Papers by Pieter De Maayer
Frontiers in Microbiology, Dec 9, 2021
The thermophilic bacterium Parageobacillus thermoglucosidasius has recently gained interest due t... more The thermophilic bacterium Parageobacillus thermoglucosidasius has recently gained interest due to its ability to catalyze the water gas shift reaction, where the oxidation of carbon monoxide (CO) is linked to the evolution of hydrogen (H 2) gas. This phenotype is largely predictable based on the presence of a genomic region coding for a carbon monoxide dehydrogenase (CODH-Coo) and hydrogen evolving hydrogenase (Phc). In this work, seven previously uncharacterized strains were cultivated under 50% CO and 50% air atmosphere. Despite the presence of the coo-phc genes in all seven strains, only one strain, Kp1013, oxidizes CO and yields H 2. The genomes of the H 2 producing strains contain unique genomic regions that code for proteins involved in nickel transport and the detoxification of catechol, a by-product of a siderophore-mediated iron acquisition system. Combined, the presence of these genomic regions could potentially drive biological water gas shift (WGS) reaction in P. thermoglucosidasius.
Springer eBooks, 2017
The Earth’s permanently cold biosphere is known to harbour abundant microbial biomass and represe... more The Earth’s permanently cold biosphere is known to harbour abundant microbial biomass and represents a rich resource for the discovery of novel cold-adapted microorganisms, many of which form part ...
IMA Fungus
Draft genome assembly of Fusarium marasasianum Sequenced strain
Systematic and Applied Microbiology, 2018
Acetylation is one of the main obstacles to the effective enzymatic conversion of hemicelluloses ... more Acetylation is one of the main obstacles to the effective enzymatic conversion of hemicelluloses to fermentable sugars. In nature, the microbial degradation of hemicellulose involves the action of deacetylating esterases that act synergistically with glycoside hydrolases. In the industrial processing of lignocelluloses biomass, alkaline pretreatments remove acetyl groups by saponification, but other non-alkaline pretreatment methods generate acetylated hemicelluloses. Complete saccharification of plant hemicelluloses can’t be achieved without the deacetylating enzymes. Recent years have witnessed considerale progress in our understanding of the mode of acetylation of hemicellulose and mode of action of microbial polysaccharide deacetylases. In this article we focus on the diversity and role of acetylxylan esterases in the breakdown of acetylxylan, the most abundant hemicellulose in nature.
Un ni iv ve er rs si it ty y o of f P Pr re et to or ri ia a DECLARATION I, the undersigned, here... more Un ni iv ve er rs si it ty y o of f P Pr re et to or ri ia a DECLARATION I, the undersigned, hereby declare that the thesis submitted herewith for the degree Philosophiae Doctor to the University of Pretoria, contains my own independent work and has hitherto not been submitted by me for a degree at this or any other tertiary institution.
Microorganisms
Parageobacillus thermoglucosidasius is known to catalyse the biological water gas shift (WGS) rea... more Parageobacillus thermoglucosidasius is known to catalyse the biological water gas shift (WGS) reaction, a pathway that serves as a source of alternative energy and carbon to a wide variety of bacteria. Despite increasing interest in this bacterium due to its ability to produce biological hydrogen through carbon monoxide (CO) oxidation, there are no data on the effect of toxic CO gas on its physiology. Due to its general requirement of O2, the organism is often grown aerobically to generate biomass. Here, we show that carbon monoxide (CO) induces metabolic changes linked to distortion of redox balance, evidenced by increased accumulation of organic acids such as acetate and lactate. This suggests that P. thermoglucosidasius survives by expressing several alternative pathways, including conversion of pyruvate to lactate, which balances reducing equivalents (oxidation of NADH to NAD+), and acetyl-CoA to acetate, which directly generates energy, while CO is binding terminal oxidases. Th...
Background Flagellar motility is an efficient means of movement that allows bacteria to successfu... more Background Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of these structures is highly energy intensive and as such flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility. Results Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4,028 (~ 20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorp...
International Journal of Molecular Sciences
Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic thermop... more Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic thermophile belonging to the family Bacillaceae. Previous studies have shown that this bacterium harbours co-localised genes coding for a carbon monoxide (CO) dehydrogenase (CODH) and Ni-Fe hydrogenase (Phc) complex and oxidises CO and produces hydrogen (H2) gas via the water-gas shift (WGS) reaction. To elucidate the genetic events culminating in the WGS reaction, P. thermoglucosidasius DSM 6285 was cultivated under an initial gas atmosphere of 50% CO and 50% air and total RNA was extracted at ~8 (aerobic phase), 20 (anaerobic phase), 27 and 44 (early and late hydrogenogenic phases) hours post inoculation. The rRNA-depleted fraction was sequenced using Illumina NextSeq, v2.5, 1x75bp chemistry. Differential expression revealed that at 8 vs.. 20, 20 vs.. 27 and 27 vs.. 44 h post inoculation, 2190, 2118 and 231 transcripts were differentially (FDR < 0.05) expressed. Cluster analysis revealed 2...
BMC Genomics
Background The order Enterobacterales encompasses a broad range of metabolically and ecologically... more Background The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized. Results Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~ 3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number ca...
Scientific Reports
Trichosporonaceae incorporates six genera of physiologically and ecologically diverse fungi inclu... more Trichosporonaceae incorporates six genera of physiologically and ecologically diverse fungi including both human pathogenic taxa as well as yeasts of biotechnological interest, especially those oleagenic taxa that accumulate large amounts of single cell oils (SCOs). Here, we have undertaken comparative genomic analysis of thirty-three members of the family with a view to gain insight into the molecular determinants underlying their lifestyles and niche specializations. Phylogenomic analysis revealed potential misidentification of three strains which could impact subsequent analyses. Evaluation of the predicted proteins coding sequences showed that the free-living members of the family harbour greater numbers of carbohydrate active enzymes (CAZYmes), metallo- and serine peptidases compared to their host-associated counterparts. Phylogenies of selected lipid biosynthetic enzymes encoded in the genomes of the studied strains revealed disparate evolutionary histories for some proteins i...
Frontiers in Bioengineering and Biotechnology
The microbial production of bulk chemicals from waste gas is becoming a pertinent alternative to ... more The microbial production of bulk chemicals from waste gas is becoming a pertinent alternative to industrial strategies that rely on fossil fuels as substrate. Acetogens can use waste gas substrates or syngas (CO, CO 2 , H 2) to produce chemicals, such as acetate or ethanol, but as the feed gas often contains oxygen, which inhibits acetogen growth and product formation, a cost-prohibitive chemical oxygen removal step is necessary. Here, we have developed a two-phase microbial system to facilitate acetate production using a gas mixture containing CO and O 2. In the first phase the facultative anaerobic carboxydotroph Parageobacillus thermoglucosidasius was used to consume residual O 2 and produce H 2 and CO 2 , which was subsequently utilized by the acetogen Clostridium ljungdahlii for the production of acetate. From a starting amount of 3.3 mmol of CO, 0.52 mmol acetate was produced in the second phase by C. ljungdahlii. In this setup , the yield achieved was 0.16 mol acetate/mol CO, a 63% of the theoretical maximum. This system has the potential to be developed for the production of a broad range of bulk chemicals from oxygen-containing waste gas by using P. thermoglucosidasius as an oxygen scrubbing tool.
AMB Express
Hydrogen gas represents a promising alternative energy source to dwindling fossil fuel reserves, ... more Hydrogen gas represents a promising alternative energy source to dwindling fossil fuel reserves, as it carries the highest energy per unit mass and its combustion results in the release of water vapour as only byproduct. The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius is able to produce hydrogen via the water–gas shift reaction catalyzed by a carbon monoxide dehydrogenase–hydrogenase enzyme complex. Here we have evaluated the effects of several operating parameters on hydrogen production, including different growth temperatures, pre-culture ages and inoculum sizes, as well as different pHs and concentrations of nickel and iron in the fermentation medium. All of the tested parameters were observed to have a substantive effect on both hydrogen yield and (specific) production rates. A final experiment incorporating the best scenario for each tested parameter showed a marked increase in the H2 production rate compared to each individual parameter. The optimis...
Advanced Techniques for Studying Microorganisms in Extreme Environments
Microbial Cell Factories
Background: Geobacillus and Parageobacillus are two ecologically diverse thermophilic genera with... more Background: Geobacillus and Parageobacillus are two ecologically diverse thermophilic genera within the phylum Firmicutes. These taxa have long been of biotechnological interest due to their ability to secrete thermostable enzymes and other biomolecules that have direct applications in various industrial and clinical fields. Despite the commercial and industrial interest in these microorganisms, the full scope of the secreted protein, i.e. the secretome, of Geobacillus and Parageobacillus species remains largely unexplored, with most studies focusing on single enzymes. A genome-wide exploration of the global secretome can provide a platform for understanding the extracellular functional "protein cloud" and the roles that secreted proteins play in the survival and adaptation of these biotechnologically relevant organisms. Results: In the present study, the global secretion profile of 64 Geobacillus and Parageobacillus strains, comprising 772 distinct proteins, was predicted using comparative genomic approaches. Thirty-one of these proteins are shared across all strains used in this study and function in cell-wall/membrane biogenesis as well as transport and metabolism of carbohydrates, amino acids and inorganic ions. An analysis of the clustering patterns of the secretomes of the 64 strains according to shared functional orthology revealed a correlation between the secreted profiles of different strains and their phylogeny, with Geobacillus and Parageobacillus species forming two distinct functional clades. Conclusions: The in silico characterization of the global secretome revealed a metabolically diverse set of secreted proteins, which include proteases, glycoside hydrolases, nutrient binding proteins and toxins.
Microbial Cell Factories
Background: The overreliance on dwindling fossil fuel reserves and the negative climatic effects ... more Background: The overreliance on dwindling fossil fuel reserves and the negative climatic effects of using such fuels are driving the development of new clean energy sources. One such alternative source is hydrogen (H 2), which can be generated from renewable sources. Parageobacillus thermoglucosidasius is a facultative anaerobic thermophilic bacterium which is frequently isolated from high temperature environments including hot springs and compost. Results: Comparative genomics performed in the present study showed that P. thermoglucosidasius encodes two evolutionary distinct H 2-uptake [Ni-Fe]-hydrogenases and one H 2-evolving hydrogenases. In addition, genes encoding an anaerobic CO dehydrogenase (CODH) are co-localized with genes encoding a putative H 2-evolving hydrogenase. The co-localized of CODH and uptake hydrogenase form an enzyme complex that might potentially be involved in catalyzing the water-gas shift reaction (CO + H 2 O → CO 2 + H 2) in P. thermoglucosidasius. Cultivation of P. thermoglucosidasius DSM 2542 T with an initial gas atmosphere of 50% CO and 50% air showed it to be capable of growth at elevated CO concentrations (50%). Furthermore, GC analyses showed that it was capable of producing hydrogen at an equimolar conversion with a final yield of 1.08 H 2 /CO. Conclusions: This study highlights the potential of the facultative anaerobic P. thermoglucosidasius DSM 2542 T for developing new strategies for the biohydrogen production.
Journal of genomics, 2018
The thermophilic 'Geobacilli' are important sources of thermostable enzymes and other bio... more The thermophilic 'Geobacilli' are important sources of thermostable enzymes and other biotechnologically relevant macromolecules. The present work reports the high quality draft genome sequences of previously unsequenced type strains of (DSM 23175), (DSM 730) and (DSM 18751). Phylogenomic analyses revealed that DSM 18751 and DSM 23175 represent later heterotypic synonyms of and , respectively, while DSM 730 represents the type strain for the species . These genome sequences will contribute towards a deeper understanding of the ecological and biological diversity and the biotechnological exploitation of the 'geobacilli'.
BMC Genomics
Background: The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces ... more Background: The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H 2) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Although little is known about the hydrogenogenic capacities of different strains of this species, these organisms offer a potentially viable process for the synthesis of this alternative energy source. Results: The WGS-catalyzed H 2 production capacities of four distinct P. thermoglucosidasius strains were determined by cultivation and gas analysis. Three strains (DSM 2542 T , DSM 2543 and DSM 6285) were hydrogenogenic, while the fourth strain (DSM 21625) was not. Furthermore, in one strain (DSM 6285) H 2 production commenced earlier in the cultivation than the other hydrogenogenic strains. Comparative genomic analysis of the four strains identified extensive differences in the protein complement encoded on the genomes, some of which are postulated to contribute to the different hydrogenogenic capacities of the strains. Furthermore, polymorphisms and deletions in the CODH-NiFe hydrogenase loci may also contribute towards this variable phenotype. Conclusions: Disparities in the hydrogenogenic capacities of different P. thermoglucosidasius strains were identified, which may be correlated to variability in their global proteomes and genetic differences in their CODH-NiFe hydrogenase loci. The data from this study may contribute towards an improved understanding of WGS-catalysed hydrogenogenesis by P. thermoglucosidasius.
Microbiology Resource Announcements
Enterobacter xiangfangensis Pb204, isolated from acid mine decant from a uranium mine, produces a... more Enterobacter xiangfangensis Pb204, isolated from acid mine decant from a uranium mine, produces a wide variety of gold nanoparticles (AuNPs), ranging from large triangular plates to small spherical AuNPs. The complete genome sequence of this isolate incorporates an integrative and conjugative element which may be pivotal to AuNP synthesis.
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Papers by Pieter De Maayer