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International Journal of Systematic and... Jul 2021Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6 and T18, were isolated from a...
Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6 and T18, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6 and T18 showed similarities with CGMCC 1.10758 and CP2C (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6 and T18, respectively; the average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus . The predominant fatty acids were summed feature 8 (Cω7Cω6), C, C 2-OH and summed feature 3 (Cω7Cω6). According to he results of the polyphasic study, strains T6 and T18 represent two novel species in the genus (which currently includes only three species), for which names sp. nov. (type strain T6 = CECT 30228=DSM 112073) and sp. nov. (type strain T18=CECT 30229=DSM 112074) are proposed, respectively.
Topics: Acetobacteraceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Desert Climate; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spain
PubMed: 34292142
DOI: 10.1099/ijsem.0.004837 -
PLoS Pathogens Apr 2006
Topics: Acetobacteraceae; Animals; Disease Models, Animal; Gram-Negative Bacterial Infections; Granulomatous Disease, Chronic; Humans; Lymph Nodes; Lymphadenitis; Mice
PubMed: 16652172
DOI: 10.1371/journal.ppat.0020036 -
Journal of Molecular Microbiology and... 2009Acetic acid bacteria are a distinct group of microorganisms within the family Acetobacteriaceae. They are characterized by their ability to incompletely oxidize a wide... (Review)
Review
Acetic acid bacteria are a distinct group of microorganisms within the family Acetobacteriaceae. They are characterized by their ability to incompletely oxidize a wide range of carbohydrates and alcohols. The great advantage of these reactions is that many substrates are regio- and stereoselectively oxidized. This feature is already exploited in several combined biotechnological-chemical procedures for the synthesis of sugar derivatives. Therefore, it is important to understand the basic concepts of this type of physiology to construct strains for improved or new oxidative fermentations. Based on the genome sequence of Gluconobacteroxydans, we will shed light on the central carbon metabolism, the composition of the respiratory chain and the analysis of uncharacterized oxidoreductases. In this context, the role of membrane-bound and -soluble dehydrogenases are of major importance in the process of incomplete oxidation. Other topics deal with the question of how these organisms generate energy and assimilate carbon. Furthermore, we will discuss how acetic acid bacteria thrive in their nutrient-rich environment and how they outcompete other microorganisms.
Topics: Acetic Acid; Acetobacteraceae; Gene Expression Regulation, Bacterial; Genome, Bacterial; Gluconobacter oxydans; Oxidation-Reduction
PubMed: 18957863
DOI: 10.1159/000142895 -
International Journal of Environmental... Jan 2022Biorefineries are attracting attention as an alternative to the petroleum industry to reduce carbon emissions and achieve sustainable development. In particular, because...
Biorefineries are attracting attention as an alternative to the petroleum industry to reduce carbon emissions and achieve sustainable development. In particular, because forests play an important role in potentially reducing greenhouse gas emissions to net zero, alternatives to cellulose produced by plants are required. Bacterial cellulose (BC) can prevent deforestation and has a high potential for use as a biomaterial in various industries such as food, cosmetics, and pharmaceuticals. This study aimed to improve BC production from lignocellulose, a sustainable feedstock, and to optimize the culture conditions for using hydrolysates as a medium. The productivity of BC was improved using statistical optimization of the major culture parameters which were as follows: temperature, 29 °C; initial pH, 5.1; and sodium alginate concentration, 0.09% (/). The predicted and actual values of BC production in the optimal conditions were 14.07 g/L and 14.88 g/L, respectively, confirming that our prediction model was statistically significant. Additionally, BC production using hydrolysates was 1.12-fold higher than in the control group (commercial glucose). Our result indicate that lignocellulose can be used in the BC production processes in the near future.
Topics: Carbon; Cellulose; Culture Media; Gluconacetobacter xylinus; Glucose
PubMed: 35055692
DOI: 10.3390/ijerph19020866 -
BMC Ecology and Evolution Aug 2023Rodents form the largest order among mammals in terms of species diversity, and home range is the area where an individual normally moves during its normal daily...
BACKGROUND
Rodents form the largest order among mammals in terms of species diversity, and home range is the area where an individual normally moves during its normal daily activities. Information about rodent home ranges is paramount in the development of effective conservation and management strategies. This is because rodent home range varies within species and different habitats. In Uganda, tropical high altitude forests such as the Mabira Central Forest Reserve are experiencing continuous disturbance. However, information on rodent home range is lacking. Therefore, a two year Capture-Mark-Release (CMR) of rodents was conducted in the intact forest habitat: Wakisi, regenerating forest habitat: Namananga, and the depleted forest habitat: Namawanyi of Mabira Central Forest Reserve in order to determine the dominant rodent species, their home ranges, and factors affecting these home ranges. The home ranges were determined by calculating a minimum convex polygon with an added boundary strip of 5 m.
RESULTS
Overall, the most dominant rodent species were: Lophuromys stanleyi, Hylomyscus stella, Praomys jacksoni Mastomys natalensis, Lophuromys ansorgei, and Lemniscomys striatus. H. stella dominated the intact forest habitat, while L. stanleyi was the most dominant both in the regenerating and the depleted forest habitats. L. stanleyi had a larger home range in the depleted forest, and the regenerating forest habitats, respectively. In the regenerating forest habitat, M. natalensis had a larger home range size, followed by L. stanleyi, and L. striatus. While in the intact forest habitat, H. stella had the largest home range followed by P. jacksoni. H. stella, L. striatus, L. stanleyi, M. natalensis, and P. jacksoni were most dominant during the wet season while L. ansorgei was relatively more dominant during the dry season. L. ansorgei, and P. jacksoni had a larger home range in the dry season, and a lower home range in the wet season. H. stella, L. stanleyi, M. natalansis and L.striatus had larger home ranges in the wet season, and lower home ranges in the dry season. The home ranges of the dominant rodent species varied across the three habitats in Mabira central forest reserve ([Formula: see text], [Formula: see text]).
CONCLUSION
The significant variation in home ranges of the dominant rodent species in Mabira Central Forest Reserve depending on the type of habitat presupposes that the rodent management strategies in disturbed forest reserves should focus on the type of habitat.
Topics: Animals; Homing Behavior; Uganda; Forests; Acetobacteraceae; Murinae
PubMed: 37605119
DOI: 10.1186/s12862-023-02148-4 -
Applied Microbiology and Biotechnology Aug 2020The strains of the Komagataeibacter genus have been shown to be the most efficient bacterial nanocellulose producers. Although exploited for many decades, the studies of... (Review)
Review
The strains of the Komagataeibacter genus have been shown to be the most efficient bacterial nanocellulose producers. Although exploited for many decades, the studies of these species focused mainly on the optimisation of cellulose synthesis process through modification of culturing conditions in the industrially relevant settings. Molecular physiology of Komagataeibacter was poorly understood and only a few studies explored genetic engineering as a strategy for strain improvement. Only since recently the systemic information of the Komagataeibacter species has been accumulating in the form of omics datasets representing sequenced genomes, transcriptomes, proteomes and metabolomes. Genetic analyses of the mutants generated in the untargeted strain modification studies have drawn attention to other important proteins, beyond those of the core catalytic machinery of the cellulose synthase complex. Recently, modern molecular and synthetic biology tools have been developed which showed the potential for improving targeted strain engineering. Taking the advantage of the gathered knowledge should allow for better understanding of the genotype-phenotype relationship which is necessary for robust modelling of metabolism as well as selection and testing of new molecular engineering targets. In this review, we discuss the current progress in the area of Komagataeibacter systems biology and its impact on the research aimed at scaled-up cellulose synthesis as well as BNC functionalisation. Key points • The accumulated omics datasets advanced the systemic understanding of Komagataeibacter physiology at the molecular level. • Untargeted and targeted strain modification approaches have been applied to improve nanocellulose yield and properties. • The development of modern molecular and synthetic biology tools presents a potential for enhancing targeted strain engineering. • The accumulating omic information should improve modelling of Komagataeibacter's metabolism as well as selection and testing of new molecular engineering targets.
Topics: Acetobacteraceae; Carbohydrate Metabolism; Cellulose; Genetic Engineering; Genotype; Phenotype; Systems Biology
PubMed: 32529377
DOI: 10.1007/s00253-020-10671-3 -
Scientific Reports Nov 2022Bacterial nanocellulose (BC) is a highly versatile biopolymer currently pursued as a material of choice in varied themes of biomedical and material science research...
Bacterial nanocellulose (BC) is a highly versatile biopolymer currently pursued as a material of choice in varied themes of biomedical and material science research fields. With the aim to extend the biotechnological applications, the genetic tractability of the BC producers within the Komagataeibacter genus and its potential as an alternative host chassis in synthetic biology have been extensively studied. However, such studies have been largely focused on the model Komagataeibacter spp. Here, we present a novel K. intermedius strain capable of utilizing glucose, and glycerol sources for biomass and BC synthesis. Genome assembly identified one bacterial cellulose synthetase (bcs) operon containing the complete gene set encoding the BC biogenesis machinery (bcsI) and three additional copies (bcsII-IV). Investigations on the genetic tractability confirmed plasmid transformation, propagation of vectors with pBBR1 and p15A origin of replications and constitutive and inducible induction of recombinant protein in K. intermedius ENS15. This study provides the first report on the genetic tractability of K. intermedius, serving as starting point towards future genetic engineering of this strain.
Topics: Acetobacteraceae; Genetic Engineering; Synthetic Biology; Biomass
PubMed: 36443480
DOI: 10.1038/s41598-022-24735-z -
Acta Crystallographica. Section F,... Mar 2018Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg...
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Å resolution. The data were merged in space group P321, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were R = 0.246 (0.3671 in the highest resolution bin) and R = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.
Topics: Acetobacteraceae; Amino Acid Sequence; Catalytic Domain; Crystallization; Crystallography, X-Ray; Models, Molecular; Protein Conformation; Pyruvate Decarboxylase
PubMed: 29497023
DOI: 10.1107/S2053230X18002819 -
MicrobiologyOpen May 2019Komagataeibacter species are well-recognized bionanocellulose (BNC) producers. This bacterial genus, formerly assigned to Gluconacetobacter, is known for its phenotypic...
Komagataeibacter species are well-recognized bionanocellulose (BNC) producers. This bacterial genus, formerly assigned to Gluconacetobacter, is known for its phenotypic diversity manifested by strain-dependent carbon source preference, BNC production rate, pellicle structure, and strain stability. Here, we performed a comparative study of nineteen Komagataeibacter genomes, three of which were newly contributed in this work. We defined the core genome of the genus, clarified phylogenetic relationships among strains, and provided genetic evidence for the distinction between the two major clades, the K. xylinus and the K. hansenii. We found genomic traits, which likely contribute to the phenotypic diversity between the Komagataeibacter strains. These features include genome flexibility, carbohydrate uptake and regulation of its metabolism, exopolysaccharides synthesis, and the c-di-GMP signaling network. In addition, this work provides a comprehensive functional annotation of carbohydrate metabolism pathways, such as those related to glucose, glycerol, acetan, levan, and cellulose. Findings of this multi-genomic study expand understanding of the genetic variation within the Komagataeibacter genus and facilitate exploiting of its full potential for bionanocellulose production at the industrial scale.
Topics: Acetobacteraceae; Cellulose; Genes, Bacterial; Genetic Variation; Genome, Bacterial; Genomics; Nanoparticles; Phylogeny; Synteny
PubMed: 30365246
DOI: 10.1002/mbo3.731 -
The Journal of Biological Chemistry Sep 2021Understanding the mechanism by which cellulases from bacteria, fungi, and protozoans catalyze the digestion of lignocellulose is important for developing cost-effective...
Understanding the mechanism by which cellulases from bacteria, fungi, and protozoans catalyze the digestion of lignocellulose is important for developing cost-effective strategies for bioethanol production. Cel7A from the fungus Trichoderma reesei is a model exoglucanase that degrades cellulose strands from their reducing ends by processively cleaving individual cellobiose units. Despite being one of the most studied cellulases, the binding and hydrolysis mechanisms of Cel7A are still debated. Here, we used single-molecule tracking to analyze the dynamics of 11,116 quantum dot-labeled TrCel7A molecules binding to and moving processively along immobilized cellulose. Individual enzyme molecules were localized with a spatial precision of a few nanometers and followed for hundreds of seconds. Most enzyme molecules bound to cellulose in a static state and dissociated without detectable movement, whereas a minority of molecules moved processively for an average distance of 39 nm at an average speed of 3.2 nm/s. These data were integrated into a three-state model in which TrCel7A molecules can bind from solution into either static or processive states and can reversibly switch between states before dissociating. From these results, we conclude that the rate-limiting step for cellulose degradation by Cel7A is the transition out of the static state, either by dissociation from the cellulose surface or by initiation of a processive run. Thus, accelerating the transition of Cel7A out of its static state is a potential avenue for improving cellulase efficiency.
Topics: Acetobacteraceae; Cellulose; Cellulose 1,4-beta-Cellobiosidase; Fungal Proteins; Hydrolysis; Hypocreales; Microscopy, Atomic Force; Microscopy, Fluorescence; Quantum Dots; Substrate Specificity
PubMed: 34339742
DOI: 10.1016/j.jbc.2021.101029