An overview of the bacteria and archaea involved in removal of inorganic and organic sulfur compounds from coal

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An overview of the bacteria and archaea involved in removal of inorganic and organic sulfur compounds from coal

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FUEL PROCESSING TECHNOLOGY ELSEVIER Fuel Processing Technology 40 (1994) 167-182 An overview of the bacteria and archaea involved in removal of inorganic and organic sulfur compounds from coal G.I Karavaiko*, L.B L o b y r e v a Institute of Microbiology, Russian Academy of Sciences, Prospect 60 Let(va Ok(vabrya 7, bldg 2, 117811 Moscow, Russian Federation Received 13 January 1994; accepted in revised form 24 May 1994 Abstract Of special importance for biohydrometallurgy are acidophilic chemolithotrophic bacteria from a number of different taxonomic groups, namely: the genera of Thiobacillus and Leptospirillum, moderately thermophilic bacteria which we combined into the group Sulfobacillus Alicyclobacillus, and archaea of the genera Sulfolobus, Acidianus, Metallosphaera, and Sulfurococcus These bacteria are able to oxidize one or more of the following compounds Fe + 2, S O and sulfide minerals and to grow under extreme environmental conditions Growth pH varies in the range from to 5, growth temprature - from to 90°C They can tolerate high concentration of metal ions They possess a great physiological, biochemical and genetic variability Some of them are important for removal of inorganic sulfur compounds from coals Some types of coals and oils contain aromatic heterocyclic compounds with the C-S bond Although a wide range of mostly heterotrophic and some chemolithotrophic bacteria, from bacteria and archaea to eucaryotes, participate in its transformation, only certain organisms have a unique capability of splitting this bond, which is impossible to be done by chemical means They can remove organic sulfur-containing compounds from coal The possibilities of application of bacteria in biological processing of coals is discussed Keywords: Chemolithotrophs; Complex sulfur organic compounds; Sulfide minerals Introduction Sulfur c o n t e n t in coals is k n o w n to v a r y widely from 0.5% to 11% I n o r g a n i c sulfur is p r e s e n t m a i n l y in the form of p y r i t e (FeS2) and, to a lesser extent, as elemental sulfur a n d sulfides of o t h e r metals P y r i t e occurs as concretia, lenses a n d finely dispersed intrusions * Corresponding author Tel.: 7-095-135-03-20 Fax: 7-095-135-65-30 0378-3820/94/$07.00 © 1994 Elsevier Science B.V All rights reserved SSDI - ( ) 0 8 - B 168 G.L Karavaiko, L.B Lobyreva/Fuel Processing Technology 40 (1994) 167-182 Organic sulfur present in coals is integrated into the structural matrix in the form of thiol, sulfide and thiophene compounds So its removal must involve splitting a covalent C-S bond, which, is resistant to chemical treatment The role of microorganisms in the oxidation of pyrite and several analogs of complex organic sulfur-containing compounds, for example, dibenzothiophene (DBT), is actively studied and has been reviewed by Klein et al [1] It has been shown that microorganisms can in principle be used for coal desulfurization, but many differences between removal of organic and inorganic sulfur have not yet been resolved Inorganic sulfur removal is technically feasible, but economically not clear yet The aim of this work is to give an overview of diversity of a main bacteria which is able to involve in oxidation of inorganic sulfur and possible organic sulfur in coal desulfurization process The diversity of chemolithotrophic bacteria and the evolution of their functions Chemolithotrophic bacteria belong to phylogenetically different groups of organisms, namely to gram-negative, gram-positive bacteria and archaea (Fig 1) It appears that chemolithotrophic bacteria have evolved by independent evolutionary patways They differ in morphology, cell wall type, nutrition type, metabolism of inorganic and organic substrates and temperature characteristics of growth (Table 1) Their important feature, however, is the ability to oxidize Fe +, So and sulfide minerals and grow D e s / u l f u r ~ 'S /1\\ !.+ Sulfol~_ / ~ lhiobacillus / I'~'c°llI Spirochaeta #tlJ ~ethanobacterium [ - i ~ / // / / Fig Schematicrepresentationof the phylogenetictree of bacteria Genus Thiobacillus Rods Typical of gramnegative bacteria Strict and facultative autotroph Fe 2÷, S°, sulfide minerals and organic compounds 2-40 1.2-5.0 Characteristic Form of cells Cell wall Type of nutrition Source of energy Temperature, °C pH 1.0-5.0 2-40 Fe ÷, FeS2 Strict autotroph Typical of gramnegative bacteria Vibrions Genus Leptospirillum Table Characteristics of different groups of chemolithotrophic bacteria 1.1-5.0 20-60 Fe ÷, S°, sulfide minerals Facultative autotroph Typical of grampositive bacteria Rods Genus Sulfobacillus and other strains 1.0 5.8 40-90 Fe +, S °, sulfide minerals Facultative autotroph gram-negative bacteria ? ¢~ t~ Metallosphaera Spherical 9~ Genera Acidianus Sulfurococcus 170 G.L Karavaiko, L.B Lobyreva/Fuel Processing Technology 40 (1994) 167-182 at low pH values under aerobic conditions T.ferrooxidans can grow anaerobically in the presence of ferric iron and elemental sulfur [2] Within different taxonomic groups of such bacteria there is also a wide diversity of species and strains According to nucleotide composition of the DNA~ the group of thiobacilli could be divided into two subgroups: T ferrooxidans (with the G + C content of DNA 55.0-57.4 mol%) and T thiooxidans (50.0-53.0 mol%) and other species with a higher G + C content of DNA (62-69 mol%) Both subgroups include species which are able to oxidize only S o (Table 2) Mesophilic leptospirilli are close in the G + C content (Table 2) while the G + C content of a moderately thermophilic strain of leptospirilli is higher On the basis of the analyses of the primary and secondary structure of the 16s rRNA, we placed moderately thermophilic bacteria of the genus Sulfobacillus into the group Sulfobacillu~Alicyclobacillus [-4] These bacteria and related unidentified organisms could also be divided into three subgroups according to their nucleotide composition of the DNA (Table 3) Strain BC is, probably, close to the bacteria of the genus Sulfobacillus Other strains might represent novel species Thermoacidophilic archaea, according to nucleotide composition of the DNA, could be divided into two groups of organisms (Table 4) A brierleyi has a more lower G + C content of DNA The variability of strains of chemolithotrophic bacteria A great diversity of strains with different physiological and biochemical capacities is known to occur among chemolithotrophic bacteria [-24-29] Chemolithotrophic bacteria in nature and experiment have to adapt to different factors: ions of metals, pH, substrate concentration and even, over a certain range, to temperature Biochemical variability is connected with changes in molecular biology of the cell and activity of enzymes caused by environmental changes The induction of the synthesis of three proteins, rusticyanin, 32 000 Da protein and 92000 Da glycoprotein was shown for T ferrooxidans transferred from a sulfur to ferrous iron medium [30] The induction of the synthesis of two proteins with molecular weight 47 000 Da and 55 000 Da was shown for T.ferrooxidans transferred from a medium with Fe 2+ to one with S O or $ 2 [,31] According to Mjoli and Kulpa [30], at least the glycoprotein with molecular weight 92 000 Da could be an integral component of the membrane iron-oxidizing system of T.ferrooxidans Osorio et al [32] found several types of acidosl~able proteins in both types of cells Proteins (60000, 30000, 25000, 17000 and 12000 main bands) found in ferrous iron-grown cells are similar to acid-stable heme proteins described previously for ferrous-iron grown cells [33] The same proteins were found in cells grown on the medium with S ° In this case, however, 60 000, 30 000, 25 000, rusticyanin (R) and 12 000 protein bands were highly reduced in size compared to those of cells grown with ferrous iron Two acid-stable proteins of molecular weight 20 000 and approximately 10000 Da were present only in sulfur-grown cells Amaro et al [34] reported changes in the general G.L Karavaiko, L.B Lobyreva/Fuel Processing Technology 40 (1994) 167-182 171 Table Bacteria species of the genera Thiobacillus and Leptospirillurn Bacteria Source of energy The DNA G + C content (mol%) Thiobacillusferrooxidians [3, 4] Fe z+, S °, Hz and sulfide minerals and ores So S °, sulfide ores Fe 2+, S °, sulfide ores PbS, H2S, H2 S °, organic compounds Fe 2+, FeS2 Fe z +, FeS2 55.0-57.4 Thiobacillus thiooxidans [5] Thiobacillus cuprinus [6] Thiohacillus prosperus [7] Thiobacillus plumbophilus [8] Thiobacillus acidophilus [9] Leptospirillumferrooxidans [10] Leptospirillum-like bacteria [11, 12] BU-I ALV BC CH LAM Leptospirillum thermoferrooxidans [13] Fe z+ 50.0-53.0 66.0 69.0 63.0 64.0 66.0 62.9-63.2 50.3 51.7 55.6 50.6 55.2 55.1 nd 65.2 Table Bacteria of genus Sulfobacillus and not classified Bacteria Source of energy The DNA G + C content (mol%l Sulfohacillus thermosulfidooxidans [14] Fe 2+, S °, sulfide minerals and organic compounds Fe 2+, S °, sulfide minerals and organic compounds 47.2 S thermosulfidooxidans subsp asporogenes [ 15] S thermotolerans [16] Other bacteria [17 20] BC ALV NAL 2b N TH3 45.5 49.3 Fe 2+, S °, sulfide minerals and organic compounds 48 56 nd nd nd 68.5 Table Thermoacidophilic archaea Bacteria Source of energy The DNA G + C content (mol%) Acidianus brierleyi [21] Metallosphaera sedula [22] Sulfurococcus yellowstonii [23] Fe +, S °, sulfide minerals and some organic compounds 30-33 43.7-46.2 44.6 172 G.I Karavaiko, L.B Lohyreva/Fuel Processing Technology 40 (1994) 167 182 protein synthesis pattern which involved significant stimulation of the synthesis of the 3.6 kDa protein when cells of T.ferrooxidans grown at pH 1.5 were transferred into the medium with pH 3.5 Vestal et al [35] observed qualitative and quantiative differences in lipopolysaccharides of cells of T ferrooxidans grown on various substrates The synthesis of rusticyanin, one of the major cell proteins of T ferrooxidans, is induced by Fe 2+ and suppressed in a medium with reduced sulfur compounds [36, 37] On a medium with Fe E+, the content of this protein in cells of T.ferrooxidans amounts to 5% of the total cell protein, whereas in sulfur medium it is present at only 20% of this amount [38] Variations in cell protein synthesis were also observed with a change of autotrophic growth to a heterotrophic growth For example, only chemolithotrophically grown cells of T cuprinus contained proteins with molecular weight about 43 kDa Also, the 18 amino acid sequence of the N-terminal and of a protein was obtained which is expressed only under heterotrophic growth conditions [39] The main part of fixed carbon of 14CO2 (about 50 80%) is incorporated into bacterial cells, while the rest (20-50%) is released into the medium as organic substrates [40-42] The composition of exometabolites produced by thiobacilli depends on the substrate oxidized as well as on other factors These results suggest that a reorganization of the entire program of biosynthesis in cells of chemolithotrophic bacteria may occur under changed growth conditions The variability mechanism so far has not been sufficiently investigated Genetically stable mutants are apparently produced both in nature and under laboratory conditions Thus, the occurrence frequency of T ferrooxidans mutants tolerant to 1.0 and 1.5 m M UO2 was approximately one per 1.3 × 10 and 9.0 × l0 s cells, respectively, but could be increased by the addition of 15-150 m M of Zn, Ni and Mn [43] It is not clear, however, what intercellular changes took place in these cases A number of works published in 1981 1992 reported the presence of one or more plasmids with a size from to 30 kb in the majority of cells of T.ferrooxidans strains isolated from different habitats However, the investigation of plasmids in T ferrooxidans failed to link them to organisms resistant to metal ions Most of the plasmids appeared to be cryptic Later, the study of the chromosomal part of the genome of T ferrooxidans was started Specifically, Shiratori et al [44] showed that the gene of mercury tolerance was localized in the chromosomal DNA Also, the CO2 fixation and synthesis of rusticyanin and Fe z +-oxidase were shown to be governed at the gene level [38, 45-47] The polymorphism of chromosomal DNA in different strains of T ferrooxidans was studied by Karavaiko et al [48] Individual patterns of chromosomal DNA restriction in these strains supported the assumption of high geneic variability of T.ferrooxidans in response to environmental factors It was found that, in a number of cases, the adaptation process was accompanied by the appearance of amplificated fragments in samples with chromosomal DNA restriction or by a change in their size A study of restrictive samples of the chromosomal DNA showed that, in strains actively oxidizing Fe + in the presence of Zn (70 g/l), the gene of zinc tolerance was probably located in the 98 kb fragment of the chromosomal DNA and is inducible G.1 Karavaiko, L.B Lobyreva /Fuel Processing Technology 40 (1994) 167-182 173 Strains of T ferrooxidans adapted to A s 3+ contained amplificated fragments of chromosomal DNA 28 kb in size This suggests that metal tolerance genes are, in fact, localized at different sites of DNA An increased tolerance of T ferrooxidans to Zn and As arises from amplification of tolerance genes and, therefore, has to with their increased activity Genetic characteristics of other chemolithotrophic bacteria are little known The question of possibility of practical application of chemolithotrophic bacteria for coal desulfurization seems to be more complicated It is also closely connected with tchnological aspects of coal utilization Inorganic forms of sulfur, present in finely graded coal could be probably oxidized by means of such bacteria as T.ferrooxidans Their successful utilization of nonferrous metals leaching and of processing of difficult-to-dress gold and silver containing concentrates in dense pulps could be used as an example Others thiobacilli (see Table 2) are either absent in the pulp, or present in the comparatively low concentration (102-103 cells/ml) That does not allow to consider them as significant for the intensive leaching processes in reactors Regarding coal desulfurization, special attention should be paid to leptospirilli and their communities with sulfur-oxidizing thiobacilli, which are able to oxidize pyrite and Fe + at lower pH values than T.ferrooxidans ([11, 49] our unpublished data) The adaptation of bacteria to concrete types of coal is essential for their application in technological processes, as the coals contain different types of pyrites Acidic pilot plant in Porto Torres (Italy) or coal treatment allows to obtain necessary data for the economical evaluation of this technology [50] The attempts to utilize moderately thermophilic bacteria and several archaea, such as S yellowstonii, [23] did not lead to the intensification of pyrite oxidation process These bacteria are more complicated for utilization; the processes require more energy and reactors should be made of highly resistant materials The diversity of heterotrophs and chemolithotrophs oxidizing complex organic substrates Microbial transformations of complex organic substrates are usually studied with dibenzothiophene as a model compound From Table it can be seen that representatives of different groups - from bacteria and archaea to eukaryotes are present among heterotrophic bacteria capable of oxidation, to a various degree, of dibenzothiophene The pathways of dibenzothiophene oxidation are also very diverse Some microorganisms (I) are able to oxidize only the peripheral aromatic ring of DBT, forming water-soluble products Other microorganisms, along with aromatic ring oxidation, can oxidize the sulfur heteroatom without its abstraction from the carbonaceous structure (II and III) Fungi, however, not interact with the aromatic ring of DBT Complete oxidation of dibenzothiophene to SO 2-, which involves splitting of the C-S bond, was shown only for a limited number of prokaryotes: Sulfolobus acidocaldarius, Brevibacterium sp and a mutant strain Pseudomonas sp CB1 (II) Oxidation of dibenzothiophene to its corresponding DBT-5-oxide, DBT-5-sulfone with and without oxidative degradation of aromatic ring Pseudomonas alkaligenes [51] Ps stutzeri [51] Ps putida [52] (I) Deoxigenation of peripheric aromatic ring resulted in the formation of water soluble compounds, the thiophene nucleus is still intact Ps putida [57, 58] Ps jianii [54, 55] Rhizobium sp., Acinetobaeter sp [56] Pseudomonas abikonensis [-54, 55] Ps aeruyinosa ERC-8 [53] Microorganisms Pathways of oxidation Table Metabolic pathways for the microbial degradation of dibenzothiophene OH CQQ H DBT3-5-sulfone O DBT-5-oxide 4-[2-(3hydroxy)thionaphtenyl]2-oxo-3buthenoic acid ~ C-H I! O 3-hydroxy-2-formyl-benzotiophene ~ Products of oxidation II O 3-hydroxy-2-formylbenzothiophene C-H II O 3-hydroxy-2-formylbenzothiophene t",, P~ (11I) Oxidationof the sulfuratom of dibenzothiopheneinto sulfate so~so~ - SO~- and ~ 2-hydroxybiphenyl SO42-, CO2, H20 Corynebacterium sp SY1 [64] Brevibacterium sp DO [65] DBT-5-sulfone II O DBT-5-oxide Pseudomonas sp CB1 (mutant) [62] Sulfolobus acidocaldarius [63] Cunninqhamella elegans [60] Rhizopus arrhizus Mortierella isabellina [61] Beyerinckia sp [59] 1,2-dihydroxy-l,2-hydrobenzothiophene t,o 4t~ Z~ 176 G.L Karavaiko, L.B Lobyreva/Fuel Processing Technologv 40 (1994) 167-182 Some microorganisms utilize DBT as the sole source of sulfur, carbon and energy for growth Other bacteria require additional substrates (cosubstrates) or growth factors It is well known that sulfur-organic compounds incorporated in coal are hardly available for bacteria Thus the achievements obtained in the experiments with DBT should not be extrapolated on coals These data demonstrate mainly the general ability of bateria to oxidize complex sulfur-organic compounds Isbister and Kobylinski have shown that a mutant strain of Pseudomonas species CB1 capable of active DBT oxidation decreased the organic sulfur content from 18% to 47% in different types of coals [66] The other strain, Pseudomonas sp CB2 capable of diphenyl sulfide oxidation removed only up to 30% of organic sulfur of coals tested [67] The culture of Pseudomonas sp CB1 was used for the desulfurization of different types of coals in continuous culture Depending on the coal type, the oxidation of organic sulfur was from 19% to 57% [66] Evidently, these results culd be improved by the utilization of highly active bacterial strains and the optimization of the process itself Control mechanisms of DBT and other organic sulfur compounds metabolism in microorganisms are not yet studied A plasmid with size 55 M G D was found in a number of bacteria of the genus Pseudomonas capable of DBT oxidation [51] The authors associate the ability to oxidize DBT with the presence of this plasmid A plasmid sized from 15.4 to 17.7 M G D was discovered in 14 isolates obtained from a mine and able to oxidize DBT to different degrees [52] More profound genetic studies are necessary not only for understanding the DBT oxidation mechanisms but also for obtaining highly active strains The mechanisms of oxidation of complex sulfur organic compounds are not clear either Since heterocyclic sulfur organic compounds are not water-soluble, two different pathways of primary reactions occuring on the cell surface are possible: (i) homogenization and subsequent transfer of aromatic compounds into cells; (ii) cleavage of the aromatic ring outside the cell and the transfer of soluble products into the cell The first mechanism of microbial cell interaction with an insoluble substrate could be illustrated by oxidation of benzpyrene representing, as well as DBT, a cyclic aromatic compound with crystallic structure In the second case, microorganisms have to possess the necessary exoenzymes The accumulation of benzpyrene predominantly in free lipids was observed in Mycobacteriumflavum and in Bacillus meyaterium (Fig 2(a) and (b)) In bacteria, benzpyrene is accumulated mainly in cytoplasm, [68, 69] while in yeasts it is accumulated in mitochondria [70] It was suggested by the authors that the solution and transport of this compound into cells was conneted with cell lipids and lipoprotein structures and that the oxidation of benzpyrene occurred on membrane structures This hypothesis might also be applied to oxidation of dibenzothiophene and of other complex aromatic compounds by certain microorganisms The cleavage of the aromatic ring in the bacterial cell occurs via its hydroxylation by means of monooxygenases (hydroxylases) with the involvement of oxygen Oxygenases are known to be inducible enzymes and are either cytochrom-P-450- or flavin-dependent [71] G.I Karavaiko, L.B Lobyreva/Fuel Processing Technology 40 (1994) 167-182 177 Fig Localization of benzpyrene in bacterial cells [64] (a) Bacillus megaterium (asporogenous mutant, × 2000); (b) Mycobacteriumflavum ( x 2000) 178 G.L Karavaiko, L.B Lobyreva/Fuel Processing Technolo~' 40 (1994) 167 182 Unlike with bacteria, the transformation of dibenzothiophene by fungi proceeds without aromatic ring rearrangement through sulfur atom oxidation It could be catalyzed by sulfoxidases similar to those of mammalian and microbial origin [71] In the case of fungi, the oxidation of dibenzothiophene probably also occurs within the cell Yet, many fungi are known to be capable of oxidizing unsoluble aromatic compounds by means of phenoloxidases (laccases) which are exocellular inducible enzymes [72, 73] Conclusions Chemolithotrophs capable of Fe 2+, So and sulfide minerals oxidation are found in different phylogenetically remote groups of bacteria Their limited number, till date, has no explanation Possibly, new species and genera of such organisms will be described in the future The physiology, biochemistry and molecular biology of chemolithotrophic bacteria are characterized by unusually large variability which is controlled at the gene level As a result, the program of biosynthetic processes in the cell can be reorganized to adapt to changing conditions of the environment Many heterotrophic microorganisms are capable of oxidizing complex organic sulfur-containing compounds with the formation of soluble products However, only a few of them are capable of splitting the C-S bond Both these processes might be of practical value given that soluble organic sulfur-containing compounds could be washed out of coal At least several thiobacilli and leptospirilli could be utilized for the pyrite elimination from the coal Scale-up testing performed by Professor G Rossi in Porto Torres (Italy) would allow to clear up the perspectives of this process and its economical value The perspectives of practical 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