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Microbial ecosystems such as biological wastewater treatment plants and the human gastrointestinal tract are home to a vast diversity of bacterial species. So far, scientists have had difficulties in analysing the dependencies between the many bacteria in a complex ecosystem such as the gut or a biological treatment plant. To achieve this, Wilmes and his group took samples from a wastewater treatment plant during different seasons. Armed with this knowledge, the researchers then went about first identifying "keystone genes" and linking these to keystone species. Naturally occurring "keystone" molecules that have powerful behavioral effects on diverse organisms often play large but unrecognized roles in structuring ecosystems, according to a theory proposed in the June issue of BioScience. Just thirteen corporations control 19-40% of the largest and most valuable stocks and 11-16 % of the global marine catch, according to new research.
Sharks, skates, and rays can detect very weak electric fields produced by prey and other animals using an array of unusual organs known as the ampullae of Lorenzini. Unique sections of coral DNA can indicate a higher tolerance to environmental stress, researchers have revealed for the first time. Researchers at The Australian National University (ANU) have found possums in New Zealand prefer to eat leaves high in available protein, giving authorities new evidence to help them limit possum damage to New Zealand's forests.
Ninety per cent of Norway's two million pairs of cliff-nesting seabirds are located in nesting colonies above the Arctic Circle. Science, Technology and Medicine open access publisher.Publish, read and share novel research.
Bioremediation of Nitroaromatic CompoundsDeepak Singh1, Keerti Mishra1 and Gurunath Ramanthan1[1] Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, IndiaAbstract: Nitroaromatics are major pollutants released in the environment during the post-industrialization era and pose toxic effects to living organisms.
They then characterized the entirety of all genes, analyzed what genes were being transcribed and gained an overview of the resulting proteins.
Scientists of the Luxembourg Centre for Systems Biomedicine (LCSB) and the Life Science Research Unit (LSRU) of the University of Luxembourg, in collaboration with US researchers, have now succeeded for the first time in determining key functional genes and the organisms encoding these in such ecological systems, working from extensive data of bacterial genetics and bacterial metabolism.
These are typically not the most abundant species but far more important are organisms carry copies of distinct, essential genes - researchers here speak of "keystone genes" - which are also transcribed disproportionately often.
In most cases, they record the different species that occur together under changing environmental conditions. They then characterised the entirety of all genes, analysed what genes were being transcribed and gained an overview of the resulting proteins. Rudi Balling explains the medical importance of the new insights: "We assume that diseases such as Parkinson's could in part be caused by a disruption in the composition of microbial communities in the human body. They are created in cells through a process called gene expression, which uses instructions from stretches of DNA called genes to build proteins. Different reductive pathways in different bacteria: (A) Clostridium acetobutylicum, Escherichia coli, Lactobacillus sp.
Schematic representation of the reactor used for the degradation of 4-nitrobenzoate and 4-aminobenzoate by B. Several bacterial strains have been isolated for the degradation of these nitroaromatic pollutants. Similar patterns of variation are hereby considered an indication of interaction and highly connected species are thought to represent keystone species.
The three stages are as follows: the conversion of the growth substrate to catechol (or substituted catechol), then ring cleavage, and finally metabolism of the ring cleavage product to central metabolites by either the ortho or meta pathways. Some of them have been used in field trial experiments for the removal of nitroaromatics from industrial water and groundwater. Paul Wilmes are also of medical importance: When microbial communities come out of balance in the course of disease, a positive health effect may be achieved by supporting keystone bacterial species in a targeted fashion. These studies for nitroaromatics clearly indicate that most of the involved genes have evolved from preexisting enzymes by using all means of gene evolution like horizontal gene transfer, mutation, and promiscuity principle.
First, dinitrotoluene dioxygenase (DNTDO) attacks on the benzene ring converting DNT into 4-methyl-5-nitrocatachol (4M5NC) with the simultaneous removal of a nitrite group. Further, MNC mono-oxygenase removes another nitrite and converts the substrate into 2-hydroxy-5-methylquinone. IntroductionMicrobes are empowered to degrade environmental pollutants under different conditions to perform unusual metabolic and physiological activities [1]. This 2-hydroxy-5-methylquinone eventually leads to the formation of 2,4,5-trihydroxytoluene, a reaction that is catalyzed by HMQ reductase. This metabolic versatility has been exploited for human benefit in various industrial products like cheese (dairy industry), insulin, antibiotics (pharmaceutical industry), etc.
Ring fission of 2,4,5-trihydroxytoluene likely occurs at position 5,6 of the aromatic ring to yield 2,4-dihydroxy-5-methyl-6-oxo-hexa-2,4-dienoic acid as ring cleavage product (Figure 10).Nishino et al. Microbial enzyme systems have also been used for the development of suitable biocatalysts for green chemistry applications [2]. When 2,4- and 2,6-DNT were used as the sole source of carbon and nitrogen together, the dioxygenation of 2,6-DNT to 3-methyl-4-nitrocatachol (3M4NC) was the initial reaction, accompanied by the release of nitrite. Organic aromatic compounds have been the main source of pollution in several water bodies [4].
3M4NC was then subjected to meta-ring cleavage (Figure 11) without releasing the second nitro group prior to the ring cleavage. Thus, a remediation and degradation study of aromatics has been a focus of intensive study.
Although 2,4-DNT-degrading strains also could convert 2,6-DNT to 3M4NC, further catabolism was halted at the point. NitroaromaticsNitroaromatic compounds have at least one nitro group attached to the aromatic ring, like nitrobenzene, nitrotoluenes, nitrophenols, etc. In the latter case, 2-hydroxy-5-nitro-6-oxohepta-2,4-dienoic acid was the first ring fission product.
In nature, nitroaromatic compounds are mostly found in natural products from different plants, fungi, and bacteria [5, 6].

The best known example of this is chloramphenicol, which is produced by Streptomyces venezuelae [7–9]. Position 3 methyl group appears as the determinant recognized by the initial dioxygenase to produce highly specific 3M4NC in the 2,6-DNT pathway proposed. The gene encoding this dioxygenase showed a nucleotide sequence similar to the ? subunit among nitroarene dioxygenase.The genes for the initial dioxygenases involved in 2,4-DNT and 2,6-DNT degradation are all closely related, but the enzymes are produced at low constitutive levels [27, 86].
These hydrocarbons produce nitroaromatic compounds after nitration with nitrogen dioxide present in the atmosphere. Synthetic nitroaromatic compounds (production and uses)The versatile chemistry of the nitro group ensures that nitroaromatic compounds serve as important feed stocks in different industrial processes. Lendenmann and Spain [88] initially failed to observe the degradation of 2,4-DNT and 2,6-DNT simultaneously. Subsequently, an aerobic biofilm, initially fed with low concentrations of DNT mixture, was tested. For example, substituted nitrobenzenes and nitropyridines are used in the production of indoles, which are active components of several drugs and agrochemicals [16]. These concentrations were then gradually increased and exhibited mineralization rates of 98% and 94% for 2,4- and 2,6-DNT, respectively. Paracetamol (an analgesic and antipyretic) is synthesized in a one-step reductive acetamidation from 4-nitrophenol [17]. Nitrobenzenes or halonitrobenzenes are used in the synthesis of derivatives of phenothiazines, a large class of drugs with antipsychotic properties [18, 19].Some nitroaromatics like nitrobenzene, nitrotoluene, and nitrophenols are used in the synthesis of pesticides. Isomer concentration needed to be kept below inhibitory levels as high concentrations of each isomer inhibited the degradation of the other.
For example, fluorodifen [20], bifenox, parathion [21], and carbofuran [22] are synthesized from nitrophenols.
Some dinitrophenols like 2,5-dinitro-o-cresol have been used in the synthesis of herbicides, insecticides, fungicides, etc. It is estimated that the worldwide consumption of aniline is approximately 3 million tons [5]. This consumption grew by 7% annually till 2014 and is expected to reach 6.2 million tons in 2015 (Global Analysts report 2014 on aniline production). Aniline is used in the synthesis of drugs, pesticides, and explosives and used as a building block for the production of polyurethane foams, rubber, azo dyes, photographic chemicals, and varnishes [24].Some nitroaromatics are used in the production of explosives like trinitrotoluene (TNT), which is produced by sequential nitration of toluenes. 1,3,5-Trinitrophenol (picric acid), which was prepared in 1771 as a yellow dye for fabrics [25], has also been used in explosive shells.
Chemical industries release these compounds into the environment through various sources, like the use of pesticides and the improper handling or storage of chemicals.
The leakage into industrial effluents by improper disposal or through accidental spills by explosive ammunitions are commonly responsible for these compounds to find their way into the environment [27].
Toxic effectsThe electron withdrawing property of the nitro groups creates a charge on the molecule. It is a unique property that makes the nitro group an important functional group for different industrial synthetic processes. This is why these compounds are given hazardous rating 3 (HR 3), where 3 shows the highest level of toxicity [29].
These are toxic to most living organisms, including humans, fishes, algae, and microorganisms [30, 31]. Their toxicity principally manifests itself due to their ability to uncouple photo or oxidative phosphorylation processes [32, 33]. Some of these compounds are also known for their ecotoxicity [34, 35], immunotoxicity [36], carcinogenicity [37], mutagenicity [38, 39], and teratogenicity [40, 41]. Physical, chemical, and physicochemical methodsDifferent physical methods are available for the treatment of these toxic chemicals, like adsorption, incineration, photo-oxidation, hydrolysis, volatilization, etc.
During adsorption, these compounds are only adsorbed on resins and separated but not destroyed completely. In incinerations, these compounds are treated at very high temperatures, which is neither cost effective nor eco-friendly because toxic NOx fumes are often released in the environment in this process. There are various reports on advanced oxidation processes (AOPs) that utilize ozone, UV radiation, hydrogen peroxide, or combinations of all these for the treatment of nitroaromatic compounds [44–47].
The use of hydrogen peroxide in these processes generates toxic intermediates and is therefore not cost-effective [48].
BioremediationBioremediation involves biological agents to catalyze the degradation and transformation of recalcitrant molecules to simpler structures.
Few common terms used in these processes are defined as follows:Biodegradation is the breakdown of organic pollutants due to microbial activity. The degradation of contaminant generates energy and microbe utilizes this energy for its growth.Biomineralization is the process of complete biodegradation. The organic contaminants are degraded completely through a series of degradation steps and finally converted to inorganic molecules like H2O and CO2.
In the process, organic molecule provides both carbon and energy to the microbe, and if organic molecule is nitroaromatic, it provides nitrogen as well.Biotransformation is the process where in one organic molecule is modified by the action of biological agents. Sometimes, biotransformation occurs with cometabolism, where a microbe uses a substrate for its growth but transforms another substrate, which is not utilized by microbe for its growth.Microbes have been isolated from almost all the parts of biosphere. Supplementing the medium with readily utilizable carbon sources can enhance degradation processes.
Thus, toxic intermediates are not generated and complete removal of toxic compounds is possible.
During the last few decades, extensive research has been carried out for isolation of microbes with the abilities of degrading wide range of toxic nitroaromatic compounds and has been reviewed nicely [5, 49, 50]. General principles of pathways for aerobic aromatic catabolismThe pathway for catabolism of aromatic compound basically has three stages (Figure 2) [51–53].
In the first stage, the substrate undergo changes in its substituent groups by the action of mono- or dioxygenases to form catechols (or substituted catechols).

The catechols then serve as substrates for the second stage of catabolism, that is, the ring opening.
Both pathways (ortho and meta cleavage) are shown in Figure 3 and meta cleavage pathway for methylcatechols is shown in Figure 4. The third stage of catabolism is the conversion of the ring cleavage products into smaller compounds that can enter into central metabolic routes.In general, aromatic compounds are initially catabolized by various pathways (known as peripheral pathways), which converge on a limited number of common intermediates (catechols or its derivatives).
Microbial degradation of nitroaromaticsWhen a nitroaromatic compound is exposed to the environment, its biodegradation takes place either by anaerobic route or by aerobic route. Anaerobic biodegradation of nitroaromaticsIn this process, nitro group is reduced to nitroso derivative, hydroxyl amines, or amines by the action of nitroreductases. The degradation of most of the (poly)nitroaromatic compounds occurs only under anaerobic conditions [49, 54, 55]. The complete mineralization of nitroaromatic by a single anaerobic strain is very rare [56].
Aerobic biodegradation of nitroaromatic compoundsMono- and dinitroaromatics are mainly subjected to aerobic biodegradation and achieve to complete mineralization. During the past few decades, several reports came up with isolation of microbes mineralizing different nitroaromatic compound and their degradation pathway.
Reactions catalyzed by mono-oxygenasesMono-oxygenases are known to add single oxygen atom at a time and cause the release of nitro group.
Simpson and Evans [62] reported the role of mono-oxygenase in a Pseudomonas sp., where 4-nitrophenol was converted to hydroquinone with the concomitant release of nitrite. Dioxygenase catalyzed reactionsDioxygenases are known to add two -OH groups simultaneously on the benzene ring of nitroaromatic compounds with the release of nitro group as nitrite. This type of mechanism is reported for 2,6-dinitrotoluene biotransformation by Alcaligenes eutrophus [63]. Meisenheimer complex formationThe addition of a hydride ion to the aromatic ring of nitroaromatic compound leads to the formation of a Meisenheimer complex [27]. Partial reduction of nitro groupsIn this mechanism, the nitro group is partially reduced to the corresponding hydroxylamine, which upon hydrolysis yields ammonia.
Bacterial degradation of nitrobenzeneThe aerobic degradation of nitrobenzene involves two major pathways: a most commonly found partial reductive pathway and a dioxygenase catalyzed pathway (Figure 6).
In the oxidative degradation of NB, degradation starts with the action of nitrobenzene-1,2-dioxygenase, which converts nitrobenzene into catechol. This catechol is further cleaved by the action of catechol 2,3-dioxygenase and degraded by the meta cleavage pathway. Bacterial degradation of mononitrotoluenesDifferent bacterial strains have been isolated from various sources, which can utilize nitrotoluenes as carbon source or both carbon and nitrogen source.
There are several reports on different degradation pathways for mononitrotoluenes as described here.Nitrotoluenes may be subjected to reductive pathways (formation of aminotoluenes) [70] or partial reductive pathway, wherein a nitro group is reduced to hydroxyl amino group and finally releases ammonia [71–72]. For example, during the degradation of 4-NT by Pseudomonas sp., initially 4-NT is converted into 4-nitrobezoic acid via the formation of 4-nitrobenzyl alcohol and 4-nitrobenzaldehyde.
Then the nitro group is partially reduced to hydroxylamino derivative (rather than amino derivative), which is further converted to protocatechuate without the utilization of oxygen and release of ammonia [71, 72]. In yet another mechanism of 4-NT metabolism by Micobacterium sp., 4-NT was first converted to 4-hydoxyl aminotoluene followed by 6-amino-m-cresol.
JS 42.The toluene mono-oxygenase encoded by TOL plasmid oxidizes only the methyl group of 3-NT and 4-NT but not of the 2-NT [77]. The enzyme, however, attacks on the aromatic ring of 4-NT to produce 2-methyl-5-nitrophenol and 3-methyl-6-nitrocatechol [81]. In both cases (either with toluene mono-oxygenase or dioxygenase as described above), the nitro group was not removed from the benzene ring and mononitrotoluene isomers did not serve as growth substrate. Degradations of monosubstituted 2-, 3-, and 4-nitrotoluenes were also reported from an adapted activated sludge system [79].The two strains of Comamonas JS47 and JS46 capable of degrading 4-nitrobenzoate and 3-nitrobenzoate respectively were immobilized on alginate beads jointly and separately, and these beads were loaded in the reactor and fed to different regimes of alternating nitrobenzoate isomer or mixed nitrobenzoate isomer.
Bacterial degradation of 4-nitrotolueneTwo different pathways are reported in bacterial strains (as shown in Figure 8). Aerobic methyl group oxidation rout is reported in Pseudomonas strains TW3 and strain 4NT.There are few well-characterized bacterial strains that degrades or biotransforms more than one mono-nitro compounds. 2-NT and 4-NT could transform to their corresponding aminotoluenes and hydroxyl nitrotoluenes (pathways A and B, Figure 9) in P.
Here 70% of the 3-NT was reduced to aminotoluene, whereas 30% was converted to 3-nitrophenol via the formation of 3-nitrobenzylalcohol, 3-nitrobenzaldehyde, and 3-nitrobenzoic acid.
This strain was able to degrade other compounds like 2-NT, 4-NT, nitrobenzene (NB), 2CNB, and 3CNB through an oxidative degradation route.
This 3NTDO gene was found to be present on the genomic DNA of the strain on a 5-kb DNA stretch. Its subunits were identified as a reductase, a ferredoxin, an oxygenase large and small subunit, and a regulatory gene product [83].
To get active enzyme, all the subunits were mixed together in a certain proportion with added NADH. Its active recombinant-reconstituted enzyme showed the conversion of nitrotoluenes and nitrobenzenes to methylcatechols and catechols as measure products with the release of nitrite [84].
Products other than (methyl)catechols are dead-end products and observed in the culture broth during the degradation of its corresponding substrates with the Diaphorobacter sp.
This strain did not grow on any dinitrotoluenes (2,4 or 2,6), but recombinant-reconstituted 3NTDO released nitrite from 2,6-dinitrotoluene.

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