Intensification of the aerobic bioremediation of an actual site soil historically contaminated by polychlorinated biphenyls (PCBs) through bioaugmentation with a non acclimated, complex source of microorganisms

Background  

The biotreatability of actual-site polychlorinated biphenyl (PCB)-contaminated soils is often limited by their poor content of autochthonous pollutant-degrading microorganisms. In such cases, inoculation might be the solution for a successful bioremediation. Some pure and mixed cultures of characterized PCB degrading bacteria have been tested to this purpose. However, several failures have been recorded mostly due to the inability of inoculated microbes to compete with autochthonous microflora and to face the toxicity and the scarcity of nutrients occurring in the contaminated biotope. Complex microbial systems, such as compost or sludge, normally consisting of a large variety of robust microorganisms and essential nutrients, would have better chances to succeed in colonizing degraded contaminated soils. However, such sources of microorganisms have been poorly applied in soil bioremediation and in particular in the biotreatment of soil with PCBs. Thus, in this study the effects of Enzyveba, i.e. a consortium of non-adapted microorganisms developed from composted material, on the slurry- and solid-phase aerobic bioremediation of an actual-site, aged PCB-contaminated soil were studied.     

A new cold-adapted β-D-galactosidase from the Antarctic Arthrobacter sp. 32c - gene cloning, overexpression, purification and properties

Background  

The development of a new cold-active β-D-galactosidases and microorganisms that efficiently ferment lactose is of high biotechnological interest, particularly for lactose removal in milk and dairy products at low temperatures and for cheese whey bioremediation processes with simultaneous bio-ethanol production.     

Life cycle assessment of polychlorinated biphenyl contaminated soil remediation processes

Purpose  

A life-cycle assessment (LCA) was performed to evaluate the environmental impacts of the remediation of industrial soils contaminated by polychlorobiphenyl (PCB). Two new bioremediation treatment options were compared with the usual incineration process. In this attributional LCA, only secondary impacts were considered. The contaminated soil used for the experiments contained 200 mg of PCB per kilogram.     

Isolation and characterisation of polychlorinated biphenyl (PCB) degrading fungi from a historically contaminated soil

Background  

Polychlorinated biphenyls (PCBs) are widespread toxic pollutants. Bioremediation might be an effective, cost competitive and environment-friendly solution for remediating environmental matrices contaminated by PCBs but it is still unsatisfactory, mostly for the limited biodegradation potential of bacteria involved in the processes. Very little is known about mitosporic fungi potential in PCB bioremediation and their occurrence in actual site historically contaminated soils. In the present study, we characterised the native mycoflora of an aged dump site soil contaminated by about 0.9 g kg^-1 of Aroclor 1260 PCBs and its changing after aerobic biotreatment with a commercial complex source of bacteria and fungi. Fungi isolated from the soil resulting from 120 days of treatment were screened for their ability to adsorb or metabolise 3 target PCBs.     

Preferential use of root litter compared to leaf litter by beech seedlings and soil microorganisms

Background and aims

Litter decomposition is regulated by e.g. substrate quality and environmental factors, particularly water availability. The partitioning of nutrients released from litter between vegetation and soil microorganisms may, therefore, be affected by changing climate. This study aimed to elucidate the impact of litter type and drought on the fate of litter-derived N in beech seedlings and soil microbes.

Methods

We quantified ¹⁵N recovery rates in plant and soil N pools by adding ¹⁵N-labelled leaf and/or root litter under controlled conditions.

Results

Root litter was favoured over leaf litter for N acquisition by beech seedlings and soil microorganisms. Drought reduced ¹⁵N recovery from litter in seedlings thereby affecting root N nutrition. ¹⁵N accumulated in seedlings in different sinks depending on litter type.

Conclusions

Root turnover appears to influence (a) N availability in the soil for plants and soil microbes and (b) N acquisition and retention despite a presumably extremely dynamic turnover of microbial biomass. Compared to soil microorganisms, beech seedlings represent a very minor short-term N sink, despite a potentially high N residence time. Furthermore, soil microbes constitute a significant N pool that can be released in the long term and, thus, may become available for N nutrition of plants.     

Bioaugmentation of carbofuran by Burkholderia cepacia PCL3 in a bioslurry phase sequencing batch reactor

The effectiveness of bioremediation technology in the removal of carbofuran from contaminated soil using a bioslurry phase sequencing batch reactor (SBR) was investigated. A 2-L laboratory glass bottle was used as a bioreactor with a working volume of 1.5 L at room temperature (27 ± 2 °C). One total cycle period of the SBR was comprised of 1 h of fill phase, 82 h of react phase, and 1 h of decant phase. The carbofuran concentration in the soil was 20 mg/kg soil. A carbofuran degrader isolated from carbofuran phytoremediated soil, namely Burkholderia cepacia PCL3 (PCL3) immobilized on corncob, was used as the inoculum. The results revealed that bioaugmentation treatment (addition of PCL3) gave the highest percentage of carbofuran removal (96.97%), followed by bioaugmentation together with biostimulation (addition of molasses) treatment (88.23%), suggesting that bioremediation was an effective technology for removing carbofuran in contaminated soil. Abiotic experiments, i.e. autoclaved soil slurry with corncob and no PCL3 treatment and autoclaved soil slurry with no PCL3 treatment, could adsorb 31.86% and 7.70% of carbofuran, respectively, which implied that soil and corncob could act as sorbents for the removal of carbofuran.     

Role of Enzyveba in the aerobic bioremediation and detoxification of a soil freshly contaminated by two different diesel fuels

The biodegradability of two commercial diesel fuels, i.e., Diesel and HiQ Diesel, herewith designated as G1 and G2, respectively, spiked to an agricultural soil at 10 g kg⁻¹ was studied under aerobic slurry-phase conditions in the absence and in the presence of Enzyveba, i.e., a characterized commercial source of microorganisms and nutrients. A quite similar hydrocarbon composition was displayed by G1 and G2, which were found to be both extensively and almost completely biodegraded under all conditions after 4.5 months of treatment with a remarkable depletion of initial soil ecotoxicity, in particular in the G2 spiked one. The addition of Enzyveba resulted in a higher availability of cultivable specialized bacteria and fungi in the reactors but this only resulted in a slight intensification of soil bioremediation, probably because of the high contents of nutrients and indigenous specialized microorganisms of the soil. A faster biodegradation of hydrocarbons and a more rapid and extensive depletion of initial ecotoxicity were generally observed in the soil reactors spiked with G2 with respect to those spiked with G1 probably for the G2 content of additives capable of improving hydrocarbons bioavailability.     

Effects of soil amendment with different carbon sources and other factors on the bioremediation of an aged PAH-contaminated soil

Carbon supplementation, soil moisture and soil aeration are believed to enhance in situ bioremediation of PAH-contaminated soils by stimulating the growth of indigenous microorganisms. However, the effects of added carbon and nitrogen together with soil moisture and soil aeration on the dissipation of PAHs and on associated microbial counts have yet to be fully assessed. In this study the effects on bioremediation of carbon source, carbon-to-nitrogen ratio, soil moisture and aeration on an aged PAH-contaminated agricultural soil were studied in microcosms over a 90-day period. Additions of starch, glucose and sodium succinate increased soil bacterial and fungal counts and accelerated the dissipation of phenanthrene and benzo(a)pyrene in soil. Decreases in phenanthrene and benzo(a)pyrene concentrations were effective in soil supplemented with glucose and sodium succinate (both 0.2 g C kg⁻¹ dry soil) and starch (1.0 g C kg⁻¹ dry soil). The bioremediation effect at a C/N ratio of 10:1 was significantly higher (P < 0.05) than at a C/N of either 25:1 or 40:1. Soil microbial counts and PAH dissipation were lower in the submerged soil but soil aeration increased bacterial and fungal counts, enhanced indigenous microbial metabolic activities, and accelerated the natural degradation of phenanthrene and benzo(a)pyrene. The results suggest that optimizing carbon source, C/N ratio, soil moisture and aeration conditions may be a feasible remediation strategy in certain PAH contaminated soils with large active microbial populations.     

Bacterial diversity and reductive dehalogenase redundancy in a 1,2-dichloroethane-degrading bacterial consortium enriched from a contaminated aquifer

Background  

Bacteria possess a reservoir of metabolic functionalities ready to be exploited for multiple purposes. The use of microorganisms to clean up xenobiotics from polluted ecosystems (e.g. soil and water) represents an eco-sustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and accurate strategies for monitoring and identification of bacteria and catabolic genes involved in the degradation of xenobiotics, key processes to follow up the activities in situ.     

Microbial Communities Associated with the Larval Gut and Eggs of the Western Corn Rootworm

Background

The western corn rootworm (WCR) is one of the economically most important pests of maize. A better understanding of microbial communities associated with guts and eggs of the WCR is required in order to develop new pest control strategies, and to assess the potential role of the WCR in the dissemination of microorganisms, e.g., mycotoxin-producing fungi.

Methodology/Principal Findings

Total community (TC) DNA was extracted from maize rhizosphere, WCR eggs, and guts of larvae feeding on maize roots grown in three different soil types. Denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene and ITS fragments, PCR-amplified from TC DNA, were used to investigate the fungal and bacterial communities, respectively. Microorganisms in the WCR gut were not influenced by the soil type. Dominant fungal populations in the gut were affiliated to Fusarium spp., while Wolbachia was the most abundant bacterial genus. Identical ribosomal sequences from gut and egg samples confirmed a transovarial transmission of Wolbachia sp. Betaproteobacterial DGGE indicated a stable association of Herbaspirillum sp. with the WCR gut. Dominant egg-associated microorganisms were the bacterium Wolbachia sp. and the fungus Mortierella gamsii.

Conclusion/Significance

The soil type-independent composition of the microbial communities in the WCR gut and the dominance of only a few microbial populations suggested either a highly selective environment in the gut lumen or a high abundance of intracellular microorganisms in the gut epithelium. The dominance of Fusarium species in the guts indicated WCR larvae as vectors of mycotoxin-producing fungi. The stable association of Herbaspirillum sp. with WCR gut systems and the absence of corresponding sequences in WCR eggs suggested that this bacterium was postnatally acquired from the environment. The present study provided new insights into the microbial communities associated with larval guts and eggs of the WCR. However, their biological role remains to be explored.     

Large-scale production of bacterial consortia for remediation of chlorinated solvent-contaminated groundwater

Chlorinated solvents such as perchloroethylene (PCE) and trichloroethylene (TCE) continue to be significant groundwater contaminants throughout the USA. In many cases efficient bioremediation of aquifers contaminated with these chemicals requires the addition of exogenous microorganisms, specifically members of the genus Dehalococcoides (DHC). This process is referred to as bioaugmentation. In this study a fed-batch fermentation process was developed for producing large volumes (to 3,200 L) of DHC-containing consortia suitable for treating contaminated aquifers. Three consortia enriched from three different sites were grown anaerobically with sodium lactate as an electron donor and PCE or TCE as an electron acceptor. DHC titers in excess of 10¹¹ DHC/L could be reproducibly obtained at all scales tested and with all three of the enrichment cultures. The mean specific DHC growth rate for culture SDC-9™ was 0.036 ± 0.005 (standard error, SE)/h with a calculated mean doubling time of 19.3 ± 2.7 (SE) h. Finished cultures could be concentrated approximately tenfold by membrane filtration and stored refrigerated (4°C) for more that 40 days without measurable loss of activity. Dehalogenation of PCE by the fermented cultures was affected by pH with no measurable activity at pH <5.0.     

Engineering plants for the phytodetoxification of explosives

Summary  Widespread contaimination of the environment by explosives resulting from the manufacture, disposal and testing of munitions is becoming a matter of increasing concern. Most explosives are considered to be a major hazard to biological systems due to their toxic and mutagenic effects. Interest on the bioremediation of land contaminated with explosives has recently been focused on phytoremediation. Unfortunately., whilst plants have many advantages for the remediation of contaminated land and water, they lack the catabolic versatility which enables microorganisms to mineralize such a wide diversity of xenobiotic compounds. This raised the interesting question as to whether the impressive biodegradative capabilities of soil bacteria could be combined with the high biomass and stability of plants to yield an optimal system for in situ bioremediation of explosive residues in soil. Our investigation into the degradation of explosive residues by soil bacteria resulted in the isolation of Enterobacter cloacae PB2, which is capable of utilizing nitrate ester explosives such as pentaerythritol tetranitrate (PETN) and nitroglycerin as the sole source of nitrogen for growth. We have successfully introduced PETN reductase, the enzyme initiating explosive degradation in this organism, into plants to create transgenic plants that degrade explosives. Since the bacterial degradative pathways for many classes of organic pollutant have been elucidated, this may be a generally applicable method of achieving bioremediation of contaminated soil in the environment.     

Geographical trends of soil-associated biodiversity changes due to tree plantations in South America: Biome and climate constraints revealed through meta-analysis

Aim

To evaluate the interaction between climate and biome structure when explaining changes in species richness of soil-associated communities due to tree plantations developed in different biomes. Compare the response of plants, soil invertebrates and soil microorganisms, and to test whether they should be considered sensitive-coupled biotas.

Location

Continental South America.

Time Period

1996–2023.

Major Taxa Studied

Plants, soil invertebrates and soil microorganisms.

Methods

Through a meta-analysis, the change in species richness (i.e. response ratio) associated with tree plantations was evaluated in 127 points of study across South America, considering soil-associated communities of plants, invertebrates and microorganisms. The influence of biome structure (open vs. closed habitats) on the response ratio, and its interaction with the actual evapotranspiration (AET) and temperature seasonality was evaluated. Differentiated responses of different taxa were tested by comparing models with and without an interaction term referring to the taxon studied. The regional agricultural cover and plantation age were considered as anthropogenic variables.

Results

Models containing the AET were better at explaining the trend of change in species richness than those with temperature seasonality. The response of the change in species richness was oppositely related to the AET in open and closed biomes. Plants presented a higher loss in species richness than soil invertebrates and microorganisms. The three taxa were positively associated with AET, while seasonality was not relevant in any case. Both anthropogenic variables significantly lessened the change in species richness in all models.

Main Conclusions

The structural contrast between the anthropogenic habitat and the biome where it is developed is a key factor influencing the response of soil-associated communities to tree plantations. Nevertheless, its influence must be assessed together with climatic and anthropogenic variables given that their interaction can explain different geographical trends in the change in species richness across regions.     

Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis

Background  

Surface contamination of smear cheese by Listeria spp. is of major concern for the industry. Complex smear ecosystems have been shown to harbor antilisterial potential but the microorganisms and mechanisms involved in the inhibition mostly remain unclear, and are likely related to complex interactions than to production of single antimicrobial compounds. Bacterial biodiversity and population dynamics of complex smear ecosystems exhibiting antilisterial properties in situ were investigated by Temporal temperature gradient gel electrophoresis (TTGE), a culture independent technique, for two microbial consortia isolated from commercial Raclette type cheeses inoculated with defined commercial ripening cultures (F) or produced with an old-young smearing process (M).     

Electrically conductive magnetite particles enhance the kinetics and steer the composition of anaerobic TCE-dechlorinating cultures

The interaction of anaerobic dechlorinating cultures with soil and aquifer geochemical components is largely unknown, although this has potentially a major impact on the bioremediation of chlorinated solvent-contaminated sites. In this study, we found that addition of magnetite (Fe₃O₄) – the end-product of Fe(III)-reduction by dissimilatory iron reducing bacteria – to anaerobic dechlorinating cultures enhances the kinetics of trichloroethene dechlorination up to 1.5-times, compared to unamended controls. Specifically, a low concentration (approx. 10 mg/L as total Fe) of small size particles (200 nm-filtered) resulted in a greater stimulatory effect compared to the addition of a higher concentration (approx. 300 mg/L as total Fe) of unfiltered particles. Notably, Desulforomonas spp. were substantially enriched in microcosms supplemented with magnetite, whereas Dehalococcoides mccartyi spp. was found to be markedly inhibited or outcompeted. Multiple lines of evidence, including the direct visualization of microbial cells and magnetite particles via Confocal Laser Scanning Microscopy (CLSM), suggest that electrically conductive particles promoted the establishment of a cooperative metabolism, based on direct interspecies electron transfer, between dechlorinating and non-dechlorinating microorganisms.     

Stable coexistence of two <Emphasis Type="Italic">Caldicellulosiruptor</Emphasis> species in a <Emphasis Type="Italic">de novo</Emphasis> constructed hydrogen-producing co-culture

Background  

Mixed culture enrichments have been used frequently for biohydrogen production from different feedstock. In spite of the several advantages offered by those cultures, they suffer poor H₂ yield. Constructing defined co-cultures of known H₂ producers may offer a better performance than mixed-population enrichments, while overcoming some of the limitations of pure cultures based on synergies among the microorganisms involved.     

Biodegradation of trinitrotoluene (TNT) by indigenous microorganisms from TNT-contaminated soil,and their application in TNT bioremediation

Soil and groundwater contaminated by munitions compounds is a crucial issue in environmental protection. Trinitrotoluene (TNT) is highly toxic and carcinogenic; therefore, the control and remediation of TNT contamination is a critical environmental issue. In this study, the authors characterized the indigenous microbial isolates from a TNT-contaminated site and evaluated their activity in TNT biodegradation. The bacteria Achromobacter sp. BC09 and Citrobacter sp. YC4 isolated from TNT-contaminated soil by enrichment culture with TNT as the sole carbon and nitrogen source (strain BC09) and as the sole nitrogen but not carbon source (strain YC4) were studied for their use in TNT bioremediation. The efficacy of degradation of TNT by indigenous microorganisms in contaminated soil without any modification was insufficient in the laboratory-scale pilot experiments. The addition of strains BC09 and YC4 to the contaminated soil did not significantly accelerate the degradation rate. However, the addition of an additional carbon source (e.g., 0.25% sucrose) could significantly increase the bioremediation efficiency (ca. decrease of 200 ppm for 10 days). Overall, the results suggested that biostimulation was more efficient as compared with bioaugmentation. Nevertheless, the combination of biostimulation and bioaugmentation using these indigenous isolates is still a feasible approach for the development of bioremediation of TNT pollution.     

Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration

Background  

Thermostable enzymes from thermophilic microorganisms are playing more and more important roles in molecular biology R&D and industrial applications. However, over-production of recombinant soluble proteins from thermophilic microorganisms in mesophilic hosts (e.g. E. coli) remains challenging sometimes.     

Screening and characterization of microorganisms with glutaryl-7 ADCA acylase activity

A screening of microorganisms producing glutaryl-7 ADCA acylase, an enzyme able to hydrolyse glutaric acid selectively from glutaryl-3-deacetoxy-7-aminocephalosporanic acid (glutaryl-7 ADCA), has been carried out in soil samples. Five microorganisms expressing acylase activity were isolated and classified as Bacillus cereus, Achromobacter xylosooxidans, Bacillus sp., Pseudomonas sp. and Pseudomonas paucimobilis. The screening was carried out by preparing enrichment cultures containing glutaryl-7-ADCA or cephalosporin C as the selective carbon source. Four model compounds (adipoyl-, glutamyl- and glutaryl-p-nitroanilide and glutarylcoumarin), mimicking the glutaryl-7 ADCA -lactam moiety, were synthesized as substrates suitable for the rapid screening of the microorganisms (2500) isolated from the enrichment cultures. A total of 300 strains were active on the model substrates and only 5 displayed acylase activity on glutaryl-7 ADCA. The fermentation parameters, such as pH and inducer concentration, for the optimal acylase expression and acylase specificity towards the model substrates were different for each strain.