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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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Zhao N, Jiao L, Xu J, Zhang J, Qi Y, Qiu M, Wei X, Fan M. Integrated transcriptomic and proteomic analysis reveals the response mechanisms of Alicyclobacillus acidoterrestris to heat stress. Food Res Int 2022; 151:110859. [PMID: 34980395 DOI: 10.1016/j.foodres.2021.110859] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/26/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
Abstract
Alicyclobacillus acidoterrestris can survive pasteurization and is implicated in pasteurized fruit juice spoilage. However, the mechanisms underlying heat responses remain largely unknown. Herein, gene transcription changes of A. acidoterrestris under heat stress were detected by transcriptome, and an integrated analysis with proteomic and physiological data was conducted. A total of 911 differentially expressed genes (DEGs) was observed. The majority of DEGs and differentially expressed proteins (DEPs) were exclusively regulated at the mRNA and protein level, respectively, whereas only 59 genes were regulated at both levels and had the same change trends. Comparative analysis of the functions of the specifically or commonly regulated DEGs and DEPs revealed that the heat resistance of A. acidoterrestris was primarily based on modulating peptidoglycan and fatty acid composition to maintain cell envelope integrity. Low energy consumption strategies were established with attenuated glycolysis, decreased ribosome de novo synthesis, and activated ribosome hibernation. Terminal oxidases, cytochrome bd and aa3, in aerobic respiratory chain were upregulated. Meanwhile, the MarR family transcriptional regulator was upregulated, reactive oxygen species (ROS) was discovered, and the concentration of superoxide dismutase (SOD) increased, indicating that the accompanied oxidative stress was induced by high temperature. Additionally, DNA and protein damage repair systems were activated. This study provided a global perspective on the response mechanisms of A. acidoterrestris to heat stress, with implications for better detection and control of its contamination in fruit juice.
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Affiliation(s)
- Ning Zhao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingxia Jiao
- School of Food Science, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Junnan Xu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yiman Qi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengzhen Qiu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinyuan Wei
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Yu K, Chen F, Yue L, Luo Y, Wang Z, Xing B. CeO 2 Nanoparticles Regulate the Propagation of Antibiotic Resistance Genes by Altering Cellular Contact and Plasmid Transfer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10012-10021. [PMID: 32806911 DOI: 10.1021/acs.est.0c01870] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The dissemination and propagation of antibiotic resistance genes (ARGs) via plasmid-mediated conjugation pose a major threat to global public health. The potential effects of nanomaterials on ARGs fates have drawn much attention recently. In this study, CeO2 nanoparticles (NPs), one of the typical nanomaterials proposed for increasing crop production, were applied at the concentration range of 1-50 mg/L to investigate their effects on ARGs transfer between Escherichia coli. Our results revealed that the conjugative transfer of RP4 plasmid was enhanced by 118-123% at relatively high concentrations (25 and 50 mg/L) of CeO2 NPs, however, CeO2 NPs at low concentrations (1 and 5 mg/L) inhibited the transfer by 22-26%. The opposite effect at low concentrations is mainly attributed to (i) the reduced ROS level, (ii) the weakened intercellular contact via inhibiting the synthesis of polysaccharides in extracellular polymeric substances, and (iii) the down-regulated expression of plasmid transfer genes due to the shortage of ATP supply. Our findings highlight the distinct dose-dependent responses of ARGs conjugative transfer, providing evidence for selecting appropriate NPs dose to reduce the spread of ARGs while applying nanoagrotechnology.
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Affiliation(s)
- Kaiqiang Yu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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Taheri R, Razmjou A, Szekely G, Hou J, Ghezelbash GR. Biodesalination-On harnessing the potential of nature's desalination processes. BIOINSPIRATION & BIOMIMETICS 2016; 11:041001. [PMID: 27387607 DOI: 10.1088/1748-3190/11/4/041001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Water scarcity is now one of the major global crises, which has affected many aspects of human health, industrial development and ecosystem stability. To overcome this issue, water desalination has been employed. It is a process to remove salt and other minerals from saline water, and it covers a variety of approaches from traditional distillation to the well-established reverse osmosis. Although current water desalination methods can effectively provide fresh water, they are becoming increasingly controversial due to their adverse environmental impacts including high energy intensity and highly concentrated brine waste. For millions of years, microorganisms, the masters of adaptation, have survived on Earth without the excessive use of energy and resources or compromising their ambient environment. This has encouraged scientists to study the possibility of using biological processes for seawater desalination and the field has been exponentially growing ever since. Here, the term biodesalination is offered to cover all of the techniques which have their roots in biology for producing fresh water from saline solution. In addition to reviewing and categorizing biodesalination processes for the first time, this review also reveals unexplored research areas in biodesalination having potential to be used in water treatment.
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Affiliation(s)
- Reza Taheri
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
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Carlson RP, Oshota O, Shipman M, Caserta JA, Hu P, Saunders CW, Xu J, Jay ZJ, Reeder N, Richards A, Pettigrew C, Peyton BM. Integrated molecular, physiological and in silico characterization of two Halomonas isolates from industrial brine. Extremophiles 2016; 20:261-74. [PMID: 26888357 DOI: 10.1007/s00792-015-0806-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/06/2015] [Indexed: 01/15/2023]
Abstract
Two haloalkaliphilic bacteria isolated from industrial brine solutions were characterized via molecular, physiological, and in silico metabolic pathway analyses. Genomes from the organisms, designated Halomonas BC1 and BC2, were sequenced; 16S ribosomal subunit-based phylogenetic analysis revealed a high level of similarity to each other and to Halomonas meridiana. Both strains were moderate halophiles with near optimal specific growth rates (≥60 % μ max) observed over <0.1-5 % (w/v) NaCl and pH ranging from 7.4 to 10.2. Isolate BC1 was further characterized by measuring uptake or synthesis of compatible solutes under different growth conditions; in complex medium, uptake and accumulation of external glycine betaine was observed while ectoine was synthesized de novo in salts medium. Transcriptome analysis of isolate BC1 grown on glucose or citrate medium measured differences in glycolysis- and gluconeogenesis-based metabolisms, respectively. The annotated BC1 genome was used to build an in silico, genome-scale stoichiometric metabolic model to study catabolic energy strategies and compatible solute synthesis under gradients of oxygen and nutrient availability. The theoretical analysis identified energy metabolism challenges associated with acclimation to high salinity and high pH. The study documents central metabolism data for the industrially and scientifically important haloalkaliphile genus Halomonas.
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Affiliation(s)
- Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
| | - Olusegun Oshota
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Matt Shipman
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA.,U.S. Navy, Washington, DC, USA
| | | | - Ping Hu
- Procter and Gamble Co., Cincinnati, OH, 45202, USA
| | | | - Jun Xu
- Procter and Gamble Co., Cincinnati, OH, 45202, USA
| | - Zackary J Jay
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Nancy Reeder
- Procter and Gamble Co., Cincinnati, OH, 45202, USA
| | - Abigail Richards
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
| | | | - Brent M Peyton
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
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