1
|
Kassem A, Abbas L, Coutinho O, Opara S, Najaf H, Kasperek D, Pokhrel K, Li X, Tiquia-Arashiro S. Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives. Front Microbiol 2023; 14:1304081. [PMID: 38075889 PMCID: PMC10703385 DOI: 10.3389/fmicb.2023.1304081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/03/2023] [Indexed: 01/02/2024] Open
Abstract
Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.
Collapse
Affiliation(s)
- Amin Kassem
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Lana Abbas
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Oliver Coutinho
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Somie Opara
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Hawraa Najaf
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Diana Kasperek
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Keshav Pokhrel
- Department of Mathematics and Statistics, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Xiaohua Li
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Sonia Tiquia-Arashiro
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| |
Collapse
|
2
|
Martínez MDLÁM, Urzúa LS, Carrillo YA, Ramírez MB, Morales LJM. Polyhydroxybutyrate Metabolism in Azospirillum brasilense and Its Applications, a Review. Polymers (Basel) 2023; 15:3027. [PMID: 37514417 PMCID: PMC10383645 DOI: 10.3390/polym15143027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Gram-negative Azospirillum brasilense accumulates approximately 80% of polyhydroxybutyrate (PHB) as dry cell weight. For this reason, this bacterium has been characterized as one of the main microorganisms that produce PHB. PHB is synthesized inside bacteria by the polymerization of 3-hydroxybutyrate monomers. In this review, we are focusing on the analysis of the PHB production by A. brasilense in order to understand the metabolism during PHB accumulation. First, the carbon and nitrogen sources used to improve PHB accumulation are discussed. A. brasilense accumulates more PHB when it is grown on a minimal medium containing a high C/N ratio, mainly from malate and ammonia chloride, respectively. The metabolic pathways to accumulate and mobilize PHB in A. brasilense are mentioned and compared with those of other microorganisms. Next, we summarize the available information to understand the role of the genes involved in the regulation of PHB metabolism as well as the role of PHB in the physiology of Azospirillum. Finally, we made a comparison between the properties of PHB and polypropylene, and we discussed some applications of PHB in biomedical and commercial areas.
Collapse
Affiliation(s)
- María de Los Ángeles Martínez Martínez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Lucía Soto Urzúa
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Yovani Aguilar Carrillo
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Mirian Becerril Ramírez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Luis Javier Martínez Morales
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| |
Collapse
|
3
|
Silva LD, Aguiar MM, Paiva AD, Bernardes PC, Gedraite R, Naves EAA. Optimization of clean-in-place (CIP) procedure of pipelines contaminated with Bacillus cereus by applying pulsed flow. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
4
|
Kamnev AA, Dyatlova YA, Kenzhegulov OA, Fedonenko YP, Evstigneeva SS, Tugarova AV. Fourier Transform Infrared (FTIR) Spectroscopic Study of Biofilms Formed by the Rhizobacterium Azospirillum baldaniorum Sp245: Aspects of Methodology and Matrix Composition. Molecules 2023; 28:molecules28041949. [PMID: 36838937 PMCID: PMC9962177 DOI: 10.3390/molecules28041949] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Biofilms represent the main mode of existence of bacteria and play very significant roles in many industrial, medical and agricultural fields. Analysis of biofilms is a challenging task owing to their sophisticated composition, heterogeneity and variability. In this study, biofilms formed by the rhizobacterium Azospirillum baldaniorum (strain Sp245), isolated biofilm matrix and its macrocomponents have for the first time been studied in detail, using Fourier transform infrared (FTIR) spectroscopy, with a special emphasis on the methodology. The accompanying novel data of comparative chemical analyses of the biofilm matrix, its fractions and lipopolysaccharide isolated from the outer membrane of the cells of this strain, as well as their electrophoretic analyses (SDS-PAGE) have been found to be in good agreement with the FTIR spectroscopic results.
Collapse
|
5
|
Etim IIN, Njoku DI, Uzoma PC, Kolawole SK, Olanrele OS, Ekarenem OO, Okonkwo BO, Ikeuba AI, Udoh II, Njoku CN, Etim IP, Emori W. Microbiologically Influenced Corrosion: A Concern for Oil and Gas Sector in Africa. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00550-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
|
6
|
Tripathi A, Ranjan MR, Verma DK, Singh Y, Shukla SK, Rajput VD, Minkina T, Mishra PK, Garg MC. ANN-GA based biosorption of As(III) from water through chemo-tailored and iron impregnated fungal biofilter system. Sci Rep 2022; 12:12414. [PMID: 35858932 PMCID: PMC9300712 DOI: 10.1038/s41598-022-14802-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/13/2022] [Indexed: 11/22/2022] Open
Abstract
The iron impregnated fungal bio-filter (IIFB) discs of luffa sponge containing Phanerochaete chrysosporium mycelia have been used for the removal of As(III) from water. Two different forms of same biomass viz. free fungal biomass (FFB) and modified free fungal biomass (chemically modified and iron impregnated; CFB and IIFB) have been simultaneously investigated to compare the performance of immobilization, chemo-tailoring and iron impregnation for remediation of As(III). IIFB showed highest uptake capacity and percentage removal of As(III), 1.32 mg/g and 92.4% respectively among FFB, CFB and IIFB. Further, the application of RSM and ANN-GA based mathematical model showed a substantial increase in removal i.e. 99.2% of As(III) was filtered out from water at optimised conditions i.e. biomass dose 0.72 g/L, pH 7.31, temperature 42 °C, and initial As(III) concentration 1.1 mg/L. Isotherm, kinetic and thermodynamic studies proved that the process followed monolayer sorption pattern in spontaneous and endothermic way through pseudo-second order kinetic pathway. Continuous mode of As(III) removal in IIFB packed bed bioreactor, revealed increased removal of As(III) from 76.40 to 88.23% with increased column height from 5 to 25 cm whereas the removal decreased from 88.23 to 69.45% while increasing flow rate from 1.66 to 8.30 mL/min. Moreover, the IIFB discs was regenerated by using 10% NaOH as eluting agent and evaluated for As(III) removal for four sorption–desorption cycles, showing slight decrease of their efficiency by 1–2%. SEM–EDX, pHzpc, and FTIR analysis, revealed the involvement of hydroxyl and amino surface groups following a non-electrostatic legend exchange sorption mechanism during removal of As(III).
Collapse
Affiliation(s)
- A Tripathi
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India.
| | - M R Ranjan
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India
| | - D K Verma
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P., 221005, India
| | - Y Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P., 221005, India
| | - S K Shukla
- Department of Transport Science and Technology, School of Engineering and Technology, Central University of Jharkhand, Ranchi, Jharkhand, 835222, India
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia, 344090
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia, 344090
| | - P K Mishra
- Department of Chemical Engineering, IIT BHU, Varanasi, U.P., 221005, India
| | - M C Garg
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India
| |
Collapse
|
7
|
Gomaa OM, Abd El Kareem H, Selim N. Nitrate modulation of Bacillus sp. biofilm components: a proposed model for sustainable bioremediation. Biotechnol Lett 2021; 43:2185-2197. [PMID: 34510307 DOI: 10.1007/s10529-021-03185-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
The presence of different pollutants in wastewater hinder microbial growth, compromise enzymatic activity or compete for electrons required for bioremediation pathway. Therefore, there is a need to use a single microorganism that is capable of tolerating different toxic compounds and can perform simultaneous bioremediation. In the present study, nitrate reducing bacteria capable of decolorizing azo dye was identified as Bacillus subtillis sp. DN using protein profiling, morphological and biochemical tests X-ray diffraction pattern, Raman spectroscopy and cyclic voltammetry confirm that the bacterium under study possesses membrane-bound nitrate reductase and that is capable of direct electron transfer. The addition of nitrate concentrations (0-50 mM) resulted in increased biofilm formation with variable exopolysaccharides, protein, and eDNA. Fourier Transform Infrared spectrum revealed the presence of a biopolymer at high nitrate concentrations. Effective capacitance and conductivity of the cells grown in different nitrate concentrations suggest changes in the relative position of polar groups, their relative orientation and permeability of cell membrane as detected by dielectric spectroscopy. The increase in biofilm shifted the removal of the azo dye from biodegradation to bioadsorption. Our results indicate that nitrate modulates biofilm components. Bacillus sp. DN granular biofilm can be used for simultaneous nitrate and azo dye removal from wastewater.
Collapse
Affiliation(s)
- Ola M Gomaa
- Radiation Microbiology Department, National Center for Radiation Research and Tecnology (NCRRT), Egyptian Atomic Energy Authority, Cairo, Egypt.
| | - Hussein Abd El Kareem
- Radiation Microbiology Department, National Center for Radiation Research and Tecnology (NCRRT), Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Nabila Selim
- Physics Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| |
Collapse
|
8
|
Al-Saadi S, Raman RS, Panter C. A Two-Step Silane Coating Incorporated with Quaternary Ammonium Silane for Mitigation of Microbial Corrosion of Mild Steel. ACS OMEGA 2021; 6:16913-16923. [PMID: 34250350 PMCID: PMC8264834 DOI: 10.1021/acsomega.1c01567] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/10/2021] [Indexed: 06/01/2023]
Abstract
Quaternary ammonium compounds have been used as antibacterial materials. However, as they are hydrophilic and produce a positively charged surface, it is challenging to develop a durable antimicrobial coating of such compounds. The objective of this study is to investigate a two-step silane coating incorporated with quaternary ammonium silane for mitigation of microbiologically influenced corrosion (MIC) of mild steel in biotic solution (a marine environment with bacteria). The corrosion resistance was characterized by electrochemical impedance spectroscopy and potentiodynamic polarization tests. The intact silane coating and that pre-exposed to the biotic solution were characterized by attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). The most probable method (MPN) was used to quantify the active microorganisms attached to the uncoated and silane-coated surfaces. Electrochemical results reveal that the coating thus developed improved the corrosion resistance of steel in the biotic solution. The MPN, FTIR, and scanning electron microscopy suggest a significant decrease in the number of active cells that get attached to the coated surface.
Collapse
Affiliation(s)
- Saad Al-Saadi
- Department
of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
- Department
of Chemical Engineering, Babylon University, Hillah 51002, Babylon, Iraq
| | - R.K. Singh Raman
- Department
of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
- Department
of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Christopher Panter
- CP
Microbiology and Analytical Laboratories, 677 Springvale Rd., Mulgrave, VIC 3170, Australia
| |
Collapse
|
9
|
Tugarova AV, Dyatlova YA, Kenzhegulov OA, Kamnev AA. Poly-3-hydroxybutyrate synthesis by different Azospirillum brasilense strains under varying nitrogen deficiency: A comparative in-situ FTIR spectroscopic analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 252:119458. [PMID: 33601223 DOI: 10.1016/j.saa.2021.119458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/23/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Monitoring of poly-3-hydroxybutyrate accumulation and changes in its relative contents in biomass of the plant-growth-promoting bacteria Azospirillum brasilense (strains Sp7, Cd and Sp245) was performed during aerobic cultivation for 1 to 8 days at various initial concentrations of bound nitrogen (0.1 to 0.5 g∙L-1 NH4Cl) in the culture medium using in-situ transmission FTIR spectroscopy. A methodology has been proposed based on calculating band areas in FTIR spectra (instead of band intensities commonly used earlier) for determining relative contents of PHB in dry bacterial biomass, using the ester ν(C=O) band as a PHB marker (in the region 1750-1720 cm-1) and amide II band of cellular proteins (at ca. 1540 cm-1). Differences in PHB accumulation levels and their changes in the course of cultivation under various trophic stress for the three strains are discussed in relation to their different ecological niches which they occupy in the rhizosphere.
Collapse
Affiliation(s)
- Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Yulia A Dyatlova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Odissey A Kenzhegulov
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia.
| |
Collapse
|
10
|
Kamnev AA, Dyatlova YA, Kenzhegulov OA, Vladimirova AA, Mamchenkova PV, Tugarova AV. Fourier Transform Infrared (FTIR) Spectroscopic Analyses of Microbiological Samples and Biogenic Selenium Nanoparticles of Microbial Origin: Sample Preparation Effects. Molecules 2021; 26:1146. [PMID: 33669948 PMCID: PMC7924863 DOI: 10.3390/molecules26041146] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/14/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022] Open
Abstract
To demonstrate the importance of sample preparation used in Fourier transform infrared (FTIR) spectroscopy of microbiological materials, bacterial biomass samples with and without grinding and after different drying periods (1.5-23 h at 45 °C), as well as biogenic selenium nanoparticles (SeNPs; without washing and after one to three washing steps) were comparatively studied by transmission FTIR spectroscopy. For preparing bacterial biomass samples, Azospirillum brasilense Sp7 and A. baldaniorum Sp245 (earlier known as A. brasilense Sp245) were used. The SeNPs were obtained using A. brasilense Sp7 incubated with selenite. Grinding of the biomass samples was shown to result in slight downshifting of the bands related to cellular poly-3-hydroxybutyrate (PHB) present in the samples in small amounts (under ~10%), reflecting its partial crystallisation. Drying for 23 h was shown to give more reproducible FTIR spectra of bacterial samples. SeNPs were shown to contain capping layers of proteins, polysaccharides and lipids. The as-prepared SeNPs contained significant amounts of carboxylated components in their bioorganic capping, which appeared to be weakly bound and were largely removed after washing. Spectroscopic characteristics and changes induced by various sample preparation steps are discussed with regard to optimising sample treatment procedures for FTIR spectroscopic analyses of microbiological specimens.
Collapse
Affiliation(s)
- Alexander A. Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia; (Y.A.D.); (O.A.K.); (A.A.V.); (P.V.M.); (A.V.T.)
| | | | | | | | | | | |
Collapse
|
11
|
Tugarova AV, Mamchenkova PV, Khanadeev VA, Kamnev AA. Selenite reduction by the rhizobacterium Azospirillum brasilense, synthesis of extracellular selenium nanoparticles and their characterisation. N Biotechnol 2020; 58:17-24. [PMID: 32184193 DOI: 10.1016/j.nbt.2020.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/24/2020] [Accepted: 02/29/2020] [Indexed: 01/25/2023]
Abstract
Microbial reduction of selenium oxyanions has attracted attention in recent years. In this study, an original and simple method for the synthesis of extracellular selenium nanoparticles (Se NPs) of relatively uniform size has been developed using strains Sp7 and Sp245 of the ubiquitous plant-growth promoting rhizobacterium Azospirillum brasilense, both capable of selenite (SeO32-) reduction. In addition, a reliable purification protocol for the recovery of the Se NPs has been perfected, which could be applied with minor modifications to cultures of other microbial species. Importantly, it was found that, by changing the conditions of bacterial reduction of selenite, extracellularly localised Se NPs can be obtained using bacteria which would otherwise produce intracellular Se NPs. In particular, bacterial cultures grown up to the end of the logarithmic growth phase, washed free of culture medium and then incubated with selenite, were used to obtain extracellular Se NPs. Their sizes depended on the initial selenite concentration (∼25-80 nm in diameter at 50-10 mM selenite, respectively). The Se NPs obtained were characterised by transmission electron microscopy (TEM), dynamic light scattering, as well as Raman and UV-vis spectroscopies. Their zeta potential was found to be negative (ca. minus 21-24 mV). Bacterial selenite reduction was also studied in the presence of the efflux pump inhibitor carbonyl cyanide m-chlorophenylhydrazone (CCCP). In this case, TEM indicated the formation only of intracellular selenium crystallites. The data show that the formation of extracellular Se NPs requires normal bacterial metabolic activity, while CCCP evidently blocks the membrane export of Se0 nuclei.
Collapse
Affiliation(s)
- Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049, Saratov, Russia.
| | - Polina V Mamchenkova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049, Saratov, Russia
| | - Vitaly A Khanadeev
- Laboratory of Nanobiotechnology, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049, Saratov, Russia
| | - Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049, Saratov, Russia.
| |
Collapse
|
12
|
Shelud’ko AV, Mokeev DI, Evstigneeva SS, Filip’echeva YA, Burov AM, Petrova LP, Ponomareva EG, Katsy EI. Cell Ultrastructure in Azospirillum brasilense Biofilms. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
13
|
Singh AK, Yadav S, Chauhan BS, Nandy N, Singh R, Neogi K, Roy JK, Srikrishna S, Singh RK, Prakash P. Classification of Clinical Isolates of Klebsiella pneumoniae Based on Their in vitro Biofilm Forming Capabilities and Elucidation of the Biofilm Matrix Chemistry With Special Reference to the Protein Content. Front Microbiol 2019; 10:669. [PMID: 31019496 PMCID: PMC6458294 DOI: 10.3389/fmicb.2019.00669] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 03/18/2019] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is a human pathogen, capable of forming biofilms on abiotic and biotic surfaces. The limitations of the therapeutic options against Klebsiella pneumoniae is actually due to its innate capabilities to form biofilm and harboring determinants of multidrug resistance. We utilized a newer approach for classification of biofilm producing Klebsiella pneumoniae isolates and subsequently we evaluated the chemistry of its slime, more accurately its biofilm. We extracted and determined the amount of polysaccharides and proteins from representative bacterial biofilms. The spatial distribution of sugars and proteins were then investigated in the biofilm matrix using confocal laser scanning microscopy (CLSM). Thereafter, the extracted matrix components were subjected to sophisticated analysis incorporating Fourier transform infrared (FTIR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, one-dimensional gel-based electrophoresis (SDS-PAGE), high performance liquid chromatography (HPLC), and MALDI MS/MS analysis. Besides, the quantification of its total proteins, total sugars, uronates, total acetyl content was also done. Results suggest sugars are not the only/major constituent of its biofilms. The proteins were harvested and subjected to SDS-PAGE which revealed various common and unique protein bands. The common band was excised and analyzed by HPLC. MALDI MS/MS results of this common protein band indicated the presence of different proteins within the biofilm. The 55 different proteins were identified including both cytosolic and membrane proteins. About 22 proteins were related to protein synthesis and processing while 15 proteins were identified related to virulence. Similarly, proteins related to energy and metabolism were 8 and those related to capsule and cell wall synthesis were 4. These results will improve our understanding of Klebsiella biofilm composition and will further help us design better strategies for controlling its biofilm such as techniques focused on weakening/targeting certain portions of the slime which is the most common building block of the biofilm matrix.
Collapse
Affiliation(s)
- Ashish Kumar Singh
- Bacterial Biofilm and Drug Resistance Research Laboratory, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Molecular Immunology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shivangi Yadav
- Bacterial Biofilm and Drug Resistance Research Laboratory, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Brijesh Singh Chauhan
- Cell and Neurobiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Nabarun Nandy
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rajan Singh
- Molecular Immunology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Kaushik Neogi
- Department of Pharmaceutics, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Jagat Kumar Roy
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Saripella Srikrishna
- Cell and Neurobiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rakesh Kumar Singh
- Molecular Immunology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Pradyot Prakash
- Bacterial Biofilm and Drug Resistance Research Laboratory, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| |
Collapse
|
14
|
Gulotta D, Villa F, Cappitelli F, Toniolo L. Biofilm colonization of metamorphic lithotypes of a renaissance cathedral exposed to urban atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:1480-1490. [PMID: 29929311 DOI: 10.1016/j.scitotenv.2018.05.277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Stone architectural heritage exposed outdoor represents a challenging habitat for biological growths; nevertheless, biocolonization on heritage structure is ubiquitous and represents a major mechanism of alteration. However, the identification of specific microorganisms with known reactivity towards the stone substrate does not necessarily imply that a biodeterioration process is in progress and, in specific conditions, bioprotection effects have been highlighted as a result of colonization. The main objective of the present research is to evaluate the biofilm formation on different lithotypes exposed to similar environmental polluted conditions, and to investigate whether the presence of subaerial biofilms can be associated to an increased magnitude of deterioration of the colonized surfaces with respect to the not colonized ones. In particular, the research examines the extensive biological colonization of the stone surfaces of the façade of the Cathedral of Monza (Italy). Four metamorphic stones widely used in the façade and showing rather different compositional, mineralogical and microstructural features were studied. The state of conservation of the stones was characterized under the mineralogical and compositional point of view by X-ray diffraction and Fourier Transformed infrared analysis. The microstructure of colonized substrates and of reference not colonized ones was studied by means of optical and electron microscopy, to comparatively evaluate the damage extent and weathering patterns in both conservative conditions. The structure and the architecture of biofilms growing on different lithic surfaces were investigated by CLSM in both fluorescence and reflection modes. Captured images were analyzed for 3D reconstructions of biofilm samples. The biovolumes were also calculated to estimate the total biomass. The results indicate that the four lithotypes showed different colonization extents. However, even in presence of extensive biological growth, chemical-physical deterioration mechanisms caused by environmental exposure were largely responsible for deterioration. A relationship between compositional and surface morphological features and biocolonization was also observed.
Collapse
Affiliation(s)
- Davide Gulotta
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano and INSTM, Italy.
| | - Federica Villa
- Department of Food, Environmental and Nutrition Sciences, Università degli Studi di Milano, Milan, Italy.
| | - Francesca Cappitelli
- Department of Food, Environmental and Nutrition Sciences, Università degli Studi di Milano, Milan, Italy.
| | - Lucia Toniolo
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Italy.
| |
Collapse
|
15
|
Shelud’ko AV, Filip’echeva YA, Telesheva EM, Burov AM, Evstigneeva SS, Burygin GL, Petrova LP. Characterization of Carbohydrate-Containing Components of Azospirillum brasilense Sp245 Biofilms. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
16
|
Kamnev AA, Tugarova AV, Dyatlova YA, Tarantilis PA, Grigoryeva OP, Fainleib AM, De Luca S. Methodological effects in Fourier transform infrared (FTIR) spectroscopy: Implications for structural analyses of biomacromolecular samples. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 193:558-564. [PMID: 29310090 DOI: 10.1016/j.saa.2017.12.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/10/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia.
| | - Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia
| | - Yulia A Dyatlova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia
| | - Petros A Tarantilis
- Laboratory of Chemistry, Department of Food Science and Human Nutrition, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens 11855, Greece
| | - Olga P Grigoryeva
- Department of Chemistry of Heterochain Polymers and Interpenetrating Polymer Networks, Institute of Macromolecular Chemistry, National Academy of Sciences of Ukraine, Kyiv 02160, Ukraine
| | - Alexander M Fainleib
- Department of Chemistry of Heterochain Polymers and Interpenetrating Polymer Networks, Institute of Macromolecular Chemistry, National Academy of Sciences of Ukraine, Kyiv 02160, Ukraine
| | - Stefania De Luca
- Institute of Biostructures and Bioimaging, National Research Council, 80134 Naples, Italy
| |
Collapse
|
17
|
Tugarova AV, Mamchenkova PV, Dyatlova YA, Kamnev AA. FTIR and Raman spectroscopic studies of selenium nanoparticles synthesised by the bacterium Azospirillum thiophilum. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 192:458-463. [PMID: 29220816 DOI: 10.1016/j.saa.2017.11.050] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/08/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
Vibrational (Fourier transform infrared (FTIR) and Raman) spectroscopic techniques can provide unique molecular-level information on the structural and compositional characteristics of complicated biological objects. Thus, their applications in microbiology and related fields are steadily increasing. In this communication, biogenic selenium nanoparticles (Se NPs) were obtained via selenite (SeO32-) reduction by the bacterium Azospirillum thiophilum (strain VKM B-2513) for the first time, using an original methodology for obtaining extracellular NPs. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) showed the Se NPs to have average diameters within 160-250nm; their zeta potential was measured to be minus 18.5mV. Transmission FTIR spectra of the Se NPs separated from bacterial cells showed typical proteinacious, polysaccharide and lipid-related bands, in line with TEM data showing a thin layer covering the Se NPs surface. Raman spectra of dried Se NPs layer in the low-frequency region (under 500cm-1 down to 150cm-1) showed a single very strong band with a maximum at 250cm-1 which, in line with its increased width (ca. 30cm-1 at half intensity), can be attributed to amorphous elementary Se. Thus, a combination of FTIR and Raman spectroscopic approaches is highly informative in non-destructive analysis of structural and compositional properties of biogenic Se NPs.
Collapse
Affiliation(s)
- Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Polina V Mamchenkova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Yulia A Dyatlova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia.
| |
Collapse
|