oak-S. citrinum ectomycorrhizosphere significantly structures the culturable bacterial communities in the two soil horizons by selecting very efficient strains for phosphorus and iron mobilization. This effect was also observed on the diversity of the phosphate-solubilizing fungal communities in the lower soil horizon. A previous study already demonstrated that Laccaria bicolor-Douglas fir ectomycorrhizosphere structures the functional diversity of Pseudomonas fluorescens population in a forest nursery soil. Comparing to it, our work highlights the consistency of the mycorrhizosphere effect on the functional diversity of bacterial and fungal communities in relation to the mineral weathering process, no matter the fungal symbiont, the age and species of the host tree, or the environment (nursery vs forest). We also demonstrated that the intensity of phosphorus and iron mobilization by the ectomycorrhizosphere bacteria isolated from the lower soil horizon was significantly higher compared to that which was isolated from the upper horizon. This reveals for the first time a stratification of the functional diversity of the culturable soil bacterial communities as related to phosphorus and iron mobilization.

Metabolic and phylogenetic analysis of microbial communities during phytoremediation of soil contaminated with weathered hydrocarbons and heavy metals

In the current study, the microbial ecology of weathered hydrocarbon and heavy metal contaminated soil undergoing phytoremediation was studied. The relationship of functional diversity, measured as carbon source utilisation in Biolog plates and extracellular enzymatic activities, and genetic diversity of bacteria was evaluated. Denaturing gradient gel electrophoresis was used for community analyses at the species level. Bulk soil and rhizosphere soil from pine and poplar plantations were analysed separately to determine if the plant rhizosphere impacted hydrocarbon degradation. Prevailing microbial communities in the field site were both genetically and metabolically diverse. Furthermore, both tree rhizosphere and fertilisation affected the compositions of these communities and increased activities of extracellular aminopeptidases. In addition, the abundance of alkane hydroxylase and naphthalene dioxygenase genes in the communities was low, but the prevalence of these genes was increased by the addition of bioavailable hydrocarbons. Tree rhizosphere communities had greater hydrocarbon degradation potential than those of bulk soil. Hydrocarbon utilising communities were dominated generally by the species Ralstonia eutropha and bacteria belonging to the genus Burkholderia. Despite the presence of viable hydrocarbon-degrading microbiota, decomposition of hydrocarbons from weathered hydrocarbon contaminated soil over four years, regardless of the presence of vegetation, was low in unfertilised soil. Compost addition enhanced the removal of hydrocarbons.

Taking the fungal highway: mobilization of pollutant-degrading bacteria by fungi

The capacity of fungi to serve as vectors for the dispersion of pollutant-degrading bacteria was analyzed in laboratory model systems mimicking water-saturated (agar surfaces) and unsaturated soil environments (glass-bead-filled columns). Two common soil fungi (Fusarium oxysporum and Rhexocercosporidium sp.) forming hydrophilic and hydrophobic mycelia, respectively, and three polycyclic aromatic hydrocarbon degrading bacteria (Achromobacter sp. SK1, Mycobacterium frederiksbergense LB501TG, and Sphingomonas sp. L138) were selected based on the absence of mutual antagonistic effects. It was shown that fungal hyphae act as vectors for bacterial transport with mobilization strongly depending on the specific microorganisms chosen: The motile strain Achromobacter sp. SK1 was most efficiently spread along hyphae of hydrophilic F. oxysporum in both model systems with transport velocities of up to 1 cm d(-1), whereas no dispersion of the two nonmotile strains was observed in the presence of F. oxysporum. By contrast, none of the bacteria was mobilized along the hydrophobic mycelia of Rhexocercosporidium sp. growing on agar surfaces. In column experiments however, strain SK1 was mobilized by Rhexocercosporidium sp. It is hypothesized that bacteria may move by their intrinsic motilitythrough continuous (physiological) liquid films forming around fungal hyphae. The results of this study suggest that the specific stimulation of indigenous fungi may be a strategy to mobilize pollutant-degrading bacteria leading to their homogenization in polluted soil thereby improving bioremediation.

Changes in microbial community composition and function during a polyaromatic hydrocarbon phytoremediation field trial

The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.

Interactions between ectomycorrhizal fungi and soil saprotrophs: implications for decomposition of organic matter in soils and degradation of organic pollutants in the rhizosphere

Ectomycorrhizal fungi and saprotrophic microorganisms coexist and interact in the mycorrhizosphere. We review what is known regarding these interactions and how they may influence processes such as ectomycorrhiza formation, mycelial growth, and the dynamics of carbon movement to and within the rhizosphere. Particular emphasis is placed on the potential importance of interactions in decomposition of soil organic matter and degradation of persistant organic pollutants in soil. While our knowledge is currently fairly limited, it seems likely that interactions have profound effects on mycorrhizosphere processes. More extensive research is warranted to provide novel insights into mycorrhizosphere ecology and to explore the potential for manipulating the ectomycorrhizosphere environment for biotechnological purposes.Key words: ectomycorrhizal fungi, ectomycorrhizosphere, rhizosphere, rhizosphere carbon flow, decomposition, rhizosphere remediation.

Microcosm-based analyses of Scots pine seedling growth, ectomycorrhizal fungal community structure and bacterial carbon utilization profiles in boreal forest humus and underlying illuvial mineral horizons

We report on the identity of indigenous mycorrhiza forming fungi and rhizosphere/mycorrhizosphere bacterial community carbon source utilization profiles of Scots pine (Pinus sylvestris L.) seedlings grown in boreal forest humus (O) or illuvial (B) mineral horizon containing microcosm growth systems. Based on rDNA (ITS)-RFLP analyses, a total of 10 fungal RFLP taxa were identified from pre-morphotyped mycorrhizas on 7-month-old seedling roots. Hierarchical cluster analysis, including corresponding RFLPs of known fungal species, confirmed root colonization by eight mycorrhizal species. In the O horizon, roots were colonized by e.g. Suillus bovinus, Suillus variegatus, Cenococcum geophilum, Piloderma croceum, Thelephora terrestris and Russula vinicolor. Mycobiont diversity in the mineral B horizon was lower but included Piceirhiza bicolorata and both Suillus species which produced extensive extramatrical mycelium. In comparison to non-colonized soils, rhizosphere and mycorrhizosphere compartments supported significantly higher numbers of bacteria (mean range 10(8)-10(11) cells g(-1) fresh weight (fw)). Specific rhizosphere/mycorrhizosphere 'niche'-linked bacterial communities were detected following multivariate analyses (PCA and CA) of bacterial carbon utilization profiles (Biolog(R) GN microplate). Distinct preferences for amino and carboxylic acids were identified in mineral B horizon rhizospheres whereas a wider range of carbon sources were utilized in the fungal-dominated mycorrhizospheres irrespective of soil types.