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Martin KR, Le HT, Abdelgawad A, Yang C, Lu G, Keffer JL, Zhang X, Zhuang Z, Asare-Okai PN, Chan CS, Batish M, Yu Y. Development of an efficient, effective, and economical technology for proteome analysis. CELL REPORTS METHODS 2024; 4:100796. [PMID: 38866007 PMCID: PMC11228373 DOI: 10.1016/j.crmeth.2024.100796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/21/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome.
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Affiliation(s)
- Katherine R Martin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ha T Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ahmed Abdelgawad
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Canyuan Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Guotao Lu
- CDS Analytical, LLC, Oxford, PA 19363, USA
| | - Jessica L Keffer
- Department of Earth Sciences, University of Delaware, Newark, DE 19716, USA
| | | | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Papa Nii Asare-Okai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE 19716, USA; School of Marine Science and Policy, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA.
| | - Yanbao Yu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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Soutelino MEM, Silva ACDO, Rocha RDS. Natural Antimicrobials in Dairy Products: Benefits, Challenges, and Future Trends. Antibiotics (Basel) 2024; 13:415. [PMID: 38786143 PMCID: PMC11117376 DOI: 10.3390/antibiotics13050415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
This review delves into using natural antimicrobials in the dairy industry and examines various sources of these compounds, including microbial, plant, and animal sources. It discusses the mechanisms by which they inhibit microbial growth, for example, by binding to the cell wall's precursor molecule of the target microorganism, consequently inhibiting its biosynthesis, and interfering in the molecule transport mechanism, leading to cell death. In general, they prove to be effective against the main pathogens and spoilage found in food, such as Escherichia coli, Staphylococcus aureus, Bacillus spp., Salmonella spp., mold, and yeast. Moreover, this review explores encapsulation technology as a promising approach for increasing the viability of natural antimicrobials against unfavorable conditions such as pH, temperature, and oxygen exposure. Finally, this review examines the benefits and challenges of using natural antimicrobials in dairy products. While natural antimicrobials offer several advantages, including improved safety, quality, and sensory properties of dairy products, it is crucial to be aware of the challenges associated with their use, such as potential allergenicity, regulatory requirements, and consumer perception. This review concludes by emphasizing the need for further research to identify and develop effective and safe natural antimicrobials for the dairy industry to ensure the quality and safety of dairy products for consumers.
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Affiliation(s)
- Maria Eduarda Marques Soutelino
- Department of Food Technology (MTA), College of Veterinary, Fluminense Federal University (UFF), 24230-340 Niterói, Brazil; (M.E.M.S.); (A.C.d.O.S.)
| | - Adriana Cristina de Oliveira Silva
- Department of Food Technology (MTA), College of Veterinary, Fluminense Federal University (UFF), 24230-340 Niterói, Brazil; (M.E.M.S.); (A.C.d.O.S.)
| | - Ramon da Silva Rocha
- Food Engineering Department (ZEA), College of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), 13635-900 Pirassununga, Brazil
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3
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Garry M, Farasin J, Drevillon L, Quaiser A, Bouchez C, Le Borgne T, Coffinet S, Dufresne A. Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer. FEMS Microbiol Ecol 2024; 100:fiae047. [PMID: 38573825 PMCID: PMC11044966 DOI: 10.1093/femsec/fiae047] [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: 11/01/2023] [Revised: 02/18/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola.
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Affiliation(s)
- Mélissa Garry
- Géosciences Rennes, CNRS, Univ Rennes, UMR 6118, Rennes, France
- OSUR, Univ Rennes, UMS 3343, Rennes, France
| | | | - Laetitia Drevillon
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Achim Quaiser
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Camille Bouchez
- Géosciences Rennes, CNRS, Univ Rennes, UMR 6118, Rennes, France
| | | | - Sarah Coffinet
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Alexis Dufresne
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
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4
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Mehić S, Saltikov C. Genome sequence and characterisation of a freshwater photoarsenotroph, Cereibacter azotoformans strain ORIO, isolated from sediments capable of cyclic light-dark arsenic oxidation and reduction. Environ Microbiol 2023; 25:3738-3752. [PMID: 37974504 DOI: 10.1111/1462-2920.16542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
A freshwater photosynthetic arsenite-oxidizing bacterium, Cereibacter azotoformans strain ORIO, was isolated from Owens River, CA, USA. The waters from Owens River are elevated in arsenic and serve as the headwaters to the Los Angeles Aqueduct. The complete genome sequence of strain ORIO is 4.8 Mb genome (68% G + C content) and comprises two chromosomes and six plasmids. Taxonomic analysis placed ORIO within the Cereibacter genus (formerly Rhodobacter). The ORIO genome contains arxB2 AB1 CD (encoding an arsenite oxidase), arxXSR (regulators) and several ars arsenic resistance genes all co-localised on a 136 kb plasmid, named pORIO3. Phylogenetic analysis of ArxA, the molybdenum-containing arsenite oxidase catalytic subunit, demonstrated photoarsenotrophy is likely to occur within members of the Alphaproteobacteria. ORIO is a mixotroph, oxidises arsenite to arsenate (As(V)) photoheterotrophically, and expresses arxA in cultures grown with arsenite. Further ecophysiology studies with Owens River sediment demonstrated the interconversion of arsenite and As(V) was dependent on light-dark cycling. arxA and arrA (As(V) respiratory reductase) genes were detected in the light-dark cycled sediment metagenomes suggesting syntrophic interactions among arsenotrophs. This work establishes C. azotoformans str. ORIO as a new model organism for studying photoarsenotrophy and light-dark arsenic biogeochemical cycling.
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Affiliation(s)
- Sanjin Mehić
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Chad Saltikov
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, USA
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Zhao C, Duan X, Liu C, Huang H, Wu M, Zhang X, Chen Y. Metabolite Cross-Feeding Promoting NADH Production and Electron Transfer during Efficient SMX Biodegradation by a Denitrifier and S. oneidensis MR-1 in the Presence of Nitrate. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18306-18316. [PMID: 37043541 DOI: 10.1021/acs.est.2c09341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Antibiotics often coexist with other pollutants (e.g., nitrate) in an aquatic environment, and their simultaneous biological removal has attracted widespread interest. We have found that sulfamethoxazole (SMX) and nitrate can be efficiently removed by the coculture of a model denitrifier (Paracoccus denitrificans, Pd) and Shewanella oneidensis MR-1 (So), and SMX degradation is affected by NADH production and electron transfer. In this paper, the mechanism of a coculture promoting NADH production and electron transfer was investigated by proteomic analysis and intermediate experiments. The results showed that glutamine and lactate produced by Pd were captured by So to synthesize thiamine and heme, and the released thiamine was taken up by Pd as a cofactor of pyruvate and ketoglutarate dehydrogenase, which were related to NADH generation. Additionally, Pd acquired heme, which facilitated electron transfer as heme, was the important composition of complex III and cytochrome c and the iron source of iron sulfur clusters, the key component of complex I in the electron transfer chain. Further investigation revealed that lactate and glutamine generated by Pd prompted So chemotactic moving toward Pd, which helped the two bacteria effectively obtain their required substances. Obviously, metabolite cross-feeding promoted NADH production and electron transfer, resulting in efficient SMX biodegradation by Pd and So in the presence of nitrate. Its feasibility was finally verified by the coculture of an activated sludge denitrifier and So.
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Affiliation(s)
- Chunxia Zhao
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xu Duan
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Chao Liu
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Meirou Wu
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xuemeng Zhang
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Chen N, Du N, Shen R, He T, Xi J, Tan J, Bian G, Yang Y, Liu T, Tan W, Yu L, Yuan Q. Redox signaling-driven modulation of microbial biosynthesis and biocatalysis. Nat Commun 2023; 14:6800. [PMID: 37884498 PMCID: PMC10603113 DOI: 10.1038/s41467-023-42561-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Microbial communication can drive coordinated functions through sensing, analyzing and processing signal information, playing critical roles in biomanufacturing and life evolution. However, it is still a great challenge to develop effective methods to construct a microbial communication system with coordinated behaviors. Here, we report an electron transfer triggered redox communication network consisting of three building blocks including signal router, optical verifier and bio-actuator for microbial metabolism regulation and coordination. In the redox communication network, the Fe3+/Fe2+ redox signal can be dynamically and reversibly transduced, channeling electrons directly and specifically into bio-actuator cells through iron oxidation pathway. The redox communication network drives gene expression of electron transfer proteins and simultaneously facilitates the critical reducing power regeneration in the bio-actuator, thus enabling regulation of microbial metabolism. In this way, the redox communication system efficiently promotes the biomanufacturing yield and CO2 fixation rate of bio-actuator. Furthermore, the results demonstrate that this redox communication strategy is applicable both in co-culture and microbial consortia. The proposed electron transfer triggered redox communication strategy in this work could provide an approach for reducing power regeneration and metabolic optimization and could offer insights into improving biomanufacturing efficiency.
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Affiliation(s)
- Na Chen
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Na Du
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Ruichen Shen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Tianpei He
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jing Xi
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Guangkai Bian
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, 518055, Shenzhen, P. R. China
| | - Yanbing Yang
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Tiangang Liu
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Lilei Yu
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China.
| | - Quan Yuan
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China.
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China.
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Qu H, Wang Y, Wang B, Li C. Pulsed electric field treatment of seeds altered the endophytic bacterial community and promotes early growth of roots in buckwheat. BMC Microbiol 2023; 23:290. [PMID: 37833633 PMCID: PMC10571398 DOI: 10.1186/s12866-023-02943-5] [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: 03/15/2023] [Accepted: 07/12/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Endophytic bacteria provide nutrients and stimulate systemic resistance during seed germination and plant growth and development, and their functional properties in combating various stresses make them a powerful tool in green agricultural production. In this paper we explored the function of the endophyte community in buckwheat seeds in order to provide a theoretical basis for the application and scientific research of endophytes in buckwheat cultivation. We used pulsed electric field (PEF) technology to treat buckwheat seeds, monitored the effect of high-voltage pulse treatment on buckwheat seed germination, and analyzed the diversity of endophytic bacteria in buckwheat seeds using the amplicon sequencing method. RESULTS PEF treatment promoted root development during buckwheat seed germination. A total of 350 Operational taxonomic units (OTUs) that were assigned into 103 genera were obtained from control and treatment groups using 16SrRNA amplicon sequencing technology. Additionally, PEF treatment also caused a significant decrease in the abundance of Actinobacteria, Proteobacteria, and Bacteroidetes. The abundance of 28 genera changed significantly as well: 11 genera were more abundant, and 17 were less abundant. The number of associated network edges was reduced from 980 to 117, the number of positive correlations decreased by 89.1%, and the number of negative correlations decreased by 86.6%. CONCLUSION PEF treatment promoted early root development in buckwheat and was able to alter the seed endophytic bacterial community. This study thus makes a significant contribution to the field of endophyte research and to the application of PEF technology in plant cultivation.
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Affiliation(s)
- Hao Qu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Trans-boundary Pests, Yunnan Agricultural University, Kunming, China
| | - Baijuan Wang
- College of Tea Science, Yunnan Agricultural University, Kunming, China.
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Trans-boundary Pests, Yunnan Agricultural University, Kunming, China.
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Saha A, Gupta A, Sar P. Metagenome based analysis of groundwater from arsenic contaminated sites of West Bengal revealed community diversity and their metabolic potential. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2023; 58:91-106. [PMID: 36852697 DOI: 10.1080/10934529.2023.2173919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The study of microbial community in groundwater systems is considered to be essential to improve our understanding of arsenic (As) biogeochemical cycling in aquifers, mainly as it relates to the fate and transport of As. The present study was conducted to determine the microbial community composition and its functional potential using As-contaminated groundwater from part of the Bengal Delta Plain (BDP) in West Bengal, India. Geochemical analyses indicated low to moderate dissolved oxygen (0.42-3.02 mg/L), varying As (2.5-311 µg/L) and Fe (0.19-1.2 mg/L) content, while low concentrations of total organic carbon (TOC), total inorganic carbon (TIC), nitrate, and sulfate were detected. Proteobacteria was the most abundant phylum, while the indiscriminate presence of an array of archaeal phyla, Euryarchaeota, Crenarchaeota, Nanoarchaeota, etc., was noteworthy. The core community members were affiliated to Sideroxydans, Acidovorax, Pseudoxanthomonas, Brevundimonas, etc. However, diversity assessed over multiple seasons indicated a shift from Sideroxydans to Pseudomonas or Brevundimonas dominant community, suggestive of microbial response to seasonally fluctuating geochemical stimuli. Taxonomy-based functional potential showed prospects for As biotransformation, methanogenesis, sulfate respiration, denitrification, etc. Thus, this study strengthened existing reports from this region by capturing the less abundant or difficult-to-culture taxa collectively forming a major fraction of the microbial community.
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Affiliation(s)
- Anumeha Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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9
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Cooper RE, Finck J, Chan C, Küsel K. Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland. FEMS Microbiol Ecol 2023; 99:6979798. [PMID: 36623865 PMCID: PMC9925335 DOI: 10.1093/femsec/fiac156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/17/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.
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Affiliation(s)
- Rebecca E Cooper
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jessica Finck
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Clara Chan
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, United States,Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713, United States,Department of Earth Sciences, University of Delaware, Newark, DE 19716, United States
| | - Kirsten Küsel
- Corresponding author. Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany. Tel: +49 3641 949461; Fax: +49 3641 949462; E-mail:
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10
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Wu M, Zhang Z, Zhang X, Dong L, Liu C, Chen Y. Propionibacterium freudenreichii-Assisted Approach Reduces N 2O Emission and Improves Denitrification via Promoting Substrate Uptake and Metabolism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16895-16906. [PMID: 36366772 DOI: 10.1021/acs.est.2c05674] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
N2O emission is often encountered during biodenitrification. In this paper, a new approach of using microorganisms to promote substrate uptake and metabolism to reduce denitrification intermediate accumulation was reported. With the introduction of Propionibacterium freudenreichii to a biodenitrification system, N2O and nitrite accumulation was, respectively, decreased by 74 and 60% and the denitrification efficiency was increased by 150% at the time of 24 h with P. freudenreichii/groundwater denitrifier of 1/5 (OD600). Propionate, produced by P. freudenreichii, only accelerated nitrate removal and was not the main reason for the decreased intermediate accumulation. The proteomic and enzyme analyses revealed that P. freudenreichii stimulated biofilm formation by upregulating proteins involved in porin forming, putrescine biosynthesis, spermidine/putrescine transport, and quorum sensing and upregulated transport proteins, which facilitated the uptake of the carbon source, nitrate, and Fe and Mo (the required catalytic sites of denitrification enzymes). Further investigation revealed that P. freudenreichii activated the methylmalonyl-CoA pathway in the denitrifier and promoted it to synthesize heme/heme d1, the groups of denitrification enzymes and electron transfer proteins, which upregulated the expression of denitrifying enzyme proteins and enhanced the ratio of NosZ to NorB, resulting in the increase of generation, transfer, and consumption of electrons in biodenitrification. Therefore, a significant reduction in the denitrification intermediate accumulation and an improvement in the denitrification efficiency were observed.
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Affiliation(s)
- Meirou Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Zhiqi Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xin Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Road, Shanghai 200092, China
| | - Lei Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
- Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Road, Shanghai 200092, China
| | - Chao Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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11
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Then A, Ewald J, Söllner N, Cooper RE, Küsel K, Ibrahim B, Schuster S. Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211553. [PMID: 35620008 PMCID: PMC9115035 DOI: 10.1098/rsos.211553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/27/2022] [Indexed: 05/03/2023]
Abstract
Iron-reducing and iron-oxidizing bacteria are of interest in a variety of environmental and industrial applications. Such bacteria often co-occur at oxic-anoxic gradients in aquatic and terrestrial habitats. In this paper, we present the first computational agent-based model of microbial iron cycling, between the anaerobic ferric iron (Fe3+)-reducing bacteria Shewanella spp. and the microaerophilic ferrous iron (Fe2+)-oxidizing bacteria Sideroxydans spp. By including the key processes of reduction/oxidation, movement, adhesion, Fe2+-equilibration and nanoparticle formation, we derive a core model which enables hypothesis testing and prediction for different environmental conditions including temporal cycles of oxic and anoxic conditions. We compared (i) combinations of different Fe3+-reducing/Fe2+-oxidizing modes of action of the bacteria and (ii) system behaviour for different pH values. We predicted that the beneficial effect of a high number of iron-nanoparticles on the total Fe3+ reduction rate of the system is not only due to the faster reduction of these iron-nanoparticles, but also to the nanoparticles' additional capacity to bind Fe2+ on their surfaces. Efficient iron-nanoparticle reduction is confined to pH around 6, being twice as high than at pH 7, whereas at pH 5 negligible reduction takes place. Furthermore, in accordance with experimental evidence our model showed that shorter oxic/anoxic periods exhibit a faster increase of total Fe3+ reduction rate than longer periods.
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Affiliation(s)
- Andre Then
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Jan Ewald
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Natalie Söllner
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Rebecca E. Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bashar Ibrahim
- Centre for Applied Mathematics and Bioinformatics, and Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
- European Virus Bioinformatics Center, Leutragraben 1 07743 Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
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Zhou N, Keffer JL, Polson SW, Chan CS. Unraveling Fe(II)-Oxidizing Mechanisms in a Facultative Fe(II) Oxidizer, Sideroxydans lithotrophicus Strain ES-1, via Culturing, Transcriptomics, and Reverse Transcription-Quantitative PCR. Appl Environ Microbiol 2022; 88:e0159521. [PMID: 34788064 PMCID: PMC8788666 DOI: 10.1128/aem.01595-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/11/2021] [Indexed: 11/20/2022] Open
Abstract
Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or by thiosulfate oxidation, in contrast to most other isolates of neutrophilic Fe(II)-oxidizing bacteria (FeOB). This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with reverse transcription-quantitative PCR (RT-qPCR). We explored the long-term gene expression response at different growth phases (over days to a week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II), even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport, and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO2 is an important electron sink for Fe(II) oxidation. IMPORTANCE Neutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans isolates are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual among neutrophilic FeOB isolates, as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment and suggest a multigene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB.
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Affiliation(s)
- Nanqing Zhou
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
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