Showing papers on "Microbial biodegradation published in 2016"

Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review

Abstract: Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed towards removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.

Anaerobic Microbial Degradation of Hydrocarbons : from Enzymatic Reactions to the Environment

Abstract: Hydrocarbons are abundant in anoxic environments and pose biochemical challenges to their anaerobic degradation by microorganisms. Within the framework of the Priority Program 1319, investigations fun

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill

Abstract: The Deepwater Horizon blowout in the Gulf of Mexico in 2010, one of the largest marine oil spills(1), changed bacterial communities in the water column and sediment as they responded to complex hydrocarbon mixtures(2-4). Shifts in community composition have been correlated to the microbial degradation and use of hydrocarbons(2,5,6), but the full genetic potential and taxon-specific metabolisms of bacterial hydrocarbon degraders remain unresolved. Here, we have reconstructed draft genomes of marine bacteria enriched from sea surface and deep plume waters of the spill that assimilate alkane and polycyclic aromatic hydrocarbons during stable-isotope probing experiments, and we identify genes of hydrocarbon degradation pathways. Alkane degradation genes were ubiquitous in the assembled genomes. Marinobacter was enriched with n-hexadecane, and uncultured Alpha- and Gammaproteobacteria populations were enriched in the polycyclic-aromatic-hydrocarbon-degrading communities and contained a broad gene set for degrading phenanthrene and naphthalene. The repertoire of polycyclic aromatic hydrocarbon use varied among different bacterial taxa and the combined capabilities of the microbial community exceeded those of its individual components, indicating that the degradation of complex hydrocarbon mixtures requires the non-redundant capabilities of a complex oil-degrading community.

Root Exudation: The Ecological Driver of Hydrocarbon Rhizoremediation

Abstract: Rhizoremediation is a bioremediation technique whereby microbial degradation of organic contaminants occurs in the rhizosphere. It is considered to be an effective and affordable “green technology” for remediating soils contaminated with petroleum hydrocarbons. Root exudation of a wide variety of compounds (organic, amino and fatty acids, carbohydrates, vitamins, nucleotides, phenolic compounds, polysaccharides and proteins) provide better nutrient uptake for the rhizosphere microbiome. It is thought to be one of the predominant drivers of microbial communities in the rhizosphere and is therefore a potential key factor behind enhanced hydrocarbon biodegradation. Many of the genes responsible for bacterial adaptation in contaminated soil and the plant rhizosphere are carried by conjugative plasmids and transferred among bacteria. Because root exudates can stimulate gene transfer, conjugation in the rhizosphere is higher than in bulk soil. A better understanding of these phenomena could thus inform the development of techniques to manipulate the rhizosphere microbiome in ways that improve hydrocarbon bioremediation.

Book Review: Advances in Biodegradation and Bioremediation of Industrial Waste

Abstract: This book covers broader aspect of bioremediation and biodegradation of environmental pollutants. The pollution due to industrialization is a global challenge for the sustainable development of human beings. Environmental pollutants may be organic or inorganic, like heavy metals, pesticides, toxic chemical fertilizers, polyaromatic hydrocarbons, polychlorinated biphenyls, detergents, antibiotics, lubricants, nanoparticles, paints, and disinfectants and many of them may cause various diseases in human beings and animals. After the green revolution, the indiscriminate use of chemical fertilizers and pesticides for enhancing agricultural productivity has destroyed the soil fertility and health as well as microbial flora and fauna. The industrial waste and sewage contain hazardous organic and inorganic chemicals comprising heavy metals, salts and extreme pH. Long term cumulative effects of heavy metals in the environment are detrimental to human health. The degradation and bioremediation of industrial wastes are a challenging task because there is no reliable technology till date which is sustainable in terms of complete removal of these pollutants. Ultimately, diverse groups of microorganism that are already present in the nature may provide solution for the degradation and bioremediation of toxic industrial wastes. Microorganisms are being used for the bioremediation and transformation of pollutants from long times (Okpokwasili, 2007). Bioremediation involves the application of microbes to detoxify and degrade environmental pollutants. Microbes have various mechanisms for removing heavy metals from contaminated environments, such as adsorption to cell surfaces, complexation of exopolysaccharides, intracellular accumulation, biosynthesis of metallothionins and other proteins that trap metals and transform them to volatile compounds (Sharma et al., 2013). Recently, research is being focused in the development of genetically modified microbes or consortia for the detoxification of environmental pollutants. The book consists of 14 chapters covering the available advanced knowledge in biodegradation and bioremediation of various environmental pollutants, which are a real challenge to environmental researchers in the current scenario. The 1st, 12th, and 14th chapters highlight recent advances in phytoremediation and the role of the bacterial ecology of the rhizosphere of wetland plants for bioremediation of complex industrial wastewater. Some plant species have the inherent capacity to uptake and accumulate the heavy metals whereas other species help in biodegradation and biotransformation of toxic pollutants to nontoxic form of pollutants for environmental management. The phytoremediation of heavy metals is broadly discussed in terms of plant mechanisms for removing theses pollutants from soils and wastewaters. The 2nd, 3rd, 7th, and 10th chapters highlight the microbial degradation and bioremediation of heavy metals, aromatic compounds, hexachlorocyclohexane (HCH) pesticides and textile dyes from industrial waste and other environmental contaminants. This book has explored the latest information related to research and development of bioremediation of various xenobiotics compounds. The 5th chapter highlights the significance and role of biosurfactants and bioemulsifiers for bioremediation and biodegradation of various pollutants discharged from industrial waste, showing to be a sustainable biotechnological tool for minimizing the toxicity of industrial waste. The 6th, 8th, 11th, and 13th chapters specially discuss the aerobic and anaerobic biodegradation of lignocellulosic, agriculture and lipid wastes. The application of potential microbial enzymatic processes for bioremediation and biodegradation of environmental pollutants is discussed in the 4th chapter. This chapter addresses laccases and their significance in the bioremediation of industrial effluents. Laccase enzyme is a type of multicopper blue oxidase which oxidize a broad range of organic substrates such as phenols, polyphenols, anilines, and even certain inorganic compounds. It is extensively disseminated in higher plants, fungi, insects, and bacteria. The 9th chapter covers few laboratory scale bioremediation experiment on petroleum hydrocarbons of contaminated wastewater of refinery plants. In general, the process of phytoremediation and microbial biodegradation is a comparatively cheaper and relevant approach on a large scale than physical and chemical remediation. The editor tried to make a holistic approach to all bioremediation and biodegradation techniques applicable for minimization of environmental pollution (soil, oily sludge, and groundwater) caused by petroleum hydrocarbons, solvents, pesticides, and other chemicals. However, management of some of the pollutants generated by tanneries, distilleries, and paper and pulp industries are a challenging task mainly due to the lack of appropriate acquaintance regarding the persistent organic pollutants discharged from these industries and the process of their detoxification. Similarly, the safe dumping and biodegradation of hospital waste is also an authentic challenge worldwide for human and animal health. In last, this book compiles and updates the recent literature related to microbial degradation and phytoremediation of industrial, agricultural waste and their biochemical and molecular processes for reducing the environmental pollution. In addition, the book also provides current available tools, techniques and literatures regarding bioremediation and biodegradation of industrial waste. It also describes the significance of various bioreactors for the treatment of complex industrial waste and provides specific chapters on bioreactors and membrane process integrated with microbial degradation processes. Thus, this book is useful to the environmental engineering students for designing sustainable technology for biodegradation and bioremediation of industrial wastes. All chapters give information regarding role of microbes and plants, and their consortium for the degradation of recalcitrant chemicals. It also covers the advances in basic knowledge as well recent technologies in environmental biotechnology. Hence, this book will be highly beneficial for a broad range of readers, including students, researchers, scientists, teachers, and consulting professionals in industrial biotechnology, environmental microbiology, biochemistry, molecular biology, life sciences and agricultural sciences.

Isolation and characterisation of crude oil sludge degrading bacteria

Abstract: The use of microorganisms in remediating environmental contaminants such as crude oil sludge has become a promising technique owing to its economy and the fact it is environmentally friendly. Polycyclic aromatic hydrocarbons (PAHs), as the major components of oil sludge, are hydrophobic and recalcitrant. An important way of enhancing the rate of PAH desorption is to compost crude oil sludge by incorporating commercial surfactants, thereby making them available for microbial degradation. In this study, crude oil sludge was composted for 16 weeks during which surfactants were added in the form of a solution. Molecular characterisation of the 16S rRNA genes indicated that the isolates obtained on a mineral salts medium belonged to different genera, including Stenotrophmonas, Pseudomonas, Bordetella, Brucella, Bacillus, Achromobacter, Ochrobactrum, Advenella, Mycobacterium, Mesorhizobium, Klebsiella, Pusillimonas and Raoultella. The percentage degradation rates of these isolates were estimated by measuring the absorbance of the 2,6-dichlorophenol indophenol medium. Pseudomonas emerged as the top degrader with an estimated percentage degradation rate of 73.7% after 7 days of incubation at 28 °C. In addition, the presence of the catabolic gene, catechol-2,3-dioxygenase was detected in the bacteria isolates as well as in evolutionary classifications based on phylogeny. The bacteria isolated in this study are potential agents for the bioremediation of crude oil sludge.

Bacterial biodegradation of neonicotinoid pesticides in soil and water systems.

Abstract: Neonicotinoids are neurotoxic systemic insecticides used in plant protection worldwide. Unfortunately, application of neonicotinoids affects both beneficial and target insects indiscriminately. Being water soluble and persistent, these pesticides are capable of disrupting both food chains and biogeochemical cycles. This review focuses on the biodegradation of neonicotinoids in soil and water systems by the bacterial community. Several bacterial strains have been isolated and identified as capable of transforming neonicotinoids in the presence of an additional carbon source. Environmental parameters have been established for accelerated transformation in some of these strains. Studies have also indicated that enhanced biotransformation of these pesticides can be accomplished by mixed microbial populations under optimised environmental conditions. Substantial research into the identification of neonicotinoid-mineralising bacterial strains and identification of the genes and enzymes responsible for neonicotinoid degradation is still required to complete the understanding of microbial biodegradation pathways, and advance bioremediation efforts.

In situ protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model

Abstract: In constructed wetlands, organic pollutants are mainly degraded via microbial processes. Helophytes, plants that are commonly used in these systems, provide oxygen and root exudates to the rhizosphere, stimulating microbial degradation. While the treatment performance of constructed wetlands can be remarkable, a mechanistic understanding of microbial degradation processes in the rhizosphere is still limited. We investigated microbial toluene removal in a constructed wetland model system combining 16S rRNA gene sequencing, metaproteomics and (13) C-toluene in situ protein-based stable isotope probing (protein-SIP). The rhizospheric bacterial community was dominated by Burkholderiales and Rhizobiales, each contributing about 20% to total taxon abundance. Protein-SIP data revealed that the members of Burkholderiaceae, the proteins of which showed about 73% of (13) C-incorporation, were the main degraders of toluene in the planted system, while the members of Comamonadaceae were involved to a lesser extent in degradation (about 64% (13) C-incorporation). Among the Burkholderiaceae, one of the key players of toluene degradation could be assigned to Ralstonia pickettii. We observed that the main pathway of toluene degradation occurred via two subsequent monooxygenations of the aromatic ring. Our study provides a suitable approach to assess the key processes and microbes that are involved in the degradation of organic pollutants in complex rhizospheric ecosystems.

Antibiotic sulfanilamide biodegradation by acclimated microbial populations

Abstract: Sulfonamide antibiotics are commonly detected in the environment. Microbial degradation can play an important role in the dissipation of sulfonamide antibiotics. However, many aspects regarding the influential factor and biodegradation pathway remain essentially unclear. Moreover, phylogenetic information on the sulfonamide-degrading microbial community is still very limited. The present study investigated the biodegradation of sulfonamide antibiotic sulfanilamide by acclimated mixed culture and its influential factors, and the sulfanilamide-degrading microbial community. At the initial sulfanilamide concentration of 100 μg/L, nearly half of the antibiotic could be removed by acclimated microbial populations after 1 week of incubation, and an average removal rate of 78.3 % could be achieved in 4 weeks. p-Phenylenediamine, benzene sulfonamide, and hydroxylamine benzene sulfonamide were identified as the potential intermediates. Sulfanilamide biodegradation could be enhanced by a temperature rise and the presence of external carbon or nitrogen sources. The richness, diversity, and structure of the bacterial community showed a remarkable change with sulfanilamide biodegradation. Firmicutes and Bacteroidetes (mainly represented by classes Bacilli and Flavobacteriia) dominated the sulfanilamide-degrading bacterial community.

Evaluation of Sulfadiazine Degradation in Three Newly Isolated Pure Bacterial Cultures.

Abstract: This study is aimed to assess the biodegradation of sulfadiazine (SDZ) and characterization of heavy metal resistance in three pure bacterial cultures and also their chemotactic response towards 2-aminopyrimidine. The bacterial cultures were isolated from pig manure, activated sludge and sediment samples, by enrichment technique on SDZ (6 mg L-1). Based on the 16S rRNA gene sequence analysis, the microorganisms were identified within the genera of Paracoccus, Methylobacterium and Kribbella, which were further designated as SDZ-PM2-BSH30, SDZ-W2-SJ40 and SDZ-3S-SCL47. The three identified pure bacterial strains degraded up to 50.0, 55.2 and 60.0% of SDZ (5 mg L-1), respectively within 290 h. On the basis of quadrupole time-of-flight mass spectrometry and high performance liquid chromatography, 2-aminopyrimidine and 4-hydroxy-2-aminopyrimidine were identified as the main intermediates of SDZ biodegradation. These bacteria were also able to degrade the metabolite, 2-aminopyrimidine, of the SDZ. Furthermore, SDZ-PM2-BSH30, SDZ-W2-SJ40 and SDZ-3S-SCL47 also showed resistance to various heavy metals like copper, cadmium, chromium, cobalt, lead, nickel and zinc. Additionally, all three bacteria exhibited positive chemotaxis towards 2-aminopyrimidine based on the drop plate method and capillary assay. The results of this study advanced our understanding about the microbial degradation of SDZ, which would be useful towards the future SDZ removal in the environment.

An effective bioremediation approach for enhanced microbial degradation of the veterinary antibiotic sulfamethazine in an agricultural soil

Abstract: The veterinary antibiotic Sulfamethazine (SMZ) contaminates soils via manure applications. Like other soil contaminants (herbicides, fungicides, and nematicides), it has to be degraded. The main challenge is that SMZ biodegradation with bacteria is impeded, since SMZ is a bacteriostatic antibiotic, designed to block microbes in their growth. In this study, we enriched the indigenous soil microbial community (including the single strain Microbacterium sp. C448, adapted to SMZ degradation) from a Canadian soil and we present a suitable approach, for soil remediation by inoculating a German soil with this microbial community established on carrier particles, at environmentally relevant concentrations of 1 mg kg−1. When compared with the isolated SMZ-degrading strain (also obtained from Canada), the microbial community outperformed the mineralization rates of the isolated strain in soil. The negligible soil native SMZ mineralization was successfully increased to 44 and 57 % within 46 days, by the microbial community. The sustainability of this increased SMZ mineralization capacity was proven by the rapid mineralization of a second application of 14C-SMZ 112 days after the first. The pronounced SMZ mineralization and the high amount of non-extractable 14C-residues (NER) in the inoculated soil indicate that the NER are mainly of biogenic origin (metabolically fixed 14C). Therefore, the applied inoculation approach decreased the risk of persistent non-extractable SMZ residues. Together with our former studies, this specific soil inoculation approach was tested for three substances with different physico-chemical properties, indicating that this soil bioremediation technique might also be used for other substances.

Enrichment of functional microbes and genes during pyrene degradation in two different soils

Abstract: Stimulating microbial degradation is a promising strategy for the remediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). To better understand the functional microbial populations and processes involved in pyrene biodegradation in situ, the dynamics of pyrene degradation and functional microbial abundance were monitored during pyrene incubation in soils. We hope our findings will provide new insights into in situ pyrene biodegradation in soils and help to identify functional microbes from soils. Pyrene (60 mg kg−1) was incubated with two different soils, one is lower PAH-containing agricultural soil (LS), and the other is higher PAH-containing industrial soil (HS). During incubation, triplicate samples were collected on days 0, 3, 7, 14, and 35. Pyrene in soil samples was analyzed using an Agilent gas chromatograph (7890A) equipped with a mass-selective detector (model 5897). DNA in soils was extracted with a FastDNA Spin kit for soil (Bio101, USA). The abundance of functional microbes and genes was monitored by a Taqman or SYBR Green based real-time PCR quantification using an iCycler iQ5 themocycler (Bio-Rad, USA). The diversity of PAH-RHDα GP genes was evaluated by constructing clone libraries and sequencing. In both soils, more than 80 % of the added pyrene was degraded within 35 days. After 35-day incubation, there was a significant enrichment of Gram-positive bacteria harboring PAH-ring hydroxylation dioxygenase (PAH-RHDα GP) genes, and the abundance of Mycobacterium increased significantly. In PAH-RHDα GP clone libraries from two soils, Mycobacterium was detected, while most sequences were closely related to uncultured Gram-positive bacteria. In addition, two pyrene catabolic pathways might be involved in pyrene degradation, as pyrene dioxygenase genes, nidA and nidA3, were dramatically enriched during incubation. Moreover, the abundance and diversity of potential degraders in two soils showed significantly difference in responding to pyrene stress. This result indicates that soil condition can significantly affect functional microbial populations and biological process for pyrene biodegradation. These results revealed that Mycobacterium as well as uncultured Gram-positive PAH-RHDα genotypes may be the important group of pyrene degraders in soils, and two pyrene catabolic pathways, targeted by nidA and nidA3, might potentially contribute to in situ biodegradation of pyrene. This study characterized the response pattern of potential pyrene degraders to pyrene stress in two different soils, which would increase our understanding of the indigenous processes of pyrene biodegradation in soil environment.

Biodegradation of Polycyclic Aromatic Hydrocarbons by Microbial Consortium: A Distinctive Approach for Decontamination of Soil

Abstract: The presence of polycyclic aromatic hydrocarbons (PAHs) in the soil is a major cause of concern due to their toxic nature and ubiquitous occurrence. As PAHs are hydrophobic substances, their solubility in water is very low. This makes them unfit for natural degradation. However, it has been found that several microorganisms have the capability to efficiently degrade soil-sorbed PAHs using different metabolic pathways. As the microbial degradation process is quite economical and does not cause ecological damage, it has been a subject of extensive research for the past several decades. In numerous studies, it has been found that a consortium of microbes is more effective than the individual microbial isolates. The process remains affected by different environmental factors. Therefore, in this article, the current status of the work done on various aspects of biodegradation of ecologically toxic PAHs using different microbial consortia has been reviewed along with the biological aspects of biosurfact...

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism

Abstract: Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase ( bssA ) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. IMPORTANCE Constructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluene-contaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results indicated stable aerobic toluene degradation by members of the Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis in these bacteria was higher during the day, suggesting that they additionally fed on organic root exudates and reutilized the stored carbon compounds during the night. Our study illuminates microbial processes occurring in the rhizosphere of an aquatic ecosystem.