Production of microbial chitinases – A revisit

Production of microbial chitinases have received increased attention in recent years due to its potential application in various fields. There has been an all around effort to increase the production of chitinases by using genetically engineered organisms and by incorporating modern fermentation techniques. This review presents a brief outline on the production of microbial chitinases which includes information on random screening and selection of chitinolytic organisms and the rationale behind the use of genetically engineered organisms. The problems and perspectives involved in large scale production of chitinases is discussed with special reference to bioreactor studies and new fermentation methods. The present limitations in the understanding of the chitinase fermentation process is also discussed and the scope for future investigation is outlined in this communication.     

A dynamic mathematical model for microbial removal of pyritic sulfur from coal

A dynamic mathematical model has been developed to describe microbial desulfurization of coal by Thiobacillus ferrooxidans. The model considers adsorption and desorption of cells on coal particles and microbial oxidation of pyritic sulfur on particle surfaces. The influence of certain parameters, such as microbial growth rate constants, adsorption-descrption constants, pulp density, coal particle size, initial cell and solid phase substrate concentration on the maximum rate of pyritic sulfur removal, have been elucidated. The maximum rate of pyritic sulfur removal was strongly dependent upon the number of attached cells per coal particle. At sufficiently high initial cell concentrations, the surfaces of coal particles are nearly saturated by the cells and the maximum leaching rate is limited either by total external surface area of coal particles or by the concentration of pyritic sulfur in the coal phase. The maximum volumetric rate of pyritic sulfur removal (mg S/h cm(3) mixture) increases with the pulp density of coal and reaches a saturation level at high pulp densities (e.g. 45%). The maximum rate also increases with decreasing particle diameter in a hyperbolic form. Increases in adsorption coefficient or decreases in the desorption coefficient also result in considerable improvements in this rate. The model can be applied to other systems consisting of suspended solid substrate particles in liquid medium with microbial oxidation occurring on the particle surfaces (e.g., bacterial ore leaching). The results obtained from this model are in good agreement with published experimental data on microbial desulfurization of coal and bacterial ore leaching.     

Microbial desulfurization of solubilized coal

Microbial desulfurization of low rank coal by Rhodococcus rhodochrous IGTS8 was investigated using three different pretreated coal samples. Solubilized coal was desulfurized more efficiently than hard coal and more sulfur was extracted from biologically solubilized coal than from chemically solubilized coal. Microbial desulfurization combined with biological solubilization removed 75% of the total sufur while the microbial desulfurization combined with chemical solubilization removed 63%.     

Microbial desulfurization of organic sulfur compounds in petroleum

Sulfur removal from petroleum is important from the standpoint of the global environment because the combustion of sulfur compounds leads to the production of sulfur oxides, which are the source of acid rain. As the regulations for sulfur in fuels become more stringent, the existing chemical desulfurizations are coming inadequate for the "deeper desulfurization" to produce lower-sulfur fuels without new and innovative processes. Biodesulfurization is rising as one of the candidates. Several microorganisms were found to desulfurize dibenzothiophene (DBT), a representative of the organic sulfur compounds in petroleum, forming a sulfur-free compound, 2-hydroxybiphenyl. They are promising as biocatalysts in the microbial desulfurization of petroleum because without assimilation of the carbon content, they remove only sulfur from the heterocyclic compounds which is refractory to conventional chemical desulfurization. Both enzymological and molecular genetic studies are now in progress for the purpose of obtaining improved desulfurization activity of organisms. The genes involved in the sulfur-specific DBT desulfurization were identified and the corresponding enzymes have been investigated. From the practical point of view, it has been proved that the microbial desulfurization proceeds in the presence of high concentrations of hydrocarbons, and more complicated DBT analogs are also desulfurized by the microorganisms. This review outlines the progress in the studies of the microbial desulfurization from the basic and practical point of view.     

Continuous microbial desulfurization of coal--application of a multistage slurry reactor and analysis of the interactions of microbial and chemical kinetics

Microbial desulfurization of coal by pyrite oxidizing bacterial enrichment cultures has been studied in air-agitated slurry reactors of 4- and 20-L volumes. Batch experiments showed that inoculation with an active bacterial culture is essential to minimize the lag phase, although a considerable number of pyrite oxidizing bacteria was found on the coal prior to desulfurization. For detailed investigations of kinetics, energy requirements, and technical applicability, a bioreactor equipment consisting of a cascade of eight stages was developed and operated continuously. Microbial desulfurization of coal-monitored by measuring the axial profile of dissolved iron concentration, real and maximum oxygen consumption rates, and cell concentration-at pulp densities to 30% was performed over a period of 200 days without any disturbances concerning the aeration system, fluidization, transport of solids and microbial growth. At a pulp density of 20%, a pyrite conversion of 68% was achieved after the third reactor stage at a total residence time of five days in the first three stages. The kinetics of pyrite degradation were found to be well described by a rate equation of first order in pyrite surface area concentration if the pyrite is directly accessible for microbial attack. Rate constants were determined to 0.48 mg pyrite/(cm(2) day) in the first and to 0.24 mg pyrite/(cm(2) day) in the following reactor stages. Kinetic models taking into account adsorption/desorption as well as growth kinetics failed to describe the observed reaction rates. However, a model treating pyrite degradation and microbial growth kinetics formalistically seems to be applicable when backmixing between the reactor stages can be avoided. The advantage of a multistage reactor in comparison to single-stage equipment was shown by calculation. To obtain a pyrite conversion of 68%, a three-stage reactor would require only 58% of the volume of single-stage equipment.Measurement of oxygen consumption rates proved to provide quickly and easily measurable parameters to observe microbial coal desulfurization in technical scale: the real oxygen consumption rate is correlated to the pyrite oxidation rate and the maximum oxygen consumption rate is correlated to the concentration of viable cells. The Y(o/s) coefficient for the amount of oxygen consumed per mass unit of pyrite oxygen was determined to approximately 0.33 in comparison to 1.0 which can be calculated from stoichiornetry. This could yet not be explained. Chemical leaching experiments as well as sulfur analyses of desulfurized coal samples showed that the microorganisms play the main role in degradation of pyrite from coal and that pyrite oxidation by ferric iron can be neglected.     

Metabolite induction via microorganism co-culture: A potential way to enhance chemical diversity for drug discovery

Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites.     

环境抗生素污染的微生物修复进展

近年来随着抗生素在畜牧业、水产养殖业以及医疗行业的广泛应用,大量抗生素通过排泄物进入环境,导致我国大面积水体及土壤环境中抗生素残留量急剧增高。环境中不同种类的抗生素的残留导致微生物种群结构失衡,对生态环境及人类造成极大危害。因此,解决抗生素残留问题是21世纪新型环境污染物领域的一个重要课题。已有研究显示,一些微生物能够以抗生素为碳源生存,可用于降解环境中残留抗生素,但人们对微生物降解抗生素的降解机制了解较少。文中概括了近十年来抗生素降解菌株和菌群对抗生素的去除情况,以及应用微生物菌群处理抗生素残留的技术方法,同时对未来利用微生物修复法减少环境中抗生素残留进行了展望。     

石油生物催化脱硫的研究进展

石油生物催化脱硫技术是新兴的极具潜力的石油非加氢脱硫技术,在降低轻质油品生产成本、提高油品质量和环境保护等方面显示出潜在的优势,被誉为21世纪的石油脱硫技术。本文主要对石油生物催化脱硫技术特点、各种降解路线和研究现状进行了综述,指出了石油生物催化脱硫技术存在的问题,并提出了进一步研究发展的方向。     

不同煤阶生物成因煤层气微生物群落的功能及多样性研究进展

生物成因煤层气是煤层气形成的主要途径之一,在各种煤阶的煤层气田中均发现有生物成因煤层气。高通量测序技术、宏基因组学等高新技术的应用逐步揭示了生物成因煤层气微生物群落的组成及多样性,为揭示煤层气资源的微生物生成机理提供了理论依据。本文综述了近年来国内外针对不同煤阶条件下微生物群落结构及多样性方面的研究进展,总结了煤层气生物成因过程中主要微生物的功能及产气途径,并探讨了生物成因煤层气领域的研究前景。     

Application of hyperthermophiles and their enzymes

Enzymes from hyperthermophiles display extreme (thermo)stability and a wide range of enzymes have been examined to explore their potential for various biotechnological processes. In addition, recent years have witnessed the development of genetic systems in a number of hyperthermophilic archaea. This has provided the means to initiate cell engineering studies in these organisms. Biofuel production is now an important topic in microbial biotechnology, and the hydrogen producing capabilities of (hyper)thermophiles, as well as their thermostable hydrogenases, are now attracting much attention.     

微生物增产煤层气技术研究进展

微生物增产煤层气技术能够产生新的煤层气,有效缓解能源紧张问题,是煤层气开采、增产的研究热点。微生物增产煤层气技术的核心机理是煤的厌氧生物降解产甲烷。国内外研究学者通过实验室模拟研究了本源和外源微生物的降解煤产甲烷能力及影响因素。部分煤层气公司富集或分离获得了高效产甲烷菌群,并研究了微生物增产煤层气技术的现场实施方法。开发煤的预处理技术、构建新型高效菌群等可进一步提高微生物的增产煤层气能力,促进微生物增产煤层气技术的应用。     

Recent advances in sea-ice microbiology

Over the past 50 years there has been much effort invested in the investigation of the ecology of sea ice. Sea ice is an ephemeral feature of the Arctic and Southern Oceans and smaller water bodies such as the Baltic and Caspian Seas. The semisolid ice matrix provides a range of habitats in which a diverse range of microbial organisms thrive. In the past 5 years there has been considerable steps forward in sea-ice research, in particular regarding the analysis of sea-ice microstructure and the investigation of the diversity and adaptation of microbial communities. These studies include: (i) controlled simulated and in situ studies on a micrometer scale to unravel the dynamic of the microhabitat with consequences for the organisms; (ii) the introduction of molecular approaches to uncover the diversity of uncultured still unknown microorganisms; and (iii) studies into the molecular adaptation of selected model organisms to the extreme environment. This minireview presents some of the most recent findings from sea-ice studies within the framework of these aims.     

Multiple Rieske proteins in prokaryotes: Where and why?

Many microbial genomes have been sequenced in the recent years. Multiple genes encoding Rieske iron-sulfur proteins, which are subunits of cytochrome bc-type complexes or oxygenases, have been detected in many pro- and eukaryotic genomes. The diversity of substrates, co-substrates and reactions offers obvious explanations for the diversity of the low potential Rieske proteins associated with oxygenases, but the physiological significance of the multiple genes encoding high potential Rieske proteins associated with the cytochrome bc-type complexes remains elusive. For some organisms, investigations into the function of the later group of genes have been initiated. Here, we summarize recent finding on the characteristics and physiological functions of multiple high potential Rieske proteins in prokaryotes. We suggest that the existence of multiple high potential Rieske proteins in prokaryotes could be one way of allowing an organism to adapt their electron transfer chains to changing environmental conditions.     

Biological and biochemical analysis of soils

Summary There is an immense literature on biological and biochemical analyses of soils. Such analyses have revealed the enormous richness of species in soil and their vast range of metabolic potentials and ecological diversity. Accordingly, the approaches used to investigate the soil biota and its biochemistry usually have to be modified or adapted depending upon the purpose of the investigation.Studies of micro-organisms in the soil environment, are complicated because microbial cells are commonly attached to surfaces where they live side-by-side with other populations in consortia usually containing different morphological and physiological types. Such assemblages of organisms cannot be described quantitatively using cultural techniques, such as plate counts, which underestimate both cell numbers and viable biomass. The development of more powerful observational and staining techniques has improved our knowledge of the diverse morphological and biochemical composition of soil micro-communities. Such findings have been amplified at a grosser level by laboratory studies with multi-component systems (microcosms) to mimic field situations and to assess the range of biochemical potentials of microbial consortia.But despite notable advances in analytical methods we are still, with a few exceptions, unable to detect or identify those microorganisms which carry out specific biochemical transformations or determine whether particular cells are alive, dormant or dead at the time of observation.Considerable work has been done to define some of the fundamental ecological attributes of microbial assemblages in soil. Productive work on the metabolic activities of the soil microbiota, specially geochemical transformations of C, N, S and P, has been under way for more than a century. But only in more recent years have more sensitive and reproducible analytical methods become available to measure viable biomass in soil. This will enable some insight to be gained into the role that microbial biomass plays as a labile source and sink for plant nutrients.Introductory lecture     

Microbiological coal desulphurization

Sulphur compounds present in coal impose severe limitations on its utilization since sulphur-containing gases emitted into the atmosphere upon direct combustion of coal cause serious environmental pollution problems. Removal of sulphur compounds from coal by microbial action has many advantages over physical and chemical desulphurization methods. The potential use of various microorganisms for the removal of sulphur compounds from coal is presented. Environmental conditions and major process variables affecting the process performance are identified and their possible effects are discussed. Various process schemes for microbial desulphurization (MDS) of coal are suggested. It is concluded that microbial methods have a high potential in removing sulphur compounds from coal. However, more research and development work is needed in this field to overcome present technological problems.     

Desulfurization of coal by microbial column flotation

Twenty-three strains capable of oxidizing iron were isolated from coal and ore storage sites as well as coal and ore mines, volcanic areas, and hot spring. Four strains were found to have high iron-oxidizing activity. One strain (T-4) was selected for this experiment since the strain showed the fastest leaching rate of iron and sulfate from pyrite among the four strains. The T-4 strain was assigned for Thiobacillus ferrooxidans from its cultural and morphological characteristics.Bacterial treatment was applied to column flotation. An increase of cell density in the microbial column flotation resulted in the increase of pyrite removal from a coal-pyrite mixture (high sulfur imitated coal) with corresponding decrease of coal recovery. The addition of kerosene into the microbial column flotation increased the recovery of the imitated coal from 55% (without kerosene) to 81% (with 50 muL/L kerosene) with the reduction of pyrite sulfur content from 11% (feed coal) to 3.9% (product coal). The kerosene addition could reduce the pyritic sulfur content by collecting the coal in the recovery. However, the addition could not enhance separation of pyrite from the coal-pyrite mixture, since pyrite rejection was not affected by the increase of the kerosene addition. An excellent separation was obtained by the microbial flotation using a long column which had a length-diameter (L/D) ratio of 12.7. The long column flotation reduced the pyritic sulfur content from 11% (feed coal) to 1.8% (product coal) when 80% of the feed coal was recovered without the kerosene addition. The long column flotation not only attained an excellent separation but also reduced the amount of cells for desulfurization to as little as one-tenth of the reported amount. (c) 1994 John Wiley & Sons, Inc.     

Microbial production and applications of 5-aminolevulinic acid

5-Aminolevulinic acid (ALA), an important intermediate in tetrapyrrole biosynthesis in organisms, has been widely applied in many fields, such as medicine, agriculture, and the food industry, due to its biochemical characteristics. Research efforts supporting the microbial production of ALA have received increasing interest due to its dominant advantages over chemical synthesis, including higher yields, lesser pollutant emissions, and a lesser monetary cost. ALA synthesis using photosynthetic bacteria (PSB) is a promising approach in various microbial synthesis methods. In this review, recent advances on the microbial production of ALA with an emphasis on PSB are summarized, the key enzymes in the biosynthesis pathway (especially the relationship between key enzymes and key genes) are detailed, regulation strategies are described, and the significant influencing factors on the ALA biosynthesis and application of ALA are outlined. Furthermore, the eco-friendly perspective involving the combination of wastewater treatment and microbial production of ALA is conceived.     

A population genomic approach to map recent positive selection in model species

Based on nearly complete genome sequences from a variety of organisms data on naturally occurring genetic variation on the scale of hundreds of loci to entire genomes have been collected in recent years. In parallel, new statistical tests have been developed to infer evidence of recent positive selection from these data and to localize the target regions of selection in the genome. These methods have now been successfully applied to Drosophila melanogaster , humans, mice and a few plant species. In genomic regions of normal recombination rates, the targets of positive selection have been mapped down to the level of individual genes.     

The influence of hydrogeological disturbance and mining on coal seam microbial communities

The microbial communities present in two underground coal mines in the Bowen Basin, Queensland, Australia, were investigated to deduce the effect of pumping and mining on subsurface methanogens and methanotrophs. The micro‐organisms in pumped water from the actively mined areas, as well as, pre‐ and post‐mining formation waters were analyzed using 16S rRNA gene amplicon sequencing. The methane stable isotope composition of Bowen Basin coal seam indicates that methanogenesis has occurred in the geological past. More recently at the mine site, changing groundwater flow dynamics and the introduction of oxygen in the subsurface has increased microbial biomass and diversity. Consistent with microbial communities found in other coal seam environments, pumped coal mine waters from the subsurface were dominated by bacteria belonging to the genera Pseudomonas and the family Rhodocyclaceae. These environments and bacterial communities supported a methanogen population, including Methanobacteriaceae, Methanococcaceae and Methanosaeta. However, one of the most ubiquitous micro‐organisms in anoxic coal mine waters belonged to the family ‘Candidatus Methanoperedenaceae’. As the Archaeal family ‘Candidatus Methanoperedenaceae’ has not been extensively defined, the one studied species in the family is capable of anaerobic methane oxidation coupled to nitrate reduction. This introduces the possibility that a methane cycle between archaeal methanogenesis and methanotrophy may exist in the anoxic waters of the coal seam after hydrogeological disturbance.