Pristine Soil Research Articles

Physical transformations of iron oxide and silver nanoparticles from an intermediate scale field transport study

In recent years, there has been increasing concern regarding the fate and transport of engineered nanoparticles (NPs) in environmental systems and the potential impacts on human and environmental health due to the exponential increase in commercial and industrial use worldwide. To date, there have been relatively few field-scale studies or laboratory-based studies on environmentally relevant soils examining the chemical/physical behavior of the NPs following release into natural systems. The objective of this research is to demonstrate the behavior and transfor- mations of iron oxide and silver NPs with different capping ligands within the unsaturated zone. Here, we show that NP transport within the vadose zone is minimal primarily due to heteroaggregation with soil surface coatings with results that (99 % of the NPs remained within 5 cm of the original source after 1 year in intermediate-scale field lysimeters. These results suggest that transport may be overestimated when compared to previous laboratory-scale studies on pristine soils and pure minerals and that future work must incorporate more environmentally relevant parameters.

Trace metal distribution in pristine permafrost-affected soils of the Lena River delta and its hinterland, northern Siberia, Russia

Abstract. Soils are an important compartment of ecosystems and have the ability to buffer and immobilize substances of natural and anthropogenic origin to prevent their movement to other environment compartments. Predicted climatic changes together with other anthropogenic influences on Arctic terrestrial environments may affect biogeochemical processes enhancing leaching and migration of trace elements in permafrost-affected soils. This is especially important since Arctic ecosystems are considered to be highly sensitive to climatic changes as well as to chemical contamination. This study characterises background levels of trace metals in permafrost-affected soils of the Lena River delta and its hinterland in northern Siberia (73.5–69.5° N), representing a remote region far from evident anthropogenic trace metal sources. Investigations on the element content of iron (Fe), arsenic (As), manganese (Mn), zinc (Zn), nickel (Ni), copper (Cu), lead (Pb), cadmium (Cd), cobalt (Co), and mercury (Hg) in different soil types developed in different geological parent materials have been carried out. The highest median concentrations of Fe and Mn were observed in soils belonging to ice-rich permafrost sediments formed during the Pleistocene (ice-complex) while the highest median values of Ni, Pb and Zn were found in soils of both the ice-complex and the Holocene estuarine terrace of the Lena River delta region, as well as in the southernmost study unit of the hinterland area. Detailed observations of trace metal distribution on the micro scale showed that organic matter content, soil texture and iron-oxide contents influenced by cryogenic processes, temperature, and hydrological regimes are the most important factors determining the metal abundance in permafrost-affected soils. The observed range of trace element background concentrations was similar to trace metal levels reported for other pristine northern areas.

DOC and CO2-C Releases from Pristine and Drained Peat Soils in Response to Water Table Fluctuations: A Mesocosm Experiment

Hydrological conditions are considered to be among the main drivers influencing the export of dissolved organic carbon (DOC) from terrestrial to aquatic ecosystems, and hydrology is likely to alter due to climate change. We built a mesocosm experiment by using peat profiles from a pristine and from a drained (drained in 1978) peatland. A several-week-long low water table period followed by a high water table period, that is, a setting mimicking drought followed by flood, released relatively more DOC from pristine peat than from drained peat. From pristine peat profiles DOC was released into soil water in such quantities that the concentration of DOC remained stable despite dilution caused by added spring water to the mesocosms. In drained peat the DOC concentrations decreased during the high water table period indicating stronger dilution effect in comparison to pristine peat. At the landscape level DOC load from a drained peatland to the recipient water body may, however, increase during flooding because of high water runoff out of the peatland containing high DOC concentrations relative to the forest and agricultural areas. During the high water table period neither peat type nor water table had any clear impact on carbon dioxide (CO2-C) fluxes.

Modelling groundwater residence time in a sub‐irrigated buffer zone

ABSTRACTThis study focuses on the short groundwater residence time induced by the development of a dense rooting system in a forested area employed as a buffer zone planned for nitrogen removal. The buffer zone consists of a rectangular area of 0·7 ha sub‐irrigated by two ditches and drained by an outflow ditch lying in the centre of the area. The pristine soil (silty clay loam) was characterized by a low hydraulic conductivity, but the agricultural practice first, and then the rooting system increased the permeability of the top soil. This was confirmed by the elevated discharge in the outflow ditch and by the elevated hydraulic conductivity values determined via slug tests. The groundwater residence time was monitored, once the rooting system was completely developed, via Rhodamine‐WT injection in the inflow ditch. The breakthrough curves were simulated using a one‐dimensional analytical model (CXTFIT) to calculate the residence time. In addition, a three‐dimensional flow and transport model (MODFLOW and MT3DMS) was calibrated using piezometric heads, groundwater fluxes and Rhodamine‐WT concentrations. The CXTFIT model overestimated the dispersivity and underestimated velocity respect to MT3DMS. This study shows that residence time can decrease respect to the value expected from the hydraulic conductivities of the pristine soils and that one‐dimensional analytical models can give a false impression compared with soil parameters respect to three‐dimensional flow and transport models. Given the importance of the residence time for biological processes in buffer zones, a greater effort is needed to improve measurement techniques on subsurface flow's heterogeneity. Copyright © 2013 John Wiley & Sons, Ltd.

Probing the functional diversity of global pristine soil communities with 3-chlorobenzoate reveals that communities of generalists dominate catabolic transformation.

Understanding of functional diversity of microbial populations has lagged description of their molecular diversity. Differences in substrate specificity, kinetics, products, and regulation can dramatically influence phenotypic variation among closely related strains, features that are missed when the strains studied are the fastest-growing and most easily isolated from serial enrichments. To investigate the broader bacterial diversity underlying degradation of anthropogenic chemicals in nature, we studied the 3-chlorobenzoate (3-CBA) degradation rate in a collection of aerobic 3-CBA degraders previously isolated from undisturbed soils in two representative ecosystems: (i) Mediterranean sclerophyllous woodlands in California, Chile, South Africa, and Australia and (ii) boreal forests in Canada and Russia. The majority of isolates degraded 3-CBA slowly and did not completely mineralize 1.0 mM 3-CBA within 1 week. Those with intermediate degradation rates had incomplete degradation pathways and produced colored intermediates indicative of chlorocatechol, a product likely metabolized by other members of the community. About 10% of the isolates grew rapidly and mineralized greater than 90% of the 3-CBA, but because of population heterogeneity in soil, they are likely not large contributors to a soil's total transformation capacity. This suggests that xenobiotic degradation in nature is carried out by a community of cometabolic generalists and not by the efficient specialists that have been traditionally studied in the laboratory. A subset of 58 genotypically distinct strains able to degrade >80% of the 3-CBA was examined for their catabolic versatility using 45 different compounds: mono- and dichlorinated benzoates, phenols, anilines, toluenes, nitrobenzenes, chlorobenzenes, and 2,4-dichlorophenoxyacetic acid. The isolates degraded from 2 to more than 30 compounds with a median of 7, but there was no correlation to habitat of isolation or 3-CBA activity. However, these findings were indicative of finer-scale functional diversity.

The microbial communities and potential greenhouse gas production in boreal acid sulphate, non-acid sulphate, and reedy sulphidic soils

Acid sulphate (AS) soils along the Baltic coasts contain significant amounts of organic carbon and nitrogen in their subsoils. The abundance, composition, and activity of microbial communities throughout the AS soil profile were analysed. The data from a drained AS soil were compared with those from a drained non-AS soil and a pristine wetland soil from the same region. Moreover, the potential production of methane, carbon dioxide, and nitrous oxide from the soils was determined under laboratory conditions. Direct microscopic counting, glucose-induced respiration (GIR), whole cell hybridisation, and extended phospholipid fatty acid (PLFA) analysis confirmed the presence of abundant microbial communities in the topsoil and also in the deepest Cg2 horizon of the AS soil. The patterns of microbial counts, biomass and activity in the profile of the AS soil and partly also in the non-AS soil therefore differed from the general tendency of gradual decreases in soil profiles. High respiration in the deepest Cg2 horizon of the AS soil (5.66μgCg−1h−1, as compared to 2.71μgCg−1h−1 in a top Ap horizon) is unusual but reasonable given the large amount of organic carbon in this horizon. Nitrous oxide production peaked in the BCgc horizon of the AS and in the BC horizon of the non-AS soil, but the peak value was ten-fold higher in the AS soil than in the non-AS soil (82.3 vs. 8.6ngNg−1d−1). The data suggest that boreal AS soils on the Baltic coast contain high microbial abundance and activity. This, together with the abundant carbon and total and mineral nitrogen in the deep layers of AS soils, may result in substantial gas production. Consequently, high GHG emissions could occur, for example, when the generally high water table is lowered because of arable farming.

Previous exposure advances the degradation of an anthropogenic s-triazine regardless of soil origin

Previous investigations—field samplings and laboratory experiments—support the hypothesis that the degradation of s-triazines is enhanced in previously exposed as compared to pristine soils in terrestrial environments. Despite this, bottlenecks of soil sampling and various soil modification practices in microcosm studies have made it difficult to guarantee that previous contamination history enhances contaminant degradation regardless of soil origin in terrestrial ecosystems. We test the hypothesis that the degradation of simazine (2-chloro-4,6-bis(ethylamino)-s-triazine) is enhanced in previously exposed soils as compared to pristine soils in 10 l buckets at the mesocosm scale. We collected soil at three separate sites consisting of a previously exposed and a pristine field. At every field, soil was collected at three separate plots and simazine degradation (days 0 and 65) and the response to atzB degrader gene primers (days 0 and 110) were followed. We analyzed the results using analysis of covariance (ANCOVA). Previous exposure and field site were assessed as fixed factors and initial simazine concentration and abiotic soil conditions as covariates. After the 65-day exposure, remaining simazine concentrations depended on previous exposure but not on collection site. The response to atzB gene primers was positive in all mesocosms where simazine degradation had been rapid. Soil moisture, pH, and organic matter content were insignificant. If soil moisture was not included in the ANCOVA model, previous exposure did not appear as a significant factor. The results support the hypothesis that simazine is degraded more rapidly in previously exposed soils as compared to pristine environments, provided that degradation genes are available. Previously exposed soil might be used to enhance the degradation of simazine in recently contaminated terrestrial soils, supposing that the central requirements for microbial growth are adequate.

The culturable soil antibiotic resistome: a community of multi-drug resistant bacteria.

Understanding the soil bacterial resistome is essential to understanding the evolution and development of antibiotic resistance, and its spread between species and biomes. We have identified and characterized multi-drug resistance (MDR) mechanisms in the culturable soil antibiotic resistome and linked the resistance profiles to bacterial species. We isolated 412 antibiotic resistant bacteria from agricultural, urban and pristine soils. All isolates were multi-drug resistant, of which greater than 80% were resistant to 16–23 antibiotics, comprising almost all classes of antibiotic. The mobile resistance genes investigated, (ESBL, bla NDM-1, and plasmid mediated quinolone resistance (PMQR) resistance genes) were not responsible for the respective resistance phenotypes nor were they present in the extracted soil DNA. Efflux was demonstrated to play an important role in MDR and many resistance phenotypes. Clinically relevant Burkholderia species are intrinsically resistant to ciprofloxacin but the soil Burkholderia species were not intrinsically resistant to ciprofloxacin. Using a phenotypic enzyme assay we identified the antibiotic specific inactivation of trimethoprim in 21 bacteria from different soils. The results of this study identified the importance of the efflux mechanism in the soil resistome and variations between the intrinsic resistance profiles of clinical and soil bacteria of the same family.

Influence of soil pollution on the composition of a microbial community

The abundance dynamics and composition of indigenous soil microbial communities were studied in soils polluted with naphthalene, dioctyl phthalate, diesel fuel, and crude oil. DGGE analysis of the 16S rRNA genes amplified from the total soil DNA revealed that the bacterial community of uncontaminated soil was more diverse and included no dominant species. In the soil samples polluted with the crude oil, diesel fuel, or dioctyl phthalate, Pseudomonas became the dominant bacteria since the third day of the experiment. In the soil polluted with naphthalene, two genera of bacteria (Pseudomonas and Paenibacillus) were dominant in population on the third day of the experiment, while on the 21th day of the experiment Arthrobacter became dominant. During the experiment, the average number of indigenous bacterial degraders increased approximately by two orders of magnitude. While the key genes of naphthalene catabolism, nahAc and nahH, were not detected in the pristine soil, they were found in a significant amount on the third day after naphthalene addition. Three degrader strains harboring the plasmids of naphthalene biodegradation (IncP-9 group) were isolated on the third day from the soil polluted with naphthalene. Two of these plasmids, although isolated from various degraders, were shown to be identical.

Using Lanthanum, Neodymium, and Thorium as Conservative Indexing Elements to Indicate Soil Lead Deposition

A critical need exists for data evaluation protocols to determine if heavy metal deposition has impacted soil or sediment. For routine reconnaissance these protocols need to be analytically precise and affordable, two issues lacking in many regions. We employed a low-cost, commercially available aqua regia digestion procedure and developed a simple protocol for isolating pristine soil horizons and conservative indexing elements to compare to more Pb impacted soil horizons. Strongly Pb impacted soil horizons are easy to ascertain; however, moderately to slightly Pb impacted soils are more problematic to identify because of the natural Pb variation in soils. Using the harmonic mean of the soil concentrations of Lanthanum (La) and Neodymium (Nd) and also the soil concentrations of Thorium (Th) as conservative indexing elements, we were able to discriminate pristine soils from slightly to moderately Pb impacted soils. Ro values are estimators of elemental gain and loss, with Ro values greater than unity implying Pb addition, providing the comparative loss of other elements or biocycling are substantial contributing factors. All pedons known to have received Pb from atmospheric addition exhibited Ro values appreciably greater than unity, whereas soils known to be not impact or at most minimally impacted showed Ro values near unity. Commercially available and relative low cost aqua regia digestion analysis provided the analytical data for Pb, Fe, La, Nd and Th.

Chlorine Isotope Effects and Composition of Naturally Produced Organochlorines from Chloroperoxidases, Flavin-Dependent Halogenases, and in Forest Soil

The use of stable chlorine isotopic signatures (δ(37)Cl) of organochlorine compounds has been suggested as a tool to determine both their origins and transformations in the environment. Here we investigated the δ(37)Cl fractionation of two important pathways for enzymatic natural halogenation: chlorination by chloroperoxidase (CPO) and flavin-dependent halogenases (FDH). Phenolic products of CPO were highly (37)Cl depleted (δ(37)Cl = -12.6 ± 0.9‰); significantly more depleted than all known industrially produced organochlorine compounds (δ(37)Cl = -7 to +6‰). In contrast, four FDH products did not exhibit any observable isotopic shifts (δ(37)Cl = -0.3 ± 0.6‰). We attributed the different isotopic effect to the distinctly different chlorination mechanisms employed by the two enzymes. Furthermore, the δ(37)Cl in bulk organochlorines extracted from boreal forest soils were only slightly depleted in (37)Cl relative to inorganic Cl. In contrast to previous suggestions that CPO plays a key role in production of soil organochlorines, this observation points to the additional involvement of either other chlorination pathways, or that dechlorination of naturally produced organochlorines can neutralize δ(37)Cl shifts caused by CPO chlorination. Overall, this study demonstrates that chlorine isotopic signatures are highly useful to understand sources and cycling of organochlorines in nature. Furthermore, this study presents δ(37)Cl values of FDH products as well of bulk organochlorines extracted from pristine forest soil for the first time.

Bioremediation Approaches in a Laboratory Activity for the Industrial Biotechnology and Applied Microbiology (IBAM) Course

Industrial Biotechnology and Applied Microbiology is an optional 128h-course for Chemistry and Biology students at the Faculty of Sciences, University of Buenos Aires, Argentina. This course is usually attended by 25 students, working in teams of two. The curriculum, with 8 lab exercises, includes an oil bioremediation practice covering an insight of bioremediation processes: the influence of pollutants on autochthonous microbiota, biodegrader isolation and biosurfactant production for bioavailability understanding. The experimental steps are: (A) evaluation of microbial tolerance to pollutants by constructing pristine soil microcosms contaminated with diesel or xylene and (B) isolation of degraders and biosurfactant production analysis. To check microbial tolerance, microcosms are incubated during one week at 25-28ºC. Samples are collected at 0, 4 and every 48 h for CFU/g soil testing. An initial decrease of total CFU/g related to toxicity is noticed. At the end of the experiment, a recovery of the CFU number is observed, evidencing enrichment in biodegraders. Some colonies from the CFU counting plates are streaked in M9-agar with diesel as sole carbon source. After a week, isolates are inoculated on M9-Broth supplemented with diesel to induce biosurfactant production. Surface tension and Emulsification Index are measured in culture supernatants to visualize tensioactive effect of bacterial products. Besides the improvement in the good microbiological practices, the students show enthusiasm in different aspects, depending on their own interests. While biology students explore and learn new concepts on solubility, emulsions and bioavailability, chemistry students show curiosity in bacterial behavior and manipulation of microorganisms for environmental benefits.

Layer of organic pine forest soil on top of chlorophenol-contaminated mineral soil enhances contaminant degradation

Chlorophenols, like many other synthetic compounds, are persistent problem in industrial areas. These compounds are easily degraded in certain natural environments where the top soil is organic. Some studies suggest that mineral soil contaminated with organic compounds is rapidly remediated if it is mixed with organic soil. We hypothesized that organic soil with a high degradation capacity even on top of the contaminated mineral soil enhances degradation of recalcitrant chlorophenols in the mineral soil below. We first compared chlorophenol degradation in different soils by spiking pristine and pentachlorophenol-contaminated soils with 2,4,6-trichlorophenol in 10-L buckets. In other experiments, we covered contaminated mineral soil with organic pine forest soil. We also monitored in situ degradation on an old sawmill site where mineral soil was either left intact or covered with organic pine forest soil. 2,4,6-Trichlorophenol was rapidly degraded in organic pine forest soil, but the degradation was slower in other soils. If a thin layer of the pine forest humus was added on top of mineral sawmill soil, the original chlorophenol concentrations (high, ca. 70 μg g(-1), or moderate, ca. 20 μg g(-1)) in sawmill soil decreased by >40 % in 24 days. No degradation was noticed if the mineral soil was kept bare or if the covering humus soil layer was sterilized beforehand. Our results suggest that covering mineral soil with an organic soil layer is an efficient way to remediate recalcitrant chlorophenol contamination in mineral soils. The results of the field experiment are promising.

Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure

Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.

Effect of ultraviolet radiation (UVR) on the tropical microalga Chlorella vulgaris

The effect of ultraviolet radiation (UVR) on the growth, lipid content and fatty acid profile of the tropical microalga Chlorella vulgaris UMACC 001 was investigated under laboratory and natural UVR conditions. The Chlorella was exposed to 10 days of PAR+UVA+UVB (1.17 Wm-2), PAR+UVA (8.54 Wm-2) and PAR alone (42 µmolm-2s-1) in the laboratory study. The natural UVR study was carried out by exposing the cultures to the natural environment on the roof-top of the Institute of Graduate Studies Building, University of Malaya for 54 hours. The average levels of UVA radiation, UVB radiation and PAR irradiance over the exposure period ranged from 3.66 to 27.95 Wm-2, 1.61 to 16.50 Wm-2 and 282 to 1480 µmol m-2s-1, respectively. UVA radiation did not affect the growth of Chlorella vulgaris UMACC 001 in both the laboratory and natural UVR studies. In contrast, growth was adversely affected by UVB radiation in the laboratory study. UVB radiation is known to decrease the stability of D1 protein (the herbicide binding protein of chloroplasts) of the photosystem II reaction centre (PSII), affect rubisco activity, pigment composition as well as generate superoxide dismutase, all of which would reduce photosynthesis and growth. No significant difference was observed in the lipid content of the cultures exposed to UVR compared to PAR alone in both laboratory and roof-top (natural UVR) cultures. Chlorella vulgaris UMACC 001 exhibited different response in fatty acid profiles under laboratory condition compared to roof-top (natural UVR) cultures. In the laboratory condition, more saturated fatty acids (SFA) were produced in the cultures exposed to laboratory-produced UVB radiation compared to PAR alone, while more polyunsaturated fatty acids (PUFAs) were produced in the cultures exposed to natural UVB radiation compared to PAR alone. Kesan radiasi ultraungu ke atas pertumbuhan, kandungan lemak dan profil asid lemak bagi mikroalga tropika Chlorella vulgaris UMACC 001 telah disiasat dalam keadaan makmal dan semulajadi. Chlorella tersebut didedah kepada PAR+UVA+UVB (1.17 Wm-2), PAR+UVA (8.54 Wm-2) dan PAR persendirian (42 mol m-2s-1) selama 10 hari dalam kajian makmal. Kajian semulajadi radiasi ultraungu dijalankan dengan mendedahkan kultur tersebut kepada persekitaran semulajadi di atas bumbung bangunan Institut Penggajian Pascasiswazah, Universiti Malaya selama 54 jam. Paras purata radiasi UVA, UVB dan PAR dalam tempoh pendedahan radiasi ultraungu semulajadi adalah 3.66 hingga 27.95 Wm-2, 1.61 hingga 16.50 Wm-2 dan 282 hingga 1480 µmol m-2s-1, masing-masing. Tiada kesan radiasi UVA ke atas tumbesaran Chlorella vulgaris UMACC 001 dalam kedua-dua eksperimen makmal dan semulajadi. Sebaliknya tumbesaran mikroalga tersebut menurun dengan ketara apabila didedahkan kepada radiasi UVB di dalam makmal. Diketahui bahawa radiasi UVB mengurangkan kestabilan protein D1 dalam fotosistem II (PSII), mempengaruhi aktiviti rubisco, komposisi pigment dan menghasilkan radikal superoxide yang mana semua akan mengurangkan fotosintesis dan tumbesaran. Tiada perbezaan ketara diperhatikan dalam kandungan lemak bagi kultur yang didedahkan kepada radiasi ultraungu berbanding dengan PAR persendirian dalam kedua-dua kajian makmal dan semulajadi. Chlorella vulgaris UMACC 001 menunjukkan tindak balas yang berbeza dalam profil asid lemak apabila kultur tersebut didedahkan kepada radiasi ultraungu dalam keadaan makmal dan semulajadi. Dalam keadaan makmal, lebih banyak asid lemak tepu (SFA) dihasilkan dalam kultur yang didedahkan kepada radiasi UVB berbanding dengan PAR persendirian, tetapi lebih banyak asid lemak poli tidak tepu (PUFAs) dihasilkan dalam kultur yang didedahkan kepada radiasi ultraungu-B semulajadi berbanding dengan PAR persendirian di atas bumbung (radiasi ultraungu semulajadi).

Distribution of alkane-degrading bacterial communities in soils from King George Island, Maritime Antarctic

The structure of alkane-degrading bacterial communities, which are present in both the hydrocarbon-polluted and pristine soils of King George Island in Maritime Antarctic, was studied using molecular methods. Polymerase Chain Reaction (PCR) amplifications of the alkane monooxygenase AlkB-coding genes, followed by Restriction Fragment Length Polymorphism (PCR-RFLP) and Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analyses, revealed the widespread presence and complex diversity of alkane-utilizing bacteria in these soils. The resulting dendrograms and Canonical Correspondence Analyses (CCA) of PCR-RFLP and PCR-DGGE patterns showed that the characteristics of the different soils, such as physicochemical properties, soil type and/or hydrocarbon contamination levels, affect the distribution of alkane-degrading bacteria. Sequencing of 20 DGGE bands revealed the presence in Antarctic soils of alkane monooxygenases with low similarity (61–91%) compared to those previously described in Gram-positive bacteria, such as Mycobacterium, Gordonia, Rhodococcus and Aeromicrobium. The high diversity of alkB genes in the soils of King George Island suggests the potential for oil pollutant degradation.

The effect of clear cutting on podzolisation and soil carbon dynamics in boreal forests (Middle Taiga zone, Russia)

Boreal forests are one of the most important terrestrial carbon sink, and a large portion of C is allocated in soil for long-term storage. However forest harvesting may quickly affect soil carbon stocks and dynamics, especially where organic substances drive the soil-forming processes, such as in Podzols. To evaluate the effects of clear cutting on carbon dynamics and podzolisation process over a short time period, a pristine boreal forest (Komi Republic, Russian Federation) and a recently clear cut site (5year-old) were selected. Soils are polygenic: podzolisation occurs within the clay-depleted eluvial horizon, formed by a previous lessivage process. Because podzolisation can start only after the eluvial horizon has reached a sort of threshold, bisequal soils allow to individuate comparable pedogenic conditions prior to anthropogenic disturbances.After harvesting, C storage tended to increase in the upper part of the soil profile (organic layer and podzolic sequum) from 2.2 to 5.0kgm−2. The abundance of woody materials on the forest floor together with an increase in soil water saturation, discernible by the vegetation survey and iron fractionation, prevented litter degradation and allowed organic matter accumulation at the soil surface. Fulvic acids (FA) in the organic layer of the pristine site showed a low incorporation of polysaccharide and proteinaceous moieties, confirming a higher degradation of the humified fraction than at the clear cut site. The lack of disturbances allowed a selection of FA with the more oxidised and mobile fractions accumulating in the deeper horizons, as currently observed in Podzols. Almost no differences were instead found in the chemical composition of FA along the profile from the clear cut site. A larger portion of FA showed the tendency to migrate through the profile after clear cutting even below the Bhs horizon (C-fulvic acid/C-humic acid >1) with a marked increase in the FA-carbon stocks with respect to the pristine forest soil (0.66 and 0.30kgm−2 down to 30cm, respectively).Clear cutting also affected Al and Fe dynamics. The reducing conditions acted upon soil mineral surfaces and enhanced Fe mobilisation probably both in the ionic form and complexed with organic matter. The Al dynamics was instead more related to short term transformations of the layer silicate phases. Traces of a poorly crystalline chlorite were detectable in the Bhs in the pristine forest, but at the clear site only hydroxy-interlayered vermiculite was present. The high amounts of organic acids that migrated through the Bhs after clear cutting may have partially complexed the Al from pedogenic chlorite, giving rise to hydroxy-interlayered behaviour, as normally occurs in Podzol eluvial horizons from where the organic Al-complexes migrate.Our findings suggested that if this trend proceeds further the whole podzolic sequum may migrate downwards. This may have important implication on C budget, as organic carbon will be transferred deeper in the soil profile limiting its losses at least over a short time period.

Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases (PAH-RHD) encoding genes in different soils from King George Bay, Antarctic Peninsula

The α-subunit of the polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases (PAH-RHDα) coding genes from Gram-positive and Gram-negative bacteria were characterized in diesel oil-contaminated and pristine soils from King George Island in Maritime Antarctica. PCR, cloning and sequencing methodologies were used, and nucleotide and deduced amino acids sequences were further analyzed using Basic Local Alignment Search Tool (BLAST), Clusters of Orthologous Groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) tools. Few PAH-RHDα sequences sharing high identities with NagAc from Ralstonia sp. U2 and with NahAc from Comamonas testosteroni strain H were found in pristine soil. In addition, PAH-RHDα sharing 44–100% identity with dioxygenases described within the Gram-negative Pseudomonas, Polaromonas, Sphingomonas, Acidovorax and Burkholderia genera and Gram-positive Mycobacterium, Gordonia, Terrabacter, Nocardioides and Bacillus genera were found in contaminated soils adjacent to the Brazilian Antarctic Station Comandante Ferraz. To our knowledge, the presence of PAH-RHDα coding genes from Gram-positive PAH-degrading bacteria has never been evidenced in Antarctic soils. Beta-diversity comparison analysis showed a different distribution of Gram-negative PAH-degrading bacteria among the Antarctic contaminated sites. This study provides important information about the PAH bioremediation potential of the Antarctic soils studied here.

High abundance of genetic Bacteroidetes markers for total fecal pollution in pristine alpine soils suggests lack in specificity for feces

Two frequently applied genetic Bacteroidetes markers for total fecal pollution (AllBac and BacUni) were found in high numbers in pristine soil samples of two alpine catchment areas casting doubt on their value as fecal indicators. This finding underlines the necessity to evaluate assays locally and against non-intestinal samples before application.

Rock Magnetic Investigations of Surface and sub-surface soil Samples from five Lake Catchments in Tropical Southern India

Iron oxide minerals in soils provide valuable insights into pedogenic processes. A wealth of such information has been obtained by rock magnetic investigations on temperate soils but similar studies on tropical soils are rare. Here, we report rock magnetic data on pristine soil profiles and surficial soils from five catchments in the tropical southern India and throw light on the pedogenic processes. We ruled out contributions from greigite, bacterial magnetite and anthropogenic sources; hence, the magnetic signal is mainly from the catchment, principally pedogenic and, thus, has a climatic signature embedded in it. The Pookot profile from a high rainfall (~4000 mm/year) region does not exhibit any magnetic enhancement at the surface. In fact, there is hardly any difference between surface and sub-surface samples, which reflects on its deeply weathered nature as a result of the high rainfall. The Shantisagara profile exhibits lessivage of magnetic minerals, resulting in a thick magnetically enhanced zone. It shows the highest χlf values among the five profiles studied. The Thimmannanayakanakere (TK) and Ayyanakere (AK) soil profiles do not exhibit any magnetic enhancement of top-soil. In fact, χlf values increase towards the profile-bottom, suggesting top-soil erosion, besides contribution of magnetic minerals from parent rocks. In the TK profile, there is a clear distinction between surface and sub-surface samples, the former being magnetically coarser grained. The Kurburukere profile exhibits moderate to strong χlf values and a mild magnetic enhancement at the surface.The data would be useful for establishing soil-sediment linkages for paleoclimatic studies of lake sediments.