Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme

Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.

Improved Thermal Stability of a Novel Acidophilic Phytase

Phytase increases the availability of phosphate and trace elements by hydrolyzing the phospho-monoester bond in phytate present in animal feed. It is also an important enzyme from an environmental perspective because it not only promotes the growth of livestocks but also prevents phosphorus contamination released into the environment. Here we present a novel phytase derived from Turicimonas muris, TmPhy, which has distinctive structure and properties compared to other previously known phytases. TmPhy gene expressed in the Pichia system was confirmed to be 41 kDa in size and was used in purified form to evaluate optimal conditions for maximum activity. TmPhy has a dual optimum pH at pH3 and pH6.8 and exhibited the highest activity at 70℃. However, the heat tolerance of the wildtype was not satisfactory for feed application. Therefore, random mutation, disulfide bond introduction, and N-terminal mutation were performed to improve the thermostability of the TmPhy. Random mutation resulted in TmPhyM with about 45% improvement in stability at 60℃. Through further improvements, a total of three mutants were screened and their heat tolerance was evaluated. As a result, we obtained TmPhyMD1 with 46.5% residual activity, TmPhyMD2 with 74.1%, and TmPhyMD3 with 66.8% at 80℃ heat treatment without significant loss of or with increased activity.

Selection and re-acclimation of bioprospected acid-tolerant green microalgae suitable for growth at low pH

For mass culture of photosynthetic green microalgae, industrial flue gases can represent a low-cost resource of CO₂. However, flue gases are often avoided, because they often also contain high levels of SO₂ and/or NO₂, which cause significant acidification of media to below pH 3 due to production of sulfuric and nitric acid. This creates an unsuitable environment for the neutrophilic microalgae commonly used in large-scale commercial production. To address this issue, we have looked at selecting acid-tolerant microalgae via growth at pH 2.5 carried out with samples bioprospected from an active smelter site. Of the eight wild samples collected, one consisting mainly of Coccomyxa sp. grew at pH 2.5 and achieved a density of 640 mg L^-1. Furthermore, three previously bioprospected green microalgae from acidic waters (pH 3-4.5) near abandoned mine sites were also re-acclimated down to their in-situ pH environment after approximately 4 years spent at neutral pH. Of those three, an axenic culture of Coccomyxa sp. was the most successful at re-acclimating and achieved the highest density of 293.1 mg L^-1 and maximum daily productivity of 38.8 mg L^-1 day^-1 at pH 3. Re-acclimation of acid-tolerant species is, therefore, achievable when directly placed at their original pH, but gradual reduction in pH is recommended to give the cells time to acclimate.

A thermostable glucose oxidase from Aspergillus heteromophus CBS 117.55 with broad pH stability and digestive enzyme resistance

In this study, the heterologous expression of an engineered thermostablle glucose oxidase from Aspergillus heteromophus CBS 117.55 was achieved in P. pastoris. This recombinant GoxAh was thermostable, with an optimal temperature range 25 °C-65 °C, and it was capable of retaining greater than 90% of its initial activity following a 10-min incubation at 75 °C. This enzyme had an optimum pH of 6.0, and it could retain above 80% of its initial activity following a 2-h incubation at a broad pH range (2.0-8.0). Moreover, GoxAh displayed excellent pepsin and trypsin resistance, and highly resistant to a range of tested metal ions and chemical reagents. These good properties make GoxAh a promising candidate for feed additive. The K_m and k_cat/K_m values of GoxAh were 187 mM and 1.09/mM/s, which limited its widespread application to some degree. However, due to its excellent characteristics, GoxAh is still of potential economic value for high value-added areas, as well as a good initial enzyme for developing applicable feed enzyme by protein engineering.

Acidophil stem cell pituitary adenoma: a case report and literature review

In this article, we describe a very rare case of pituitary acidophilic stem cell adenoma, accompanied by a literature review. We present the case of 33-year-old woman with a history of amenorrhea, galactorrhea, elevated prolactin levels, and pituitary tumor. Despite suppression of prolactin levels with cabergoline, the pituitary tumor continued to increase in size and the patient developed clinical symptoms and biochemistry consistent with the diagnosis of acromegaly due to acidophilic stem cell adenoma, an extremely rare subtype of mixed growth hormone/prolactin adenoma, which behaves more aggressively and has a lower surgical cure rate compared to the pure GH-secreting adenoma. The patient had in vitro fertilization 2 years after the successful pituitary surgery and delivered healthy twins. To our knowledge, this is the only case report which describes acromegaly developing during cabergoline treatment. This case also highlights the importance of having a correct histopathological diagnosis to determine the behavior of the tumor and decide on further management.

A statistical approach of zinc remediation using acidophilic bacterium via an integrated approach of bioleaching enhanced electrokinetic remediation (BEER) technology

The aim of the present study was to isolate an indigenous acidophilic bacterium from tannery effluent contaminated sludge (TECS) sample and evaluate its potentiality towards the removal of zinc using an integrated approach of bioleaching enhanced electrokinetic remediation (BEER) technology in zinc spiked soil at an initial concentration of 1000 mg/kg. The isolated acidophilic bacterium was characterized by biochemical and 16S rRNA molecular identification and was named as Serratia marcescens SMAR1 bearing an accession no. MG742410 in NCBI database. The effect of pH and inoculum dosage of SMAR 1 strain showed an optimal growth at pH 5.0 and 4% (v/v) respectively. Based on these experimental data, a statistical analysis was done using Design Expert computer software, v11 to study the interaction between the process parameters with respect to zinc reduction as an output response. Electrokinetic experiments were conducted in a customised EK cell under optimised process conditions, employing titanium electrodes. Experiments for zinc removal were demonstrated for bioleaching, electrokinetic (EK) and BEER technology. On comparing, the integrated process was found to evidence as an excellent metal remediation option with a maximum zinc removal of 93.08% in 72 h than plain bioleaching (72.86%) and EK (56.67%) in 96 h. This is the first report of zinc removal in a short period of time using Serratia marcescens. It is therefore concluded that the BEER approach can be regarded as an effective technology in cleaning up the metal contaminated environment with an easy recovery and reuse option within short period of time.

Genome Mining and Predictive Functional Profiling of Acidophilic Rhizobacterium Pseudomonas fluorescens Pt14

Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic soil (pH 4.65). Genome sequencing of strain Pt14 was performed using Single Molecule Real Time (SMRT) sequencing to get insights into unique existence of this strain in acidic environment. Complete genome sequence of this strain revealed a chromosome of 5,841,722 bp having 5354 CDSs and 88 RNAs. Phylogenomic reconstruction based on 16S rRNA gene, Average Nucleotide Identity (ANI) values and marker proteins revealed that strain Pt14 shared a common clade with P. fluorescens strain A506 and strain SS101. ANI value of strain Pt14 in relation to strain A506 was found 99.23% demonstrating a very close sub-species association at genome level. Further, orthology determination among these three phylogenetic neighbors revealed 4726 core proteins. Functional analysis elucidated significantly higher abundance of sulphur metabolism (>1×) which could be one of the reasons for the survival of strain Pt14 under acidic conditions (pH 4.65). Acidophilic bacteria have capability to oxidize sulphur into sulphuric acid which in turn can make the soil acidic and genome-wide analysis of P. fluorescens Pt14 demonstrated that this strain contributes towards making the soil acidic.

Production and characterization of an acido-thermophilic, organic solvent stable cellulase from Bacillus sonorensis HSC7 by conversion of lignocellulosic wastes

The acidophilic and thermophilic cellulase would facilitate the conversion of lignocellulosic biomass to biofuel. In this study, Bacillus sonorensis HSC7 isolated as the best thermophilic cellulose degrading bacterium from Gorooh hot spring. 16S rRNA gene sequencing showed that, this strain closely related to the B. sonorensis. CMCase production was considered under varying environmental parameters. Results showed that, sucrose and (NH4)2SO4 were obtained as the best carbon and nitrogen sources for CMCase production. B. sonorensis HSC7 produced CMCase during the growth in optimized medium supplemented with agricultural wastes as sole carbon sources. The enzyme was active with optimum temperature of 70 °C and the optimum CMCase activity and stability observed at pH 4.0 and 5.0, respectively. These are characteristics indicating that, this enzyme could be an acidophilic and thermophilic CMCase. Furthermore, the CMCase activity improved by methanol (166%), chloroform (152%), while it was inhibited by DMF (61%). The CMCase activity was enhanced in the presence of Mg+2 (110%), Cu+2 (116%), Triton X-100 (118%) and it retained 57% of its activity at 30% NaCl. The compatibility of HSC7 CMCase varied for each laundry detergent, with higher stability being observed in the presence of Taj® and darya®. This enzyme, that is able to work under extreme conditions, has potential applications in various industries.

Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park

The Norris Geyser Basin in Yellowstone National Park contains a large number of hydrothermal systems, which host microbial populations supported by primary productivity associated with a suite of chemolithotrophic metabolisms. We demonstrate that Metallosphaera yellowstonensis MK1, a facultative autotrophic archaeon isolated from a hyperthermal acidic hydrous ferric oxide (HFO) spring in Norris Geyser Basin, excretes formaldehyde during autotrophic growth. To determine the fate of formaldehyde in this low organic carbon environment, we incubated native microbial mat (containing M. yellowstonensis) from a HFO spring with (13)C-formaldehyde. Isotopic analysis of incubation-derived CO2 and biomass showed that formaldehyde was both oxidized and assimilated by members of the community. Autotrophy, formaldehyde oxidation, and formaldehyde assimilation displayed different sensitivities to chemical inhibitors, suggesting that distinct sub-populations in the mat selectively perform these functions. Our results demonstrate that electrons originally resulting from iron oxidation can energetically fuel autotrophic carbon fixation and associated formaldehyde excretion, and that formaldehyde is both oxidized and assimilated by different organisms within the native microbial community. Thus, formaldehyde can effectively act as a carbon and electron shuttle connecting the autotrophic, iron oxidizing members with associated heterotrophic members in the HFO community.

Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile

Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod-shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.

Acanthamoeba and other free-living amoebae in bat guano, an extreme habitat

Several representatives of the so-called free-living amoebae (FLA) are of medical relevance, not only as facultative pathogens but also as vehicles for pathogenic bacteria. Some FLA can survive and even grow under extreme environmental conditions. Bat guano is an exceptional habitat, the conditions becoming gradually more extreme with aging. In the current study, samples of bat guano of different ages from five caves in Slovenia were screened for the presence of FLA. FLA were isolated from almost all guano samples, including guano with a pH of 3.5. Only the two samples that had been drawn from >20-year-old guano were negative for FLA. Generally, FLA diversity correlated to high concentrations of cultivable bacteria (∼10(8) CFU/g) and fungi (∼10(5) CFU/g). Interestingly, the absence of FLA in seasoned guanos was mirrored by the presence of dictyostelid slime moulds. The isolated amoebae were identified as belonging to the genera Acanthamoeba, Copromyxa, Naegleria, Sappinia, Tetramitus, Thecamoeba, Vahlkampfia, Vannella and Vermamoeba. To the best of our knowledge, this is the first study on the diversity of FLA in guano.