Microbiology of rice soils

Changes in arsenic mobility and speciation across a 2000-year-old paddy soil chronosequence

Rice accumulates arsenic (As) when cultivated under flooded conditions in paddy soils threatening rice yield or its safety for human consumption, depending on As speciation. During long-term paddy use, repeated redox cycles systematically alter soil biogeochemistry and microbiology. In the present study, incubation experiments from a 2000-year-old paddy soil chronosequence revealed that As mobilization and speciation also change with paddy soil age. Younger paddies (≤100 years) showed the highest total As mobilization, with speciation dominated by carcinogenic inorganic oxyarsenic species and highly mobile inorganic thioarsenates. Inorganic thioarsenates formed by a high availability of reduced sulfur (S) due to low concentrations of reducible iron (Fe) and soil organic carbon (SOC). Long-term paddy use (>100 years) resulted in higher microbial activity and SOC, increasing the share of phytotoxic methylated As. Methylated oxyarsenic species are precursors for cytotoxic methylated thioarsenates. Methylated thioarsenates formed in soils of all ages being limited either by the availability of methylated As in young soils or that of reduced-S in older ones. The present study shows that via a linkage of As to the biogeochemistry of Fe, S, and C, paddy soil age can influence the kind and the extent of threat that As poses for rice cultivation.

Efficient biodegradation of the recalcitrant organochlorine pesticide chlordecone under methanogenic conditions

Anaerobic digestion (AD) has long been studied as an effective environmental and economic strategy for treating matrices contaminated with recalcitrant pollutants. In the present work, we investigated the bioremediation potential of AD on organic waste contaminated with chlordecone (CLD), an organochlorine pesticide extensively used in the French West Indies and classified among the most persistent organic pollutants. Digestates from animal and plant origins were supplemented with CLD and incubated under methanogenic conditions for over 40 days. The redox potential and pH monitoring showed that methanogenic conditions were preserved during the entire incubation period despite the presence of CLD. In addition, the comparison of the total biogas generated from digestates with and without CLD demonstrated no adverse effects of CLD on biogas production. For the first time, a QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) extraction method, followed by GC-MS and LC-HRMS analyses, was developed to quantify CLD and its main known transformation products (TPs) in AD experiments. A decrease in CLD concentrations was evident to a greater extent under thermophilic conditions (55 °C) compared to mesophilic conditions (37.5 °C) (CLD removal of 85 % and 42 %, respectively, after 40 days of incubation). CLD degradation was confirmed by the detection and quantification of several TPs: 10-monohydroCLD (A1), two dihydroCLDs different from 2,8-dihydroCLD (A3), pentachloroindene (B1), tetrachloroindenes (B2, B3/B4), tetra- and tri-chloroindenecarboxylic acids (C1/C2, C3/C4). Determining TPs concentrations using the QuEChERS method provided an overview of CLD fate in AD. Overall, these results reveal that AD processes can efficiently degrade CLD into several TPs from A, B, and C families while maintaining satisfactory biogas production. They pave the way to developing a scaled-up AD process capable of treating CLD-contaminated organic wastes produced by farming, thus stopping any further transfer of CLD.

Degradation of Alpha-, Beta-, and Gamma-Hexachlorocyclohexane by a Soil Bacterium under Aerobic Conditions

A Pseudomonas sp., isolated from sugarcane rhizosphere soil, readily metabolized not only alpha and gamma isomers of hexachlorocyclohexane, but also the thermodynamically more stable beta isomer, under aerobic conditions. Bacterial degradation of the three isomers led to the accumulation of a transitory metabolite and eventual release of covalently linked chlorine as chloride in stoichiometric amounts.

Application of zerovalent iron (Fe(0)) to enhance degradation of HCHs and DDX in soil from a former organochlorine pesticides manufacturing plant

Remediation of pesticide-polluted soil is particularly challenging when pesticides in soil are aged and a mixture of pesticides is present. Application of zerovalent iron (Fe(0)) was investigated to accelerate the degradation of HCHs (alpha-, beta-, gamma- and delta-hexachlorocyclohexane) and DDX (DDT, DDE and DDD) in the soil from a former organochlorine pesticide manufacturing plant. Ultrasonic extraction was used extract the organochlorine pesticides from soil. The identification and quantification of organochlorine pesticides in the extracts were accomplished by gas chromatograph. The addition of Fe(0) facilitated the degradation of the beta-HCH isomer, but had little effect on the degradation of alpha-HCH, gamma-HCH and delta-HCH. Zerovalent iron significantly increased the degradation of p,p'-DDT and o,p'-DDT in soil, and the percentage degradation of p,p'-DDT and o,p'-DDT increased with increased Fe(0) concentration during the first period of incubation. However, the amount of p,p'-DDD, the main dechlorinated product of p,p'-DDT, basically kept increased except in the unamended soil. The addition of Fe(0) therefore did not increased the percent degradation of summation SigmaDDT (p,p'-DDT+p,p'-DDD+p,p'-DDE) markedly.

Biodegradation of hexachlorocyclohexane (HCH) by microorganisms

The organochlorine pesticide Lindane is the gamma-isomer of hexachlorocyclohexane (HCH). Technical grade Lindane contains a mixture of HCH isomers which include not only gamma-HCH, but also large amounts of predominantly alpha-, beta- and delta-HCH. The physical properties and persistence of each isomer differ because of the different chlorine atom orientations on each molecule (axial or equatorial). However, all four isomers are considered toxic and recalcitrant worldwide pollutants. Biodegradation of HCH has been studied in soil, slurry and culture media but very little information exists on in situ bioremediation of the different isomers including Lindane itself, at full scale. Several soil microorganisms capable of degrading, and utilizing HCH as a carbon source, have been reported. In selected bacterial strains, the genes encoding the enzymes involved in the initial degradation of Lindane have been cloned, sequenced, expressed and the gene products characterized. HCH is biodegradable under both oxic and anoxic conditions, although mineralization is generally observed only in oxic systems. As is found for most organic compounds, HCH degradation in soil occurs at moderate temperatures and at near neutral pH. HCH biodegradation in soil has been reported at both low and high (saturated) moisture contents. Soil texture and organic matter appear to influence degradation presumably by sorption mechanisms and impact on moisture retention, bacterial growth and pH. Most studies report on the biodegradation of relatively low (< 500 mg/kg) concentrations of HCH in soil. Information on the effects of inorganic nutrients, organic carbon sources or other soil amendments is scattered and inconclusive. More in-depth assessments of amendment effects and evaluation of bioremediation protocols, on a large scale, using soil with high HCH concentrations, are needed.

Metabolism of gamma-hexachlorocyclohexane by Arthrobacter citreus strain BI-100: Identification of metabolites

Growth characteristics of the aerobic bacterial strain Arthrobacter citreus BI-100 in mineral salts medium with gamma-hexachlorocyclohexane (gamma-HCH) as the sole source of carbon and degradation of gamma-HCH by the strain are reported. The highest yield of the bacteria is observed at a gamma-HCH concentration of 100 mg/L. At this concentration, the bacteria entered the exponential phase of growth without any lag. At 8 h of growth, no residual HCH, but its metabolites, was detectable in the medium. The bacterium attained its stationary phase at 48 h and at 72 h; no metabolite of gamma-HCH could be detected by gas chromatography. Six metabolic intermediates of gamma-HCH produced by A. citreus BI-100 at different periods of growth were characterized by using gas chromatography-mass spectrometry and high-performance liquid chromatography, which furnished evidence for the presence of gamma-1,3,4,5,6-pentachlorocyclohexene, tetrachlorocyclohexene, trichlorocyclohexa-diene, 2-chlorophenol, phenol, and catechol, among others.

Biodegradation of hexachlorocyclohexane isomers in soil and food environment

Persistence of chlorinated hydrocarbon insecticides in the environment is well documented. One early introduced insecticide, hexachlorocyclohexane (HCH), popularly called BHC, was used in large quantities all over the world until recently. In India, even today, technical grade HCH is being used extensively. Theoretically, HCH has eight possible stereoisomers of which four (alpha, beta, gamma, and delta) predominate in the technical product. These isomers significantly differ between themselves with respect to their persistence and toxicity toward insects, birds, mammals, and other nontarget organisms. The relative proportion of HCH isomers is, therefore, crucial from a toxicology standpoint. This problem assumes importance in light of reports that the HCH isomers undergo interconversion in soil, water, animals, plants, insects, etc. The persistence of HCH can be attributed in part to the interconversion of HCH isomers, which also restrict their solubility. In the present review, biotransformation of HCH isomers, both under aerobic and anaerobic conditions, and their degradation pathways have been described. In addition, emphasis is given to the interconversion of HCH isomers, including interconversion mechanisms, as this area has not received adequate coverage in earlier reviews on HCH.

Microbial reductive dehalogenation

A wide variety of compounds can be biodegraded via reductive removal of halogen substituents. This process can degrade toxic pollutants, some of which are not known to be biodegraded by any other means. Reductive dehalogenation of aromatic compounds has been found primarily in undefined, syntrophic anaerobic communities. We discuss ecological and physiological principles which appear to be important in these communities and evaluate how widely applicable these principles are. Anaerobic communities that catalyze reductive dehalogenation appear to differ in many respects. A large number of pure cultures which catalyze reductive dehalogenation of aliphatic compounds are known, in contrast to only a few organisms which catalyze reductive dehalogenation of aromatic compounds. Desulfomonile tiedjei DCB-1 is an anaerobe which dehalogenates aromatic compounds and is physiologically and morphologically unusual in a number of respects, including the ability to exploit reductive dehalogenation for energy metabolism. When possible, we use D. tiedjei as a model to understand dehalogenating organisms in the above-mentioned undefined systems. Aerobes use reductive dehalogenation for substrates which are resistant to known mechanisms of oxidative attack. Reductive dehalogenation, especially of aliphatic compounds, has recently been found in cell-free systems. These systems give us an insight into how and why microorganisms catalyze this activity. In some cases transition metal complexes serve as catalysts, whereas in other cases, particularly with aromatic substrates, the catalysts appear to be enzymes.

Dissipation of some organochlorine insecticides in cropped and uncropped soil

Dissipation of four organochlorine insecticides, viz. aldrin, HCH, chlordane and heptachlor was studied in a sandy loam soil with and without crops during a period of 10 cropping seasons. Dissipation of all chemicals followed first-order kinetics (r(2)=0.537 - 0.976) with almost similar persistence in cropped and uncropped soils for all the insecticides. The average half-lives, (t(1/2) values) for total residues of aldrin, HCH, chlordane, and heptachlor in cropped treatments were 80.7, 58.8, 93.2, and 110 days. Their respective values in fallow plots were 78.4, 83.8, 154, and 116 days. None of the parent compounds or their isomers could be detected below the 20 cm depth at the termination of the experiment. Highest residue concentrations were observed in the surface 10 cm layer in fallow plots, but in the deeper (10-20 cm) layer in cropped plots. Analysis of plants and grains showed significant residues of all the chemicals. Degradation of these compounds in cropped and uncropped plots is discussed with regard to their volatilization, microbial degradation, leaching, and plant uptake.

Dynamics of Methane Production, Sulfate Reduction, and Denitrification in a Permanently Waterlogged Alder Swamp

The dynamics of sulfate reduction, methane production, and denitrification were investigated in a permanently waterlogged alder swamp. Molybdate, an inhibitor of sulfate reduction, stimulated methane production in soil slurries, thus suggesting competition for common substrates between sulfate-reducing and methane-producing bacteria. Acetate, hydrogen, and methanol were found to stimulate both sulfate reduction and methane production, while trimethylamine mainly stimulated methane production. Nitrate addition reduced both methane production and sulfate reduction, either as a consequence of competition or poisoning of the bacteria. Sulfate-reducing bacteria were only slightly limited by the availability of electron acceptors, while denitrifying bacteria were seriously limited by low nitrate concentrations. Arrhenius plots of the three processes revealed different responses to temperature changes in the slurries. Methane production was most sensitive to temperature changes, followed by denitrification and sulfate reduction. No significant differences between slope patterns were observed when comparing summer and winter measurements, indicating similar populations regarding temperature responses.