The potential for reductive dehalogenation of chlorinated phenol in a sulphidogenic environment inin situ enhanced biodegradation

An investigation of the reductive dechlorination of 2, 4, 6-trichlorophenol (2, 4, 6-TCP) under sulphate-reducing conditions was made. Sulphate-reducing and dechloro-respiring activities were studied in a mixed microbial population operated in batch-fed as well as continuous pine chip-packed fluidised bed reactors. Results showed that reductive dechlorination of 2, 4, 6-TCP by the dechloro-respiring bacteria may be indirectly stimulated by the fermentative activity of the sulphate-reducing population affected by sulphate and lactate concentrations. Sulphate was administered in excess (900 mg·ℓ-1) and limiting (110 mg·ℓ-1) concentrations. At these concentrations, SO42- was available in quantities sufficient and lower than that required to bring about consumption of lactate. Transformation to 2,4-dichlorophenol (2,4-DCP), 4-chlorophenol (4-CP) and phenol was enhanced in sulphate-limiting conditions with average 47.7% TCP reduction compared to 11.6% in sulphate-enriched administered reactors. The potential application requirements for dechlorination under sulphate-reducing conditions for in situ biodegradation are considered. The input electron donor: SO42- ratio is manipulated to effect accelerated dechlorination rates for chlorinated organic compound-contaminated soil/groundwater bioremediation applications where oxygen is frequently limited. Water SA Vol. 32(2) 2006: pp.243-24

Technical note: Development of a Linear Flow Channel Reactor for sulphur removal in acid mine wastewater treatment operations

Where sulphate removal is targeted in the biological treatment of acid mine drainage wastewaters, a step additional to sulphate reduction is required to prevent the complete oxidation of sulphide back to sulphate. This linearisation of the biological sulphur cycle has presented a technological bottleneck, particularly in passive treatment operations. We report an investigation of sulphur production in floating sulphur biofilms as a means for addressing this problem. These 50 μm to 500 μm structures may be seen to form on the surface of sulphidic, organic waters and in which sulphide is partly oxidised to So and polysulphide. A Linear Flow Channel Reactor was developed in which the formation of the floating sulphur biofilm could be optimised and studied under controlled conditions. In this study the sulphide feed was sourced from a lignocellulose packed bed reactor treating a synthetic acid mine water (2 000 mg∙ℓ-1 Na2SO4 solution) and the Liner Flow Channel Reactors (surface area 1.1 m2 and 2.2 m2) were operated in a controlled environment chamber. The floating sulphur biofilm was harvested by settling to the bottom of the reactor where it remained largely unreacted until removed. It was shown that up to 88% of sulphide in the feed stream may be removed in this way and that this was achieved mainly by oxidation of sulphide to sulphur (including a polysulphide fraction). A mass balance accounting for the process showed that up to 66% of total sulphur species entering the system were recovered as So. Oxidation of sulphide to thiosulphate and sulphate was not found to be significant. A fraction of fine particulate sulphur is released into the stream on harvesting of the biofilm which does not readily settle in the reactor and may thus be lost to the mass balance account. The effects of temperature, loading rate and reactor surface area were investigated in optimising the performance of the reactor. Scale-up application studies in the use of the Linear Flow Channel Reactor in an acid mine drainage passive treatment environment have been undertaken in field studies.Keywords: floating sulphur biofilms, acid mine drainage, AMD passive treatment, linear flow channel reactor, sulphur biotechnolog

Molecular microbial ecology of lignocellulose mobilisation as a carbon source in mine drainage wastewater treatment

The community structure of complex microbial consortia which develop in lignocellulose packed passive treatment systems for acid mine drainage remediation were investigated. An understanding of interactions between these populations is important in determining mechanisms by which such systems operate. A degrading packed bed reactor was packed with lignocellulositic material as a sole carbon source and fed continuously with simulated acid mine drainage. Samples were collected every two months at different depths of the reactor to isolate the total genomic DNA and PCR amplify section of 16S rDNA gene. PCR primers, GM5F and 907R incorporating GC clamp were used to amplify 586-bp region of 16S rDNA gene. Denaturing gradient gel electrophoresis (DGGE) indicated clearly a highly differentiated pattern of r-DNA – derived amplificates between different depths of the bioreactor. Predominant DGGE bands were further excised, reamplified, cloned and sequenced. Sequencing analysis revealed phylogenetic affiliation of specific bacterial populations in different depths of the bioreactor. Water SA Vol. 30 (5) 2005: pp.658-66

An investigation into the mechanism underlying enhanced hydrolysis of complex carbon in a biosulphidogenic recycling sludge bed reactor (RSBR)

The potential for using readily available and cost-effective complex carbon sources such as primary sewage sludge for a range of biological processes, including the bioremediation of acid mine drainage, has been constrained by the slow rate of solubilisation and low yield of soluble products, which drive the above mentioned processes. Previous research into the hydrolysis of complex organic matter, such as primary sludge, under biosulphidogenic conditions within a novel Recycling Sludge Bed Reactor (RSBR) demonstrated solubilisation in excess of 50%. However, further investigation was required into the mechanism of this enhanced hydrolysis. The current study was aimed at confirming that hydrolysis is enhanced under biosulphidogenic conditions, and to obtain an estimate of the relative rates of hydrolysis using toluene as a specific metabolic inhibitor. The solubilisation of primary sewage sludge under sulphate reducing conditions was conducted in controlled flask studies and previously reported findings of enhanced hydrolysis were confirmed. The maximum percentage solubilisation obtained in this study over a 10-day period was 31% and 64% for the methanogenic and sulphidogenic systems respectively. By using toluene as an inhibitor of bacterial uptake of soluble carbohydrates, it was possible to determine the rate of production of various key products of the hydrolytic step. From the results of the current experiment, the rate of production of soluble carbohydrate, and therefore the rate of hydrolysis of complex carbohydrates, in terms of COD equivalents was estimated at 543 mgCOD·l-1·d-1 and 156 mgCOD·l- 1·d-1 under sulphidogenic and methanogenic conditions, respectively.. Water SA Vol. 30 (5) 2005: pp.150-15

Technical note: Development of a gradient tube method for examining microbial population structures in floating sulphur biofilms

Floating biofilms occur in thin layers of between 50 μm and 500 μm on the surface of certain organic, sulphidic aquatic environments and, at times, may only be several cells deep. While these structures may be important in terms of energy flow pathways, and possibly also in wastewater treatment operations, little is known about their structural/functional properties. This is due, in part, to their flimsy nature but also to methodological constraints related to their sampling and manipulation. We have investigated floating sulphur biofilms that appear as white layers on the surface of anoxic sulphidic organic wastewaters and describe here the development of a novel gradient tube method for investigating these systems. This approach enables testing of the hypothesis that these floating sulphur biofilms are complex well-differentiated structures rather than disordered dispersions of microbial biomass as has been previously thought. Furthermore, if the former is correct, they would seem to resemble the structure and functionality of comparable complex bioflms that are attached to solid substrates. The gradient tube method involves the establishment of apposing gradients of sulphide and oxygen that are expanded across a tube of agarose 10 cm in length; this simulates the oxic/anoxic interface that occurs over only several micrometres in the natural biofilm system. A plug of sulphide-enriched agarose is first placed in the base of the tube. Samples of the floating sulphur biofilm are then mixed into agarose growth medium and, before it sets, this is overlaid on top of the plug. The tubes are then open capped and incubated. A variety of different microbial populations may thus become established in the separate physiological niches that are set up in this way within the gradient tube. The populations may be quite robustly sampled by extruding and then sectioning the agarose plug. This expansion of the biofilm enables more detailed molecular phylogenetic studies of the populations found in the various niches within the biofilm and also measurement of physico-chemical parameters within the system.Keywords: gradient tube method, floating biofilms, floating sulphur biofilms, microbial ecology, sulphur biotechnology, acid mine drainage wastewater

Nuclear Quadrupole Hyperfine Structure in HC14N/H14NC and DC15N/D15NC Isomerization: A Diagnostic Tool for Characterizing Vibrational Localization

Large-amplitude molecular motions which occur during isomerization can cause significant changes in electronic structure. These variations in electronic properties can be used to identify vibrationally-excited eigenstates which are localized along the potential energy surface. This work demonstrates that nuclear quadrupole hyperfine interactions can be used as a diagnostic marker of progress along the isomerization path in both the HC14N/H14NC and DC15N/D15NC chemical systems. Ab initio calculations at the CCSD(T)/cc-pCVQZ level indicate that the hyperfine interaction is extremely sensitive to the chemical bonding of the quadrupolar 14N nucleus and can therefore be used to determine in which potential well the vibrational wavefunction is localized. A natural bonding orbital analysis along the isomerization path further demonstrates that hyperfine interactions arise from the asphericity of the electron density at the quadrupolar nucleus. Using the CCSD(T) potential surface, the quadrupole coupling constants of highly-excited vibrational states are computed from a one-dimensional internal coordinate path Hamiltonian. The excellent agreement between ab initio calculations and recent measurements demonstrates that nuclear quadrupole hyperfine structure can be used as a diagnostic tool for characterizing localized HCN and HNC vibrational states.Comment: Accepted by Physical Chemistry Chemical Physic

Change and Aging Senescence as an adaptation

Understanding why we age is a long-lived open problem in evolutionary biology. Aging is prejudicial to the individual and evolutionary forces should prevent it, but many species show signs of senescence as individuals age. Here, I will propose a model for aging based on assumptions that are compatible with evolutionary theory: i) competition is between individuals; ii) there is some degree of locality, so quite often competition will between parents and their progeny; iii) optimal conditions are not stationary, mutation helps each species to keep competitive. When conditions change, a senescent species can drive immortal competitors to extinction. This counter-intuitive result arises from the pruning caused by the death of elder individuals. When there is change and mutation, each generation is slightly better adapted to the new conditions, but some older individuals survive by random chance. Senescence can eliminate those from the genetic pool. Even though individual selection forces always win over group selection ones, it is not exactly the individual that is selected, but its lineage. While senescence damages the individuals and has an evolutionary cost, it has a benefit of its own. It allows each lineage to adapt faster to changing conditions. We age because the world changes.Comment: 19 pages, 4 figure

Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense

Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species. This results in the maintenance of genetic diversity at pathogen antigens (or so-called effectors) and host resistance genes such as the major histocompatibility complex (MHC) in mammals or resistance (R) genes in plants. In plant-pathogen interactions, the current paradigm posits that a specific defense response is activated upon recognition of pathogen effectors via interaction with their corresponding R proteins. According to the''Guard-Hypothesis,'' R proteins (the ``guards'') can sense modification of target molecules in the host (the ``guardees'') by pathogen effectors and subsequently trigger the defense response. Multiple studies have reported high genetic diversity at R genes maintained by balancing selection. In contrast, little is known about the evolutionary mechanisms shaping the guardee, which may be subject to contrasting evolutionary forces. Here we show that the evolution of the guardee RCR3 is characterized by gene duplication, frequent gene conversion, and balancing selection in the wild tomato species Solanum peruvianum. Investigating the functional characteristics of 54 natural variants through in vitro and in planta assays, we detected differences in recognition of the pathogen effector through interaction with the guardee, as well as substantial variation in the strength of the defense response. This variation is maintained by balancing selection at each copy of the RCR3 gene. Our analyses pinpoint three amino acid polymorphisms with key functional consequences for the coevolution between the guardee (RCR3) and its guard (Cf-2). We conclude that, in addition to coevolution at the ``guardee-effector'' interface for pathogen recognition, natural selection acts on the ``guard-guardee'' interface. Guardee evolution may be governed by a counterbalance between improved activation in the presence and prevention of auto-immune responses in the absence of the corresponding pathogen