The Genus Gluconobacter Oxydans: Comprehensive Overview of Biochemistry and Biotechnological Applications

ABSTRACT

The genus Gluconobacter comprises some of the most frequently used microorganisms when it comes to biotechnological applications. Not only has it been involved in “historical” production processes, such as vinegar production, but in the last decades many bioconversion routes for special and rare sugars involving Gluconobacter have been developed. Among the most recent are the biotransformations involved in the production of L-ribose and miglitol, both very promising pharmaceutical lead molecules. Most of these processes make use of Gluconobacter's membrane-bound polyol dehydrogenases. However, recently other enzymes have also caught the eye of industrial biotechnology. Among them are dextran dextrinase, capable of transglucosylating substrate molecules, and intracellular NAD-dependent polyol dehydrogenases, of interest for co-enzyme regeneration. As such, Gluconobacter is an important industrial microbial strain, but it also finds use in other fields of biotechnology, such as biosensor-technology. This review aims to give an overview of the myriad of applications for Gluconobacter, with a special focus on some recent developments.     

Mineral and Bacterial Diversities of Desert Sand Grains from South-East Morocco

Mineralogy and microbiology of sand from Merzouga (Morocco) were simultaneously characterized, with the purpose of contributing to a better understanding of the geomicrobiology of deserts. In spite of very low measured bacterial biomass, bacterial diversity on each of the five defined mineralogical classes, was found high. An original grain by grain cultivation method enabled to obtain bacterial isolates with an unusually high recovery rate. The results of this study show that the genus Arthrobacter is well adapted to this environment with a preference for grains other than the dominant mineral quartz, and that the genera Chelatococcus and Saccharotrix are strongly attached to the grains.     

Biosignatures and Bacterial Diversity in Hydrothermal Deposits of Solfatara Crater,Italy

We have combined mineralogy, organic geochemistry and molecular microbiology to study hydrothermal deposits from Solfatara Crater, a geologically young volcanic formation (～4,000 years old) displaying hot (45–95°C) and acidic (pH 1.7) mud pools and fumaroles. The search for inorganic (mineral) biosignatures revealed the presence of delicate structures, most likely mineralized extracellular polymers (EPSs), and the presence of potential biologically induced minerals: sulfides, sulfates (barite and alunite), elemental sulfur, and iron oxides. Geochemical analyses revealed a low total organic carbon content, 0.13 to 0.53%, displaying δ¹³C values from ?17.09 to ?27.39‰, and total nitrogen contents from 0.03 to 0.12%, which are characteristic of hydrothermal systems and suggest the presence of autotrophic carbon fixation. Lipid biomarker analysis showed the presence of hopanoids and linear alkanes, and the absence of detectable steroids, implying the occurrence of bacteria in our samples. We constructed 16S rRNA gene libraries from the environmental samples. Most environmental sequences obtained were affiliated to the Alpha- and Betaproteobacteria (Hydrogenophilus-like), the Acidobacteria, and to a lesser extent, the Gammaproteobacteria and Actinobacteria. When known, the closest cultivated relatives were often thermophilic or thermotolerant bacteria oxidizing iron, hydrogen, or methane/methanol, suggesting an important microbial contribution to the formation of biominerals.     

Formation of Hydroxysulphate Green Rust 2 as a Single Iron(II-III) Mineral in Microbial Culture

Although GR2(SO₄ ^2-) can be easily formed by abiotic synthesis, the biotic formation of hydroxysulphate as a single iron(II-III) mineral in microbial culture and its characterization was not achieved. This study was carried out to investigate the sole formation of GR2(SO₄ ^2-) during the reduction of γ-FeOOH by a dissimilatory iron-respiring bacterium, Shewanella putrefaciens CIP 8040^T. Reduction experiments were performed in a non-buffered medium devoid of organic compounds, with 25 mM of sulphate and with a range of lepidocrocite concentrations with H₂ as the electron donor under nongrowth conditions. The resulting biogenic solids, after iron-respiring activity, were characterized by X-ray diffraction (XRD), transmission Mössbauer spectroscopy (TMS) and electron microscopy (SEM and TEM). The sulphate has been identified as the intercalated anion by diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). In addition, the structure of this sulphate anion was discussed. Our experimental study demonstrated that, under H₂ atmosphere, the biogenic solid was a GR2(SO₄ ^2-), as the sole iron(II-III) bearing mineral, whatever the initial lepidocrocite concentration. The crystals of the biotically formed GR2(SO₄ ^2-) are significantly larger than those observed for GR2(SO₄ ^2-) obtained through abiotic preparation, < 15 μ m diameter as against 0.5–4 μm, respectively.     

FTIR Spectroscopic Study of Biogenic Mn-Oxide Formation by Pseudomonas putida GB-1

Biomineralization in heterogeneous aqueous systems results from a complex association between pre-existing surfaces, bacterial cells, extracellular biomacromolecules, and neoformed precipitates. Fourier transform infrared (FTIR) spectroscopy was used in several complementary sample introduction modes (attenuated total reflectance [ATR], diffuse reflectance [DRIFT], and transmission) to investigate the processes of cell adhesion, biofilm growth, and biological Mn-oxidation by Pseudomonas putida strain GB-1. Distinct differences in the adhesive properties of GB-1 were observed upon Mn oxidation. No adhesion to the ZnSe crystal surface was observed for planktonic GB-1 cells coated with biogenic MnO _x , whereas cell adhesion was extensive and a GB-1 biofilm was readily grown on ZnSe, CdTe, and Ge crystals prior to Mn-oxidation. IR peak intensity ratios reveal changes in biomolecular (carbohydrate, phosphate, and protein) composition during biologically catalyzed Mn-oxidation. In situ monitoring via ATR-FTIR of an active GB-1 biofilm and DRIFT data revealed an increase in extracellular protein (amide I and II) during Mn(II) oxidation, whereas transmission mode measurements suggest an overall increase in carbohydrate and phosphate moieties. The FTIR spectrum of biogenic Mn oxide comprises Mn-O stretching vibrations characteristic of various known Mn oxides (e.g., “acid” birnessite, romanechite, todorokite), but it is not identical to known synthetic solids, possibly because of solid-phase incorporation of biomolecular constituents. The results suggest that, when biogenic MnO _x accumulates on the surfaces of planktonic cells, adhesion of the bacteria to other negatively charged surfaces is hindered via blocking of surficial proteins.     

34S/32S and 18O/16O Fractionation During Sulfur Disproportionation by Desulfobulbus propionicus

In the present study, coupled stable sulfur and oxygen isotope fractionation during elemental sulfur disproportionation according to the overall reaction: 4H₂O + 4S^? → 3H₂S + SO₄ ^{2 ?} + 2H⁺, was experimentally investigated for the first time using a pure culture of the sulfate reducer Desulfobulbus propionicus at 35^?C. Bacterial disproportionation of elemental sulfur is an important process in the sulfur cycle of natural surface sediments and leads to the simultaneous formation of sulfide and sulfate. A dual-isotope approach considering both sulfur and oxygen isotope discrimination has been shown to be most effective in evaluating specific microbial reactions. The influence of iron- and manganese bearing-solids (Fe(II)CO₃, Fe(III)OOH, Mn(IV)O₂) acting in natural sediments as scavengers for hydrogen sulfide, was considered, too. Disproportionation of elemental sulfur was observed in the presence of iron solids at a cell-specific sulfur disproportionation rate of about 10^{? 9.5± 0.4} μ mol S^? cell^{? 1} h^{? 1}. No disproportionation, however, was observed with MnO₂. In the presence of iron solids, newly formed sulfate was enriched in ¹⁸ O compared to water by about +21‰ (≡ ? _H2O ), in agreement with a suggested oxygen isotope exchange via traces of intra- or extracellular sulfite that is formed as a disproportionation intermediate. Dissolved sulfate was also enriched in ³⁴S compared to elemental sulfur by up to +35%. Isotope fractionation by Desulfobulbus propionicusis highest for all disproportionating bacteria investigated, so far, and may impact on the development of isotope signals at the redox boundary of surface sediments.     

Lower Abundance of Ammonia-Oxidizing Archaea Than Ammonia-Oxidizing Bacteria Detected in the Subsurface Sediments of the Northern South China Sea

Diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in samples of the northern South China Sea subsurface sediment were assessed by analyzing the amoA gene sequences retrieved from the samples. The microbial diversity was assessed using rarefaction and phylogenetic analyses. The deep-sea subsurface sediments harbored diverse and distinct AOA and AOB communities, but the abundance of AOA was lower than that of AOB, consistent with many other studies about bacteria and archaea in subsurface sediments. Diversity of AOA shown in the OTUs and Shannon index was correlated with the concentration of nitrite in the Pearson analysis, but no obvious relationships between the diversity or abundance of AOB and the physicochemical parameters could be identified in the present study, indicating the concentration of ammonium may not be an important factor to determine the diversity and abundance of ammonia-oxidizing prokaryotes in the subsurface sediments. Additionally, Nitrosomonas-like AOB was found to be dominant in subsurface sediments of the northern South China Sea showing a different adaption strategy comparing with some Nitrosospira-like AOB lineages. Concentration of nitrite was correlated with diversity of AOA, but no correlations between diversity and abundance of AOB and the physicochemical parameters were established in the study. Supplementary materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files.     

Microbial Diversity and Community Structure on Corroding Concretes

The objective of this study was to analyze bacterial diversity in two different concrete samples to understand the dominant types of bacteria that may contribute to concrete corrosion. Two concrete samples, HN-1 from the sunny side and HN-2 from dark and damp side, were collected from Zijin Mountain in Nanjing and genomic DNA was extracted. The partial bacterial 16S rRNA gene fragment was PCR amplified and two clone libraries were constructed. Amplified ribosomal DNA restriction analysis (ARDRA) was performed by digestion of the 16S rRNA gene and each unique restriction fragment polymorphism pattern was designated as an operational taxonomic unit (OTU). Phylogenetic trees of bacterial 16S rDNA nucleotide sequences were constructed. Sample HN-1 and HN-2 contained 21 OTUs and 26 OTUs, respectively. Proteobacteria and Planctomycetes were the predominant bacteria in both samples, and they are distributed among Herbaspirillum, Archangium, Phyllobacteriaceae and Planctomycetaceae. Cyanobacteria and Rubrobacter sp. are dominant in HN-1; while Acidobacteriaceae, Adhaeribacter sp. and Nitrospira sp. are predominant in HN-2. This distribution pattern was consistent with local environmental conditions of these two samples. The inferred physiological characteristics of these bacteria, based on relatedness of the DNA clone sequences to cultivated species, revealed different mechanisms of concrete corrosion depending on the local environmental conditions.     

Competitive Formation of Hydroxycarbonate Green Rust 1 versus Hydroxysulphate Green Rust 2 in Shewanella putrefaciens Cultures

The formation of hydroxysulphate green rust 2, a Fe(II-III) compound commonly found during corrosion processes of iron-based materials in seawater, has not yet been reported in bacterial cultures. Here we used Shewanella putrefaciens, a dissimilatory iron-reducing bacterium to anaerobically catalyze the transformation of a ferric oxyhydroxide, lepidocrocite (γ-FeOOH), into Fe(II) in the presence of various sulphate concentrations. Biotransformation assays of γ-FeOOH were performed with formate as the electron donor under a variety of concentrations. The results showed that the competitive formation of hydroxycarbonate green rust 1 (GR1(CO₃ ^2?)) and hydroxysulphate green rust 2 (GR2(SO₄ ^{2 ?})) depended upon the relative ratio (R) of bicarbonate and sulphate concentrations. When R ≥ 0.17, GR1(CO₃ ^{2 ?}) only was formed whereas when R < 0.17, a mixture of GR2(SO₄ ^{2 ?}) and GR1(CO₃ ^{2 ?}) was obtained. These results demonstrated that the hydroxysulphate GR2 can originate from the microbial reduction of γ-FeOOH and confirmed the preference for carbonate over sulphate during green rust precipitation. The solid phases were characterized by X-ray diffraction, transmission Mössbauer spectroscopy and scanning electron microscopy. Diffuse reflectance infrared Fourier transform spectroscopy confirmed the presence of intercalated carbonate and sulphate in green rust's structure. This study sheds light on the influence of dissimilatory iron-reducing bacteria on microbiologically influenced corrosion.     

Seasonal Dynamics of Dimethylarsenic Acid Degrading Bacteria Dominated in Lake Kibagata

Degradation processes of organoarsenic compounds significantly influence arsenic cycles in aquatic environments and would depend on the bacterial activities. The bacterial population involving dimethylarsinic acid (DMAA) degradation was investigated in Lake Kibagata from April to December in 2003. During the experimental period, the methylated arsenic was not detected, although the inorganic arsenic concentration ranged from 3.4 nM to 9.2 nM. Moreover, in the sample water of Lake Kibagata to which DMAA added, DMAA decreased while inorganic arsenic increased for 25 days. These facts suggested that the bacteria remineralized methylate arsenic species to inorganic arsenic. In fact, monitoring the use of Most Probable Number (MPN) procedure demonstrated that the DMAA-degrading bacteria exist at cell densities ranged from 41 cells/ml to 510 cells/ml. To determine the composition of DMAA-degrading bacteria, the total 110 isolates obtained as dominated bacterial species were analyzed by the restriction-fragment-length polymorphism (RFLP) analysis of 16S rDNA. As a result, total 110 isolates were classified into 12 types, of which 4 types dominated during the spring and/or fall seasons, and the rest 8 types dominated during summer season. DMAA degrading activities of the 110 isolates ranged at various degrees. Especially, the some isolates of fall season tend to show high degradation activities. The phylogenetic analysis using 16S rDNA revealed that the representative isolates formed several clusters in the gram-positive bacterial group and the proteobacteria subdivision. The diverse compositions of DMAA-degrading bacteria would seasonally change to control the rates of organoarsenic degradation in Kibagata.