-
Proceedings of the National Academy of... Jun 2022Biological functionality is often enabled by a fascinating variety of physical phenomena that emerge from orientational order of building blocks, a defining property of...
Biological functionality is often enabled by a fascinating variety of physical phenomena that emerge from orientational order of building blocks, a defining property of nematic liquid crystals that is also pervasive in nature. Out-of-equilibrium, "living" analogs of these technological materials are found in biological embodiments ranging from myelin sheath of neurons to extracellular matrices of bacterial biofilms and cuticles of beetles. However, physical underpinnings behind manifestations of orientational order in biological systems often remain unexplored. For example, while nematiclike birefringent domains of biofilms are found in many bacterial systems, the physics behind their formation is rarely known. Here, using cellulose-synthesizing bacteria, we reveal how biological activity leads to orientational ordering in fluid and gel analogs of these soft matter systems, both in water and on solid agar, with a topological defect found between the domains. Furthermore, the nutrient feeding direction plays a role like that of rubbing of confining surfaces in conventional liquid crystals, turning polydomain organization within the biofilms into a birefringent monocrystal-like order of both the extracellular matrix and the rod-like bacteria within it. We probe evolution of scalar orientational order parameters of cellulose nanofibers and bacteria associated with fluid-gel and isotropic-nematic transformations, showing how highly ordered active nematic fluids and gels evolve with time during biological-activity-driven, disorder-order transformation. With fluid and soft-gel nematics observed in a certain range of biological activity, this mesophase-exhibiting system is dubbed "biotropic," analogously to thermotropic nematics that exhibit solely orientational order within a temperature range, promising technological and fundamental-science applications.
Topics: Cellulose; Gels; Gluconacetobacter xylinus; Liquid Crystals; Water
PubMed: 35671425
DOI: 10.1073/pnas.2200930119 -
MicrobiologyOpen Feb 2022Electronic scraps (e-scraps) represent an attractive raw material to mine demanded metals, as well as rare earth elements (REEs). A sequential microbial-mediated process...
Electronic scraps (e-scraps) represent an attractive raw material to mine demanded metals, as well as rare earth elements (REEs). A sequential microbial-mediated process developed in two steps was examined to recover multiple elements. First, we made use of an acidophilic bacteria consortium, mainly composed of Acidiphilium multivorum and Leptospidillum ferriphilum, isolated from acid mine drainages. The consortium was inoculated in a dissolution of e-scraps powder and cultured for 15 days. Forty-five elements were analyzed in the liquid phase over time, including silver, gold, and 15 REEs. The bioleaching efficiencies of the consortium were >99% for Cu, Co, Al, and Zn, 53% for Cd, and around 10% for Cr and Li on Day 7. The second step consisted of a microalgae-mediated uptake from e-scraps leachate. The strains used were two acidophilic extremotolerant microalgae, Euglena sp. (EugVP) and Chlamydomonas sp. (ChlSG) strains, isolated from the same extreme environment. Up to 7.3, 4.1, 1.3, and 0.7 µg by wet biomass (WB) of Zn, Al, Cu, and Mn, respectively, were uptaken by ChlSG biomass in 12 days, presenting higher efficiency than EugVP. Concerning REEs, ChlSG biouptake 14.9, 20.3, 13.7, 8.3 ng of Gd, Pr, Ce, La per WB. Meanwhile, EugVP captured 1.1, 1.5, 1.4, and 7.5, respectively. This paper shows the potential of a microbial sequential process to revalorize e-scraps and recover metals and REEs, harnessing extremotolerant microorganisms.
Topics: Acidiphilium; Bacteria; High-Throughput Nucleotide Sequencing; Industrial Waste; Metals; Microscopy, Electron, Scanning; Mining; Recycling
PubMed: 35212477
DOI: 10.1002/mbo3.1265 -
International Journal of Environmental... Jan 2022Consumers' preference towards healthy and novel foods dictates the production of organic unfiltered bottled vinegar that still contains acetic acid bacteria. After...
Consumers' preference towards healthy and novel foods dictates the production of organic unfiltered bottled vinegar that still contains acetic acid bacteria. After ingesting vinegar, the bacteria come into close contact with the human microbiota, creating the possibility of horizontal gene transfer, including genetic determinants for antibiotic resistance. Due to the global spread of antimicrobial resistance (AMR), we analyzed the AMR of and species originating mainly from vinegars. Six antibiotics from different structural groups and mechanisms of action were selected for testing. The AMR was assessed with the disk diffusion method using various growth media. Although the number of resistant strains differed among the growth media, 97.4%, 74.4%, 56.4%, and 33.3% of strains were resistant to trimethoprim, erythromycin, ciprofloxacin, and chloramphenicol, respectively, on all three media. Moreover, 17.9% and 53.8% of all strains were resistant to four and three antibiotics of different antimicrobial classes, respectively. We then looked for antimicrobial resistance genes in the genome sequences of the reference strains. The most common genetic determinant potentially involved in AMR encodes an efflux pump. Since these genes pass through the gastrointestinal tract and may be transferred to human microbiota, further experiments are needed to analyze the probability of this scenario in more detail.
Topics: Acetic Acid; Acetobacter; Anti-Bacterial Agents; Bacteria; Drug Resistance, Bacterial; Humans; Microbial Sensitivity Tests
PubMed: 35010733
DOI: 10.3390/ijerph19010463 -
Soft Matter Dec 2019A facile and effective method is described to engineer original bacterial cellulose fibrous networks with tunable porosity. We showed that the pore shape, volume, and...
A facile and effective method is described to engineer original bacterial cellulose fibrous networks with tunable porosity. We showed that the pore shape, volume, and size distribution of bacterial nanocellulose membranes can be tailored under appropriate culture conditions specifically carbon sources. Pore characterization techniques such as capillary flow porometry, the bubble point method, and gas adsorption-desorption technique as well as visualization techniques such as scanning electron and atomic force microscopy were utilized to investigate the morphology and shape of the pores within the membranes. Engineering various shape, size and volume characteristics of the pores available in pristine bacterial nanocellulose membranes leads to fabrication and development of eco-friendly materials with required characteristics for a broad range of applications.
Topics: Acetobacteraceae; Bioengineering; Cellulose; Nanostructures; Porosity; Surface Tension
PubMed: 31697286
DOI: 10.1039/c9sm01895f -
Archives of Microbiology Dec 2021Strain SYSU D01096 was isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, PR China. Phylogenetic analysis of the nearly full-length 16S...
Strain SYSU D01096 was isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, PR China. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence revealed that strain SYSU D01096 belonged to the family Acetobacteraceae and was closest to Rubritepida flocculans DSM 14296 (96.0% similarity). Cells of strain SYSU D01096 were observed to be non-motile, short rod-shaped and Gram-staining negative. The colonies were observed to be translucent, reddish orange, circular, convex and smooth. Growth occurred at 15-37 °C (optimum, 28-30 °C), pH 4.0-8.0 (optimum, pH 7.0) and 0-0.5% NaCl (w/v; optimum, 0%) on Reasoner's 2A medium. The predominant ubiquinone was identified as ubiquinone 9 and the major fatty acids were Summed Feature 8 (C ω7c and/or C ω6c) and C. The polar lipids consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), one unidentified phospholipid (PL), three unidentified aminolipids (AL1-3) and one unidentified aminophospholipid (APL). The genomic DNA G + C content was 69.1%. Phylogenetic tree based on 16S rRNA gene sequences indicated strain SYSU D01096 represented an individual lineage in the family Acetobacteraceae, which was supported by 30 core gene-based phylogenomic tree. Based on the multi-analysis including physiological, chemotaxonomic and phylogenetic comparison, strain SYSU D01096 was proposed to represent a novel species of a novel genus, named Sabulicella rubraurantiaca gen. nov., sp. nov., within the family Acetobacteraceae. The type strain is SYSU D01096 (= CGMCC 1.8619 = KCTC 82268 = MCCC 1K04998).
Topics: Acetobacteraceae; Bacterial Typing Techniques; DNA, Bacterial; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil
PubMed: 34870748
DOI: 10.1007/s00203-021-02604-z -
PloS One 2023Lactobacilli and Acetobacter sp. are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in...
Lactobacilli and Acetobacter sp. are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in the digestive tract of the fruit fly Drosophila melanogaster. Communities of these bacteria are widespread and prolific, despite numerous strain-specific auxotrophies, suggesting they have evolved nutrient interdependencies that regulate their growth. The use of a chemically-defined medium (CDM) supporting the growth of both groups of bacteria would facilitate the identification of the molecular mechanisms for the metabolic interactions between them. While numerous CDMs have been developed that support specific strains of lactobacilli or Acetobacter, there has not been a medium formulated to support both genera. We developed such a medium, based on a previous CDM designed for growth of lactobacilli, by modifying the nutrient abundances to improve growth yield. We further simplified the medium by substituting casamino acids in place of individual amino acids and the standard Wolfe's vitamins and mineral stocks in place of individual vitamins and minerals, resulting in a reduction from 40 to 8 stock solutions. These stock solutions can be used to prepare several CDM formulations that support robust growth of numerous lactobacilli and Acetobacters. Here, we provide the composition and several examples of its use, which is important for tractability in dissecting the genetic and metabolic basis of natural bacterial species interactions.
Topics: Animals; Acetobacter; Lactobacillus; Drosophila melanogaster; Bacteria; Vitamins
PubMed: 37824485
DOI: 10.1371/journal.pone.0292585 -
ACS Applied Materials & Interfaces Sep 2021The formation of cellulose nanofibrous skin with a colloidal suspension is challenging due to the diffusion of colloidal particles and bacteria to the bulk and a limited...
The formation of cellulose nanofibrous skin with a colloidal suspension is challenging due to the diffusion of colloidal particles and bacteria to the bulk and a limited supply of oxygen for bacteria in the liquid culture environment. A composite-actuating string was fabricated with magnetic nanoparticles (MNPs) and in a solid matrix of hydrophobic microparticles. synthesizes a dense skin layer of cellulose nanofibers enclosing MNPs in the solid matrix to form an actuator string responsive to an external magnetic field. The nanofibrous actuator string is transformable to fit the diverse shapes of tubular structures in cross section due to its softness and plastic deformability, which reduce friction and stress against the walls of organ tissues. The nanofibrous skin string is bendable at an acute angle by magnetic actuation and is applicable as an endoscopic guidewire to reach a target deep inside a model kidney structure.
Topics: Cellulose; Endoscopy; Gluconacetobacter xylinus; Hydrogels; Kidney Calculi; Magnetic Iron Oxide Nanoparticles; Magnetic Phenomena; Membranes, Artificial; Nanofibers
PubMed: 34495638
DOI: 10.1021/acsami.1c09410 -
Food Research International (Ottawa,... Feb 2022Microbial ecosystems of fermented foods are largely interfered by human activities in myriad ways. The aim of this study was to illuminate the impacts of various...
Microbial ecosystems of fermented foods are largely interfered by human activities in myriad ways. The aim of this study was to illuminate the impacts of various starters and environmental variables on the fermentation process of Zhenjiang aromatic vinegar (ZAV), one of the four representative cereal vinegars in China. The effects of environmental variables (e.g., ethanol, total acidity, temperature) and starters (e.g., jiuqu, maiqu, seed pei) on the profiles of microbiome and metabolome (e.g., organic acids, amino acids and volatiles) during fermentation process of ZAV were analyzed. Amongst the four fermentation stages, acetic acid fermentation was the main stage for the accumulation of flavor substances, and subsequently, the contents of acids (mainly acetic, lactic and citric acids) and volatile metabolites (e.g., 2,3-butanedione, acetoin, etc.) continued to enrich in sealed fermentation stage. Principal coordinate analysis (PCoA) and analysis of similarities (ANOSIM) showed that the fungal and bacterial community structures of four fermentation stages were significantly different. As for bacterial community, the dominant OTUs with average relative abundance over 10% in at least one fermentation stage were assigned to the genera Acetilactobacillus, Acetobacter, Acinetobacter, Aeromonas, Lactobacillus, and Pseudomonas. The dominant fungal populations in each fermentation stage were obviously divergent, including Wickerhamomyces, Saccharomyces, Alternaria, Fusarium, etc. SourceTracker analysis demonstrated that jiuqu and seed pei provided microorganisms to initiate starch saccharification and acetic acid fermentation stages, respectively, and maiqu was mainly the donor of enzymes in alcohol fermentation. Spearman correlation coefficients revealed positive relationships between fungal community and various flavor metabolites, indicating the essential role of fungi in the flavor formation of ZAV. This study systematically reveals the effects of fermentation starters and environmental variables on vinegar production and deepens the understanding of the traditional production craft.
Topics: Acetic Acid; Acetobacter; Bacteria; Fermentation; Humans; Microbiota
PubMed: 35181076
DOI: 10.1016/j.foodres.2021.110900 -
Archives of Microbiology Dec 2021Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing...
Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing at the time of rock deposition. Here we show that an anaerobic bacterium produces 3-methylhopanoids, pentacyclic lipids previously detected only in aerobic bacteria and widely used as biomarkers for methane-oxidizing bacteria. Both Rhodopila globiformis, a phototrophic purple nonsulfur bacterium isolated from an acidic warm spring in Yellowstone, and a newly isolated Rhodopila species from a geochemically similar spring in Lassen Volcanic National Park (USA), synthesized 3-methylhopanoids and a suite of related hopanoids and contained the genes encoding the necessary biosynthetic enzymes. Our results show that 3-methylhopanoids can be produced under anoxic conditions and challenges the use of 3-methylhopanoids as biomarkers of oxic conditions in ancient rocks and as prima facie evidence that methanotrophic bacteria were active when the rocks were deposited.
Topics: Acetobacteraceae; Anaerobiosis; Base Composition; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 34528111
DOI: 10.1007/s00203-021-02561-7 -
Microbial Ecology Jul 2021Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions...
Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH and CO gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.
Topics: Bacteria; Greenhouse Gases; Humans; Microbiota; Mycobiome; Soil
PubMed: 31942666
DOI: 10.1007/s00248-020-01483-z