Structure of microbial community in soils contaminated with heavy metals assessed by culture and fatty acid approaches

Badano wpływ Cu, Zn i Cd na liczebność, biomasę oraz strukturę ogólnej i zdolnej do wzrostu na podłożach hodowlanych populacji bakterii w warunkach laboratoryjnych. Glebę skażono Cu lub Zn w dawce 1000 lub 2000 pg g oraz Cd w dawce 500 lub 1000 pg g' gleby. Po 15, 60 i 90 dniach od skażenia gleby określono w niej zawartość wymywalnych wodą jonów wprowadzonych metali, ogólną liczebność bakterii na podłożu TSA oraz biomasę bakterii i grzybów na podstawie zawartości wybranych fosfolipidowych kwasów tłuszczowych (PLFA). Strukturę zdolnej do wzrostu frakcji bakterii określano na podstawie profili komórkowych kwasów tłuszczowych (FAMĘ) oraz na podstawie koncepcji r- i K-strategów. Do oceny bioróżnorodności populacji bakterii zastosowano współczynnik ekofizjologiczny (EP) i rozwoju kolonii (CD). Strukturę całego zespołu bakterii glebowych oceniano, opierając się na profilach PLFA izolowanych bezpośrednio z gleby. Zawartość wymywalnych wodą jonów Cu, Zn i Cd stanowiła jedynie kilka procent wprowadzonych do gleby metali i zmniejszała się w czasie trwania doświadczenia. Wykazano, że metale ciężkie mają jedynie krótkotrwały negatywny wpływ na ogólną liczebność bakterii. Po 60 dniach inkubacji nie stwierdzono istotnych różnic pomiędzy liczebnością mikroorganizmów w glebach skażonych a kontroli. Obserwowano natomiast istotny wpływ wprowadzonych metali na biomasę mikroorganizmów. W glebach skażonych wyższymi dawkami metali biomasa bakterii była zawsze niższa w porównaniu z biomasą bakterii w glebie kontrolnej. Wartości parametrów EP i CD wskazują na wyraźne zmiany w strukturze zespołów bakterii zdolnych do wzrostu w glebach skażonych Cu, Zn i Cd. Wszystkie metale powodowały przebudowę struktury zespołów bakterii w kierunku dominacji K-strategów. Największą redukcję bioróżnorodności stwierdzono w glebach skażonych Zn i Cd, w których wartość parametru EP (od 0,518 do 0,553) była istotnie niższa od wartości EP w kontroli (0,707). Profil komórkowych kwasów tłuszczowych (FAMĘ) izolowanych z wyrosłych komórek wskazuje na dominację bakterii Gram-dodatnich zarówno w glebie kontrolnej, jak i skażonej metalami. Nie zaobserwowano istotnych zmian w profilach FAME badanych zespołów, jakkolwiek procentowy udział rozgałęzionych kwasów tłuszczowych w glebach zanieczyszczonych Cu, Zn i Cd był wyższy niż w glebie kontrolnej. Zespoły wyrosłych na podłożu TSA bakterii były mniej zróżnicowane w porównaniu z zespołami mikroorganizmów określanymi za pomocą fosfolipidowych kwasów tłuszczowych, izolowanych bezpośrednio z gleby. Analiza profili tych kwasów wskazuje na wyraźne zmiany w obrębie struktury badanych zespołów bakterii w glebach potraktowanych różnymi metalami i kontrolą. Zmiany w profilu PLFA zależały od rodzaju metalu, jego dawki i czasu, w którym pobierano próbki. Po 90 dniach inkubacji w glebach skażonych Cu, Zn i Cd stwierdzono spadek zawartości rozgałęzionych kwasów tłuszczowych i 14:0 i i 15:0 oraz wzrost ilości kwasów i 17:0 i a 17:0 w stosunku do kontroli. W glebach skażonych metalami wzrosła również ilość kwasu 16:ko7t, natomiast zawartość innych kwasów nienasyconych, jak i kwasów cyklopropanowych zmieniała się w zależności od rodzaju metalu wprowadzonego do gleby. Analiza dendrogramów, utworzonych na podstawie uzyskanych profili PLFA, obrazujących podobieństwa między zespołami bakterii w badanych glebach, wskazuje, że mikroorganizmy w różny sposób reagują na skażenie gleby Cu, Zn i Cd

Pyrethroid-Degrading Microorganisms and Their Potential for the Bioremediation of Contaminated Soils: A Review

Pyrethroid insecticides have been used to control pests in agriculture, forestry, horticulture, public health and for indoor home use for more than 20 years. Because pyrethroids were considered to be a safer alternative to organophosphate pesticides (OPs), their applications significantly increased when the use of OPs was banned or limited. Although, pyrethroids have agricultural benefits, their widespread and continuous use is a major problem as they pollute the terrestrial and aquatic environments and affect non-target organisms. Since pyrethroids are not degraded immediately after application and because their residues are detected in soils, there is an urgent need to remediate pyrethroid-polluted environments. Various remediation technologies have been developed for this purpose; however, bioremediation, which involves bioaugmentation and/or biostimulation and is a cost-effective and eco-friendly approach, has emerged as the most advantageous method for cleaning-up pesticide-contaminated soils. This review presents an overview of the microorganisms that have been isolated from pyrethroid-polluted sites, characterized and applied for the degradation of pyrethroids in liquid and soil media. The paper is focused on the microbial degradation of the pyrethroids that have been most commonly used for many years such as allethrin, bifenthrin, cyfluthrin, cyhalothrin, cypermethrin, deltamethrin, fenpropathrin, fenvalerate, and permethrin. Special attention is given to the bacterial strains from the genera Achromobacter, Acidomonas, Bacillus, Brevibacterium, Catellibacterium, Clostridium, Lysinibacillus, Micrococcus, Ochrobactrum, Pseudomonas, Serratia, Sphingobium, Streptomyces, and the fungal strains from the genera Aspergillus, Candida, Cladosporium, and Trichoderma, which are characterized by their ability to degrade various pyrethroids. Moreover, the current knowledge on the degradation pathways of pyrethroids, the enzymes that are involved in the cleavage of pesticide molecules, the factors/conditions that influence the survival of strains that are introduced into soil and the rate of the removal of pyrethroids are also discussed. This knowledge may be useful to optimize the environmental conditions of bioremediation and may be crucial for the effective removal of pyrethroids from polluted soils

Molecular basis of active cooper resistance mechanisms in Gram-negative bacteria

Copper is a metallic element that is crucial for cell metabolism; however, in extended concentrations, it is toxic for all living organisms. The dual nature of copper has forced organisms, including bacteria, to keep a tight hold on cellular copper content. This challenge has led to the evolution of complex mechanisms that on one hand enable them to deliver the essential element and on the other to protect cells against its toxicity. Such mechanisms have been found in both eukaryotic and prokaryotic cells. In bacteria a number of different systems such as extra- and intracellular sequestration, enzymatic detoxification, and metal removal from the cell enabling them to survive in the presence of high concentration of copper have been identified. Gram-negative bacteria, due to their additional compartment, need to deal with both cytoplasmic and periplasmic copper. Therefore, these bacteria have evolved intricate and precisely regulated systems which interact with each other. In this review the active mechanisms of copper resistance at their molecular level are discussed

Community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil treated with the insecticide imidacloprid

The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10× FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4 +, known as the most important factor which determines the contribution of these microorganisms to soil nitrification

Use of the PCR-DGGE method for the analysis of the bacterial community structure in soil treated with the cephalosporin antibiotic cefuroxime and/or inoculated with a multidrug-resistant Pseudomonas putida strain MC1

The widespread use of cefuroxime (XM) has resulted in the increase in its concentration in hospital and domestic wastewaters. Due to the limited removal of antibiotics and antibiotic-resistant genes in conventional systems, the drugs enter the surface water and soils. Moreover, the introduction of XM and/or XM-resistant bacteria into soil may cause a significant modification of the biodiversity of soil bacterial communities. Therefore, the goal of this research was to assess the genetic diversity of a bacterial community in the cefuroxime (XM1-1 mg/kg and XM10-10 mg/kg) and/or antibiotic-resistant Pseudomonas putida strain MC1 (Ps - 1.6 × 107 cells/g)-treated soils as determined by the DGGE (denaturing gradient gel electrophoresis) method. The obtained data were also evaluated using a multivariate analysis and the resistance (RS)/resilience (RL) concept. Strain MC1 was isolated from raw sewage in the presence of XM and was resistant not only to this antibiotic but also to vancomycin, clindamycin and erythromycin. The DGGE patterns revealed that the XM10 and XM10+Ps treatments modified the composition of the bacterial community by the alteration of the DGGE profiles as well as a decline in the DGGE indices, in particular on days 30, 60, and 90. In turn, the XM1 and XM1+Ps or Ps treatments did not affect the values of richness and diversity of the soil bacteria members. A principal component analysis (PCA) also indicated that XM markedly changed the diversity of bacterial assemblages in the second part of the experiment. Moreover, there were differences in the RS/RL of the DGGE indices to the disturbances caused by XM and/or Ps. Considering the mean values of the RS index, the resistance was categorized in the following order: diversity (0.997) > evenness (0.993) > richness (0.970). The soil RL index was found to be negative, thus reflecting the progressing detrimental impact of XM on the genetic biodiversity of bacteria within the experiment. These results indicate that the introduction of XM at higher dosages into the soil environment may exert a potential risk for functioning of microorganis

FAME profiles in Pseudomonas vesicularis during catechol and phenol degradation in the presence of glucose as an additional carbon source

The aim of this study was to evaluate the impact of catechol and phenol added to culture media separately and with glucose as an additional, easily-degradable carbon source on fatty acid methyl ester (FAME) composition in Pseudomonas vesicularis. Simultaneously, the degradation rates of aromatic substrates used were investigated in single and binary substrate systems. Both catechol and phenol treatments caused changes in the distribution of tested groups of fatty acids. The most noticeable changes included an increase in degree of fatty acid saturation, the appearance of branched and disappearance of hydroxy fatty acids as compared to the control sample with glucose. Under catechol or phenol treatment sat/unsat ratio showed the values of 8.63 and 11.38, respectively, whereas in contr ol cells it reached the value of 2.66. The high level of saturation comes from the high content of cyclopropane fatty acids in bacteria under exposure to aromatic substrates, regardless of the presence of glucose. In these treatments their content was more than 3-fold higher compared to the control. It has been demonstrated that glucose supplementation of culture media containing single aromatic substrate extended the degradation rates of catechol and phenol by P. vesicularis, caused an increase in number of cells but did not significantly change the fatty acid profiles in comparison with bacteria growing on catechol and phenol added to the media individually

Symbioza owady-bakterie

Insects are among the most successful animals on Earth both with regard to their biomass and biodiversity. In 1965, Paul Buchner first described the symbiotic, intracellular specific microorganisms. It is estimated that up to 20% of all insects are associated with microorganisms. This relationship has greatly contributed to insects’ evolutionary success. Symbiotic bacteria live in specialized cells called the bacteriocytes (mycetocytes), fat body or insects gut. These bacteria may have a role in nutritional upgrading of their hosts’ diets. For example, all aphids require a primary endosymbiont, the bacterium Buchnera sp., to synthesize the nutrients missing in their xylem food source. The improvement of health condition of the host resistance to pathogens and high temperature is associated with the presence of specific microflora. Extremely stable interactions between insects and bacteria are the result of specific genetic mechanisms. Analysis of 16S rRNA gene sequence allowed the identification of these microorganisms because their culture is not possible on traditional microbiological media. The genome sequence analysis enabled the discovery of their metabolic functions. Researches on insect-symbiotic bacteria interactions allowed for the application of new strategies to pest control. New methods are less toxic to the environment

Enhancement of deltamethrin degradation by soil bioaugmentation with two different strains of "Serratia marcescens"

Deltamethrin is one of the most commonly used pyrethroid in agricultural practice in different geographic regions of the world. It is detected in many environments, especially in soil and water, and can exhibit toxic effect to human and other organisms. In this study, we describe two bacterial strains DeI-1 and DeI-2, isolated from soil, and both identified as Serratia marcescens based on profile of the fatty acid methyl esters, biochemical test, and 16S RNA gene analysis, which were shown to efficiently degrade deltamethrin. Degradation of deltamethrin in mineral salt medium (50 mg l -1 ) proceeded by strains DeI-1 or DeI-2 reached the values of 88.3 or 82.8 % after 10 days, and DT50 was 2.8 or 4.0 days, respectively. Bioaugmentation of deltamethrin-contaminated non-sterile soils (100 mg kg -1 ) with strains DeI-1 or DeI-2 (3 × 10 6 cells g -1 of soil) enhanced the disappearance rate of pyrethroid, and its DT50 was reduced by 44.9, 33.1, 44.4, and 58.2 days or 39.1, 25.8, 35.6, and 46.0 days in sandy, sandy loam, silty loam, and silty soils, respectively, in comparison with non-sterile soils with only indigenous microflora. The three-way ANOVA indicated that DT50 of deltamethrin was significantly (P < 0.01) affected by soil type, microflora presence, and inoculum, and the interaction between these factors. Generally, the lower content of clay and organic carbon in soil, the higher degradation rate of deltamethrin was observed. Obtained results show that both strains of S. marcescens may possess potential to be used in bioremediation of deltamethrin-contaminated soils

Non-target impact of fungicide tetraconazole on microbial communities in soils with different agricultural management

Effect of the fungicide tetraconazole on microbial community in silt loam soils from orchard with long history of triazole application and from grassland with no known history of fungicide usage was investigated. Triazole tetraconazole that had never been used on these soils before was applied at the field rate and at tenfold the FR. Response of microbial communities to tetraconazole was investigated during 28-day laboratory experiment by determination of changes in their biomass and structure (phospholipid fatty acids method—PLFA), activity (fluorescein diacetate hydrolysis—FDA) as well as changes in genetic (DGGE) and functional (Biolog) diversity. Obtained results indicated that the response of soil microorganisms to tetraconazole depended on the management of the soils. DGGE patterns revealed that both dosages of fungicide affected the structure of bacterial community and the impact on genetic diversity and richness was more prominent in orchard soil. Values of stress indices—the saturated/monounsaturated PLFAs ratio and the cyclo/monounsaturated precursors ratio, were almost twice as high and the Gram-negative/Gram-positive ratio was significantly lower in the orchard soil compared with the grassland soil. Results of principal component analysis of PLFA and Biolog profiles revealed significant impact of tetraconazole in orchard soil on day 28, whereas changes in these profiles obtained for grassland soil were insignificant or transient. Obtained results indicated that orchards soil seems to be more vulnerable to tetraconazole application compared to grassland soil. History of pesticide application and agricultural management should be taken into account in assessing of environmental impact of studied pesticides

Activity and functional diversity of microbial communities in long-term hydrocarbon and heavy metal contaminated soils

The impacts of long-term polycyclic aromatic hydrocarbons (PAHs) and heavy metal pollution on soil microbial communities functioning were studied in soils taken from an old coke plant. The concentrations of PAHs in the tested soils ranged from 171 to 2137 mg kg-1. From the group of tested heavy metals, concentrations of lead were found to be the highest, ranging from 57 to 3478 mg kg-1, while zinc concentrations varied from 247 to 704 mg kg-1 and nickel from 10 to 666 mg kg-1. High dehydrogenase, acid and alkaline phosphatase activities were observed in the most contaminated soil. This may indicate bacterial adaptation to long-term heavy metal and hydrocarbon contamination. However, the Community Level Physiological Profiles (CLPPs) analysis showed that the microbial functional diversity was reduced and influenced to a higher extent by some metals (Pb, Ni), moisture and conductivity than by PAHs