Characterisation and identification of carbofuran-utilising bacteria isolated from agricultural soil

A total of 96 bacterial cultures were isolated from soil. Seventeen bacterial isolates were selected following their cultivation on solid media containing 100 mg · L^?1 carbofuran as the sole source of carbon and nitrogen. Of the 17 isolates, 10F, 11M, 17N, 23B and 26M were specifically chosen because of their relatively higher growth efficiency and genetic diversity based on Box-polymerase chain reaction analysis. These bacterial cultures had 16S rRNA gene sequences that were most similar to Acinetobacter baumannii (10F), Agrobacterium tumefaciens (11M), Ochrobactrum anthropi (17N), Escherichia coli (23B) and Agrobacterium tumefaciens (26M) with 97, 95, 93, 95 and 94% similarity in their 16S rDNA gene sequence, respectively. Degradation rates of carbofuran in soil inoculated with these isolates were 1.9, 1.5, 1.6, 1.7 and 1.6 times, respectively, faster in comparison with uninoculated soil after 10 days of incubation. The maximum degradation rates of carbofuran (45 and 91%) were detected in soil inoculated with A. baumannii (10F) after 10 and 20 days’ incubation, respectively. These data indicate that these isolates may have the potential for use in bioremediation of pesticide contaminated soil.     

Changes in desert steppe soil culturable bacteria from northwestern China and correlation with physicochemical parameters

Seasonal variations effects on desert steppe soil culturable bacteria in northwestern China and physicochemical parameters were investigated. Soil temperature ranged from 5.37 to 23.73 °C. Moisture content varied from 3.22% to 7.62%. The pH was between 7.98 and 8.72. Soil nutrients were altered in different seasons. Total potassium (K) remained the same, but available K levels ranged from 101.29 to 227.55 mg/kg. The culturable bacterial counts in January, April, July and October were 0.13 × 10⁷, 4.09 × 10⁷, 5.33 × 10⁷ and 1.8 × 10⁷ colony forming units (cfu)/g, respectively. Bacterial populations were most abundant in surface layers and declined with increase of soil depth. Seventy-two bacterial strains were isolated and classified according to 27 genera of 5 phyla groups: Firmicutes, Actinobacteria, Alphaproteobacteria, Gammaproteobacteria and Bacteroidates. The bacterial diversities varied according to seasons. In spring, only Firmicutes and Actinobacteria were isolated. In summer, Firmicutes, Actinobacteria and Bacteroidetes were detected with Firmicutes the dominant species. In autumn and winter, Firmicutes, Actinobacteria, α-Proteobacteria and γ-Proteobacteria predominated. Our results indicated that climatic variations, vegetation coverage and soil physicochemical parameters are critical factors for maintaining culturable bacterial populations and diversity in the desert steppe. Soil moisture content and temperature exerted marked influence on bacterial quantities and diversities.     

Impact of litter removal on soil characteristics under a Pinus caribaea stand

ABSTRACT

Forest productivity is dependent on soil quality, which in turn is related to litter; yet there is limited understanding of the relationships between litter and soil quality. The effects of litter removal treatment on tree growth and soil properties were examined in a Pinus caribaea stand with the aim of providing an understanding of consequences of litter removal on soil patterns. This knowledge is important for planning appropriate long-term forest management. Three pairs of 30 × 30 m² plots (each pair a control and treatment) were established in the center of a P. caribaea stand in April 2002. The controls were left undisturbed with an intact litter layer, while litter was removed monthly from treated plots. The diameter and height of the P. caribaea decreased and soil quality was degraded over the experimental period in litter-removed (treated) plots. Litter removal also produced a significant increase in soil bulk density at 0–20 and 20–40 cm depths. The capillary porosity, capillary moisture capacity, and natural water content in controls at 0–20 and 20–40 cm depths were significantly greater than treated plots. The non-capillary porosity in controls at the 0–20 cm depth was also significantly higher than treated plots. The organic carbon, total nitrogen (N), total potassium (K) and alkalized N content in each layer, and available P and exchangeable K at 0–20 and 40–60 cm depths in control plots were significantly greater than litter-removed plots. The numbers of bacteria at 0–20 and 40–60 cm depths and of fungi at 20–40 and 40–60 cm depths were higher in control than treated plots. The number of actinomyces and urease, catalase, and acid phosphatase activities in controls at each depth were significantly greater than litter-removed plots.     

Fungicidal activity and molecular modeling of fusarubin analogues from Fusarium oxysporum

Abstract

Fusarubin analogues of Fusarium oxysporum f. sp. ciceris were investigated for antifungal activity in vitro against five soil borne phytopathogenic fungi. 3-O-Methyl-8-O-methyl-fusarubin was inhibitory towards S. sclerotiorum (EC₅₀ 0.33?mmol L^?1) and Sclerotium rolfsii (EC₅₀ 0.38?mmol L^?1). A structure–antifungal activity relationship of fusarubin analogues was established from their activity performance. Possible mechanism of action of these compounds was studied using molecular docking and simulations against three target enzymes which revealed receptor ligand binding affinity. Docking of 3-O-methyl-8-O-methyl-fusarubin into the succinate dehydrogenase site revealed formation of salt bridge, hydrogen bond, π–anion, π–alkyl, and Van der Waals interactions.     

Biomass and carbon budgeting of sustainable agroforestry systems as ecosystem service in Indian Himalayas

Adoption of agroforestry is paramount as a climate change mitigation and adaptation strategy. The assessment of plant biomass is crucial for understanding the vulnerability of biological systems to climate change. In the present study, agroforestry systems viz., agrisilviculture (AS), agrihorticulture (AH), agrihortisilviculture (AHS) and agrisilvihorticulture (ASH) were investigated for biomass production and carbon stock in vegetation as well as in soil in the Indian central Himalaya along the elevation i.e. E₁ (<1100 m), E₂ (1100–1400 m), E₃ (1400–1700 m), E₄ (1700–2000 m) and E₅ (>2000 m). Mean aboveground and belowground biomass were 73.9% and 26.1%, respectively, of total biomass (64.4 t ha^?1) in agroforestry systems. Fodder and/or timber trees accounted for 31% (in AHS) to 74% (in AS) of total biomass, while fruit trees accounted for 18% (in ASH) to 73% (in AH) of total biomass. The contribution of agriculture crops to total biomass fluctuated between 19% (in ASH) and 26% (in AH). Total vegetation biomass, soil carbon and total carbon density in agroforestry systems increased significantly along the elevation, with maximum biomass at elevation E₅ (32.0 t ha^?1, 64.7 t C ha^?1 and 96.7 t C ha^?1). Total biomass of vegetation among agroforestry systems differed significantly. Soil carbon stock was highest in AHS (59.5 t C ha^?1) and total carbon density (vegetation + soil) was highest in ASH (93.0 t C ha^?1). Thus, in Indian Himalayas, vegetation biomass, carbon stock, soil and total carbon (vegetation + soil) stock increased along the elevation.

Abbrviations: AG: aboveground; BG: belowground; WD: wood density; VOB: volume over bark; BEF: biomass expansion factor; AS: agrisilviculture; AH: agrihorticulture; ASH: agrisilvihorticulture; AHS: agrihortisilviculture; E: elevation; C: carbon; CO₂: carbon-di-oxide; IPCC: Intergovernmental Panel on Climate Change; DBH: diameter at breast height; AGBD: aboveground biomass density; BGBD: belowground biomass density; GSVD: growing stock volume density     

Isolation and characterisation of a carbofuran degrading Burkholderia sp. PCL3 from carbofuran-phytoremediated rhizosphere soil

A bacterial strain capable of degrading carbofuran as the sole carbon source was isolated from carbofuran-phytoremediated rhizosphere soil of rice. A 16S rRNA study identified the strain as Burkholderia sp. (isolate PCL3). Free cells of isolate PCL3 possessed inhibitory-type degradation kinetics with a q _max of 0.087 day^?1 and S _m of 248.76 mg·L^?1. Immobilised PCL3 on corncob and sugarcane bagasse possessed Monod-type degradation kinetics with a q _max of 0.124 and 0.098 day^?1, respectively. The optimal pH and temperature with the highest degradation rate coefficient of carbofuran were pH 7.5 and 35 °C, respectively.     

Single-species bacteria in sediments induce larval settlement of the infaunal polychaetes Polydora cornuta and Streblospio benedicti

Larval settlement of the infaunal spionid polychaetes Polydora cornuta and Streblospio benedicti is mediated by sediment-associated microorganisms. To investigate if larval preference for certain sediment is guided by individual sediment-associated bacteria, 13 bacterial isolates (5 phyla) obtained from the natural habitat of adult polychaetes (Wadden Sea, Germany) in 2008 were screened in still-water, no-choice settlement assays. Two isolates (α-Proteobacterium-Strain DF11 and Flavobacterium-Strain 54) significantly triggered larval settlement in comparison with sterile sediment. In still-water, multiple-choice settlement assays comprising natural and sterile sediment and sediment re-inoculated with isolates DF11 and 54, significant preferences for natural sediment and sediment containing bacterial isolates at 10⁸ cells g^?1 were observed. Larval settlement was influenced by bacterial abundance in sediment but the correlation was not strictly positive; thus, maximum larval settlement in response to single bacterial species may occur at certain optimum densities. Non-viable or suspended bacteria and water-soluble bacterial products did not induce larval settlement, suggesting that sediment-associated bacterial settlement cues for P. cornuta and S. benedicti were either produced in situ and/or consisted of heat-labile bacterial products.     

Effects of ethyl 2-methyl acetoacetate (EMA) on the growth of Phaeodactylum tricornutum and Skeletonema costatum

We investigated the effects of ethyl 2-methyl acetoacetate (EMA) on growth of the marine diatom algae Phaeodactylum tricornutum (P. tricornutum) and Skeletonema costatum (S. costatum). Growth of P. tricornutum was significantly inhibited by the minimum concentration (3.5 mmol·L ^?1) of EMA at lower initial algal densities (IADs) (3.6×10⁴ and 3.3×10⁵ cells·mL ^?1). However, at the highest IAD, significant growth inhibition was found at above 7 mmol·L ^?1 of EMA exposure. In S. costatum, EMA concentrations of 10.5 mmol·L ^?1 or more significantly inhibited growth at lower IAD (3×10⁴ and 1.8×10⁵ cells·mL ^?1); at the highest IAD, only EMA concentrations above 14 mmol·L ^?1 obviously inhibited the growth of S. costatum. Changes in specific growth rates and pigment were consistent with algal growth, but only at higher EMA concentrations or lower IAD values was the ratio of chlorophyll a (Chla) to carotenoid significantly lower than the control. Medium effective concentration (EC ₅₀) values were in the order 4.07, 8.03 and 12.27 mmol·L ^?1 for P. tricornutum and 7.48, 11.92 and 17.22 mmol·L ^?1 for S. costatum. All these results show that the effect of EMA on the growth of algae was species specific and mainly depended on IAD, which might be an important factor to influence algal growth.     

铜胁迫对农田土壤酶活性、细菌和古菌数量的影响

为了研究铜矿周边农田土壤中不同Cu含量对土壤酶活性、细菌和古菌基因拷贝数的影响,在铜矿周边农田土壤中采集了8个不同Cu含量的土壤,测定土壤的酶活性、细菌和古菌基因拷贝数,结果表明,土壤总Cu含量为28.30~1 019.27mg·kg~(-1),酸可提取态Cu含量为335~415.11 mg·kg~(-1),细菌16S rRNA基因拷贝数在每克干土3.10×10~(10)~1.84×10~(11)个之间,古茵16S rRNA基因拷贝数在每克干土737×10~8~6.82×10~9个之间。土壤总Cu和酸可提取态Cu含量对土壤脲酶活性影响较大,但对土壤脱氢酶和转化酶活性影响不显著。土壤细菌基因拷贝数均与总Cu含量、各形态Cu含量呈极显著的负相关关系,同样土壤古菌基因拷贝数与总Cu含量、各形态Cu含量也均呈极显著的负相关关系,说明Cu胁迫对土壤细菌和古菌活性具有较大的抑制作用。     

Impact of organic manure on the phytoremediation potential of Vetiveria zizanioides in chromium-contaminated soil

Chromium is a pollutant present in electroplating waste water and its removal is necessary for the protection of the environment. Vetiveria zizanioides (VZ) was grown in chromium effluent concentrations of 50, 100 and 200 mg kg ^?1 soil amended with organic manure and the potential for phytoremediation was determined. The amounts of Cr in plant tissues (root and shoot), soil and percentage electrolyte leakage of VZ roots were analysed. From the results, VZ amended with organic manure showed the greatest potential for Cr removal because of its faster growth and larger biomass achieved over the whole length of the experiment. In this study, 92.25% Cr removal efficiency was obtained with a Cr concentration of 50 mg kg ^?1 soil and removal efficiencies of 90.5% and 85% were obtained with 100 and 200 mg kg^?1, respectively after a period of two months of VZ growth.     

Influence of americium-241 on the microbial population and biodegradation of organic waste

The present study investigated the influence of ²⁴¹Am on microbial growth and the degradation of organic waste. Leachate samples collected in a lysimeter were periodically analyzed for bacterial growth, under both aerobic and anaerobic conditions. ²⁴¹Am inhibited bacterial growth, and the degradation of organic matter was delayed in comparison with the control. Minimal inhibitory concentration assays and survival curves revealed that it inhibits the growth of Pseudomonas putida F1. The assay also revealed that ²⁴¹Am is more toxic than ²³⁸U, Zn²⁺ and Cd²⁺. This study further led to the finding of four new radionuclide-tolerant bacterial strains: Flavobacterium spp., Pseudomonas gladioli, Chryseobacterium indologenes and Ochrobactrum anthropi. The survival curves of P. gladioli, C. indologenes revealed that these bacteria are resistant to metal as consortia.     

As(V)-reduction to As(III) by arsenic-resistant Bacillus spp. bacterial strains isolated from low-contaminated sediments of the Oliveri-Tindari Lagoon,Italy

Five arsenic-resistant bacterial strains designated MT1, MT2, MT3, V1 and V2 were isolated from sediments of the Oliveri-Tindari Lagoon (Italy), which comprises six small lakes whose sediments contain low arsenic concentrations. Phylogenetic analysis of the 16S rRNA gene sequences assigned them to the genus Bacillus. Bacillus sp. strain MT3 showed higher tolerance to As(III) and As(V), as indicated by minimum inhibitory concentrations of 14 and 135 mmol^?1, respectively. Bacillus sp. strain V1 showed growth inhibition at 14 mmol^?1 in the presence of As(III) and at 68 mmol^?1 in the presence of As(V), whereas the arsenic resistance of Bacillus sp. strain MT1 was 10 and 27 mmol^?1 for As(III) and As(V), respectively. The strains Bacillus spp. MT2 and V2 showed low levels of As(III) and As(V) resistance, as it was unable to grow at concentrations>7 and 14 mmol^?1, respectively. The isolated arsenic-resistant Bacillus spp. strains were able to reduce As(V) to As(III), especially Bacillus spp. strain MT3. This study suggests that the isolated bacterial strains play a role in the arsenic biogeochemical cycle of arsenic-poor sediments in the Oliveri-Tindari Lagoon.     

In vitro antioxidant and antibacterial activities of certain 3-{4-(5-mercapto-1,3,4-oxadiazole-2-yl)phenylimino}-indolin-2-one derivatives

A new series of 5- or 7-substituted 3-{4-(5-mercapto-1,3,4-oxadiazol-2-yl)phenylimino}-indolin-2-one derivatives were screened for in vitro antioxidant and antimicrobial activities. The results of this study revealed that all synthesized compounds were significantly scavenged DPPH free radicals in a concentration-dependant manner. The IC₅₀ values of all test compounds were found to be between 18.34 and 50.54?µM. All compounds significantly inhibited growth of bacteria and most of the minimum inhibitory concentration values were between 20 and 100?mg?mL^?1 indicating potent to moderate antibacterial activity. In conclusion, 3-{4-(5-mercapto-1,3,4-oxadiazole-2-yl)phenylimino)-5 or 7-substituted indolin-2-ones derivatives exhibited moderate antioxidant and antimicrobial activities.     

Phytoextraction of Cr(VI) from soil using Portulaca oleracea

Cr(VI) represents an environmental challenge in both soil and water as it is soluble and bioavailable over a wide range of pH. In previous investigations, Portulaca oleracea (a plant local to the United Arab Emirates (UAE)) demonstrated particular ability for the phytoextraction of Cr(VI) from calcareous soil of the UAE. In this publication, the results of the evaluation of P. oleracea phytoextraction of Cr(VI) from UAE soil at higher concentrations are reported. P. oleracea was exposed to nine different concentrations of Cr(VI) in soil from 0 to 400 mg kg^?1. The uptake of Cr(VI) increased as its concentration in soil increased between 50 and 400 mg kg^?1, with the most efficient removal in the range from 150 to 200 mg kg^?1. The total chromium concentrations exceeded 4600 mg kg^?1 in roots and 1400 mg kg^?1 in stems, confirming the role of P. oleracea as an effective Cr(VI) accumulator. More than 95% of the accumulated Cr(VI) was reduced to the less toxic Cr(III) within the plant.     

Crop demand of manganese

The objectives of this study were to evaluate some of the popular rotation crops grown in Hungary for tolerance to low external Mn²⁺ levels and to determine the critical tissue concentration of Mn²⁺ deficiency during early stages of growth. The minimum Mn²⁺ concentration required in soil nutrient contents was 42.5 mg kg⁻¹ for sunflower, 24.3 mg kg⁻¹ for tobacco and 10.2 mg kg⁻¹ for triticale. Sunflower, tobacco and triticale achieved optimum growth at 48.0–65.0 mg Mn²⁺ kg⁻¹, 24.9–32.1 mg Mnⁿ⁺ kg⁻¹ and 28.7 to 29.6 mg Mn²⁺ kg⁻¹, respectively. Critical shoot Mn²⁺ concentration at early stages of growth was 53.6 mg kg⁻¹ in sunflower, 458.0 mg kg⁻¹ in tobacco and 193.8 mg kg⁻¹ in triticale. Our results demonstrate that the tolerance to low external Mn²⁺ (triticale: <30.2 mg kg⁻¹; sunflower: <56.2 mg kg⁻¹; tobacco: <69.3 mg kg⁻¹) and the critical tissue Mn²⁺ levels for deficiency varied significantly between crop species tested.

     

Evaluation of the effect of antimicrobials in marine cultures,using the copepod Acartia tonsa as a bioindicator

Cultures of the copepod Acartia tonsa are used both in aquaculture and ecotoxicology studies. However, the cultivation of these crustaceans at high densities results in the proliferation of microorganisms that can affect the organisms of interest, leading to illness or death. Antimicrobials inhibit microbial growth and may favour the cultivated species, aiding the development of ecological studies. This study investigated the potential of antimicrobials (antibiotic + antifungal) to inhibit bacteria and fungi when applied to marine zooplankton cultures, using the copepod A. tonsa as a bioindicator of acute toxicity. Treatment with 0.025?g?L^?1 of penicillin G potassium + 0.08?g?L^?1 of streptomycin sulphate + 0.04?g?L^?1 of neomycin sulphate + 0.005?g?L^?1 of nystatin resulted in 95% bacterial inhibition (after 12?h of exposure); however, after this time, the inhibitory effect was lost. The antimicrobial combination tested in this study prevented colonisation by fungi until 168?h after exposure, without causing acute toxicity to A. tonsa. Thus, it has potential for use in marine cultures of less sensitive organisms.     

Biodegradation of Hexachlorocyclohexane by two species of Bacillus isolated from contaminated soil

Biodegradation of α, β, γ and δ hexachlorocyclohexane (HCH) isomers was studied in broth medium and soil microcosm by Bacillus circulans and Bacillus brevis isolated from contaminated soil. Degradation of α and γ isomers by both the bacterial isolates was higher than thermodynamically stable β and δ isomers. However, B. circulans was found more effective than B. brevis for β and δ isomers. Maximum rate of degradation was recorded at 150 mg/L followed by 100 and 50 mg/L. Soil microcosm study revealed maximum degradation of HCH isomers in the treatment containing natural soil, pesticide and bacterial inocula than the treatment having sterilised soil, pesticide and bacterial isolates. Chloride release was positively co-related with HCH degradation in broth medium as well as in soil microcosm, suggesting that B. circulans and B. brevis hold promising potential by having efficient enzyme(s) required for dechlorination of HCH from contaminated sites.     

Organochlorine pesticides (HCHs and DDTs) in soils along the north coastal areas of the Bohai Sea,China

A systematic survey of organochlorine pesticides (OCPs) including hexachlorocyclohexane isomers (α-HCH, β-HCH, γ-HCH, δ-HCH and ΣHCH) and dichlorodiphenyltrichloroethane metabolites (p,p′-DDT, p,p′-DDE, o,p′-DDT, p,p′-DDD and ∑DDT) in soils along the north coastal areas of the Bohai Sea, China, has been lacking. In this study, 31 representative surface soil samples were collected along the north coastal and riverine areas of the Bohai Sea to characterise the potential for adverse effects of ∑HCH, ∑DDT and their individual isomers and transformation products. Concentrations of ΣHCH and ΣDDT in soils ranged from less than the limit of detection (1 ng · g^?1 dw (mean: 3.5 ng · g^?1 dw) and2 ng · g^?1 dw (mean: 1.7 × 10¹ ng · g^?1 dw), respectively. Compared with studies of OCPs in soils from other locations, concentrations of HCHs and DDTs observed in this study were moderate. Concentrations of OCPs observed in soils were generally less than proposed reference values. HCH residues were a mixture of historical technical HCH and current lindane sources. The pattern of DDTs was consistent with historical releases of technical DDTs. Selected soil physicochemical properties did not explain the sorption and/or partitioning of HCHs or DDTs.     

Phytotoxicity assessment of phenanthrene and pyrene in soil using two barley genotypes

This study investigated the toxicity extent of phenanthrene and pyrene to two cultivars (CM-72 and Gairdner) of barley (Hordeum vulgare). Germination of barley seeds was evaluated in 69-d aged soil, separately spiked with phenanthrene at extractable concentrations of 0.95, 6.3, 59, and 300 mg kg^?1 (dry soil) and pyrene at 1.0, 9.0, 73, and 400 mg kg^?1 (dry soil). Although germination was not inhibited, significant (P < 0.05) reduction in root and shoot length occurred at concentrations of phenanthrene ≥6.3 mg kg^?1 and pyrene ≥9.0 mg kg^?1 after both 72 and 240 h. Fresh and dry biomass of both cultivars reduced with increasing concentrations of both polycyclic aromatic hydrocarbons (PAHs). Barley cultivar CM-72 was more sensitive than Gairdner, and it can be considered suitable for toxicity assessment of PAH-contaminated soils.     

Growth and Cd accumulation of two halophytes and a non-halophyte grown in a non-saline and a saline soil with different Cd levels

Two halophytes, Salicornia europaea and Atriplex verucifera, and the non-halophyte Chenopodium album were grown in pots on sodic and non-sodic Iranian soils spiked with up to 100 mg Cd kg^?1. The halophytes grew best on the sodic soil in the absence of Cd spiking, while C. album performed better on non-sodic soil. Cadmium spiking reduced the growth of all plants, with Cd tolerance decreasing in the order S. europaea>A. verucifera>C. album. The observed order of Cd tolerance corresponds to the abilities of the plants to tolerate sodic soil properties. The variation of Cd concentration in shoots in response to sodicity was related to different mechanism, including dilution (C. album) Cd solubilisation by Ca²⁺ (S. europea) and Ca²⁺ competition for uptake and translocation of Cd (A. verucifera). Improved understanding of these complex interactions will help to design phytoextraction technology for Cd-polluted soils in arid regions.