Isolation and characterization of a novel simazine-degrading bacterium from agricultural soil of central Chile, Pseudomonas sp. MHP41

Isolation of 2 simazine-degrading bacteria and development of a microbial agent for bioremediation of simazine pollution

Simazine was one of the most commonly used herbicides and was widely used to control broadleaf weeds in agriculture and forestry. Its widespread use had caused wide public concern for its high ecological toxicity. In order to remove simazine residues, 2 strains capable of effectively degrading simazine were isolated from the soil and named SIMA-N5 and SIMA-N9. SIMA-N5 was identified as Bacillus licheniformis by 16SrRNA sequence analysis, and SIMA-N9 was Bacillus altitudinis. According to the degradation ratio of simazine in a certain period of time, the degradation ability of different strains was evaluated. The degradation efficiency of simazine (5 mg/L) by SIMA-N9 could reach about 98% in 5d, and the strain SIMA-N5 could reach 94% under the same conditions. In addition, the addition of Pennisetum rhizosphere soil during the process of degrading simazine by strain SIMA-N9 could effectively improve the degradation efficiency. The strain SIMA-N9 has been developed as a microbial agent for the bioremediation of simazine contamination in soil. The new microbial agent developed by using SIMA-N9 has achieved satisfactory application effects. Based on the research results already obtained in this study, it was considered that strain SIMA-N9 and its live bacterial agent could play an important role in bioremediation of simazine pollution. This study could not only provide a set of solutions to the simazine pollution, but also provide a reference for the treatment of other pesticide pollution.

Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants

Cold stress decreases the growth and productivity of agricultural crops. Psychrotolerant plant growth-promoting bacteria (PGPB) may protect and promote plant growth at low temperatures. The aims of this study were to isolate and characterize psychrotolerant PGPB from wild flora of Andes Mountains and Patagonia of Chile and to formulate PGPB consortia. Psychrotolerant strains were isolated from 11 wild plants (rhizosphere and phyllosphere) during winter of 2015. For the first time, bacteria associated with Calycera, Orites, and Chusquea plant genera were reported. More than 50% of the 130 isolates showed ≥33% bacterial cell survival at temperatures below zero. Seventy strains of Pseudomonas, Curtobacterium, Janthinobacterium, Stenotrophomonas, Serratia, Brevundimonas, Xanthomonas, Frondihabitans, Arthrobacter, Pseudarthrobacter, Paenarthrobacter, Brachybacterium, Clavibacter, Sporosarcina, Bacillus, Solibacillus, Flavobacterium, and Pedobacter genera were identified by 16S rRNA gene sequence analyses. Ten strains were selected based on psychrotolerance, auxin production, phosphate solubilization, presence of nifH (nitrogenase reductase) and acdS (1-aminocyclopropane-1-carboxylate (ACC) deaminase) genes, and anti-phytopathogenic activities. Two of the three bacterial consortia formulated promoted tomato plant growth under normal and cold stress conditions. The bacterial consortium composed of Pseudomonas sp. TmR5a & Curtobacterium sp. BmP22c that possesses ACC deaminase and ice recrystallization inhibition activities is a promising candidate for future cold stress studies.

Activated Carbon and Ozone to Reduce Simazine in Water

In this study, the reduction of the pesticide simazine at an initial concentration of 0.7 mg L−1 in water has been investigated using two different technologies: adsorption with powdered and granulated activated carbon, advanced oxidation processes with ozone and finally, the combination of both technologies. The results obtained for a carbon dose of 16 mg L−1 show that powdered activated carbon, with contact times of 60 min, obtained 81% of reduction and in 24 h 92%, while granulated activated carbon at 60 min obtained a reduction of 2%, rising to 34% after 24 h of contact time. Therefore, powdered activated carbon achieves better reductions compared to granulated; when ozone was applied at a dose of 19.7 mg L−1, with a reaction time of 18 min, a reduction of 93% was obtained, achieving a better reduction in less time than with adsorption treatments; however, during oxidation, by-products of simazine were produced. In the combined treatments, with the same doses of carbon and ozone mentioned above, the treatment that starts with ozone followed by activated carbon powder is recommended due to the adsorption in the last phase reaching a 90% reduction of the simazine and its by-products in 38 min of time.

Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application

The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.

Responses of Vitis vinifera cv. Cabernet Sauvignon roots to the arbuscular mycorrhizal fungus Funneliformis mosseae and the plant growth-promoting rhizobacterium Ensifer meliloti include changes in volatile organic compounds

Arbuscular mycorrhizal (AM) fungi and plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms that may associate with grapevine roots, improving stress tolerance, growth, and nutrition. AM fungi and PGPR enhance the production of plant secondary metabolites, including volatile organic compounds (VOCs) that play a key role in the interaction of plants with the environment and are involved in defence mechanisms. The aim of this study was to analyse the effects of an AM fungus and a rhizobacterium on plant growth and VOCs in Vitis vinifera cv. Cabernet Sauvignon roots to gain insight into the potential role of plant-rhizosphere microorganisms in vine growth and defence. Grapevines were inoculated or not with the AM fungus Funneliformis mosseae IN101 and/or the plant growth-promoting rhizobacterium Ensifer meliloti TSA41. Both microbial strains enhanced plant growth. Fifty-eight VOCs extracted from ground roots were identified using headspace solid-phase microextraction coupled to gas chromatography/mass spectrometry. VOCs were induced by F. mosseae IN101, increasing up to 87% compared with control plants. Monoterpenes were strongly enhanced by F. mosseae IN101, increasing up to 113% compared with control plants. Interestingly, monoterpene alcohols related to plant defence, such as myrtenol, p-cymen-7-ol, and p-mentha-1.8-dien-7-ol were increased. By contrast, E. meliloti TSA41 did not significantly affect VOCs. The knowledge of the effects of AM fungi and PGPR on grapevine VOCs may contribute to an integrated and sustainable management of vineyards.

Microbial Enrichment Culture Responsible for the Complete Oxidative Biodegradation of 3-Amino-1,2,4-triazol-5-one (ATO), the Reduced Daughter Product of the Insensitive Munitions Compound 3-Nitro-1,2,4-triazol-5-one (NTO)

3-Nitro-1,2,4-triazol-5-one (NTO) is one of the main ingredients of many insensitive munitions, which are being used as replacements for conventional explosives. As its use becomes widespread, more research is needed to assess its environmental fate. Previous studies have shown that NTO is biologically reduced to 3-amino-1,2,4-triazol-5-one (ATO). However, the final degradation products of ATO are still unknown. We have studied the aerobic degradation of ATO by enrichment cultures derived from the soil. After multiple transfers, ATO degradation was monitored in closed bottles through measurements of inorganic carbon and nitrogen species. The results indicate that the members of the enrichment culture utilize ATO as the sole source of carbon and nitrogen. As ATO was mineralized to CO₂, N₂, and NH₄⁺, microbial growth was observed in the culture. Co-substrates addition did not increase the ATO degradation rate. Quantitative polymerase chain reaction analysis revealed that the organisms that enriched using ATO as carbon and nitrogen source were Terrimonas spp., Ramlibacter-related spp., Mesorhizobium spp., Hydrogenophaga spp., Ralstonia spp., Pseudomonas spp., Ectothiorhodospiraceae, and Sphingopyxis. This is the first study to report the complete mineralization of ATO by soil microorganisms, expanding our understanding of natural attenuation and bioremediation of the explosive NTO.

Plasmids associated with heavy metal resistance and herbicide degradation potential in bacterial isolates obtained from two Brazilian regions

The use of pesticides has been increasing due to the great agricultural production worldwide. The pesticides are used to eradicate pests and weeds; however, these compounds are classified as toxic to non-target organisms. Atrazine and diuron are herbicides widely used to control grassy and broadleaf weeds and weed control in agricultural crops and non-crop areas. Heavy metals are also important environmental contaminants that affect the ecological system. This study aimed to investigate the presence of herbicides-degrading genes and heavy metal resistance genes in bacterial isolates from two different soil samples from two Brazilian regions and to determine the genetic location of these genes. In this study, two isolates were obtained and identified as Escherichia fergusonii and Bacillus sp. Both isolates presented atzA, atzB, atzC, atzD, atzE, atzF, puhA, and copA genes and two plasmids each, being the major with ~ 60 Kb and a smaller with ~ 3.2 Kb. Both isolates presented the atzA-F genes inside the larger plasmid, while the puhA and copA genes were detected in the smaller plasmid. Digestion reactions were performed and showed that the ~ 60-Kb plasmid presented the same restriction profile using different restriction enzymes, suggesting that this plasmid harboring the complete degradation pathway to atrazine was found in both isolates. These results suggest the dispersion of these plasmids and the multi-herbicide degradation potential in both isolates to atrazine and diuron, which are widely used in different culture types worldwide.

Living at the Frontiers of Life: Extremophiles in Chile and Their Potential for Bioremediation

Extremophiles are organisms capable of adjust, survive or thrive in hostile habitats that were previously thought to be adverse or lethal for life. Chile gathers a wide range of extreme environments: salars, geothermal springs, and geysers located at Altiplano and Atacama Desert, salars and cold mountains in Central Chile, and ice fields, cold lakes and fjords, and geothermal sites in Patagonia and Antarctica. The aims of this review are to describe extremophiles that inhabit main extreme biotopes in Chile, and their molecular and physiological capabilities that may be advantageous for bioremediation processes. After briefly describing the main ecological niches of extremophiles along Chilean territory, this review is focused on the microbial diversity and composition of these biotopes microbiomes. Extremophiles have been isolated in diverse zones in Chile that possess extreme conditions such as Altiplano, Atacama Desert, Central Chile, Patagonia, and Antarctica. Interesting extremophiles from Chile with potential biotechnological applications include thermophiles (e.g., Methanofollis tationis from Tatio Geyser), acidophiles (e.g., Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum from Atacama Desert and Central Chile copper ores), halophiles (e.g., Shewanella sp. Asc-3 from Altiplano, Streptomyces sp. HKF-8 from Patagonia), alkaliphiles (Exiguobacterium sp. SH31 from Altiplano), xerotolerant bacteria (S. atacamensis from Atacama Desert), UV- and Gamma-resistant bacteria (Deinococcus peraridilitoris from Atacama Desert) and psychrophiles (e.g., Pseudomonas putida ATH-43 from Antarctica). The molecular and physiological properties of diverse extremophiles from Chile and their application in bioremediation or waste treatments are further discussed. Interestingly, the remarkable adaptative capabilities of extremophiles convert them into an attractive source of catalysts for bioremediation and industrial processes.

Activity, biomass and composition of microbial communities and their degradation pathways in exposed propazine soil

Propazine is a s-triazine herbicide widely used for controlling weeds for crop production. Its persistence and contamination in environment nagatively affect crop growth and food safety. Elimination of propazine residues in the environment is critical for safe crop production. This study identified a microbial community able to degrade propazine in a farmland soil. About 94% of the applied propazine was degraded within 11 days of incubation when soil was treated with 10mgkg^-1 propazine as the initial concentration. The process was accompanied by increased microbial biomass and activities of soil enzymes. Denaturing gradient gel electrophoresis (DGGE) revealed multiple bacterial strains in the community as well as dynamic change of the composition of microbial community with a reduced microbial diversity (H' from 3.325 to 2.78). Tracking the transcript level of degradative genes AtzB, AtzC and TrzN showed that these genes were induced by propazine and played important roles in the degradation process. The activities of catalase, dehydrogenase and phenol oxidase were stimulated by propazine exposure. Five degradation products (hydroxyl-, methylated-, dimeric-propazine, ammeline and ammelide) were characterized by UPLC-MS², revealing a biodegradation of propazine in soil. Several novel methylated and dimeric products of propazine were characterized in thepropazine-exposed soil. These data help understand the pathway, detailed mechanism and efficiency of propazine biodegradation in soil under realistic field condition.

Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes

Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.

Bioaugmentation as a strategy for the remediation of pesticide-polluted soil: A review

Bioaugmentation, a green technology, is defined as the improvement of the degradative capacity of contaminated areas by introducing specific microorganisms, has emerged as the most advantageous method for cleaning-up soil contaminated with pesticides. The present review discusses the selection of pesticide-utilising microorganisms from various sources, their potential for the degradation of pesticides from different chemical classes in liquid media as well as soil-related case studies in a laboratory, a greenhouse and field conditions. The paper is focused on the microbial degradation of the most common pesticides that have been used for many years such as organochlorinated and organophosphorus pesticides, triazines, pyrethroids, carbamate, chloroacetamide, benzimidazole and derivatives of phenoxyacetic acid. Special attention is paid to bacterial strains from the genera Alcaligenes, Arthrobacter, Bacillus, Brucella, Burkholderia, Catellibacterium, Pichia, Pseudomonas, Rhodococcus, Serratia, Sphingomonas, Stenotrophomonas, Streptomyces and Verticillum, which have potential applications in the bioremediation of pesticide-contaminated soils using bioaugmentation technology. Since many factors strongly influence the success of bioaugmentation, selected abiotic and biotic factors such as pH, temperature, type of soil, pesticide concentration, content of water and organic matter, additional carbon and nitrogen sources, inoculum size, interactions between the introduced strains and autochthonous microorganisms as well as the survival of inoculants were presented.

Assessing environmental drivers of microbial communities in estuarine soils of the Aconcagua River in Central Chile

Aconcagua River basin (Central Chile) harbors diverse economic activities such as agriculture, mining and a crude oil refinery. The aim of this study was to assess environmental drivers of microbial communities in Aconcagua River estuarine soils, which may be influenced by anthropogenic activities taking place upstream and by natural processes such as tides and flood runoffs. Physicochemical parameters were measured in floodplain soils along the estuary. Bacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Pseudomonas, Bacillus and Fungi were studied by DGGE fingerprinting of 16S rRNA gene and ribosomal ITS-1 amplified from community DNA. Correlations between environment and communities were assessed by distance-based redundancy analysis. Mainly hydrocarbons, pH and the composed variable copper/arsenic/calcium but in less extent nitrogen and organic matter/phosphorous/magnesium correlated with community structures at different taxonomic levels. Aromatic hydrocarbons degradation potential by bacterial community was studied. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases genes were detected only at upstream sites. Naphthalene dioxygenase ndo genes were heterogeneously distributed along estuary, and related to Pseudomonas, Delftia, Comamonas and Ralstonia. IncP-1 plasmids were mainly present at downstream sites, whereas IncP-7 and IncP-9 plasmids showed a heterogeneous distribution. This study strongly suggests that pH, copper, arsenic and hydrocarbons are main drivers of microbial communities in Aconcagua River estuarine soils.

Isolation and characterization of a Pseudomonas aeruginosa from a virgin Brazilian Amazon region with potential to degrade atrazine

The use of pesticides to increase agricultural production can result in the contamination of the environment, causing changes in the genetic structure of organisms and in the loss of biodiversity. This practice is also inducing changes in the rainforest ecosystem. In this work, a Pseudomonas aeruginosa isolated from a preservation soil area of the Brazilian Amazon Forest, without usage of any pesticide, was evaluated for its potential to degrade atrazine. This isolate presented all responsible genes (atzA, atzB, atzC, atzD, atzE, and atzF) for atrazine mineralization and demonstrated capacity to use atrazine as a nitrogen source, having achieved a reduction of 44 % of the initial concentration of atrazine after 24 h. These results confirm gene dispersion and/or a possible contamination of the area with the herbicide, which reinforces global concern of the increase and intensive use of pesticides worldwide.

Simazine biodegradation and community structures of ammonia-oxidizing microorganisms in bioaugmented soil: impact of ammonia and nitrate nitrogen sources

The objective of the present study was to investigate the impact of ammonia and nitrate nitrogen sources on simazine biodegradation by Arthrobacter sp. strain SD1 and the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in non-agricultural soil. Soil microcosms with different treatments were constructed for herbicide biodegradation test. The relative abundance of the strain SD1 and the structures of AOA and AOB communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. The co-existence of two inorganic nitrogen sources (ammonia and nitrate) had certain impact on simazine dissipation by the strain SD1. Bioaugmentation could induce a shift in the community structures of both AOA and AOB, but AOA were more responsive. Nitrogen application had significant impacts on AOA and AOB communities in bioaugmented soils. Moreover, in non-bioaugmented soil, the community structure of AOA, instead of AOB, could be quickly recovered after herbicide application. This study could add some new insights towards the impacts of nitrogen sources on s-triazine bioremediation and ammonia-oxidizing microorganisms in soil ecosystem.

Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics

Quaternary ammonium compounds (QACs) represent widely used cationic biocides that persist in natural environments. Although microbial degradation, sensitivity and resistance to QACs have been extensively documented, a quantitative understanding of how whole communities adapt to QAC exposure remain elusive. To gain insights into these issues, we exposed a microbial community from a contaminated river sediment to varied levels of benzalkonium chlorides (BACs, a family of QACs) for 3 years. Comparative metagenomic analysis showed that the BAC-fed communities were dramatically decreased in phylogenetic diversity compared with the control (no BAC exposure), resulting presumably from BAC toxicity, and dominated by Pseudomonas species (> 50% of the total). Time-course metagenomics revealed that community adaptation occurred primarily via selective enrichment of BAC-degrading Pseudomonas populations, particularly P. nitroreducens, and secondarily via amino acid substitutions and horizontal transfer of a few selected genes in the Pseudomonas populations, including a gene encoding a PAS/PAC sensor protein and ring-hydroxylating dioxygenase genes. P. nitroreducens isolates were reproducibly recoverable from communities after prolonged periods of no-BAC exposure, suggesting that they are robust BAC-degraders. Our study provides new insights into the mechanisms and tempo of microbial community adaptation to QAC exposure and has implications for treating QACs in biological engineered systems.

Nitrogen impacts on atrazine-degrading Arthrobacter strain and bacterial community structure in soil microcosms

The objective of this study was to investigate the impacts of exogenous nitrogen on a microbial community inoculated with the atrazine-degrading Arthrobacter sp. in soil amended with a high concentration of atrazine. Inoculated and uninoculated microcosms for biodegradation tests were constructed. Atrazine degradation capacity of the strain DAT1 and the strain's atrazine-metabolic potential and survival were assessed. The relative abundance of the strain DAT1 and the bacterial community structure in soils were characterized using quantitative PCR in combination with terminal restriction fragment length polymorphism. Atrazine degradation by the strain DAT1 and the strain's atrazine-metabolic potential and survival were not affected by addition of a medium level of nitrate, but these processes were inhibited by addition of a high level of nitrate. Microbial community structure changed in both inoculated and uninoculated microcosms, dependent on the level of added nitrate. Bioaugmentation with the strain DAT1 could be a very efficient biotechnology for bioremediation of soils with high concentrations of atrazine.

Isolation and characterization of a lipopeptide bioemulsifier produced by Pseudomonas nitroreducens TSB.MJ10 isolated from a mangrove ecosystem

Pseudomonas nitroreducens TSB.MJ10 exhibiting growth and bioemulsifier production with 0.5% sodium benzoate as the sole carbon source was isolated from a mangrove ecosystem in the vicinity of a petroleum pump. The bioemulsifier is a lipopeptide that is stable over a pH range of 5-11 and a temperature range of 20-90°C and showed emulsifying activity in the presence of relatively high NaCl concentrations (up to 25%). The bioemulsifier formed stable emulsions with aliphatic (hexadecane, n-heptane, cyclohexane), aromatic (xylene, benzene, toluene) and petroleum (gasoline, diesel, kerosene, crude oil) compounds. It exhibited a maximum emulsification activity with weathered crude oil (97%) and was capable of transforming the rheological behavior of the pseudoplastic to a Newtonian fluid. The results reveal the potential of the bioemulsifier for use in bioremediation of hydrocarbons in marine environments and in enhanced oil recovery.

Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile

Background

Copper mining has led to Cu pollution in agricultural soils. In this report, the effects of Cu pollution on bacterial communities of agricultural soils from Valparaiso region, central Chile, were studied. Denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA genes was used for the characterization of bacterial communities from Cu-polluted and non-polluted soils. Cu-resistant bacterial strains were isolated from Cu-polluted soils and characterized.

Results

DGGE showed a similar high number of bands and banding pattern of the bacterial communities from Cu-polluted and non-polluted soils. The presence of copA genes encoding the multi-copper oxidase that confers Cu-resistance in bacteria was detected by PCR in metagenomic DNA from the three Cu-polluted soils, but not in the non-polluted soil. The number of Cu-tolerant heterotrophic cultivable bacteria was significantly higher in Cu-polluted soils than in the non-polluted soil. Ninety two Cu-resistant bacterial strains were isolated from three Cu-polluted agricultural soils. Five isolated strains showed high resistance to copper (MIC ranged from 3.1 to 4.7 mM) and also resistance to other heavy metals. 16S rRNA gene sequence analyses indicate that these isolates belong to the genera Sphingomonas, Stenotrophomonas and Arthrobacter. The Sphingomonas sp. strains O12, A32 and A55 and Stenotrophomonas sp. C21 possess plasmids containing the Cu-resistance copA genes. Arthrobacter sp. O4 possesses the copA gene, but plasmids were not detected in this strain. The amino acid sequences of CopA from Sphingomonas isolates (O12, A32 and A55), Stenotrophomonas strain (C21) and Arthrobacter strain (O4) are closely related to CopA from Sphingomonas, Stenotrophomonas and Arthrobacter strains, respectively.

Conclusions

This study suggests that bacterial communities of agricultural soils from central Chile exposed to long-term Cu-pollution have been adapted by acquiring Cu genetic determinants. Five bacterial isolates showed high copper resistance and additional resistance to other heavy metals. Detection of copA gene in plasmids of four Cu-resistant isolates indicates that mobile genetic elements are involved in the spreading of Cu genetic determinants in polluted environments.

Aerobic biotransformation of n-tetradecylbenzyldimethylammonium chloride by an enriched Pseudomonas spp. community

The biotransformation of n-tetradecylbenzyldimethylammonium chloride (C(14)BDMA-Cl), a quaternary ammonium compound (QAC), under aerobic conditions by an enriched microbial community growing on benzalkonium chlorides (BACs) was investigated. Biotransformation of C(14)BDMA-Cl commenced with cleavage of the C(alkyl)-N bond and formation of benzyldimethylamine (BDMA). BDMA was further degraded, but in contrast to a previously reported BAC biotransformation pathway, neither benzylmethylamine (BMA) nor benzylamine (BA) was detected as a BDMA biotransformation product. Kinetic assays further confirmed that BMA and BA were not intermediates of C(14)BDMA-Cl transformation by the enriched community. Thus, BDMA is thought to be transformed to dimethylamine and benzoic acid via debenzylation. The biomass-normalized rate of C(14)BDMA-Cl biotransformation was 0.09 μmol/[mg of volatile suspended solids (VSS)·h]. The Microtox acute toxicity EC(50) value of BDMA was 500 times higher than that of C(14)BDMA-Cl. Thus, the aerobic biotransformation of C(14)BDMA-Cl to BDMA results in substantial toxicity reduction. Phylogenetic analysis of Bacteria diversity indicated that the majority of the sequenced clones (98% of the clone library) belonged to the genus Pseudomonas.

Influence of microorganisms and leaching on simazine attenuation in an agricultural soil

Simazine is an s-triazine herbicide world widely used for the control of broadleaf weeds. The influence of leaching and microorganisms on simazine attenuation in an agricultural soil long-term treated with this herbicide was studied. To elucidate the leaching potential of simazine in this soil, undisturbed soil columns amended with simazine were placed in a specially designed system and an artificial precipitation was simulated. To evaluate the simazine removal by soil microorganisms, three soil microcosm sets were established: i) control soil; ii) soil subjected to gamma irradiation (γ-soil) and iii) γ-soil inoculated with the simazine-degrading bacterium Pseudomonas sp. strain MHP41. The simazine-degrading microorganisms in soil were estimated using an indicator for respiration combined with MPN enumeration. The simazine removal in soil was monitored by GC-ECD and HPLC. In this agricultural soil the leaching of the applied simazine was negligible. The gamma irradiation decreased in more than one order of magnitude the cultivable heterotrophic bacteria and reduced the simazine-degrading microorganisms. Simazine was almost completely depleted (97%) in control soil by natural attenuation after 23 d, whereas in γ-soil only 70% of simazine was removed. The addition of the simazine-degrading strain MHP41 to γ-soil restored and upheld high stable simazine catabolic microorganisms as well as increased the simazine removal (87%). The results indicated that simazine is subjected to microbial degradation with negligible leaching in this agricultural soil and pointed out the crucial role of native microbiota in the herbicide removal.

Prevalence of the gene trzN and biogeographic patterns among atrazine-degrading bacteria isolated from 13 Colombian agricultural soils

The following study evaluated the diversity and biogeography of 83 new atrazine-degrading bacteria and the composition of their atrazine degradation genes. These strains were isolated from 13 agricultural soils and grouped according to rep-PCR genomic fingerprinting into 11 major clusters, which showed biogeographic patterns. Three clusters (54 strains) belonged to the genus Arthrobacter, seven clusters (28 strains) were similar to the genus Nocardioides and only one strain was a gram-negative from the genus Ancylobacter. PCR assays for the detection of the genes atzA, B, C, D, E, F and trzN conducted with each of the 83 strains revealed that 82 strains (all gram positive) possessed trzN, 74 of them possessed the combination of trzN, atzB and atzC, while only the gram-negative strain had atzA. A similar PCR assay for the two analogous genes, atzA and trzN, responsible for the first step of atrazine degradation, was performed with DNA extracted directly from the enrichment cultures and microcosms spiked with atrazine. In these assays, the gene trzN was detected in each culture, while atzA was detected in only six out of 13 soils. These results raise an interesting hypothesis on the evolutionary ecology of the two atrazine chlorohydrolase genes (i.e. atzA and trzN) and about the biogeography of atrazine-degrading bacteria.

Agronomic and environmental implications of enhanced s-triazine degradation

Novel catabolic pathways enabling rapid detoxification of s-triazine herbicides have been elucidated and detected at a growing number of locations. The genes responsible for s-triazine mineralization, i.e. atzABCDEF and trzNDF, occur in at least four bacterial phyla and are implicated in the development of enhanced degradation in agricultural soils from all continents except Antarctica. Enhanced degradation occurs in at least nine crops and six crop rotation systems that rely on s-triazine herbicides for weed control, and, with the exception of acidic soil conditions and s-triazine application frequency, adaptation of the microbial population is independent of soil physiochemical properties and cultural management practices. From an agronomic perspective, residual weed control could be reduced tenfold in s-triazine-adapted relative to non-adapted soils. From an environmental standpoint, the off-site loss of total s-triazine residues could be overestimated 13-fold in adapted soils if altered persistence estimates and metabolic pathways are not reflected in fate and transport models. Empirical models requiring soil pH and s-triazine use history as input parameters predict atrazine persistence more accurately than historical estimates, thereby allowing practitioners to adjust weed control strategies and model input values when warranted.

Bioaugmentation with Pseudomonas sp. strain MHP41 promotes simazine attenuation and bacterial community changes in agricultural soils

Bioremediation is an important technology for the removal of persistent organic pollutants from the environment. Bioaugmentation with the encapsulated Pseudomonas sp. strain MHP41 of agricultural soils contaminated with the herbicide simazine was studied. The experiments were performed in microcosm trials using two soils: soil that had never been previously exposed to s-triazines (NS) and soil that had >20 years of s-triazine application (AS). The efficiency of the bioremediation process was assessed by monitoring simazine removal by HPLC. The simazine-degrading microbiota was estimated using an indicator for respiration combined with most-probable-number enumeration. The soil bacterial community structures and the effect of bioaugmentation on these communities were determined using 16S RNA gene clone libraries and FISH analysis. Bioaugmentation with MHP41 cells enhanced simazine degradation and increased the number of simazine-degrading microorganisms in the two soils. In highly contaminated NS soil, bioaugmentation with strain MHP41 was essential for simazine removal. Comparative analysis of 16S rRNA gene clone libraries from NS and AS soils revealed high bacterial diversity. Bioaugmentation with strain MHP41 promoted soil bacterial community shifts. FISH analysis revealed that bioaugmentation increased the relative abundances of two phylogenetic groups (Acidobacteria and Planctomycetes) in both soils. Although members of the Archaea were metabolically active in these soils, their relative abundance was not altered by bioaugmentation.

Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil

A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6(T), the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6(T) did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5-4.5 % NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5 %; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA-DNA hybridization data revealed low levels of genomic DNA similarity (less than 30 %) between strain CPDB6(T) and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16 : 1ω7c) and hexadecanoic (16 : 0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6(T) was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6(T) (=CCUG 55948(T)=CCM-A-29:1289(T)) as the type strain.

Adsorption studies of the herbicide simazine in agricultural soils of the Aconcagua valley, central Chile

Simazine is a s-triazine herbicide that has been applied worldwide for agriculture. This herbicide is the second most commonly detected pesticide in surface and groundwater in the United States, Europe and Australia. In this study, simazine adsorption behaviour was studied in two agricultural soils of the Aconcagua valley, central Chile. The two studied soils were soil A (loam, 8.5% organic matter content) and soil B (clay-loam, 3.5% organic matter content). Three times higher simazine adsorption capacity was observed in soil A (68.03 mg kg(-1)) compared to soil B (22.03 mg kg(-1)). The simazine adsorption distribution coefficients (K(d)) were 9.32 L kg(-1) for soil A and 7.74 L kg(-1) for soil B. The simazine adsorption enthalpy in soil A was -21.0 kJ mol(-1) while in soil B the adsorption enthalpy value was -11.5 kJ mol(-1). These results indicate that simazine adsorption process in these soils is exothermic, governing H bonds the adsorption process of simazine in both the loam and clay-loam soils. These results and the potentiometric profiles of both soils, suggest that simazine adsorption in soil A is mainly governed by simazine-organic matter interactions and in soil B by simazine-clay interactions. The understanding of simazine sorption-desorption processes is essential to determine the pesticide fate and availability in soil for pest control, biodegradation, runoff and leaching.