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Bai S, Shang K, Zeng S, Huang Z, Han Z. Genome analysis of Salinimicrobium sp. 3283s, a deep-sea bacterium isolated from the sediments of South China Sea, China. Mar Genomics 2024; 76:101125. [PMID: 39009496 DOI: 10.1016/j.margen.2024.101125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/12/2024] [Indexed: 07/17/2024]
Abstract
Salinimicrobium sp. 3283s is an aerobic, golden-yellow pigment-producing, Flavobacteriaceae bacterium isolated from the sediments at the depth of 1751 m in the South China Sea. In this study, we present the complete genome sequence of strain 3283s, which only have a single circular chromosome comprising 3,702,683 bp with 41.41% G + C content and no circular plasmid. In total, 3257 protein coding genes, 45 tRNA, 9 rRNA, and 13 sRNA genes were obtained. In terms of the function of gene annotation, strain 3283s was more different from Salinimicrobium oceani J15B91, which was isolated from the South China Sea at a similar depth, and more similar to a Mariana Trench-derived strain Salinimicrobium profundisediminis MT39, which was closer in phylogenetic taxonomic status, suggesting that strain 3283s possesses a stronger potential to adapt to the deep-sea environment. Furthermore, the high- pressure simulations also confirmed that strain 3283s can grow in both 30 MPa and 60 MPa hydrostatic pressure environments, and that it grows better in 30 MPa hydrostatic pressure environments than in 60 MPa hydrostatic pressure environments. In addition, we found a large number of genes in strain 3283s that can promote better adaptation of the bacteria to the low oxygen and high hydrostatic pressure (HHP) environment of the deep sea, such as biosynthetic enzymes of antioxidant pigments, genes encoding cytochromes with enhanced affinity for oxygen, proteins for adaptation to HHP, and genes encoding TonB-dependent transporters in the absence of flagella.
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Affiliation(s)
- Shijie Bai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Kun Shang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Shuqian Zeng
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; Hainan Tropical Ocean University, Sanya 572022, China
| | - Ziming Huang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; Hainan Tropical Ocean University, Sanya 572022, China
| | - Zhuang Han
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
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2
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Hu X, Wang H, Ji B, Wang B, Guo W, Chen R, Jiang C, Chen Y, Zhou D, Zhang Q. Metagenomic insights into the mechanism for the rapid enrichment and high stability of Candidatus Brocadia facilitated by Fe(Ⅲ). WATER RESEARCH 2024; 252:121224. [PMID: 38309072 DOI: 10.1016/j.watres.2024.121224] [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: 09/12/2023] [Revised: 12/09/2023] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
The rapid enrichment of anammox bacteria and its fragile resistance to adverse environment are the critical problems facing of anammox processes. As an abundant component in anammox bacteria, iron has been proved to promote the activity and growth of anammox bacteria in the mature anammox systems, but the functional and metabolic profiles in Fe(III) enhanced emerging anammox systems have not been evaluated. Results indicated that the relative abundance of functional genes involved in oxidative phosphorylation, nitrogen metabolism, cofactors synthesis, and extracellular polymers synthesis pathways was significantly promoted in the system added with 5 mg/L Fe(III) (R5). These enhanced pathways were crucial to energy generation, nitrogen removal, cell activity and proliferation, and microbial self-defense, thereby accelerating the enrichment of anammox bacteria Ca. Brocadia and facilitating their resistance to adverse environments. Microbial community analysis showed that the proportion of Ca. Brocadia in R5 also increased to 64.42 %. Hence, R5 could adapt rapidly to the increased nitrogen loading rate and increase the nitrogen removal rate by 108 % compared to the system without Fe(III) addition. However, the addition of 10 and 20 mg/L Fe(III) showed inhibitory effects on the growth and activity of anammox bacteria, which exhibited the lower relative abundance of Ca. Brocadia and unstable or even collapsed nitrogen removal performance. This study not only clarified the concentration range of Fe(III) that promoted and inhibited the enrichment of anammox bacteria, but also deepened our understanding of the functional and metabolic mechanisms underlying enhanced enrichment of anammox bacteria by Fe(III), providing a potential strategy to hasten the start-up of anammox from conventional activated sludge.
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Affiliation(s)
- Xiaoling Hu
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Hongyu Wang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China.
| | - Bin Ji
- Department of Water and Wastewater Engineering, School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Bin Wang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Wenbin Guo
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Rongfan Chen
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Can Jiang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Yanfang Chen
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Dao Zhou
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Qian Zhang
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan 430070, China
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3
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Wu Z, Yu X, Ji Y, Liu G, Gao P, Xia L, Li P, Liang B, Freilich S, Gu L, Qiao W, Jiang J. Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132762. [PMID: 37837778 DOI: 10.1016/j.jhazmat.2023.132762] [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: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhan Ji
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xia
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Lifeng Gu
- ChangXing AISHENG Environmental Technology Co., Ltd, Zhejiang 313199, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Alio I, Moll R, Hoffmann T, Mamat U, Schaible UE, Pappenfort K, Alawi M, Schie M, Thünauer R, Stamm J, Rohde H, Streit WR. Stenotrophomonas maltophilia affects the gene expression profiles of the major pathogens Pseudomonas aeruginosa and Staphylococcus aureus in an in vitro multispecies biofilm model. Microbiol Spectr 2023; 11:e0085923. [PMID: 37819084 PMCID: PMC10714729 DOI: 10.1128/spectrum.00859-23] [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: 03/02/2023] [Accepted: 08/21/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE In the past, studies have focused on bacterial pathogenicity in mono-species infections, in part ignoring the clinical relevance of diseases caused by more than one pathogen (i.e., polymicrobial infections). However, it is now common knowledge that multiple bacteria species are often involved in the course of an infection. For treatment of such infections, it is absolutely important to understand the dynamics of species interactions at possible infection sites and the molecular mechanisms behind these interactions. Here, we studied the impact of Stenotrophomonas maltophilia on its commensals Pseudomonas aeruginosa and Staphylococcus aureus in multispecies biofilms. We analyzed the 3D structural architectures of dual- and triple-species biofilms, niche formation within the biofilms, and the interspecies interactions on a molecular level. RNAseq data identified key genes involved in multispecies biofilm formation and interaction as potential drug targets for the clinical combat of multispecies infection with these major pathogens.
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Affiliation(s)
- Ifey Alio
- Department of Microbiology and Biotechnology, University Hamburg, Hamburg, Germany
| | - Raphael Moll
- Department of Microbiology and Biotechnology, University Hamburg, Hamburg, Germany
| | - Tim Hoffmann
- Department of Microbiology and Biotechnology, University Hamburg, Hamburg, Germany
| | - Uwe Mamat
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center,Leibniz Research Alliance Infection , Borstel Gemany, Borstel, Germany
| | - Ulrich E. Schaible
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center,Leibniz Research Alliance Infection , Borstel Gemany, Borstel, Germany
| | - Kai Pappenfort
- Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Malik Alawi
- Bioinformatics Core, UKE Hamburg, Hamburg, Germany
| | - Marcel Schie
- LIV, Leibniz Institute of Experimental Virology, Hamburg, Germany
| | - Roland Thünauer
- LIV, Leibniz Institute of Experimental Virology, Hamburg, Germany
| | - Johanna Stamm
- Institute for Medical Microbiology, Virology and Hygiene, UKE, Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, UKE, Eppendorf, Hamburg, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, University Hamburg, Hamburg, Germany
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Schroven K, Putzeys L, Kerremans A, Ceyssens PJ, Vallino M, Paeshuyse J, Haque F, Yusuf A, Koch MD, Lavigne R. The phage-encoded PIT4 protein affects multiple two-component systems of Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0237223. [PMID: 37962408 PMCID: PMC10714779 DOI: 10.1128/spectrum.02372-23] [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: 06/08/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE More and more Pseudomonas aeruginosa isolates have become resistant to antibiotics like carbapenem. As a consequence, P. aeruginosa ranks in the top three of pathogens for which the development of novel antibiotics is the most crucial. The pathogen causes both acute and chronic infections, especially in patients who are the most vulnerable. Therefore, efforts are urgently needed to develop alternative therapies. One path explored in this article is the use of bacteriophages and, more specifically, phage-derived proteins. In this study, a phage-derived protein was studied that impacts key virulence factors of the pathogen via interaction with multiple histidine kinases of TCSs. The fundamental insights gained for this protein can therefore serve as inspiration for the development of an anti-virulence compound that targets the bacterial TCS.
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Affiliation(s)
- Kaat Schroven
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Leena Putzeys
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | | | - Marta Vallino
- Institute of Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Jan Paeshuyse
- Host and Pathogen Interactions, KU Leuven, Leuven, Belgium
| | - Farhana Haque
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Ahmed Yusuf
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Matthias D. Koch
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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Maybin JA, Thompson TP, Flynn PB, Skvortsov T, Hickok NJ, Freeman TA, Gilmore BF. Cold atmospheric pressure plasma-antibiotic synergy in Pseudomonas aeruginosa biofilms is mediated via oxidative stress response. Biofilm 2023; 5:100122. [PMID: 37214348 PMCID: PMC10196807 DOI: 10.1016/j.bioflm.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
Cold atmospheric-pressure plasma (CAP) has emerged as a potential alternative or adjuvant to conventional antibiotics for the treatment of bacterial infections, including those caused by antibiotic-resistant pathogens. The potential of sub-lethal CAP exposures to synergise conventional antimicrobials for the eradication of Pseudomonas aeruginosa biofilms is investigated in this study. The efficacy of antimicrobials following or in the absence of sub-lethal CAP pre-treatment in P. aeruginosa biofilms was assessed. CAP pre-treatment resulted in an increase in both planktonic and biofilm antimicrobial sensitivity for all three strains tested (PAO1, PA14, and PA10548), with both minimum inhibitory concentrations (MICs) and minimum biofilm eradication concentrations (MBECs) of individual antimicrobials, being significantly reduced following CAP pre-treatment of the biofilm (512-fold reduction with ciprofloxacin/gentamicin; and a 256-fold reduction with tobramycin). At all concentrations of antimicrobial used, the combination of sub-lethal CAP exposure and antimicrobials was effective at increasing time-to-peak metabolism, as measured by isothermal microcalorimetry, again indicating enhanced susceptibility. CAP is known to damage bacterial cell membranes and DNA by causing oxidative stress through the in situ generation of reactive oxygen and nitrogen species (RONS). While the exact mechanism is not clear, oxidative stress on outer membrane proteins is thought to damage/perturb cell membranes, confirmed by ATP and LDH leakage, allowing antimicrobials to penetrate the bacterial cell more effectively, thus increasing bacterial susceptibility. Transcriptomic analysis, reveals that cold-plasma mediated oxidative stress caused upregulation of P. aeruginosa superoxide dismutase, cbb3 oxidases, catalases, and peroxidases, and upregulation in denitrification genes, suggesting that P. aeruginosa uses these enzymes to degrade RONS and mitigate the effects of cold plasma mediated oxidative stress. CAP treatment also led to an increased production of the signalling molecule ppGpp in P. aeruginosa, indicative of a stringent response being established. Although we did not directly measure persister cell formation, this stringent response may potentially be associated with the formation of persister cells in biofilm cultures. The production of ppGpp and polyphosphate may be associated with protein synthesis inhibition and increase efflux pump activity, factors which can result in antimicrobial tolerance. The transcriptomic analysis also showed that by 6 h post-treatment, there was downregulation in ribosome modulation factor, which is involved in the formation of persister cells, suggesting that the cells had begun to resuscitate/recover. In addition, CAP treatment at 4 h post-exposure caused downregulation of the virulence factors pyoverdine and pyocyanin; by 6 h post-exposure, virulence factor production was increasing. Transcriptomic analysis provides valuable insights into the mechanisms by which P. aeruginosa biofilms exhibits enhanced susceptibility to antimicrobials. Overall, these findings suggest, for the first time, that short CAP sub-lethal pre-treatment can be an effective strategy for enhancing the susceptibility of P. aeruginosa biofilms to antimicrobials and provides important mechanistic insights into cold plasma-antimicrobial synergy. Transcriptomic analysis of the response to, and recovery from, sub-lethal cold plasma exposures in P. aeruginosa biofilms improves our current understanding of cold plasma biofilm interactions.
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Affiliation(s)
- Jordanne-Amee Maybin
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Padrig B Flynn
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Timofey Skvortsov
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Noreen J Hickok
- Department of Orthopaedic Surgery Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Theresa A Freeman
- Department of Orthopaedic Surgery Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
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Ramdass AC, Rampersad SN. Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains. DNA Res 2023; 30:dsad025. [PMID: 37952165 PMCID: PMC10710014 DOI: 10.1093/dnares/dsad025] [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: 07/20/2023] [Revised: 10/29/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.
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Affiliation(s)
- Amanda Christine Ramdass
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies
| | - Sephra Nalini Rampersad
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies
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8
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Li G, Wei M, Wei G, Chen Z, Shao Z. Efficient heterotrophic nitrification by a novel bacterium Sneathiella aquimaris 216LB-ZA1-12 T isolated from aquaculture seawater. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115588. [PMID: 37839193 DOI: 10.1016/j.ecoenv.2023.115588] [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: 05/13/2023] [Revised: 09/10/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
High concentration of ammonia poses a common threat to the healthy breeding of marine aquaculture organisms. Since aquaculture water is rich in organic matter, heterotrophic nitrifying bacteria might play a crucial role in ammonia removal. However, their roles in ammonia oxidation remain unknown. Here, we report a novel strain isolated from shrimp aquaculture seawater, identified as Sneathiella aquimaris 216LB-ZA1-12T, capable of heterotrophic nitrification. It is the first characterized heterotrophic nitrifier of the order Sneathiellales in the class Alphaproteobacteria. It exhibits high activity in heterotrophic nitrification, removing nearly 94% of ammonium-N under carbon-constrained conditions in 8 days with no observed nitrite accumulation. The heterotrophic nitrification pathway, inferred based on detection and genomic data was as follows: NH4+→NH2OH→NO→NO2-→NO3-. While this pathway aligns with the classical nitrification pathway, while the significant difference lies in the absence of classical HAO and HOX encoding genes in the genome, which is common in heterotrophic nitrifying bacteria. In summary, this bacterium is not only valuable for studying the nitrifying mechanism, but also holds potential for practical applications in ammonia removal in marine aquaculture systems and saline wastewater.
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Affiliation(s)
- Guizhen Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Mengjiao Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; College of Oceans and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai)/School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Zhen Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai)/School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China.
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9
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Bertagnolli AD, Maritan AJ, Tumolo BB, Fritz SF, Oakland HC, Mohr EJ, Poole GC, Albertson LK, Stewart FJ. Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome. ISME COMMUNICATIONS 2023; 3:111. [PMID: 37848489 PMCID: PMC10582121 DOI: 10.1038/s43705-023-00315-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023]
Abstract
Larval net-spinning caddisflies (Hydropsychidae) function as ecosystem engineers in streams where they construct protective retreats composed of organic and inorganic material affixed with silk filtration nets that alter streambed hydrology. We hypothesized that hydropsychid bio-structures (retreats, nets) are microhabitats for microbes with oxygen-sensitive metabolisms, and therefore increase the metabolic heterogeneity of streambed microbial assemblages. Metagenomic and 16 S rRNA gene amplicon analysis of samples from a montane stream (Cherry Creek, Montana, USA) revealed that microbiomes of caddisfly bio-structures are taxonomically and functionally distinct from those of the immediately adjacent rock biofilm (~2 cm distant) and enriched in microbial taxa with established roles in denitrification, nitrification, and methane production. Genes for denitrification, high oxygen affinity terminal oxidases, hydrogenases, oxidative dissimilatory sulfite reductases, and complete ammonia oxidation are significantly enriched in caddisfly bio-structures. The results suggest a novel ecosystem engineering effect of caddisflies through the creation of low-oxygen, denitrifier-enriched niches in the stream microbiome. Facilitation of metabolic diversity in streambeds may be a largely unrecognized mechanism by which caddisflies alter whole-stream biogeochemistry.
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Affiliation(s)
- Anthony D Bertagnolli
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| | - Andrew J Maritan
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Benjamin B Tumolo
- Department of Ecology, Montana State University, Bozeman, MT, 59717, USA
| | - Samuel F Fritz
- Department of Ecology, Montana State University, Bozeman, MT, 59717, USA
| | - Hayley C Oakland
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Elizabeth J Mohr
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Geoffrey C Poole
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
- Montana Institute on Ecosystems, Montana State University, Bozeman, MT, 59717, USA
| | | | - Frank J Stewart
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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10
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Azarkina NV, Borisov VB, Oleynikov IP, Sudakov RV, Vygodina TV. Interaction of Terminal Oxidases with Amphipathic Molecules. Int J Mol Sci 2023; 24:ijms24076428. [PMID: 37047401 PMCID: PMC10095113 DOI: 10.3390/ijms24076428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
The review focuses on recent advances regarding the effects of natural and artificial amphipathic compounds on terminal oxidases. Terminal oxidases are fascinating biomolecular devices which couple the oxidation of respiratory substrates with generation of a proton motive force used by the cell for ATP production and other needs. The role of endogenous lipids in the enzyme structure and function is highlighted. The main regularities of the interaction between the most popular detergents and terminal oxidases of various types are described. A hypothesis about the physiological regulation of mitochondrial-type enzymes by lipid-soluble ligands is considered.
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Affiliation(s)
- Natalia V Azarkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
| | - Vitaliy B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
| | - Ilya P Oleynikov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
| | - Roman V Sudakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
| | - Tatiana V Vygodina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
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11
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Metagenome-Assembled Genome of a Novel Cyclobacteriaceae Epibiont of a Heterotrophic Diazotroph. Microbiol Resour Announc 2023; 12:e0059422. [PMID: 36688647 PMCID: PMC9933675 DOI: 10.1128/mra.00594-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Here, we describe the metagenome-assembled genome (MAG) HetDA_MAG_SS2, in the family Cyclobacteriaceae. It was found in association with a HetDA cyanobiont isolated from a Station ALOHA Trichodesmium colony. Annotation suggests that HetDA_MAG_SS2 is a chemoorganoheterotroph with the potential for lithoheterotrophy, containing genes for aerobic respiration, mixed acid fermentation, dissimilatory nitrate reduction to ammonium, and sulfide oxidation.
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12
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Martin LW, Gray AR, Brockway B, Lamont IL. Pseudomonas aeruginosa is oxygen-deprived during infection in cystic fibrosis lungs, reducing the effectiveness of antibiotics. FEMS Microbiol Lett 2023; 370:fnad076. [PMID: 37516450 PMCID: PMC10408701 DOI: 10.1093/femsle/fnad076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
Pseudomonas aeruginosa infects the lungs of patients with cystic fibrosis. Sputum expectorated from the lungs of patients contains low levels of oxygen, indicating that P. aeruginosa may be oxygen-deprived during infection. During in vitro growth under oxygen-limiting conditions, a P. aeruginosa reference strain increases expression of a cytochrome oxidase with a high affinity for oxygen, and of nitrate and nitrite reductases that enable it to use nitrate instead of oxygen during respiration. Here, we quantified transcription of the genes encoding these three enzymes in sputum samples from 18 infected patients, and in bacteria isolated from the sputum samples and grown in aerobic and anaerobic culture. In culture, expression of all three genes was increased by averages of 20- to 500-fold in anaerobically grown bacteria compared with those grown aerobically, although expression levels varied greatly between isolates. Expression of the same genes in sputum was similar to that of the corresponding bacteria in anaerobic culture. The isolated bacteria were less susceptible to tobramycin and ciprofloxacin, two widely used anti-pseudomonal antibiotics, when grown anaerobically than when grown aerobically. Our findings show that P. aeruginosa experiences oxygen starvation during infection in cystic fibrosis, reducing the effectiveness of antibiotic treatment.
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Affiliation(s)
- Lois W Martin
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Andrew R Gray
- Biostatistics Centre, University of Otago, Dunedin 9016, New Zealand
| | - Ben Brockway
- Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
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13
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Nie Z, Tang K, Wang W, Wang P, Guo Y, Wang Y, Kao SJ, Yin J, Wang X. Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris. Front Microbiol 2023; 14:1138751. [PMID: 37152757 PMCID: PMC10158934 DOI: 10.3389/fmicb.2023.1138751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb 3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.
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Affiliation(s)
- Zhaolong Nie
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Kaihao Tang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Kaihao Tang,
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Jianping Yin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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14
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Yang Y, Lu Z, Azari M, Kartal B, Du H, Cai M, Herbold CW, Ding X, Denecke M, Li X, Li M, Gu JD. Discovery of a new genus of anaerobic ammonium oxidizing bacteria with a mechanism for oxygen tolerance. WATER RESEARCH 2022; 226:119165. [PMID: 36257158 DOI: 10.1016/j.watres.2022.119165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems.
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Affiliation(s)
- Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Zhongyi Lu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Mohammad Azari
- Department of Aquatic Environmental Engineering, Institute for Water and River Basin Management, Karlsruhe Institute of Technology (KIT), Gotthard-Franz-Str. 3, Karlsruhe 76131, Germany
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen 28359, Germany
| | - Huan Du
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Xinghua Ding
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Martin Denecke
- Department of Urban Water- and Waste Management, University of Duisburg-Essen, Universitätsstraße 15, Essen 45141, Germany
| | - Xiaoyan Li
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai, Guangdong 519082, People's Republic of China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China.
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15
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Mulkern AJ, Oyama LB, Cookson AR, Creevey CJ, Wilkinson TJ, Olleik H, Maresca M, da Silva GC, Fontes PP, Bazzolli DMS, Mantovani HC, Damaris BF, Mur LAJ, Huws SA. Microbiome-derived antimicrobial peptides offer therapeutic solutions for the treatment of Pseudomonas aeruginosa infections. NPJ Biofilms Microbiomes 2022; 8:70. [PMID: 36038584 PMCID: PMC9424236 DOI: 10.1038/s41522-022-00332-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Microbiomes are rife for biotechnological exploitation, particularly the rumen microbiome, due to their complexicity and diversity. In this study, antimicrobial peptides (AMPs) from the rumen microbiome (Lynronne 1, 2, 3 and P15s) were assessed for their therapeutic potential against seven clinical strains of Pseudomonas aeruginosa. All AMPs exhibited antimicrobial activity against all strains, with minimum inhibitory concentrations (MICs) ranging from 4–512 µg/mL. Time-kill kinetics of all AMPs at 3× MIC values against strains PAO1 and LES431 showed complete kill within 10 min to 4 h, although P15s was not bactericidal against PAO1. All AMPs significantly inhibited biofilm formation by strains PAO1 and LES431, and induction of resistance assays showed no decrease in activity against these strains. AMP cytotoxicity against human lung cells was also minimal. In terms of mechanism of action, the AMPs showed affinity towards PAO1 and LES431 bacterial membrane lipids, efficiently permeabilising the P. aeruginosa membrane. Transcriptome and metabolome analysis revealed increased catalytic activity at the cell membrane and promotion of β-oxidation of fatty acids. Finally, tests performed with the Galleria mellonella infection model showed that Lynronne 1 and 2 were efficacious in vivo, with a 100% survival rate following treatment at 32 mg/kg and 128 mg/kg, respectively. This study illustrates the therapeutic potential of microbiome-derived AMPs against P. aeruginosa infections.
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Affiliation(s)
- Adam J Mulkern
- IBERS, Aberystwyth University, Aberystwyth, SY23 3DA, Wales, UK. .,TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany.
| | - Linda B Oyama
- Institute for Global Food Security, 19 Chlorine Gardens, Queen's University of Belfast, Belfast, Northern Ireland, BT9 5DP, UK
| | - Alan R Cookson
- IBERS, Aberystwyth University, Aberystwyth, SY23 3DA, Wales, UK
| | - Christopher J Creevey
- Institute for Global Food Security, 19 Chlorine Gardens, Queen's University of Belfast, Belfast, Northern Ireland, BT9 5DP, UK
| | - Toby J Wilkinson
- IBERS, Aberystwyth University, Aberystwyth, SY23 3DA, Wales, UK.,The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Roslin, Edinburgh, EH25 9RG, UK
| | - Hamza Olleik
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397, Marseille, France
| | - Marc Maresca
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397, Marseille, France
| | - Giarla C da Silva
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Patricia P Fontes
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Denise M S Bazzolli
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Hilario C Mantovani
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Bamu F Damaris
- TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Luis A J Mur
- IBERS, Aberystwyth University, Aberystwyth, SY23 3DA, Wales, UK
| | - Sharon A Huws
- Institute for Global Food Security, 19 Chlorine Gardens, Queen's University of Belfast, Belfast, Northern Ireland, BT9 5DP, UK.
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16
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Trutschel LR, Chadwick GL, Kruger B, Blank JG, Brazelton WJ, Dart ER, Rowe AR. Investigation of microbial metabolisms in an extremely high pH marine-like terrestrial serpentinizing system: Ney Springs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155492. [PMID: 35476949 DOI: 10.1016/j.scitotenv.2022.155492] [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] [Received: 12/01/2021] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Ney Springs, a continental serpentinizing spring in northern California, has an exceptionally high reported pH (12.4) for a naturally occurring water source. With high conductivity fluids, it is geochemically more akin to marine serpentinizing systems than other terrestrial locations. Our geochemical analyses also revealed high sulfide concentrations (544 mg/L) and methane emissions (83% volume gas content) relative to other serpentinizing systems. Thermodynamic calculations were used to investigate the potential for substrates resulting from serpentinization to fuel microbial life, and were found to support the energetic feasibility of sulfate reduction, anaerobic methane oxidation, denitrification, and anaerobic sulfide oxidation within this system. Assessment of the microbial community via 16S rRNA taxonomic gene surveys and metagenome sequencing revealed a community composition dominated by poorly characterized members of the Izemoplasmatales and Clostridiales. The genomes of these dominant taxa point to a fermentative lifestyle, though other highly complete (>90%) metagenome assembled genomes support the potential for organisms to perform sulfate reduction, sulfur disproportionation and/or sulfur oxidation (aerobic and anaerobic). Two chemolithoheterotrophs identified in the metagenome, a Halomonas sp. and a Rhodobacteraceae sp., were isolated and shown to oxidize thiosulfate and were capable of growth in conditions up to pH 12.4. Despite being characteristic products of serpentinization reactions, little evidence was seen for hydrogen and methane utilization in the Ney Springs microbial community. Hydrogen is not highly abundant and could be consumed prior to reaching the spring community. Other metabolic strategies may be outcompeted by more energetically favorable heterotrophic or fermentation reactions, or even inhibited by other compounds in the spring such as ammonia. The unique geochemistry of Ney Springs provides an opportunity to study how local geology interacts with serpentinized fluids, while its microbial community can better inform us of the metabolic strategies employed in hyperalkaline environments.
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Affiliation(s)
- Leah R Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Grayson L Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Jennifer G Blank
- Blue Marble Space Institute of Science, Livermore, CA, USA; NASA Ames Research Center in Silicon Valley, Moffett Field, CA, USA
| | | | - Emily R Dart
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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17
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Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps. mSystems 2022; 7:e0032022. [PMID: 35938718 PMCID: PMC9426478 DOI: 10.1128/msystems.00320-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation. IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.
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18
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Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming. BIOLOGY 2022; 11:biology11060913. [PMID: 35741434 PMCID: PMC9220171 DOI: 10.3390/biology11060913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Bottom sediments are usually classified as extreme habitats for microorganisms. They are defined as matter deposited on the bottom of water bodies through the sedimentation process. The quality of sediments is extremely important for the good environmental status of water, because they are an integral part of the surface water environment. Microorganisms living in sediments are involved in biogeochemical transformations and play a fundamental role in maintaining water purity, decomposition of organic matter, and primary production. As a rule, studies on bottom sediments focus on monitoring their chemistry and pollution, while little is known about the structure of bacterial communities inhabiting this extreme environment. In this study, Next-Generation Sequencing (NGS) was combined with the Community-Level Physiological Profiling (CLPP) technique to obtain a holistic picture of bacterial biodiversity in the bottom sediments from Cardinal Pond intended for ecological king carp farming. It was evident that the bottom sediments of the studied pond were characterized by a rich microbiota composition, whose structure and activity depended on the season, and the most extensive modifications of the biodiversity and functionality of microorganisms were noted in summer. Abstract The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.
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19
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Yan J, Sun D, Kuang X, Liang M, Luo L. Quantitative proteomic analysis reveals the metabolic characteristics and adaptive mechanism of Cupriavidus oxalaticus T2 in the process of simultaneous nitrogen and phenol removal. J Proteomics 2022; 251:104426. [PMID: 34781029 DOI: 10.1016/j.jprot.2021.104426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/07/2021] [Accepted: 11/06/2021] [Indexed: 11/20/2022]
Abstract
Phenol and ammonia in wastewater pose a serious threat to ecosystems and human health. However, the currently limited studies on single bacterium simultaneously removing phenol and nitrogen pollution have not fully elucidated the relevant metabolic mechanisms. The differences in proteomic profile after supplementing with phenol and ammonia for 6 and 24 h, respectively, were evaluated to explore the metabolic characteristics and adaptive mechanism of Cupriavidus oxalaticus T2 during the simultaneous removal process of phenol and nitrogen. Results revealed that a new potential phenol para-degradation pathway appeared in T2. Phenol induced changes in nitrogen metabolism, resulting in increased denitrification and decreased synthesis of glutamate from ammonia at 6 h. In addition, phenol exposure enhanced the expression of cytochrome oxidases with high oxygen affinity and increased ATP synthesis. The increase in chemotaxis and flagellar assembly was conducive to the uptake and utilization of phenol. The synthesis of lipoic acid and biotin was also promoted to resist phenol toxicity. Moreover, phenol triggered cellular stress response, thereby leading to the upregulation of anti-stress proteins, such as universal stress protein, iron‑sulfur cluster protein, and chaperones. This study contributes to revealing the metabolic characteristics and adaptive mechanism of T2 during simultaneous nitrogen and phenol removal. SIGNIFICANCE: Phenol and ammonia often co-exist in wastewater, causing serious environmental problems. The information on the metabolic mechanism of simultaneously removing these two pollutants by bacteria is insufficient at present. Moreover, phenol is toxic to microbial and causes cells damage. Therefore, exploring the response mechanism of bacteria to phenol stress is conducive to understand their tolerance mechanism to aromatic compounds. In this study, the metabolic characteristics and adaptive mechanism of C. oxalaticus T2 during the simultaneous removal of phenol and nitrogen process were evaluated by comparing the proteome profiles at different stages. The results revealed the degradation pathways of phenol and nitrogen by strain T2. A variety of phenol response mechanisms were determined, including enhanced energy production, improved cell motility, increased the synthesis of lipoic acid and biotin, and combined action of multiple anti-stress proteins. This study is potentially useful to future phenol and nitrogen co-pollution bioremediation strategies and provides insight into the phenolic compound resistance mechanism in bacteria.
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Affiliation(s)
- Junwei Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Dongdong Sun
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Xiaoxian Kuang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Minghua Liang
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, Guangdong 510640, PR China
| | - Lixin Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, PR China.
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Lichtenberg M, Line L, Schrameyer V, Jakobsen TH, Rybtke ML, Toyofuku M, Nomura N, Kolpen M, Tolker-Nielsen T, Kühl M, Bjarnsholt T, Jensen PØ. Nitric-oxide-driven oxygen release in anoxic Pseudomonas aeruginosa. iScience 2021; 24:103404. [PMID: 34849468 PMCID: PMC8608891 DOI: 10.1016/j.isci.2021.103404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/29/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
Denitrification supports anoxic growth of Pseudomonas aeruginosa in infections. Moreover, denitrification may provide oxygen (O2) resulting from dismutation of the denitrification intermediate nitric oxide (NO) as seen in Methylomirabilis oxyfera. To examine the prevalence of NO dismutation we studied O2 release by P. aeruginosa in airtight vials. P. aeruginosa rapidly depleted O2 but NO supplementation generated peaks of O2 at the onset of anoxia, and we demonstrate a direct role of NO in the O2 release. However, we were not able to detect genetic evidence for putative NO dismutases. The supply of endogenous O2 at the onset of anoxia could play an adaptive role when P. aeruginosa enters anaerobiosis. Furthermore, O2 generation by NO dismutation may be more widespread than indicated by the reports on the distribution of homologues genes. In general, NO dismutation may allow removal of nitrate by denitrification without release of the very potent greenhouse gas, nitrous oxide. Pseudomonas aeruginosa was found to release O2 at the onset of anoxia Peaks of O2 were amplified in a nitric oxide reductase (NOR) mutant The O2 release was mediated by nitric oxide (NO)
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Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Laura Line
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Verena Schrameyer
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Morten Levin Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Masanori Toyofuku
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8577 Tsukuba, Japan
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8577 Tsukuba, Japan
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
- Center for Rheumatology and Spine Diseases, Institute for Inflammation Research, Rigshospitalet, 2100 Copenhagen, Denmark
- Corresponding author
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Shen L, Gao L, Yang M, Zhang J, Wang Y, Feng Y, Wang L, Wang S. Deletion of the PA4427-PA4431 Operon of Pseudomonas aeruginosa PAO1 Increased Antibiotics Resistance and Reduced Virulence and Pathogenicity by Affecting Quorum Sensing and Iron Uptake. Microorganisms 2021; 9:microorganisms9051065. [PMID: 34069209 PMCID: PMC8156433 DOI: 10.3390/microorganisms9051065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/06/2022] Open
Abstract
The respiratory chain is very important for bacterial survival and pathogenicity, yet the roles of the respiratory chain in P. aeruginosa remain to be fully elucidated. Here, we not only proved experimentally that the operon PA4427-PA4431 of Pseudomonas aeruginosa PAO1 encodes respiratory chain complex III (cytobc1), but also found that it played important roles in virulence and pathogenicity. PA4429–31 deletion reduced the production of the virulence factors, including pyocyanin, rhamnolipids, elastase, and extracellular polysaccharides, and it resulted in a remarkable decrease in pathogenicity, as demonstrated in the cabbage and Drosophila melanogaster infection models. Furthermore, RNA-seq analysis showed that PA4429–31 deletion affected the expression levels of the genes related to quorum-sensing systems and the transport of iron ions, and the iron content was also reduced in the mutant strain. Taken together, we comprehensively illustrated the function of the operon PA4427–31 and its application potential as a treatment target in P. aeruginosa infection.
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Khademian M, Imlay JA. How Microbes Evolved to Tolerate Oxygen. Trends Microbiol 2021; 29:428-440. [PMID: 33109411 PMCID: PMC8043972 DOI: 10.1016/j.tim.2020.10.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022]
Abstract
Ancient microbes invented biochemical mechanisms and assembled core metabolic pathways on an anoxic Earth. Molecular oxygen appeared far later, forcing microbes to devise layers of defensive tactics that fend off the destructive actions of both reactive oxygen species (ROS) and oxygen itself. Recent work has pinpointed the enzymes that ROS attack, plus an array of clever protective strategies that abet the well known scavenging systems. Oxygen also directly damages the low-potential metal centers and radical-based mechanisms that optimize anaerobic metabolism; therefore, committed anaerobes have evolved customized tactics that defend these various enzymes from occasional oxygen exposure. Thus a more comprehensive, detailed, and surprising view of oxygen toxicity is coming into view.
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Affiliation(s)
- Maryam Khademian
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
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Yamazaki C, Kashiwa S, Horiuchi A, Kasahara Y, Yamamura S, Amachi S. A novel dimethylsulfoxide reductase family of molybdenum enzyme, Idr, is involved in iodate respiration by Pseudomonas sp. SCT. Environ Microbiol 2020; 22:2196-2212. [PMID: 32190953 DOI: 10.1111/1462-2920.14988] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/30/2020] [Accepted: 03/16/2020] [Indexed: 10/24/2022]
Abstract
Pseudomonas sp. strain SCT is capable of using iodate (IO3 - ) as a terminal electron acceptor for anaerobic respiration. A possible key enzyme, periplasmic iodate reductase (Idr), was visualized by active staining on non-denaturing gel electrophoresis. Liquid chromatography-tandem mass spectrometry analysis revealed that at least four proteins, designated as IdrA, IdrB, IdrP1 , and IdrP2 , were involved in Idr. IdrA and IdrB were homologues of catalytic and electron transfer subunits of respiratory arsenite oxidase (Aio); however, IdrA defined a novel clade within the dimethylsulfoxide (DMSO) reductase family. IdrP1 and IdrP2 were closely related to each other and distantly related to cytochrome c peroxidase. The idr genes (idrABP 1 P 2 ) formed an operon-like structure, and their transcription was upregulated under iodate-respiring conditions. Comparative proteomic analysis also revealed that Idr proteins and high affinity terminal oxidases (Cbb3 and Cyd), various H2 O2 scavengers, and chlorite (ClO2 - ) dismutase-like proteins were expressed specifically or abundantly under iodate-respiring conditions. These results suggest that Idr is a respiratory iodate reductase, and that both O2 and H2 O2 are formed as by-products of iodate respiration. We propose an electron transport chain model of strain SCT, in which iodate, H2 O2 , and O2 are used as terminal electron acceptors.
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Affiliation(s)
- Chihiro Yamazaki
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba, 271-8510, Japan
| | - Sumie Kashiwa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba, 271-8510, Japan
| | - Ayaka Horiuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba, 271-8510, Japan
| | - Yasuhiro Kasahara
- Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan
| | - Shigeki Yamamura
- Center for Regional Environmental Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Seigo Amachi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba, 271-8510, Japan
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Active sulfur cycling in the terrestrial deep subsurface. ISME JOURNAL 2020; 14:1260-1272. [PMID: 32047278 DOI: 10.1038/s41396-020-0602-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 11/09/2022]
Abstract
The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.
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Rinaldo S, Giardina G, Mantoni F, Paone A, Cutruzzolà F. Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms. FEMS Microbiol Lett 2019; 365:4834012. [PMID: 29401255 DOI: 10.1093/femsle/fny029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
The nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans. In this minireview, we summarise the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3',5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings.
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Affiliation(s)
- Serena Rinaldo
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Federico Mantoni
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
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Abstract
Bacteria can communicate through diffusible signaling molecules that are perceived by cognate receptors. It is now well established that bacterial communication regulates hundreds of genes. Hydrophobic molecules which do not diffuse in aqueous environments alone have been identified in bacterial communication, that raised the question on how these molecules are transported between cells and trigger gene expressions. Recent studies show that these hydrophobic signaling molecules, including a long-chain N-acyl homoserine lactone signal produced in Paracoccus denitrificans, are carried by membrane vesicles (MVs). MVs were thought to be formed only through the blebbing of the cell membrane, but new findings in Pseudomonas aeruginosa and Bacillus subtilis revealed that different types of MVs can be formed through explosive cell lysis or bubbling cell death, which findings have certain implications on our view of bacterial interactions.
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Affiliation(s)
- Masanori Toyofuku
- a Faculty of Life and Environmental Sciences, University of Tsukuba , Tsukuba , Japan.,b Microbiology Research Center for Sustainability (MiCS), University of Tsukuba , Tsukuba , Japan
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27
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Zhang H, Zhao Z, Chen S, Kang P, Wang Y, Feng J, Jia J, Yan M, Wang Y, Xu L. Paracoccus versutus KS293 adaptation to aerobic and anaerobic denitrification: Insights from nitrogen removal, functional gene abundance, and proteomic profiling analysis. BIORESOURCE TECHNOLOGY 2018; 260:321-328. [PMID: 29631182 DOI: 10.1016/j.biortech.2018.03.123] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
A novel strain KS293 exhibiting excellent aerobic and anaerobic denitrification performance was isolated and identified as Paracoccus versutus KS293. Nitrate nitrogen and total organic carbon could be effectively removed by P. versutus KS293 without nitrite accumulation, whilst 82% and 85% of total nitrogen was converted into gaseous products under aerobic and anaerobic conditions (P > .05), respectively. Based on the ratio of anaerobic to aerobic, relative abundance values were increased 1.41, 1.45, and 2.31 folds for nirS, nosZ, and narG, respectively. A comparison of the two-dimensional gel electrophoresis and principal component analysis showed significant differences in proteomic profiles between aerobic and anaerobic conditions. In total, 78 proteins that displayed fluctuations in relative expression were observed. 10 proteins including nitrate reductase, maintenance of cell membrane (TolA), and RNA polymerase-binding transcription factor (DksA) were differentially expressed. These findings demonstrated that P. versutus KS293 was effective for nitrogen removal under aerobic or anaerobic conditions.
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Affiliation(s)
- Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China.
| | - Zhenfang Zhao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Shengnan Chen
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Pengliang Kang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Yue Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Ji Feng
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Jingyu Jia
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Miaomiao Yan
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Yan Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Lei Xu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
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Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is characterized by its versatility that enables persistent survival under adverse conditions. It can grow on diverse energy sources and readily acquire resistance to antimicrobial agents. As an opportunistic human pathogen, it also causes chronic infections inside the anaerobic mucus airways of cystic fibrosis patients. As a strict respirer, P. aeruginosa can grow by anaerobic nitrate ( [Formula: see text] ) respiration. Nitric oxide (NO) produced as an intermediate during anaerobic respiration exerts many important effects on the biological characteristics of P. aeruginosa. This review provides information regarding (i) how P. aeruginosa grows by anaerobic respiration, (ii) mechanisms by which NO is produced under such growth, and (iii) bacterial adaptation to NO. We also review the clinical relevance of NO in the fitness of P. aeruginosa and the use of NO as a potential therapeutic for treating P. aeruginosa infection.
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Favre L, Ortalo-Magné A, Pichereaux C, Gargaros A, Burlet-Schiltz O, Cotelle V, Culioli G. Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8. BIOFOULING 2018; 34:132-148. [PMID: 29319346 DOI: 10.1080/08927014.2017.1413551] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
A number of bacteria adopt various lifestyles such as planktonic free-living or sessile biofilm stages. This enables their survival and development in a wide range of contrasting environments. With the aim of highlighting specific metabolic shifts between these phenotypes and to improve the overall understanding of marine bacterial adhesion, a dual metabolomics/proteomics approach was applied to planktonic and biofilm cultures of the marine bacterium Pseudoalteromonas lipolytica TC8. The liquid chromatography mass spectrometry (LC-MS) based metabolomics study indicated that membrane lipid composition was highly affected by the culture mode: phosphatidylethanolamine (PEs) derivatives were over-produced in sessile cultures while ornithine lipids (OLs) were more specifically synthesized in planktonic samples. In parallel, differences between proteomes revealed that peptidases, oxidases, transcription factors, membrane proteins and the enzymes involved in histidine biosynthesis were over-expressed in biofilms while proteins involved in heme production, nutrient assimilation, cell division and arginine/ornithine biosynthesis were specifically up-regulated in free-living cells.
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Affiliation(s)
- Laurie Favre
- a MAPIEM EA 4323 , Université de Toulon , Toulon , France
| | | | - Carole Pichereaux
- b Fédération de Recherche FR3450 , CNRS , Toulouse , France
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Audrey Gargaros
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Odile Burlet-Schiltz
- c Institut de Pharmacologie et de Biologie Structurale, IPBS , Université de Toulouse, CNRS, UPS , Toulouse , France
| | - Valérie Cotelle
- d Laboratoire de Recherche en Sciences Végétales , Université de Toulouse, CNRS, UPS , Castanet-Tolosan , France
| | - Gérald Culioli
- a MAPIEM EA 4323 , Université de Toulon , Toulon , France
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Cao H, Lai Y, Bougouffa S, Xu Z, Yan A. Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853. BMC Genomics 2017; 18:459. [PMID: 28606056 PMCID: PMC5467263 DOI: 10.1186/s12864-017-3842-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/05/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome. RESULTS Here we sequenced and assembled the complete genome of P. aeruginosa ATCC 27853 using the Pacific Biosciences SMRT (PacBio) technology and Illumina sequencing platform. We found that accessory genes of ATCC 27853 including prophages and genomic islands (GIs) mainly contribute to the difference between P. aeruginosa ATCC 27853 and other P. aeruginosa strains. Seven prophages were identified within the genome of P. aeruginosa ATCC 27853. Of the predicted 25 GIs, three contain genes that encode monoxoygenases, dioxygenases and hydrolases that could be involved in the metabolism of aromatic compounds. Surveying virulence-related genes revealed that a series of genes that encode the B-band O-antigen of LPS are lacking in ATCC 27853. Distinctive SNPs in genes of cellular adhesion proteins such as type IV pili and flagella biosynthesis were also observed in this strain. Colony morphology analysis confirmed an enhanced biofilm formation capability of ATCC 27853 on solid agar surface compared to Pseudomonas aeruginosa PAO1. We then performed transcriptome analysis of ATCC 27853 and PAO1 using RNA-seq and compared the expression of orthologous genes to understand the functional genome and the genomic details underlying the distinctive colony morphogenesis. These analyses revealed an increased expression of genes involved in cellular adhesion and biofilm maturation such as type IV pili, exopolysaccharide and electron transport chain components in ATCC 27853 compared with PAO1. In addition, distinctive expression profiles of the virulence genes lecA, lasB, quorum sensing regulators LasI/R, and the type I, III and VI secretion systems were observed in the two strains. CONCLUSIONS The complete genome sequence of P. aeruginosa ATCC 27853 reveals the comprehensive genetic background of the strain, and provides genetic basis for several interesting findings about the functions of surface associated proteins, prophages, and genomic islands. Comparative transcriptome analysis of P. aeruginosa ATCC 27853 and PAO1 revealed several classes of differentially expressed genes in the two strains, underlying the genetic and molecular details of several known and yet to be explored morphological and physiological potentials of P. aeruginosa ATCC 27853.
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Affiliation(s)
- Huiluo Cao
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Yong Lai
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,Present address: Interdisciplinary research group in Infectious Diseases, The Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore
| | - Salim Bougouffa
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Zeling Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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31
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Puigvert M, Guarischi-Sousa R, Zuluaga P, Coll NS, Macho AP, Setubal JC, Valls M. Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii. FRONTIERS IN PLANT SCIENCE 2017; 8:370. [PMID: 28373879 PMCID: PMC5357869 DOI: 10.3389/fpls.2017.00370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/02/2017] [Indexed: 05/03/2023]
Abstract
Bacterial wilt of potatoes-also called brown rot-is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by sequencing transcripts from infected tissue avoiding prokaryotic RNA enrichment.
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Affiliation(s)
- Marina Puigvert
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | | | - Paola Zuluaga
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | - Núria S. Coll
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | - Alberto P. Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences (CAS)Shanghai, China
| | - João C. Setubal
- Department of Biochemistry, University of São PauloSão Paulo, Brazil
| | - Marc Valls
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
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32
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Flavin as an Indicator of the Rate-Limiting Factor for Microbial Current Production in Shewanella oneidensis MR-1. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). Stand Genomic Sci 2016; 11:38. [PMID: 27274784 PMCID: PMC4891895 DOI: 10.1186/s40793-016-0162-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 05/24/2016] [Indexed: 02/01/2023] Open
Abstract
Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1T is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1T is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
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Abstract
The formation of the organized bacterial community called biofilm is a crucial event in bacterial physiology. Given that biofilms are often refractory to antibiotics and disinfectants to which planktonic bacteria are susceptible, their formation is also an industrially and medically relevant issue. Pseudomonas aeruginosa, a well-known human pathogen causing acute and chronic infections, is considered a model organism to study biofilms. A large number of environmental cues control biofilm dynamics in bacterial cells. In particular, the dispersal of individual cells from the biofilm requires metabolic and morphological reprogramming in which the second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) plays a central role. The diatomic gas nitric oxide (NO), a well-known signaling molecule in both prokaryotes and eukaryotes, is able to induce the dispersal of P. aeruginosa and other bacterial biofilms by lowering c-di-GMP levels. In this review, we summarize the current knowledge on the molecular mechanisms connecting NO sensing to the activation of c-di-GMP-specific phosphodiesterases in P. aeruginosa, ultimately leading to c-di-GMP decrease and biofilm dispersal.
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Ahn S, Jung J, Jang IA, Madsen EL, Park W. Role of Glyoxylate Shunt in Oxidative Stress Response. J Biol Chem 2016; 291:11928-38. [PMID: 27036942 DOI: 10.1074/jbc.m115.708149] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Indexed: 12/16/2022] Open
Abstract
The glyoxylate shunt (GS) is a two-step metabolic pathway (isocitrate lyase, aceA; and malate synthase, glcB) that serves as an alternative to the tricarboxylic acid cycle. The GS bypasses the carbon dioxide-producing steps of the tricarboxylic acid cycle and is essential for acetate and fatty acid metabolism in bacteria. GS can be up-regulated under conditions of oxidative stress, antibiotic stress, and host infection, which implies that it plays important but poorly explored roles in stress defense and pathogenesis. In many bacterial species, including Pseudomonas aeruginosa, aceA and glcB are not in an operon, unlike in Escherichia coli In P. aeruginosa, we explored relationships between GS genes and growth, transcription profiles, and biofilm formation. Contrary to our expectations, deletion of aceA in P. aeruginosa improved cell growth under conditions of oxidative and antibiotic stress. Transcriptome data suggested that aceA mutants underwent a metabolic shift toward aerobic denitrification; this was supported by additional evidence, including up-regulation of denitrification-related genes, decreased oxygen consumption without lowering ATP yield, increased production of denitrification intermediates (NO and N2O), and increased cyanide resistance. The aceA mutants also produced a thicker exopolysaccharide layer; that is, a phenotype consistent with aerobic denitrification. A bioinformatic survey across known bacterial genomes showed that only microorganisms capable of aerobic metabolism possess the glyoxylate shunt. This trend is consistent with the hypothesis that the GS plays a previously unrecognized role in allowing bacteria to tolerate oxidative stress.
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Affiliation(s)
- Sungeun Ahn
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - Jaejoon Jung
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - In-Ae Jang
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
| | - Eugene L Madsen
- the Department of Microbiology, Cornell University, Ithaca, New York 14853
| | - Woojun Park
- From the Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea and
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Identification and Characterization of the Novel Subunit CcoM in the cbb3₃Cytochrome c Oxidase from Pseudomonas stutzeri ZoBell. mBio 2016; 7:e01921-15. [PMID: 26814183 PMCID: PMC4742706 DOI: 10.1128/mbio.01921-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c oxidases (CcOs), members of the heme-copper containing oxidase (HCO) superfamily, are the terminal enzymes of aerobic respiratory chains. The cbb3-type cytochrome c oxidases (cbb3-CcO) form the C-family and have only the central catalytic subunit in common with the A- and B-family HCOs. In Pseudomonas stutzeri, two cbb3 operons are organized in a tandem repeat. The atomic structure of the first cbb3 isoform (Cbb3-1) was determined at 3.2 Å resolution in 2010 (S. Buschmann, E. Warkentin, H. Xie, J. D. Langer, U. Ermler, and H. Michel, Science 329:327–330, 2010, http://dx.doi.org/10.1126/science.1187303). Unexpectedly, the electron density map of Cbb3-1 revealed the presence of an additional transmembrane helix (TMH) which could not be assigned to any known protein. We now identified this TMH as the previously uncharacterized protein PstZoBell_05036, using a customized matrix-assisted laser desorption ionization (MALDI)–tandem mass spectrometry setup. The amino acid sequence matches the electron density of the unassigned TMH. Consequently, the protein was renamed CcoM. In order to identify the function of this new subunit in the cbb3 complex, we generated and analyzed a CcoM knockout strain. The results of the biochemical and biophysical characterization indicate that CcoM may be involved in CcO complex assembly or stabilization. In addition, we found that CcoM plays a role in anaerobic respiration, as the ΔCcoM strain displayed altered growth rates under anaerobic denitrifying conditions. The respiratory chain has recently moved into the focus for drug development against prokaryotic human pathogens, in particular, for multiresistant strains (P. Murima, J. D. McKinney, and K. Pethe, Chem Biol 21:1423–1432, 2014, http://dx.doi.org/10.1016/j.chembiol.2014.08.020). cbb3-CcO is an essential enzyme for many different pathogenic bacterial species, e.g., Helicobacter pylori, Vibrio cholerae, and Pseudomonas aeruginosa, and represents a promising drug target. In order to develop compounds targeting these proteins, a detailed understanding of the molecular architecture and function is required. Here we identified and characterized a novel subunit, CcoM, in the cbb3-CcO complex and thereby completed the crystal structure of the Cbb3 oxidase from Pseudomonas stutzeri, a bacterium closely related to the human pathogen Pseudomonas aeruginosa.
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Toyofuku M, Inaba T, Kiyokawa T, Obana N, Yawata Y, Nomura N. Environmental factors that shape biofilm formation. Biosci Biotechnol Biochem 2015; 80:7-12. [PMID: 26103134 DOI: 10.1080/09168451.2015.1058701] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Cells respond to the environment and alter gene expression. Recent studies have revealed the social aspects of bacterial life, such as biofilm formation. Biofilm formation is largely affected by the environment, and the mechanisms by which the gene expression of individual cells affects biofilm development have attracted interest. Environmental factors determine the cell's decision to form or leave a biofilm. In addition, the biofilm structure largely depends on the environment, implying that biofilms are shaped to adapt to local conditions. Second messengers such as cAMP and c-di-GMP are key factors that link environmental factors with gene regulation. Cell-to-cell communication is also an important factor in shaping the biofilm. In this short review, we will introduce the basics of biofilm formation and further discuss environmental factors that shape biofilm formation. Finally, the state-of-the-art tools that allow us investigate biofilms under various conditions are discussed.
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Affiliation(s)
- Masanori Toyofuku
- a Graduate School of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Japan
| | - Tomohiro Inaba
- a Graduate School of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Japan
| | - Tatsunori Kiyokawa
- a Graduate School of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Japan
| | - Nozomu Obana
- a Graduate School of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Japan
| | - Yutaka Yawata
- b Departoment of Civil and Environmental Engineering , Massachusetts Institute of Technology , Cambridge , USA
| | - Nobuhiko Nomura
- a Graduate School of Life and Environmental Sciences , University of Tsukuba , Tsukuba , Japan
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An aerobic exercise: defining the roles of Pseudomonas aeruginosa terminal oxidases. J Bacteriol 2014; 196:4203-5. [PMID: 25266389 DOI: 10.1128/jb.02336-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa encodes a large and diverse complement of aerobic terminal oxidases, which is thought to contribute to its ability to thrive in settings with low oxygen availability. In this issue, Arai et al. (J. Bacteriol. 196:4206-4215, 2014, doi:http://dx.doi.org/10.1128/JB.02176-14) present a thorough characterization of these five complexes, enabling a more detailed understanding of aerobic respiration in this organism.
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