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Profiling of heavy metal(loid)-resistant bacterial community structure by metagenomic-DNA fingerprinting using PCR–DGGE for monitoring and bioremediation of contaminated environment
Abstract
Frequent exposure of microbes to hazardous metalloids/heavy metals in contaminated environment results in the development of heavy metal(loid)-resistance properties. The study attempted to assess the profile of elevated arsenic (As), cadmium (Cd) and mercury (Hg)—resistant bacterial community structures of sludge (S1, India), sludge and sediment (S2 and S3, Japan) and sediment (S4, Vietnam) samples by metagenomic-DNA fingerprinting using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) for monitoring and bioremediation of hazardous metal(loid) contamination in environment. The results revealed that As-resistant bacteria were dominant compared to Cd- and Hg-resistant bacteria with higher species diversity (Lysinibacillus sp., Uncultured soil bacterium clone, Staphylococcus sciuri, Bacillus fastidiosus, Bacillus niacini, Clostridium sp. and Bacillus sp.) in S1 and S4 than that of S2 and S3 samples. The occurrence of dominant As-resistant bacteria may indicate arsenic contamination in the investigated coastal habitats of India, Japan and Vietnam. The As-, Cd- and Hg-resistant bacteria/bacterial consortiums showed appreciable uptake ability of respective metal(loid) (0.042–0.125 mg As/l, 0.696–0.726 mg Cd/l and 0.34–0.412 mg Hg/l). Therefore, it might be concluded that the profiling of metalloids/heavy metal-resistant bacterial community structure by metagenomic-DNA fingerprinting using PCR–DGGE could be used to explore high metal(loid)-resistant bacteria for applying in metal(loid) bioremediation and as an indicator for monitoring hazardous metal(loid) contamination in environment.
... Exploration of diversified microbes of the environment is impossible by common cultural method. Metagenomic profiling using various advanced techniques brought unprecedented development in exploring and profiling of the unculturable microbes of environment (Bhakta et al., 2017). ...
... A thorough analysis of each of these molecules extracted from an environmental community yields key insights into the taxonomic composition of a community, the functional potential for community, or the genes and proteins currently being expressed (Techtmann and Hazen, 2016;Bhakta et al., 2017). ...
... The elucidation of how microbial communities change due to the effects of environmental disturbances like pollution, investigations need to rely on rapid methods that can characterize cellular constituents such as nucleic acids, proteins (enzymes) and other taxa-specific compounds (Maila, 2005). These molecules can be extracted directly from the soil without the need for culturing and thus can be used to elucidate the microbial community composition of such polluted environments during bioremediation (Simon et al., 2011;Bhakta et al., 2017). ...
Bioenergy refers to sustainable power source generated from biomass. Energy Independence and Security Act stated that the volume standards for advanced biofuels were set to grow from a meager 0.6 billion gallons in 2009 to 21 billion gallons in 2022, which will worth multihundred-billion-dollar industry. Biofuels can be utilized alone or in blend with other nonrenewable energy sources, for example, oil. Biofuels are categorized into first, second, and third-era biofuels. The first-generation biofuels are created from starch and sugars (bioethanol) and from seed oils (biodiesel). The immediate utilization of vegetable oils and nonconsumable oils can cause problems for the diesel motors because of their high thickness. So, there is a need of changing over these sources into biodiesel with the goal that it may be utilized as a swap for oil-based diesel. Another vital biofuel suggested to as bioethanol has picked up a great deal of significance. The process of managing the transformation of noneatable oils to biodiesel or by adjusting the procedure of transesterification and additionally the transformation of sugars to bioethanol by genetic alteration of yeast cells and by changing the substrates required for ethanol production by yeast are of paramount importance. Genetic engineering plays a key role in the transformation of microbes into the desired cell factories with high efficiency of biodiesel production. In this chapter, we present an overview of principal microorganisms, especially filamentous fungi, used in the microbial biodiesel production and recent advances in metabolic engineering for the modification required. Overexpression or deletion of the related enzymes for de novo synthesis of biodiesel is highlighted with relevant examples.
... Exploration of diversified microbes of the environment is impossible by common cultural method. Metagenomic profiling using various advanced techniques brought unprecedented development in exploring and profiling of the unculturable microbes of environment (Bhakta et al., 2017). ...
... A thorough analysis of each of these molecules extracted from an environmental community yields key insights into the taxonomic composition of a community, the functional potential for community, or the genes and proteins currently being expressed (Techtmann and Hazen, 2016;Bhakta et al., 2017). ...
... The elucidation of how microbial communities change due to the effects of environmental disturbances like pollution, investigations need to rely on rapid methods that can characterize cellular constituents such as nucleic acids, proteins (enzymes) and other taxa-specific compounds (Maila, 2005). These molecules can be extracted directly from the soil without the need for culturing and thus can be used to elucidate the microbial community composition of such polluted environments during bioremediation (Simon et al., 2011;Bhakta et al., 2017). ...
A vast array of microbes is being omnipresent in different domains of the environment.
Diversified microbial community of environment is dynamic in nature due to
environmental dynamicity caused by geogenic and anthropogenic activities. Exploration
of diversified microbes of environment is impossible by common cultural methods.
Metagenomic profiling using various advanced techniques brought unprecedented
development in exploring and profiling the unculturable microbes of environment.
Metagenomic had proposed to understand how the unculturable microorganisms genome
worked on the environmental contaminants and how the biostimulation could affect on
microbial community’s genes. In this chapter, an updated knowledge about different metagenomic techniques which facilitated by the recent advances in gene sequence and
used in studying environmental biology have been covered. The process of monitoring of
environmental microorganisms genomes that had been adapted to contaminants
elimination from environments is of a paramount importance, because it might help in
engineering microorganisms capable to clean up the environment.
... Thus, metagenomics is an essential tool for studying soil bacterial communities and provides an excellent way to assess bacteriocenosis structure. High-throughput sequencing based on 16S rRNA is currently a common tool for in-depth study of soil bacterial community composition and abundance [2,13]. ...
... Agriculture 2023,13, 653 ...
The increasing rate of natural resource use leads to an increase in the anthropogenic load on the soil. As the result of industrial, metallurgical and mining activities, excessive amounts of heavy metals (HMs) enter the soil. In addition, they can be introduced with waste and drainage water from various enterprises. Accumulating in the soil, HMs can negatively affect the soil bacterial community, which is one of the main factors of its “health”. Molecular genetic methods based on shotgun sequencing or metabarcoding of standard DNA sequences (for example, the 16S rRNA gene for bacteria) are the modern ways to assess the bacterial diversity of soils. This review presents the results of modern studies on the effect of HMs on the soil bacterial communities, using metagenomic methods. Based on the analysis of publications over the past two decades, a generally negative effect of pollutants on the taxonomic composition and diversity of bacterial communities has been shown. The influence of factors modulating the toxicity of metals and metalloids was noted: the amount and composition of salts, soil pH, ecosystem type, rhizosphere presence and other soil properties. In this paper, promising directions of research are outlined.
... Very preliminary research isolated cadmium and leadresistant lactic acid bacteria (LAB), Enterococcus faecium and Lactobacillus reuteri (Limosilactobacillus reuteri) for possible application as cadmium and lead removal probiotic [17,31]. Some studies isolated As-resistant bacteria for possible application in As removal and bioremediation in the environment [36][37][38]. Bhakta et al. explored some As-resistant lactic acid bacteria for uptaking As from an aqueous medium [37]. Halttunen et al. showed the heavy metal removal of Lactobacillus casei DSM20011 from water [39,40]. ...
... To obtain the As-resistant LAB, the enrichment culture process was followed according to the method described by Bhakta et al. [31,38]. The morphologically different colonies of distinct yellow colour ( Supplementary Fig. S1) were randomly picked up from the MRS (Hi-Media, Mumbai, India) agar plates to represent the As-resistant LAB. ...
Arsenic (As) contamination of water and food is a global problem posing a severe threat to environmental and human health; therefore, fish as an aquatic animal is immensely affected by the hazardous impacts of As. The present study aimed to explore the As-resistant probiotic bacteria and characterize their potential for applying as an As bioremediation tool in fish. As-resistant lactic acid bacteria (LAB) were isolated from sludge samples of an old stabilization pond/lagoon of wastewater treatment plant using spared plate techniques. The potential probiotic was selected by assessing the sequential probiotic characterization, As resistance and removal properties. The selected probiotic was identified by PCR-based molecular method using 16S rDNA. A total of 51 As-resistant LAB were isolated from sludge samples. Potential six As-resistant LAB strains (As4, 11, 20, 21, 41 and 48) were selected from 51 isolates through sequential probiotic characterizations using mimic fish gastrointestinal conditions. The selected probiotics displayed relatively elevated As (> 1000 mg L⁻¹), cadmium (20–100 mg L⁻¹) and lead (> 2000 mg L⁻¹)–resistant patterns and excellent As-removal efficiencies (0.0012–0.0044 mg As mg cell⁻¹ h⁻¹) from water along with favourable various associative probiotic properties. The 16S rDNA sequence-based molecular identification and phylogenetic analysis revealed that the strains As4, 11, 20, 21, 41 and 48 belong to Limosilactobacillus fermentum (Lactobacillus fermentum according to old taxonomy). The As removal and survival in mimic gastrointestinal conditions of fish indicated that new Limosilactobacillus fermentum strains could be employed as the novel and potential probiotic tools for possible bioremediation of As and other pollutants in the fish to prevent the bioaccumulation and toxicity impacts of As in fish for cleaner and safe fish food production.
... For decades, unreasonable mining, smelting and agricultural activities have contributed much in excessive heavy metal contamination in water resources and soils (Bhakta et al., 2018;Hmt et al., 2021;Iftikhar et al., 2021;Tauqeer et al., 2021), which has posed significant threat to agri-ecosystems, soil quality, food safety, as well as the health of animals and human (Turan, 2019(Turan, , 2020. Heavy metal (loid)s can significantly affect multi-functionality of arable ecosystems by changing the microbial abundance, manipulating the diversity of soil microbes and reducing soil enzymes activity (Chen et al., 2020;Luo et al., 2018;Shahid et al., 2016;Tipayno et al., 2018). ...
... Hence, it's essential to understand the effects of geochemical factors in contaminated soil on bacterial community assembly for maintaining arable sustainable development (Chen et al., 2020;Crowther et al., 2019;Fierer, 2017). Recently, 16S rDNA-based high-throughput sequencing technicality has been frequently employed to explore complicated native bacterial composition and abundance (Bhakta et al., 2018;Fierer, 2017;Wan et al., 2020). However, the factors that determine the assembling process and the mechanisms of how communities respond to geochemical changes have rarely understood (Prosser, 2019). ...
Soil microbes play crucial roles in biochemical and geochemical processes in contaminated arable ecosystems. However, what factors determine the assembling process of soil bacterial community under multiple heavy metal (loid)s (HMs) stress and how communities respond to geochemical changes have rarely been understood. Therefore, a number of contaminated soils were sampled to explore the interactions among geochemical parameters, HMs and innate bacterial community. The results showed that soil biochemical activities were inhibited obviously with the increase of HMs. Significant differences were observed in bacterial composition and abundance in studied areas, with Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria and Firmicutes governing the bacterial community structure. Redundancy analysis and variation partition analysis revealed that about 67.33% of the variation in bacterial assemblages could be explained by physiochemical parameters (21.59%), biochemical parameters (11.64%), toxic metal (loid)s (9.11%) and the interaction effect of these variables (24.99%), among which total-arsenic and moisture were the main factors. Spearman correlation analysis also demonstrated that dehydrogenase, moisture and TOC have a positive correlation with bacterial community structure with As–Cd–Pb gradient. Altogether, this study would provide a comprehensive relationship between major environmental factors and bacterial assemblages, which could offer some baseline data to investigate the mechanisms of how communities respond to physiochemical changes.
... For decades, excessive and unreasonable producing activities have caused serious heavy metals pollution problems, which has posed significant threat to biodiversity and functioning of soil microorganisms, food safety and public health (Bhakta et al., 2018). Soil microorganisms are crucial role in natural and managed soil ecosystems (Fierer, 2017). ...
... Recent methodological development provided opportunities to chart complex microbial community structure and potential mechanisms for the full variation with dominant environmental parameters (Wu et al., 2017). 16S rRNA-based high-throughput sequencing is now relatively common tool for in-depth exploring soil microbial community composition and abundance (Bhakta et al., 2018;Fierer, 2017). Toxic stress of heavy metal(loid)s would adversely influence the diversity and abundance of soil sensitive microorganisms, while resistant bacteria could readily adapt and increase in abundance (Xu et al., 2018;Zhao et al., 2019), thereby structuring microbial community (Guo et al., 2017). ...
Microorganisms play a vital role in soil biochemical process in contaminated managed ecosystems. In the present study, a field investigation was conducted in farmland around an industrial intensive region contaminated with cadmium, and the changes of microbial assemblages in contaminated soils were assessed by 16S rRNA sequencing and the further statistical analysis. The results revealed obvious variations in microbial richness between referenced and contaminated soils, with Proteobacteri, Chloroflexi, Actinobacteria, Acidobacteria and Nitrospirae dominating the studied communities around the industrial intensive region. Redundancy analysis and Spearman correlation heatmap revealed that about 68.95% of overall variation in microbial community composition was explained by soil physiochemical properties and Cd existence, among which pH, soil total phosphorus, total nitrogen, organic carbon (OC) and available Cd were identified as dominant factors. No significant difference was found in the similarities and Beta-diversity analysis among different groups. In conclusion, this study revealed the ecological effects of physiochemical parameters and Cd stress on the diversity and abundance of microbial communities, and these findings provided the detailed and integrated correlation between the main factors and microbial indexes in Cd contaminated farmland around the industrial intensive region.
... These bioassays offer a rapid and effective method for evaluating environmental quality, facilitating ongoing monitoring and expedited reactions to pollution incidents. These strategies leverage biological systems that respond to environmental stressors, yielding expedited results and facilitating continuous, localized environmental evaluations without the necessity for extensive sample transportation and analysis [16,20,[33][34][35][36]. ...
Near real-time biomonitoring, particularly through enzyme assays, offers exceptional sensitivity to bioavailable pollutants, delivering rapid results that facilitate timely intervention. This method is crucial for reducing pollution in drinking water systems and safeguarding human and animal health. The marriage of biological and instrumental process of monitoring allows only positive samples be sent for instrumental analysis vastly increasing the frequency of monitoring and reducing cost at the same time. This study demonstrates the application of ficin as an inhibitive enzyme assay for biomonitoring, in a near real time setting, specifically targeting heavy metals in environmental samples from waters near Kuah’s Jetty, Langkawi. Using the ficin dye-binding assay, designed to detect mercury silver (Ag+), (Hg2+), and copper (Cu2+) at sub-ppm levels, we validated its ability to identify trace concentrations of these metals in waters. The assay proved to be sensitive, rapid, and cost-effective, with minimal inhibition (<10%) during a 6-hour field trial, indicating low pollution levels, which was further corroborated through instrumental analysis. This method enables the swift identification of pollutants, prompting timely action and supporting the preservation of ecotourism sites by providing empirical data for policy development. The simplicity and visual appeal of enzyme assays make them excellent tools for education, fostering environmental awareness and conservation efforts. Our findings underscore the potential of enzyme assays for large-scale environmental monitoring, aligning local practices with international standards and promoting global cooperation in environmental conservation. This study enhances our understanding of ecological health in marine and brackish ecosystems, emphasizing the need for continuous monitoring to protect natural habitats.
... The Cd sorption capacity of the biosorbent was calculated by the following equation [29]: ...
... Intercropping systems similarly cause changes in inter-root microbial community composition, which are mainly due to fertilization (Guo et al., 2020), crop type (Prommer et al., 2020), and changes associated with crop diversity, such as root secretions (Mommer et al., 2016) and soil environmental factors (Stefan et al., 2021). High-throughput sequencing of 16S rRNA is now an established approach (Bhakta et al., 2017) for deep exploration of soil microbial community composition and abundance. Li et al. (2022) found that Acidobacteriota and Proteobacteria were the dominant phyla in the maize intercropping system, and Proteobacteria relative abundance in the intercropped maize root soil increased significantly, primarily due to interspecific root interactions resulting in differences in bacterial community structure during intercropping. ...
We investigated the effects of the complex cultivation of Salvia miltiorrhiza on microbial communities, secretions, yield, and active ingredients, and the mechanism of action between microbial communities, secretions, and S. miltiorrhiza growth and development. Neither maize nor soybean was suitable to grow with S. miltiorrhiza, but sesame significantly increased salvinone content, the active ingredient of S. miltiorrhiza, and Tanshinone IIA, Tanshinone I, and Cryptotanshinone increased by 27.06%, 22.76%, and 26.41%, respectively, which increased the abundance and number of microbial communities in S. miltiorrhiza roots. 16S rRNA results showed that the most abundant bacterial phyla were Proteobacteria and Acidobacteriota, and their number increased with compound planting of sesame and S. miltiorrhiza. Salvia inter-root secretions affected the microbial community and Salvia growth and development, and lipids and lipid-like molecules significantly reduced Salvia yield and active ingredients. Overall, different plant secretions can lead to differences in the natural environment and Salvia root growth and development, and the composite planting of sesame with Salvia can improve inter-root microbial communities, enhance Salvia quality, and make fuller use of land resources.
... Tracking pathogenic bacteria and multi-resistant strains needs DNA fingerprinting (Bhakta et al, 2018). Variable Number of Tandem Repeat Regions (VNTRs) are repeated DNA loci present in bacterial genes that can vary between strains and are used as an effective identification tool for pathogenic bacteria (Burgueño-Rodríguez et al, 2020). ...
Forty isolates of Staphylococcus aureus were activated, 10 from blood, 10 from urine and 20 from vaginal swabs. All isolates were diagnosed by 16S rRNA. The results of the virulence factor tests showed that 13 (32.5%) of these isolates were producing extended-spectrum â-Lactamase enzymes (ESBLs), while 36 (90%) of them produced the metallo â-lactase enzymes. MBLs and the cefoxetine resistance test was used to detect the production of AMPs, and the results were 9 isolates. (22.5%) produced the enzyme. Antimicrobial sensitivity of Staphylococcus aureus isolates was determined by disc diffusion method, for 7 antibiotics, and the results of isolate resistance were as follows: Azithromycin (87.5%), Cefotaxim (37.5%), Cefoxitin (62.5%), Gentamycin (37.5%), Methicillin (100%), Norfloxacin (40%) and Vancomycin (75%). The minimum inhibitory concentration (MIC) was determined for all isolates for Vancomycin between (16-128) mg/ml. Molecular profiling of S.aureus by variable number tandem repeats depending on the sites clfA, and sdrC. The results of the current study showed that, the gene scan analysis revealed 6 different kinds of amplicons in 10 isolates for clfA gene, which were 993bp (4 isolates), 957bp (2 isolate), 1029bp (1 isolate), 101bp (1isolate), 921bp (1 isolate) and 939bp (1 isolate). In case of sdrC gene locus 3 different types of amplicons were obtained with MRSA isolates. These amplicon sizes were 610bp (7 isolates), 646bp (2 isolates) and 592bp (1 isolate). Key words : Multi locus variable number tandem repeat analysis, capillary electrophoresis. How to cite : Zahraa Ali Fadhil, Hadi R. Rasheed Al-Taai and Asaal Abdul-Ghani Shyeaa (2021) Use of multiple locus variable number tandem repeat analysis for genotyping of Staphylococcus aureus isolates in Diyala Governorate. Biochem. Cell. Arch. 21, 4553-4557. DocID: https://connectjournals.com/03896.2021.21.4553
... The Cd sorption capacity of the biosorbent was calculated by the following equation [29]: ...
... Bhakta et al. (2012) showed high Cd-(50-1000 mg/l) and Pb (> 2000 mg/l)-resistant properties of several lactic acid bacteria (Lactobacillus reuteri, L. amylovorus, L. dextrinicus, etc.).Bhakta et al. (2017) isolated a number of As-, Cd-and Hgresistant bacteria (Lysinibacillus sp.Temporal changes of CD, HZD, and PSI (inset showing the hollow zone around the EGM8 colony in the petri plate)Fig. 4The changes of inorganic phosphate solubilization efficiency of PSB strain, EGM8 in liquid MPIK media with time Org. ...
Phosphorus (P), a primary macronutrient nutrient of soil, plays a vital role in plant nutrition and growth promotion. The objective of the present study was to explore potential phosphate solubilizing bacteria (PSB) from earthworms (Metaphire posthuma). A total of 8 PSB colonies were isolated from the gut content of earthworm using Pikovskaya’s agar media following the spread plate method. Out of eight isolates, one isolate (EGM8) of the gut of earthworm was selected as potential PSB using phosphate solubilization index and inorganic phosphate solubilizing activity. The isolate showing the highest phosphate solubilization index (4.8 ± 0.5) and inorganic phosphate solubilization activity (1.053 ± 0.18 mg/l) was selected for biochemical characterizations, plants (Vigna unguiculata, Amaranthus dubius, and Abelmoschus esculentus) seed germination, and growth studies. The EGM8 isolate showed a higher rate of seed germination (10–50%) and plant growth (shoot length — 21% and leaf number — 77%) properties compared to that of the control in A. esculentus. The EGM8 revealed higher plant growth due to producing the highest bioavailable P in the rhizosphere zone of plants. The selected PSB strain, EGM8, exhibited 99% similarity with Pseudomonas aeruginosa and hence identified as P. aeruginosa EGM8 strain. Summarily, it can be concluded that the P. aeruginosa EGM8 bacterial strain could be utilized as a potential biofertilizer for high crop production and may also be suggested that the earthworm would be a potential source for microbial biofertilizer.
Graphical abstract
... Estomas anomocíticos a nivel de las células epidérmicas fueron observados por Abubakar et al., Bhakta et al., (2017), además de los hábitos y condiciones de crecimiento de las plantas, este fenómeno morfológico de los estomas, habitualmente se relaciona con la especie de plantas con la que se esté experimentando. ...
The species Moringa oleifera Lam. It is a deciduous tree that is used in food and treatment of human and animal diseases. The objective of the present study was to characterize the growth, production, development, stomatal morphology and biochemical composition of M. oleifera Lam. inoculated with plant growth promoting rhizobacteria (PGPR) (Bacillus niacini (Y11), Moraxella osloensis (Y13), Bacillus cereus (A11) and Azospirillum brasilense Cd (DSM 1843)) under greenhouse conditions. The stomatal morphology results, the leaves of plants inoculated with B. cereus presented smaller stomata, compared to the rest of the inoculums and control (CT). In the case of M. osloensis, this induced changes (P≤0.001) in the length and width of the stomata; the leaves were hypostomatic with wavy anticline walls and anomocytic stomatal apparatuses. In the evaluation of the growth and development of plants inoculated with PGPR, A. brasilense promoted a greater height in the plant (67.17 cm) (P≤0.01) compared to the control. (43.54 cm); M. osloensis and B. cereus as a whole, increased (P≤0.001) the number of leaves (11.45 and 11.85, Vs 8.68 of the TC, respectively). Regarding the dry biomass yield (DBY) of leaves and whole plant (WP). The plants inoculated with B. cereus led to higher (P≤0.01) yields of dry biomass of leaves (0.80 Vs 0.26 t DBY ha-1 of the control) and WP (12.92 Vs 5.52 t DBY ha-1 of the control). Regarding the morphophysiology of the plant, B. cereus promoted (P≤0.01) the development of leaf area
(LA) (20.28 cm2); leaf area index (LAI) (21.13) and duration of leaf area (DLA) (4.78 cm2day-1) with respect to TC (13.9 cm2; 14.71; -1.57 cm2day-1, for LA, LAI and DLA, respectively), absolute growth rate (AGR) and relative (RGR) growth rate were higher with the A. brasilense and M. osloensis inocula in AGR (1.037 and 0.93 cm2 day-1 Vs 0.12 cm2 day-1 of the CT) and RGR (0.014 cm day-1 * 10-3 with both inoculums Vs 0.002 cm day-1 * 10-3 of the CT). Bacterial inocula did not promote differences (P≥0.05) in the
concentration of photosynthetic pigments or total polyphenols, but did (P≤0.001) in the content of total flavonoids with respect to TC (6.22 mg equivalent of Quercetin g extract-1). Regarding the mineral composition of the plant, the concentration of mineral elements in leaves only showed significant differences (P≤0.001) in the content of Mg2+ and K+ promoted by B. niacini. Through principal component analysis (PCA) of the mineral content of roots, it was possible to explain 79.1% of the variance in two components, the PGPR facilitated the increase of the content of K+, Br+ and P3+, and for the analysis of leaves, it was observed in the PCA with three components and 80.24% of the variance explanation, the presence of Mn2+, Zn2+, Si4+ and Al3+. In conclusion, the inocula of PGPR inoculated to Moringa plants under greenhouse conditions modified the morphology of leaves and stomata, highlighting B. cereus, all the inoculars stimulated growth as a function of height with respect to CT, prevailing the effects of A. brasilense; in the diversification of the antioxidant profile B niacini promoted concentrations of total flavonoids and differentiated the content of Mg2+ and K+ in the order of minerals, in the concentration of photosynthetic pigments and total polyphenols the PGPR were not effective.
... KS-Kim et al., 2003) Two-dimensional gel electrophoresis Proteomics and transcriptomics Identification of upregulated genes by cis-dichloroethene (cDCE), an assumed carcinogen in JS666 strain of Polaromonas sp. Chakraborty and Das, 2017)PCR-DGGE MetagenomicsProfiling of heavy metal-resistant microbial community(Bhakta et al., 2018) ...
The quality of life on Earth is inevitably related to the quality of environment. Industrialization has led to the production of pollutants and contaminants especially inorganic contaminants such as mineral acids, metals, and inorganic salts. Numerous innovative and novel techniques have been designed to minimize the hazardous effects of these contaminants, and bioremediation is one of these approaches. In contrast to conventional remediation techniques, the key advantage of bioremediation is its low cost and environmentally friendly operation as compared with other typical approached. Researchers were previously focused on typical bioremediation approaches, but now advanced molecular techniques of bioremediation using multi omics approaches have been introduced to explore and comprehend the functional and structural characteristics of participating biotic factors. Several molecular techniques including 16S rRNA sequences analysis, denaturing gradient gel electrophoresis, ecological diversity, and omics approaches have been established and considered to be potent and vital tool for the degradation, eradication, and detoxification of contaminants from the nature.
... According to many researchers, metallotolerant bacteria isolated from heavy metal-contaminated sites are more potent candidates of bioremediation due to their better adaptation and heavy metal resistance mechanism (Al-Gheethi et al. 2015). The bacteria Lysinibacillus sp., Staphylococcus sciuri, B. fastidiosus, B. niacini, Clostridium sp., and Bacillus sp. were reported to be tolerant to As, Cd, and Hg, which were also applied in bioremediation (Bhakta et al. 2018). Similarly, various gram-negative bacteria like Enterobacter sp., Stenotrophomonas sp., Providencia sp., Chryseobacterium sp., Comamonas sp., Ochrobactrum sp., and Delftia sp. were isolated from activated sludge, which appear to tolerate Cu, Cd, and Co, and can be efficiently utilized for bioaugmentation of activated sludge to treat the industrial effluents efficiently (Bestawy et al. 2013). ...
The book compiles the latest studies on microorganisms thriving in extreme conditions. Microbes have been found in extremely high and low temperatures, highly acidic to saline conditions, from deserts to the Dead sea, from hot-springs to underwater hydrothermal vents- the diversity is incredible. The various chapters highlight the microbial life and describe the mechanisms of tolerance to these harsh conditions, and show how an understanding of these phenomena can help us exploit the microbes in biotechnology. The theme of the book is highly significant since life in these environments can give vital clues about the origin and evolution of life on earth, as a lot of these conditions simulate the environment present billions of years ago. Additionally, the study of adaptation and survival of organisms in such environments can be important for finding life on other planets.
This book shall be useful for students, researchers and course instructors interested in evolution, microbial adaptations and ecology in varied environments.
... Arsenic (As), a colorless and odorless element found in air, water, and soil in trace quantities (Matschullat 2000;Prashant et al. 2009;Bhakta et al. 2016Bhakta et al. , 2017, is one of the priority hazardous pollutants posing severe environmental and human health hazardous impacts worldwide. According to the International Agency for Research on Cancer, As and its compounds are Group 1 carcinogen to human beings (Bhakta et al. 2016;Bhakta and Munekage 2009;IARC 1987). ...
The Middle Ganga Plain (MGP) is the second largest arsenic (As) contaminated groundwater zone in south-east Asia after the Bengal Delta Plain. About 90% of the total population in the MGP depends on shallow aquifer based groundwater supply for their drinking and irrigation need. More than ten million people in the alluvial belt of MGP are exposed to elevated levels of As (more than the limit set by Bureau of Indian Standards (BIS) 2012 drinking limit of 50 μgL⁻¹) in their drinking water. In the light of synthesis of groundwater As distribution in MGP, the availability of safe sources of water for drinking have been analyzed. The current study delineates two aquifer systems in MGP through the study of borehole lithologs (n = 27). The first aquifer system persists from below the top aquitard to up to ~87–126 m below ground level (bgl), while the second aquifer system starts at various depths ranging from ~116 to 139 m bgl and continues up to the depth of ~250 m bgl. Suitability of the deeper (second) aquifer system for As free drinking water has been assessed through analysis of pumping test data. The Newer Alluvium comprising the top aquitard and the upper 15–20 m slice of the first aquifer system hosts the contaminated aquifers for the depth of ~50 m below ground surface. The Pleistocene aquifers (the bottom three-fourth part of the first aquifer system and the entire second aquifer system) are low in groundwater As. The second aquifer system, existing in confined condition, can be used for community water supply through the installation of deep tube wells with a regulated draft. Community hand pumps in the depth range of 5–15 m below ground can be constructed in the sandy areas in the floodplain for drinking need of the local people. Large diameter dug wells can also be constructed to tap the replenished dynamic groundwater, which normally remains oxic and low in As.
Cadmium (Cd) contamination poses serious risks to soil ecosystems and human health. Herein, the effect of two drunken horse grasses (Achnatherum inebrians) including endophytes Epichloë gansuensis infected (E+ ) and uninfected (E-) on the phytoremediation of Cd-contaminated soils were analyzed by coupling high-throughput sequencing and soil metabolomics. The results showed that the high-risk soil Cd decreased and the medium- and low-risk Cd fraction increased to varying degrees after planting E+ and E- plants in the soil. Meanwhile, total Cd content decreased by 19.7 % and 35.1 % in E+ and E- A. inebrians-planted soils, respectively. Principal coordinate analysis revealed a significant impact of E+ and E- plants on the soil microbial community. Most stress-tolerant and gram-positive functional bacterial taxa were enriched to stabilize Cd(II) in E+ planted soil. Several beneficial fungal groups related to saprotroph and symbiotroph were enriched to absorb Cd(II) in E- soil. Soil metabolomic analysis showed that the introduction of A. inebrians could weaken the threat of CdCl2 to soil microbe metabolism and improve soil quality, which in turn promoted plant growth and improved phytoremediation efficiency in Cd-contaminated soil. In conclusion, A. inebrians plants alleviate soil Cd pollution by regulating soil microbial metabolism and microbial community structure. These results provide valuable information for an in-depth understanding of the phytoremediation mechanisms of A. inebrians.
The study was conducted to investigate the growth of mercury-resistant bacterial consortium under the influence of different pHs, temperatures, and C:N ratios, as a part of mercury bioremediation research. The consortium consisted of five bacterial isolates selected due to their resistance to HgCl 2 up to 100 ppm and was proven to effectively reduce mercury from the culture media. Consortium suspension was inoculated into two sets of media: 1) Tryptic soy broth (TSB) with pHs of 4.8, 6.1, 8.5, and 9.7; 2) Mineral salt with the addition of glucose and peptone to create C:N ratios of 20:1, 30:1, and 40:1 while the pH was set to 7.4. For comparison, a solution containing mercury-contaminated soil was added to the same set of media and regarded as a microbial community. The growth curves show that the bacterial consortium tended to grow better compared to the microbial community, especially in the TSB medium at incubation temperatures of 20 and 35 °C. In the same medium at a temperature of 45 °C, the growth of both consortium and community under high pHs (8.5 and 9.7) was higher than the one under lower pHs (4.8 and 6.1). Meanwhile, in the mineral salt medium, the influence of the inoculant was not remarkable except under an incubation temperature of 35 °C. Moreover, the C:N ratio did not affect the growth of either the bacterial consortium or the microbial community (p > 0.05). The variance analysis also indicated that the growths were significantly different only when the pH was 4.8.
This study investigated the structure of fungal and bacterial communities in different types of Cd-contaminated soils. The results showed that obvious variations in microbial structure between contaminated alkaline soils and acidic soils. Proteobacteria, Gemmatimonadetes, Bacteroidetes and Basidiomycota dominated the studied communities in the alkaline soils, whereas Actinobacteria, Chloroflexi, Firmicutes, Acidobacteria, Saccharibacteria and Ascomycota were more abundant in the acidic soils. Additionally, Cd tolerant (Proteobacteria, Bacteroidetes, Ascomycota) and sensitive (Actinobacteria, Acidobacteria, Basidiomycota) in alkaline soils and JL-soils, Cd tolerant (Actinobacteria, Acidobacteria, Basidiomycota) and sensitive (Saccharibacteria, Proteobacteria, Bacteroidetes, Ascomycota, Mucoromycota) in the acidic soils were identified. Redundancy analysis and correlation analysis demonstrated that it was significantly affected by different environment parameters in alkaline soils and acidic soils. Varied bacterial community structures in all soils were dominantly influenced by pH and SOM. The similarities among different groups indicated the effect of soil type on microbial community structure was greater than that of Cd level. The above conclusions may provide a new perspective for the bio-remediation of Cd in different types of soils.
Arsenic intoxication through contaminated water and food is a challenging problem worldwide. The objective of the present study was to isolate the As-resistant lactic acid bacteria (LAB) and assess the As sorption stoichiometry of LAB to validate its practical application as a bioremediation tool. The present study isolated 50 As-resistant LAB colonies from human (HS1-25) and albino mice (MM1-25) fecal samples. Out of 50 As-resistant LAB, the HS12 isolate exhibited the highest As removal efficiency (0.021 mg/h/g). The As bioremediation kinetic study determined the contact time 10 min and the pH between 5 and 7 for optimum As biosorption from the water. The Langmuir isotherm model ( R ² = 0.993) was well fitted with the data than the Freundlich isotherm model ( R ² = 0.876). The As bioaccumulation and scanning electron microscopy studies proved that binding of As onto cell membrane (0.000037 mg/g) and within the cell (0.000036 mg/g) are the mechanism of As sequestration of LAB HS12. The biosorption of As (2.28–20.37%) from fruit juice, soft drink and coffee as well as multimetals (0.025–0.179 mg/l; 16.22–98.69%) along with As (0.00024 mg/l) from water validated the practical application potential of HS12. The phylogenetic analysis of 16S rDNA amplicon (500 bp) of isolated potential HS12 LAB strains showed 97% similarity to Lactobacillus reuteri. Due to having As biosorption efficiency from water and liquid foods, it can be concluded that the human origin identified L. reuteri HS12 strain could be employed as a novel candidate of As bioremediation to safe environmental and human health.
In the modern era of microbial ecology studies, use of high-throughput methods for culture-independent assessment of microbial communities from contaminated sites can pave the way of development of sustainable bioremediation approaches. Numerous culture-independent techniques involving molecular tools can provide a mechanistic understanding of the structure and functions of microbial communities, including their observable changes in contaminated sites. In particular, next-generation sequencing (NGS) approaches have revolutionized assessment of microbial communities across contaminated sites and have provided deeper understanding of their metabolism linked to breakdown of contaminants. Therefore these techniques help toward direct analysis of natural microbial communities and can help toward restoration of contaminated sites. This chapter discusses the application of some of the well-established molecular tools, including NGS toward characterization of microbial communities in contaminated sites.
Effluents from different industries are rampantly being discharged into the natural water bodies. Thus it is pertinent to treat this wastewater pollution from different sources before discharging it to the environment. The most extensively used biological process for the treatment of wastewater plant is the activated sludge process. The activated sludge process has shown high nutrient removal, biomass retention capacities, and removal of toxins, due to which activated sludge processes are a lucrative option for treating the wastewater. The diverse microbial communities comprising bacteria, fungi, protozoa, viruses, algae, and metazoa account for 95% of the microbes and play a chief role in the wastewater treatment. Many high-throughput techniques, such as metagenomics, metatranscriptomics, and metaproteomics, are utilized to decipher the functional aspects of these microbial communities.
Zinc (Zn) is one of the hazardous metal pollutants commonly found in industrial effluents and poses severe environmental and human health impacts. The present study chosen the leaves of Corchorus olitorius as a potential biosorbent among four different types of leaves employed for removing Zn from aqueous solution. The process parameters—contact time, pH, biosorbent dose, and initial Zn concentration were optimized for maximum removal of Zn using standard protocols. The Fourier‐transform infrared spectroscopy study was performed to identify the functional groups involved in Zn biosorption mechanism. The biosorption equilibrium was achieved at 120 min of contact time. The biosorption of Zn was highest at pH 6 and biosorbent dose of 2 g/L. The sorption equilibrium data were well fitted with the Freundlich isotherm model (R² = 0.995). Highest adsorption capacity of C. olitorius leaves was 11.63 mg/g. It is concluded that the leaves of C. olitorius could be used as a potentially low‐cost novel biosorbent to remove Zn from contaminated water.
Practitioner points
• Optimum Zn sorption process parameters of Corchorus olitorius leaf biosorbent were determined.
• Zn sorption kinetic data of C. olitorius leaf were well fitted by Freundlich isotherm model.
• C. olitorius leaf biosorbent showed excellent Zn sorption capacity (11.63 mg/g) from water.
• Leaves of C. olitorius could be used as a potentially low‐cost novel biosorbent.
The overall condition of the environment is inevitably linked to nature of life on the Earth. However, due to industrial revolution, the global upsurge of accumulation of toxic metals has increased enormously which is posing a serious problem to human health. In such environment, where survival of indigenous microorganisms is difficult, metallotolerant bacteria are able to thrive by tolerating high levels of heavy metals. To cope with this extreme condition, they employ diverse mechanisms to overcome the toxic effects of metals and metalloids with alteration of different genes and proteins, and these mechanisms also help their possible commercial exploitation. Hence, it is essential to understand their unique metabolic capacity or physical structure which encourages thriving in these metal-rich environments. This chapter also sheds light on evolutionary strategies that facilitate the metallotolerant bacteria to adapt to the environment and associated ecophysiological aspects.
Arsenic (As) contamination of drinking water and its severe human health impacts have been a global concern during the last few decades. In order to control the problem of As in drinking water, various chemical based treatment methods, such as coagulation, ion-exchange, adsorption, and reverse osmosis, are used in removing As from water. Most of these methods are not eco-friendly and have several limitations (high material cost, high energy requirements, generation of sludge, etc.) in large-scale practical applications. To overcome these limitations, several studies considered various biological agents as potential low-cost and eco-friendly sound biosorbents in treating As-contaminated water. It has been found that a wide range of biomass such as algae, fungi, bacteria, plant parts, fruit wastes, and agricultural wastes are low-cost, recyclable, no sludge generating and highly effective biosorbents in removing arsenic from water. Thus, biosorption has emerged as an eco-friendly and cost-effective technique in arsenic remediation. The present chapter provides a review of recent literature on As biosorption technologies. The utilization of various biosorbents including their optimum treatment conditions also is extensively summarized to get a better concept about the future scope of As remediation using biosorption method.
Conventional leaching methods in metal mobilization and recovery is a troublesome
process require strong acids and other associated facilities, which are not favourable and
ecofriendly, posing severe hazardous threats to the environment. Discovery of microbial
leaching properties opens a new avenue in metal mobilization and recovery. Various
technologies have been developed concerning the application of microbes in metal mobilization and recovery from the sources employing microbial leaching mechanism. The
present chapter attempted to draw an updated picture on the current advancement of
bioleaching in metal mobilization considering the brief historical perspective, bioleaching
mechanism, microbes in bioleaching, factores influencing the bioleaching process and its
application as green technology and nanoparticle processing. The chapter summarily
concluded that bioleaching is a green and environment friendly biotechnological
application, has broad future prospects and its current research and advancement openning newer avenues for developing cleaner and greener environment.
Contamination, pollution and degradation of air, water, and soil environments by
geogenically and anthropogenically generated various pollutants are severe and life
threatening problems globally. Recently, bioremediation has evolved as the most
promising eco-friendly approach in the field of environmental remediation technology,
playing a pivotal role in solving the menacing problems of environmental pollution in
2018. Several innovative and advanced bioremediation technologies have been developed
using genomics and metagenomics, proteomics, transcriptomics and metabolomics in order to overcome the limitations concerning the process. The present chapter has attempted to briefly discuss the advancement of bioremediation in respect to significant
biotechnological improvement for applying as green technology in order to eco-friendly
cleaning the air, water, and soil environments.
Thirty-one mercury-resistant bacterial strains were isolated from the effluent discharge sites of the SIPCOT industrial area. Among them, only one strain (CASKS5) was selected for further investigation due to its high minimum inhibitory concentration of mercury and low antibiotic susceptibility. In accordance with 16S ribosomal RNA gene sequences, the strain CASKS5 was identified as Vibrio fluvialis. The mercury-removal capacity of V. fluvialis was analyzed at four different concentrations (100, 150, 200, and 250 í µí¼g/ml). Efficient bioremediation was observed at a level of 250 í µí¼g/ml with the removal of 60% of mercury ions. The interesting outcome of this study was that the strain V. fluvialis had a high bioremediation efficiency but had a low antibiotic resistance. Hence, V. fluvialis could be successfully used as a strain for the ecofriendly removal of mercury.
Heavy metal pollution is one of the most important environmental issues of today. Bioremediation by microorganisms is one of technologies extensively used for pollution treatment. In this study, we investigated the heavy metal resistance and zinc bioaccumulation by microbial consortium isolated from nickel sludge disposal site near Sereď (Slovakia). The composition of consortium was analyzed based on MALDI-TOF MS of cultivable bacteria and we have shown that the consortium was dominated by bacteria of genus Arthrobacter. While consortium showed very good growth in the zinc presence, it was able to remove only 15 % of zinc from liquid media. Selected members of consortia have shown lower growth rates in the zinc presence but selected isolates have shown much higher bioaccumulation abilities compared to whole consortium (up to 90 % of zinc removal for NH1 strain). Bioremediation is frequently accelerated through injection of native microbiota into a contaminated area. Based on data obtained in this study, we can conclude that careful selection of native microbiota could lead to the identification of bacteria with increased bioaccumulation abilities.
The population dynamics of bacterial community was investigated in three Agricultural soils, designated as Loamy sand (A), Peaty coarse (B) and Loamy coarse sand (C) in North-East, Nigeria. The soil chemical properties were characterized to fully understand their nature. Metagenomic approach was used to extract soil DNA using the fast DNA Spin Kit extraction technique. The PCR-electrophoresed DNA bands were excised and subjected to a full scale Denaturing Gradient Gel Electrophoresis (DGGE) analysis. DGGE fingerprinting for the PCR-16S rDNA product revealed a diverse profile of complex population of bacterial community in the study area. The study shows that more bacterial community can be fully investigated using molecular techniques rather than traditional culture method. The implication of the results obtained is discussed.
The rapid progression of technology has significantly impacted population growth, urbanization, and industrialization in modern society. These developments, while positive on the surface, have created critical environmental problems in recent years. The Handbook of Research on Inventive Bioremediation Techniques is a comprehensive reference source for the latest scholarly information on optimizing bioremediation technologies and methods to control pollution and enhance sustainability and conservation initiatives for the environment. Highlighting pivotal research perspectives on topics such as biodegradation, microbial tools, and green technology, this publication is ideally designed for academics, professionals, graduate students, and practitioners interested in emerging techniques for environmental decontamination.
In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.
Regional water pollution and use of unregulated water sources can be an important mixed metals exposure pathway for rural populations located in areas with limited water infrastructure and an extensive mining history. Using censored data analysis and mapping techniques we analyzed the joint geospatial distribution of arsenic and uranium in unregulated water sources throughout the Navajo Nation, where over 500 abandoned uranium mine sites are located in the rural southwestern United States. Results indicated that arsenic and uranium concentrations exceeded national drinking water standards in 15.1 % (arsenic) and 12.8 % (uranium) of tested water sources. Unregulated sources in close proximity (i.e., within 6 km) to abandoned uranium mines yielded significantly higher concentrations of arsenic or uranium than more distant sources. The demonstrated regional trends for potential co-exposure to these chemicals have implications for public policy and future research. Specifically, to generate solutions that reduce human exposure to water pollution from unregulated sources in rural areas, the potential for co-exposure to arsenic and uranium requires expanded documentation and examination. Recommendations for prioritizing policy and research decisions related to the documentation of existing health exposures and risk reduction strategies are also provided.
Inorganic arsenic (i-As) is a non-threshold human carcinogen that has been associated with several adverse health outcomes. Exposure to i-As is of particular concern among pregnant women, infants and children, as they are specifically vulnerable to the adverse health effects of i-As, and in utero and early-life exposure, even low to moderate levels of i-As, may have a marked effect throughout the lifespan. Ion chromatography-mass spectrometry detection (IC-ICP-MS) was used to analyse urinary arsenic speciation, as an exposure biomarker, in samples of 4-year-old children with relatively low-level arsenic exposure living in different regions in Spain including Asturias, Gipuzkoa, Sabadell and Valencia. The profile of arsenic metabolites in urine was also determined in samples taken during pregnancy (1st trimester) and in the children from Valencia of 7 years old. The median of the main arsenic species found in the 4-year-old children was 9.71 μg/l (arsenobetaine—AsB), 3.97 μg/l (dimethylarsinic acid—DMA), 0.44 μg/l (monomethylarsonic acid—MMA) and 0.35 μg/l (i-As). Statistically significant differences were found in urinary AsB, MMA and i-As according to the study regions in the 4-year-old, and also in DMA among pregnant women and their children. Spearman’s correlation coefficient among urinary arsenic metabolites was calculated, and, in general, a strong methylation capacity to methylate i-As to MMA was observed.
In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.
Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well publicized case of this occurs within Glasgow, UK, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI) contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria have been identified that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively non-toxic and less mobile Cr(III) oxidation state, predominantly under circum-neutral pH conditions. Recently, however, alkaliphilic bacteria have been identified that have the potential to reduce Cr(VI) under alkaline conditions. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI) contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using TEM-EDX and XPS. The effectiveness of this haloalkaliphilic bacteria for Cr(VI) reduction at high pH, suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI) contaminated environments.
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The present study proposed the isolation of arsenic resistant bacteria from wastewater. Only three
bacterial isolates (MNZ1, MNZ4 and MNZ6) were able to grow in high concentrations of arsenic.
The minimum inhibitory concentrations of arsenic against MNZ1, MNZ4 and MNZ6 were 300
mg/L, 300 mg/L and 370 mg/L respectively. The isolated strains showed maximum growth at 37 °C
and at 7.0 pH in control but in arsenite stress Luria Bertani broth the bacterial growth is lower than
control. All strains were arsenite oxidizing. All strains were biochemically characterized and
ribotyping (16S rRNA) was done for the purpose of identification which confirmed that MNZ1 was
homologous to Enterobacter sp. while MNZ4 and MNZ6 showed their maximum homology with
Klebsiella pneumoniae. The protein profiling of these strains showed in arsenic stressed and non
stressed conditions, so no bands of induced proteins appeared in stressed conditions. The bacterial
isolates can be exploited for bioremediation of arsenic containing wastes, since they seem to have the
potential to oxidize the arsenite (more toxic) into arsenate (less toxic) form.
The contamination of hazardous metal(loid) is one of the serious environmental and human health risks. This study isolated a total of 40 cadmium (Cd)- and arsenic (As)-resistant bacterial isolates from coastal sediments by pour plate technique using tryptic soy agar supplemented with Cd or As (50 mg l−1) for use as metal(loid) bioremediation agents. Out of 40, 4 isolates, RCd3, RCd6, RAs7, and RAs10, showed a relatively higher growth rate in Cd- or As-supplemented culture media which were selected for further study. The selected isolates showed a high minimum inhibitory concentration (60–400 mg l−1 for Cd and 400–2200 mg l−1 for As), which demonstrated their remarkable Cd and As resistance capabilities. The metal(loid) removal efficiencies (0.032–0.268 μg Cd h−1 mg−1 and 0.0003–0.0172 μg As h−1 mg−1 [wet weight cell]) of selected isolates indicated their greater magnitude in absorbing Cd compared to As from water. Phylogenetic analysis of the 16S rDNA sequences revealed that isolates RCd3, RCd6, RAs7, and RAs10 were closely related to Acinetobacter brisouii, Pseudomonas abietaniphila, Exiguobacterium aestuarii, and Planococcus rifietoensis, respectively. Because of high Cd and As resistance and removal efficiency, the selected isolates can survive in a high metal(loid)-contaminated environment and could be a potential tool for bioremediation of high metal(loid)-contaminated effluents to protect the aquatic environment.
Three bacterial strains were isolated from industrial effluents of Penang, Malaysia. The strains RZ1, RZ2, and RZ3 were identified as Pantoea sp. RL32.2, Salmonella enterica, and Enterobacter sp. OCPSB1, respectively, based on morphological observation, biochemical, physiological characterization, and 16S rDNA sequence analysis. The strains RZ1, RZ2, and RZ3 removed 89.89, 82.10, and 89.14% of cadmium, respectively, when the 100 μg/mL of cadmium was added in the medium. The minimum inhibitory concentrations of strains RZ1, RZ2, and RZ3 were 750, 410, and 550 μg/mL, respectively. Cured strain showed resistance and sensitivity against some range of antibiotics. The molecular weights of induced proteins were 35 and 25 kDa in the presence of cadmium which points out a possible role of this protein in cadmium removal. Overall, these strains could be useful for the removal of cadmium in industrial wastewater.
Arsenic is a toxic metalloid which is widely distributed in nature. It is normally present as arsenate under oxic conditions while arsenite is predominant under reducing condition. The major discharges of arsenic in the environment are mainly due to natural sources such as aquifers and anthropogenic sources. It is known that arsenite salts are more toxic than arsenate as it binds with vicinal thiols in pyruvate dehydrogenase while arsenate inhibits the oxidative phosphorylation process. The common mechanisms for arsenic detoxification are uptaken by phosphate transporters, aquaglyceroporins, and active extrusion system and reduced by arsenate reductases via dissimilatory reduction mechanism. Some species of autotrophic and heterotrophic microorganisms use arsenic oxyanions for their regeneration of energy. Certain species of microorganisms are able to use arsenate as their nutrient in respiratory process. Detoxification operons are a common form of arsenic resistance in microorganisms. Hence, the use of bioremediation could be an effective and economic way to reduce this pollutant from the environment.
The field of microbial ecology has grown tremendously with the advent of novel molecular techniques, allowing the study of uncultured microbes in the environment, and producing a paradigm shift: now, rather than using bacteria cultures for evaluating cell-specific questions, researchers use RNA and DNA techniques to examine more broad-based ecological and evolutionary constructs such as biogeography and the long-debated biological species concept. Recent work has begun to relate bacteria functional genes to ecosystem processes and functioning, thereby enabling a better understanding of the interactive role of bacteria in different and often-changing environments. The field continues to mature and will most likely make substantial contributions in the future with additional efforts that include metagenomics and genomics. Here we review progress in the application of molecular techniques to study microbial communities in freshwater environments.
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.
A cultivation-independent approach based on polymerase chain reaction (PCR)-amplified partial small subunit rRNA genes was used to characterize bacterial populations in the surface soil of a commercial pear orchard consisting of different pear cultivars during two consecutive growing seasons. Pyrus communis L. cvs Blanquilla, Conference, and Williams are among the most widely cultivated cultivars in Europe and account for the majority of pear production in Northeastern Spain. To assess the heterogeneity of the community structure in response to environmental variables and tree phenology, bacterial populations were examined using PCR-denaturing gradient gel electrophoresis (DGGE) followed by cluster analysis of the 16S ribosomal DNA profiles by means of the unweighted pair group method with arithmetic means. Similarity analysis of the band patterns failed to identify characteristic fingerprints associated with the pear cultivars. Both environmentally and biologically based principal-component analyses showed that the microbial communities changed significantly throughout the year depending on temperature and, to a lesser extent, on tree phenology and rainfall. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant bacterial populations. Most DGGE band sequences were related to bacterial phyla, such as Bacteroidetes, Cyanobacteria, Acidobacteria, Proteobacteria, Nitrospirae, and Gemmatimonadetes, previously associated with typical agronomic crop environments.
As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.
Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
Cultured soil microorganisms have provided a rich source of natural-product chemistry. Because only a tiny fraction of soil microbes from soil are readily cultured, soil might be the greatest untapped resource for novel chemistry. The concept of cloning the metagenome to access the collective genomes and the biosynthetic machinery of soil microflora is explored here.
This study focused on the screening of cadmium-resistant bacterial strains from Pb-Zn tailing. We investigated the diversity of microbial community inhabiting Dong-san-cha Pb-Zn tailing in Beijing, China, by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene of bacterial strain, and found two dominant strains in the DGGE profile. Using special culture media, we isolated two strong cadmium-resistant bacterial strains. On the basis of morphological, physiological, and biochemical characteristics, BIOLOG, and 16S rDNA sequencing, the two strains were identified as Bacillus cereus and Enterobacter cloacae. Minimal inhibitory concentrations (MICs) of heavy metals for the bacteria were determined. E. cloacae showed higher MIC values for heavy metals and a larger range of antibiotic resistance than B. cereus.
An awful consequence of metal contamination in environment is one of the global problems posing severe hazardous and toxic impacts in microorganisms. The objective of the present chapter is to elucidate how metals cause toxicity at biochemical and molecular levels in microorganisms. The excess concentration of metals is responsible for causing various toxicity reactions in microbial cell, such as, over production of reactive oxygen species; protein and enzyme dysfunction, destruction of thiol and iron-sulfide cluster, metal substitution and inhibition of nutrient assimilation; lipid peroxidation; and DNA damage. Consequently, toxicity causes mutagenicity effects and/or cell death that lead to immeasurable damage in microorganisms and microbial community. The biochemical and molecular mechanisms of metal toxicity may be helpful to depth metal toxicity study in microbes and other organisms for controlling and treating the metal toxicity in further. Moreover, metal-resistant microbes have potential significance in environmental and human health perspectives.
This study investigates the efficiency of six types of soil, upper, lower and shell fossil layer of shirasu soils of Kagoshima; tuff soil of Shimane; Akadama and Kanuma soils of Tochigi, Japan in removing Hg from aquatic phase by analyzing the morphological and chemical properties. Morphological and chemical characterization of each soil was executed by SEM-EDS analysis as well as Hg removal study was performed by batch operation mode. SEM-EDS characteristics revealed soils particles predominantly constituted of SiO2 (21.8-78.5%), Al2O3 (4.1 - 38%) and FeO (0.8 - 7.7%) in all soil types excepting tuff soil where CaO showed highest percentage (65.3%). Organic matter and CuO were exclusively observed in Kanuma and Akadama soils. A critical appraisal of total Hg removal (36.4 - 48.15 μg/L) data clearly revealed that though maximum Hg removal efficiencies were observed in Kanuma (0.27μg/L/g/h) and Akadama (0.26 μg/L/g/h) soils, but former one was superior. Obtained results also demonstrated Hg removal of soils is potentiality governed by higher percentage Al2O3 lower percentage SiO2, CuO and organic matter content of soils. Therefore, it may be concluded that Kanuma and Akadama soils can be used as a low-cost potential Hg adsorbing agent for treating the Hg contaminated effluents in order to reclaim the aquatic environment.
The growing health hazardous impact of arsenic (As) contamination in environment is the impetus of the present investigation. Application of lactic acid bacteria (LAB) for the removal of toxic and heavy metals from water has been reported. This study was performed in order to isolate and characterize the Asresistant LAB from mud and sludge samples for using as efficient As uptaking probiotic. Isolation of As-resistant LAB colonies was performed by spread plate technique using bromocresol purple impregnated-MRS (BP-MRS) agar media provided with As @ 50 μg/ml. Isolated LAB were employed for probiotic characterization process, acid and bile tolerance, lactic acid production, antibacterial activity and antibiotic tolerance assays. After As-resistant and removal characterizations, the LAB were identified using 16S rDNA sequencing. A total of 103 isolates were identified as As-resistant strains of LAB. The survival of 6 strains (As99-1, As100-2, As101-3, As102-4, As105-7, and As112-9) was found after passing through the sequential probiotic characterizations. Resistant pattern pronounced hollow zones at As concentration >2000 μg/ml in As99-1, As100-2, and As101-3 LAB strains, whereas it was found at ~1000 μg/ml in rest 3 strains. Among 6 strains, the As uptake efficiency of As102-4 (0.006 μg/h/mg wet weight of cell) was higher (17 - 209%) compared to remaining LAB. 16S rDNA sequencing data of 3 (As99- 1, As100-2, and As101-3) and 3 (As102-4, As105-7, and As112-9) LAB strains clearly showed 97 to 99% (340 bp) homology to Pediococcus dextrinicus and Pediococcus acidilactici, respectively. Though, there was no correlation between the metal resistant and emoval efficiency of LAB examined but identified elevated As removing LAB would probably be a potential As uptaking probiotic agent. Since present experiment concerned with only As removal from pure water, As removal and removal mechanism in natural condition of intestinal milieu should be assessed in future studies.
Bioremediation to remove toxic heavy metals from the environment relies on metal‐tolerant plants or microbes to do the job, but with varying degrees of success. Understanding the ecology and evolution of metal‐resistant bacterial societies could drastically improve the efficiency of microbial bioremediation.
The current study was aimed at using immobilized mercury bioaccumulating Bacillus cereus cells for the remediation of mercury from synthetic effluent. The remediation process was attempted under different experimental conditions. The different adsorption kinetics, equilibria, and thermodynamics were also investigated in an attempt to develop an effective and better biosorbent for mercury remediation. The maximum biosorption capacity of the immobilized cells was found to be 104.1 mg g(-1). The mean free energy value, as evaluated using the Dubinin-Radushkevich (D-R) model, was 15.8 kJ mol(-1). This indicates that the mercury remediation process under investigation was chemically more favorable than the physical adsorption process. The remediation process was seen to follow pseudo-second-order kinetics. The apparent free energy change showed that the biosorption process of mercury was thermodynamically feasible and spontaneous in nature. The feasibility of using immobilized cells in a continuous column for effective mercury remediation was also attempted. The breakthrough point was obtained after 11 h of continuous flow. Thus, according to the study, the alginate immobilized B. cereus cells constitute a prospective mercury remediation system, which can effectively be used in mercury contaminated aqueous environment.
A heavy-metal resistant bacterial consortium was obtained from a contaminated river in São Paulo, Brazil and utilized for the design of a fixed-bed column for the removal of copper. Prior to the design of the fixed-bed bioreactor, the copper removal capacity by the live consortium and the effects of copper in the consortium biofilm formation were investigated. The Langmuir model indicated that the sorption capacity of the consortium for copper was 450.0 mg/g dry cells. The biosorption of copper into the microbial biomass was attributed to carboxyl and hydroxyl groups present in the microbial biomass. The effect of copper in planktonic cells to form biofilm under copper rich conditions was investigated with confocal microscopy. The results revealed that biofilm formed after 72 h exposure to copper presented a reduced thickness by 57% when compared to the control; however 84% of the total cells were still alive. The fixed-bed bioreactor was set up by growing the consortium biofilm on granular activated carbon (GAC) and analyzed for copper removal. The biofilm-GAC (BGAC) column retained 45% of the copper mass present in the influent, as opposed to 17% in the control column that contained GAC only. These findings suggest that native microbial communities in sites contaminated with heavy metals can be immobilized in fixed-bed bioreactors and used to treat metal contaminated water.
In this study, for the first time the potential use of dried Vibrio parahaemolyticus PG02 to remove mercury from synthetic effluent was investigated by considering equilibrium, kinetic, and thermodynamic aspects. The results indicated that Hg2+ biosorption was best described by the pseudo-second order model. In addition, it was found that intraparticle diffusion was not the sole rate-limiting step. The ion-exchange mechanism was a predominant biosorption mechanism in the first 15 min of contact. The Langmuir isotherm better described the equilibrium data of Hg2+ biosorption than the Freundlich isotherm. According to this model, the maximum biosorption capacity was found to be 9.63 × 10−4 mol g−1 at optimum conditions (pH = 6.0 and temperature =35 °C).
The purpose of the present study was to isolate and identify the metal-resistant lactic acid bacteria from sediments of coastal aquaculture habitats for removal of cadmium and lead from ambience. Collected sediment samples were used to isolate the cadmium- and lead-resistant bacterial colonies by spread plate technique using agar media (De Man, Rogosa and Sharpe) supplemented with cadmium or lead at 50 mg/l. Isolates were identified by bacterial colony polymerase chain reaction and sequencing of 16S ribosomal deoxyribonucleic acid. Metal removing probiotic was determined by characterizing the lactic acid yield in culture media, viability in fish intestine, metal-resistant and metal-removal efficiencies. 16S ribosomal deoxyribonucleic acid sequencing data of five (Cd10, Cd11, Pb9, Pb12 and Pb18) and other all isolates clearly showed 99 % similarities to Enterococcus faecium and Bacillus cereus, respectively. The Pb12 exhibited higher lactic acid yield (180 mmol) than that of the remaining E. faecium strains and excellent viability without pathogenicity; therefore, further study was carried out using Pb12 strain. The selected Pb12 strain showed elevated metal resistant (minimum inhibitory concentrations 120 and 800 mg/l for cadmium and lead, respectively) and removal efficiencies [Cadmium 0.0377 mg/h/g and lead 0.0460 mg/h/g of cells (wet weight)]. From the viability and metal removal points of view, it can be concluded that isolated metal-resistant E. faecium Pb12 strains might be used as potential probiotic strains for removing heavy metals from fish intestinal milieu to control the progressive bioaccumulation of heavy metals in the fish.
In nature, trace element toxicities occur in all living organisms. The consequences of these toxicities have been described in crops, livestock and humans. In some instances, the toxicities are a direct consequence of the organism's position in the food chain and their environment, while in others, they are based upon genetic abnormalities resulting in physiological impairment.Nutrient toxicities in crops are more frequent for manganese (Mn) and boron (B) than for other nutrients. Manganese toxicity is found on acid soils in many parts of the world. Boron toxicities occur in irrigated regions where the well or irrigation waters are exceptionally high in B. Most other nutrient toxicities occur when large amounts of nutrients in question have been added in waste, e.g., sewage sludge. Crops grown near mines and smelters are prone to nutrient toxicities. Generally, the symptoms of toxicity in crops occur as burning, chlorosis and yellowing of leaves. Toxicities can result in decreased yield and/or impaired crop quality. Toxicity levels of trace elements range from 20 to 50 μg g for copper (Cu) and B to several hundred μg g for Mn, molybdenum (Mo) and zinc (Zn). With the exception of Mo, toxicity of other nutrients can be reduced by liming. Following recommended rates of fertilizers and the safe and controlled use of waste materials, such as sewage sludge and coal fly ash, should reduce metal loading and nutrient toxicity in crops. Use of crop species and genotypes less susceptible to toxicity are recommended where toxicity is suspected. Toxicities of trace elements in animals are caused by the consumption of either feeds or grazing on pastures with high contents of the element in question. Accidental excess applications of minerals in grain mixes or oral ingestions of elements have been described as causing toxicity. Some toxicities, e.g., of Mo result in deficiency of other elements such as Cu. Some of the most toxic elements for livestock include Cu, lead (Pb), mercury (Hg), Mo, and selenium (Se). Under certain conditions, toxicities of arsenic (As), cobalt (Co), fluoride (Fl), iodine (I), iron (Fe), Mn, and Zn have also been reported. Symptoms of toxicity have been described in detail in the animal section. Trace elements, when in excess quantities, accumulate chiefly in the blood, liver, and kidneys. Measures of control for various trace element toxicities include removal of animals from affected areas or removal of the source of toxicity; gastric lavage and the specific use of oral doses of salts and chelates depending upon the element in question. Trace element/metal toxicities in humans are not common under normal conditions. Most toxicities are caused by environmental and/or genetic abnormalities, from excessive intake, by deliberate or accidental overdose, or from induced deficiencies (e.g. excess Zn causing Fe deficiency). Among the elements causing relatively frequent cases of toxicity are Pb, cadmium (Cd), Hg, Cu, Zn, and Fe. Selenium toxicity is generally limited to those areas/regions of the world, e.g. in certain parts of China, where soils with abnormally high Se content produce food crops containing highly toxic Se concentrations. Effective measures to control metal toxicities include gastric lavage, resuscitation, and the use of chelating agents in the acute phase. Protective legislation against the use of metal alloy utensils used for cooking is the long‐term control strategy.
a b s t r a c t This paper presents the results of experimental work on the possibility of removal of environmentally sensitive trace elements from coal through treatment with mixed bacterial consortium. In the coals of Kalimantan area, Indonesia the metals like Cd, Cu, Cr, Ni, Pb and Zn have been found to occur in concen-trations of 1.96, 59.34, 26.98, 102.68, 14.4 and 172.54 ppm respectively. The concentrations of these ele-ments are higher when compared with Clarke values in bituminous coals. Mixed bacterial consortium has been used to explore the possibility of removal of these toxic trace elements. The result reveals that the bacterial consortium is efficient to remove more than 80% of metals like Ni, Zn, Cd, Cu and Cr while the removal of Pb is nearly 45%. The removal is seen in the order: Zn > Ni > Cd > Cu > Cr > Pb.
Bacteria, and other microorganisms, exhibit a number of metabolism-dependent and-independent processes or the uptake and accumulation of heavy metals and radionuclides. The removal of such harmful substances from effluents and waste waters by microbe-based technologies may provide an alternative or additional means of metal/radionuclide recovery for economic reasons and/or environmental protection. Both living and dead cells as well as products derived from or produced by microorganisms can be effective metal accumulators and there is evidence that some biomass-based clean-up processes are economically viable. However, many aspects of metal-microbe interactions remain unexploited in biotechnology and further development and application is necessary, particularly to the problem of radionuclide release into the environment.
The accumulation of heavy metals by microbial biomass with high surface area-to-volume ratio holds great potential for heavy
metal removal in both soluble and paritcular forms, especially when the heavy metal concentrations are low (<50 mg/L). E. coli and B. subtilis are effective agents for metal removal. We further investigated the effect of pH, temperature, equilibration time, and pre-treatment
reagents on the removal of Pb(II), Cd(II) and Cr(VI) from aqueous solutions by E. coli and B. subtilis. E. coli and B. subtilis were cultivated for 60 hours, the experimentally determined optimal cultivation time before they were used in metal removal
experiments. Under the optimal conditions of pH 6.0, equilibration temperature 30 C and equilibration time 1 hour, 63.39%
and 69.90% Cd(II) can be removed by E. coli and B. subtilis. Under the optimal conditions of pH 5.5, equilibration temperature 30 C and equilibration time 1 hour, 68.51% and 67.36%
Pb(II) can be removed by E. coli and B. subtilis. And under the optimal conditions of pH 5. 5, equilibration temperature 30 C, and equilibration time 1 hour, 60.26 % and
54.56 % Cr(W) can be removed by E. coli and B. subtilis. Chemical treatment of cultivated bacteria (0.1 mol/L NaOH, 0.1 mol/L HC1, 30% ethanol, and distilled water) affects the
efficiency of metal removal by E. coli and B. subtilis. Pretreatment of biomass by NaOH enhanced Cd(II), Pb(II) and Cr(VI) removal, while pretreatment by HC1, ethanol and distilled
water reduced Cd(II), Pb(I) and Cr(YI) removal. For metal removal from industrial waste discharges, pretreated biomass of
E. coli can remove 68.5% of Cd and 58.1% of Cr from solutions, while pretreated biomass of B. subtilis can remove 62.6% of Cd and 57% of Cr from solutions.
An increasing body of evidence suggests that microorganisms are far more sensitive to heavy metal stress than soil animals or plants growing on the same soils. Not surprisingly, most studies of heavy metal toxicity to soil microorganisms have concentrated on effects where loss of microbial function can be observed and yet such studies may mask underlying effects on biodiversity within microbial populations and communities. The types of evidence which are available for determining critical metal concentrations or loadings for microbial processes and populations in agricultural soil are assessed, particularly in relation to the agricultural use of sewage sludge. Much of the confusion in deriving critical toxic concentrations of heavy metals in soils arises from comparison of experimental results based on short-term laboratory ecotoxicological studies with results from monitoring of long-term exposures of microbial populations to heavy metals in field experiments. The laboratory studies in effect measure responses to immediate, acute toxicity (disturbance) whereas the monitoring of field experiments measures responses to long-term chronic toxicity (stress) which accumulates gradually. Laboratory ecotoxicological studies are the most easily conducted and by far the most numerous, but are difficult to extrapolate meaningfully to toxic effects likely to occur in the field. Using evidence primarily derived from long-term field experiments, a hypothesis is formulated to explain how microorganisms may become affected by gradually increasing soil metal concentrations and this is discussed in relation to defining “safe” or “critical” soil metal loadings for soil protection.
An experiment was conducted using 15 glass aquariums to ascertain the pathways of removal of cadmium through numerical and compositional manipulation of ecosystem components and their role in Cd removal in different aquatic ecosystems. Each aquarium was provided with surface sediment @ 2 kg, filled with 15 L tap water and randomly distributed into five treatments having three replicates in each. Cadmium chloride (CdCl2) of analytical grade was added @ 2 mg/L to the water of each aquarium and mixed gently. Except for the first one, the other four systems received unio (Lamellidens marginalis, 55 ± 2.5 g) @ 6 pieces/aquarium. Tilapia (Oreochromis mossambicus, 35 ± 3 g) was introduced @ 6 fish/aquarium in the third and fifth systems, whereas pistia (Pistia stratiotes) was introduced @ 50 g/aquarium in the fourth and fifth systems for a 28-day observation period. The samples of water, sediment, unio, fish and pistia were collected from different systems at 7-day intervals and analyzed. Results revealed that mean substantial reduction of Cd in water varied between 1.820 and 1.994 mg/L in different simulated ecosystems. Ecosystem efficiency of Cd removal varied in the different ecosystems and showed highest (11%) value in the ecosystem carrying five components, which suggested a cumulative effect of increasing number of components employed in different simulated aquatic ecosystems significantly facilitated the reduction of the level of Cd concentration in water column. Pistia exerted (12.88–547.5 times) higher rate of Cd accumulation over the other components employed in five simulated ecosystems of various component structures. Therefore, in the present study, it may be concluded that ecosystems carrying five components exhibited the best performance for optimum minimization of Cd removal from water column. It can also be concluded that ecosystem components showed a variable performance and pistia was the efficient component from the perspective of Cd removal.
To isolate and characterize lactic acid bacteria (LAB) and determine whether they could potentially be used as heavy metal (cadmium and lead) absorbing probiotics.
The study used 53 environmental (mud and sludge) samples to isolate cadmium- and lead-resistant LAB, by following spared plate technique. A total of 255 cadmium- and lead-resistant LAB were isolated from these samples. The survival of 26 of the LAB was found after passing through sequential probiotic characterizations. These 26 probiotic LAB exhibited remarkable variations in their metal-resistant and metal-removal abilities. Of 26, seven (Cd54-2, Cd61-7, Cd69-12, Cd70-13, Pb82-8, Pb96-19 and Cd109-16) and four (Pb71-1, Pb73-2, Pb85-9 and Pb96-19) strains displayed relatively elevated cadmium- and lead-removal efficiencies from water, respectively, compare with that of the remaining strains. Strains Cd70-13 and Pb71-1 showed the highest cadmium (25%) and lead (59%) removal capacity from MRS (De Man, Rogosa and Sharpe) culture medium, respectively, amongst the selected strains and showed a good adhesive ability on fish mucus. A phylogenetic analysis of their 16S rDNA sequences revealed that the strains Cd70-13 and Pb71-1 belong to Lactobacillus reuteri.
Excellent probiotic, metal sorption and adhesive characteristics of newly identified Lact. reuteri strains Cd70-13 and Pb71-1 were isolated, which indicated their high potential abilities to survive in the intestinal milieu and to uptake the tested metals from the environment.
To our knowledge, this is the first study that has aimed to isolate, characterize and identify metal-resistant LAB strains that have potential to be a probiotic candidate for food and in vivo challenge studies in the intestinal milieu of fish for the uptake and control of heavy metal bioaccumulation.
Metagenomics as a new field of research has been developed over the past decade to elucidate the genomes of the non-cultured microbes with the goal to better understand global microbial ecology on the one side, and on the other side it has been driven by the increasing biotechnological demands for novel enzymes and biomolecules. Since it is well accepted that the majority of all microbes has not yet been cultured, the not-yet-cultivated microbes represent a shear unlimited and intriguing resource for the development of novel genes, enzymes and chemical compounds for use in biotechnology. However, with respect to biotechnology, metagenomics faces now two major challenges. Firstly, it has to identify truly novel biocatalysts to fulfil the needs of industrial processes and green chemistry. Secondly, the already available genes and enzymes need to be implemented in production processes to further prove the value of metagenome-derived sequences.
The polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) has been used widely to determine species richness and structure of microbial communities in a variety of environments. Researchers commonly archive soil samples after routine chemical or microbial analyses, and applying PCR-DGGE technology to these historical samples offers evaluation of long-term patterns in bacterial species richness and community structure that was not available with previous technology. However, use of PCR-DGGE to analyze microbial communities of archived soils has been largely unexplored. To evaluate the stability of DGGE patterns in archived soils in comparison with fresh soils, fresh and archived soils from five sites along an elevational gradient in the Chihuahuan Desert were compared using PCR-DGGE of 16S rDNA. DNA from all archived samples was extracted reliably, but DNA in archived soils collected from a closed-canopy oak forest site could not be amplified. DNA extraction yields were lower for most archived soils, but minimal changes in bacterial species richness and structure due to archiving were noted in bacterial community profiles from four sites. Use of archived soils to determine long-term changes in bacterial community structure via PCR-DGGE appears to be a viable option for addressing microbial community dynamics for particular ecosystems or landscapes.
Soil has the largest population of microbes of any habitat, but only about 0.3% of soil microbes are cultivable with current techniques. Cultured soil microbes have been an incredibly productive source of drugs, for example the cancer chemotherapeutics doxorubicin hydrochloride, bleomycin, daunorubicin and mitomycin. Unfortunately, the current yield of new drugs from soil microbes is low due to repeated cultivation of the same small fraction of cultivable microbes. Uncultured soil species represent a tremendous untapped resource of new antineoplastic agents. Methods have recently been developed to access the diversity of secondary metabolites from uncultured soil microbes. Briefly, total DNA is extracted from soil samples, purified, partially digested, and fragments inserted into vectors for expression in readily fermented microbes such as Escherichia coli. Clones expressing enzymatic and antibiotic activities that are encoded by novel sequences have been reported.
Recent advances in the estimation of prokaryotic diversity have brought us insight into two questions: what is the extent of prokaryotic diversity, and perhaps more importantly, why bother finding out. In this review, we highlight the insights about the extent of diversity that may be gained by considering patterns that occur, or are likely to occur, in the relative abundance of prokaryotic taxa. We posit that global reservoirs of diversity are an important driving force behind patterns in localised diversity seen in leaves, intestines and wastewater treatment reactors. Thus, where the reservoir community is very large and relatively even, chance alone will prevent physically identical communities from having the same, or sometimes even stable, communities. By contrast, communities that tend to be similar (even when not physically identical) and stable are observed where the source diversity is low. Thus the relationship between structure and function in a community can only be understood, predicted and engineered through an understanding of the source of diversity from which the community is drawn.
It is widely accepted that up to 99.8% of the microbes present in many environments are not readily culturable. 'Metagenome technology' tries to overcome this bottleneck by developing and using culture-independent approaches. From the outset, metagenome-based approaches have led to the accumulation of an increasing number of DNA sequences, but until this time the sequences retrieved have been those of uncultured microbes. These genomic sequences are currently exploited for novel biotechnological and pharmaceutical applications and to increase our knowledge on microbial ecology and physiology of these microbes. Using the metagenome sequences to fully understand how complex microbial communities function and how microbes interact within these niches represents a major challenge for microbiologists today.
Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.
Seven soils were sampled from farmland at different distances (0.01-5 km) from a copper and zinc smelter. The total contents of heavy metals in these soils ranged from 46 to 4895 mg Cu kg-1, 96 to 1133 mg Zn kg-1, and 6.9 to 28.8 mg Cd kg-1, respectively. The available fractions were highly correlated with total contents of the metals. In order to assess the impact of combined contamination of heavy metals on soil bacterial communities, denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplicons of 16S rDNA sequence of bacteria in soil was used. Bacterial community structure was affected to some extent by heavy metals. The number of DGGE bands in soils increased with increasing distance from the copper and zinc smelter. Clustering analysis of the DGGE profiles showed that bacteria in the seven soils belonged to three clusters. Bacterial communities in three soils sampled at 0.01-0.60 km from the smelter belonged to one cluster, and those in three soils sampled at 0.8-1.2 km from the smelter belong to another cluster. Bacterial community in soil farthest from the smelter belonged to a single cluster. This study demonstrated that heavy metal contamination decreased both biomass and diversity of bacterial community in the soil.
The environmental risk of heavy metal pollution is pronounced in soils adjacent to large industrial complexes. It is important to investigate the functioning of soil microorganisms in ecosystems exposed to long-term contamination by heavy metals. We studied the potential effects of heavy metals on microbial biomass, activity, and community composition in soil near a copper smelter in China. The results showed that microbial biomass C was negatively affected by the elevated metal levels and was closely correlated with heavy metal stress. Enzyme activity was greatly depressed by conditions in the heavy metal-contaminated sites. Good correlation was observed between enzyme activity and the distance from the smelter. Elevated metal loadings resulted in changes in the activity of the soil microbe, as indicated by changes in their metabolic profiles from correlation analysis. Significant decrease of soil phosphatase activities was found in the soils 200 m away from the smelter. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis demonstrated that heavy metals pollution had a significant impact on bacterial and actinomycetic community structure. There were negative correlations between soil microbial biomass, phosphatase activity, and NH(4)NO(3) extractable heavy metals. The soil microorganism activity and community composition could be predicted significantly using the availability of Cu and Zn. By combining different monitoring approaches from different viewpoints, the set of methods applied in this study were sensitive to site differences and contributed to a better understanding of heavy metals effects on the structure, size and activity of microbial communities in soils. The data presented demonstrate the role of heavy metals pollution in understanding the heavy metal toxicity to soil microorganism near a copper smelter in China.
The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modifications were assessed by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using B- and F-ARISA (bacterial and fungal automated ribosomal intergenic spacer analysis). In the field study, no significant modifications were observed in C-biomass whereas microcosm incubation showed a decrease in B3 contamination only. ARISA fingerprinting showed slight but significant modifications of bacterial and fungal communities in field and microcosm incubation. These modifications were transient in all cases, suggesting a short-term effect of Cu stress. Microcosm experiments detected the microbial community modifications with greater precision in the short-term, while field experiments showed that the biological effects of Cu contamination may be overcome or hidden by pedo-climatic variations.
Bacterial communities of four arable soils--pelosol, gley, para brown soil, and podsol brown soil--were analysed by fingerprinting of 16S rRNA gene fragments amplified from total DNA of four replicate samples for each soil type. Fingerprints were generated in parallel by denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and single strand conformation polymorphism (SSCP) to test whether these commonly applied techniques are interchangeable. PCR amplicons could be separated with all three methods resulting in complex ribotype patterns. Although the fragments amplified comprised different variable regions and lengths, DGGE, T-RFLP and SSCP analyses led to similar findings: (a) a clustering of fingerprints which correlated with soil physico-chemical properties, (b) little variability between the four replicates of the same soil, (c) the patterns of the two brown soils were more similar to each other than to those of the other two soils, and (d) the fingerprints of the different soil types revealed significant differences in a permutation test, which was recently developed for this purpose.