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Aso RE, Obuekwe IS. Polycyclic aromatic hydrocarbon: underpinning the contribution of specialist microbial species to contaminant mitigation in the soil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:654. [PMID: 38913190 DOI: 10.1007/s10661-024-12778-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024]
Abstract
The persistence of PAHs poses a significant challenge for conventional remediation approaches, necessitating the exploration of alternative, sustainable strategies for their mitigation. This review underscores the vital role of specialized microbial species (nitrogen-fixing, phosphate-solubilizing, and biosurfactant-producing bacteria) in tackling the environmental impact of polycyclic aromatic hydrocarbons (PAHs). These resistant compounds demand innovative remediation strategies. The study explores microbial metabolic capabilities for converting complex PAHs into less harmful byproducts, ensuring sustainable mitigation. Synthesizing literature from 2016 to 2023, it covers PAH characteristics, sources, and associated risks. Degradation mechanisms by bacteria and fungi, key species, and enzymatic processes are examined. Nitrogen-fixing and phosphate-solubilizing bacteria contributions in symbiotic relationships with plants are highlighted. Biosurfactant-producing bacteria enhance PAH solubility, expanding microbial accessibility for degradation. Cutting-edge trends in omics technologies, synthetic biology, genetic engineering, and nano-remediation offer promising avenues. Recommendations emphasize genetic regulation, field-scale studies, sustainability assessments, interdisciplinary collaboration, and knowledge dissemination. These insights pave the way for innovative, sustainable PAH-contaminated environment restoration.
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Affiliation(s)
- Rufus Emamoge Aso
- Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin, Edo State, Nigeria
| | - Ifeyinwa Sarah Obuekwe
- Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin, Edo State, Nigeria.
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2
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Teffera M, Veith AC, Ronnekleiv-Kelly S, Bradfield CA, Nikodemova M, Tussing-Humphreys L, Malecki K. Diverse mechanisms by which chemical pollutant exposure alters gut microbiota metabolism and inflammation. ENVIRONMENT INTERNATIONAL 2024; 190:108805. [PMID: 38901183 DOI: 10.1016/j.envint.2024.108805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/28/2024] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
The human gut microbiome, the host, and the environment are inextricably linked across the life course with significant health impacts. Consisting of trillions of bacteria, fungi, viruses, and other micro-organisms, microbiota living within our gut are particularly dynamic and responsible for digestion and metabolism of diverse classes of ingested chemical pollutants. Exposure to chemical pollutants not only in early life but throughout growth and into adulthood can alter human hosts' ability to absorb and metabolize xenobiotics, nutrients, and other components critical to health and longevity. Inflammation is a common mechanism underlying multiple environmentally related chronic conditions, including cardiovascular disease, multiple cancer types, and mental health. While growing research supports complex interactions between pollutants and the gut microbiome, significant gaps exist. Few reviews provide descriptions of the complex mechanisms by which chemical pollutants interact with the host microbiome through either direct or indirect pathways to alter disease risk, with a particular focus on inflammatory pathways. This review focuses on examples of several classes of pollutants commonly ingested by humans, including (i) heavy metals, (ii) persistent organic pollutants (POPs), and (iii) nitrates. Digestive enzymes and gut microbes are the first line of absorption and metabolism of these chemicals, and gut microbes have been shown to alter compounds from a less to more toxic state influencing subsequent distribution and excretion. In addition, chemical pollutants may interact with or alter the selection of more harmful and less commensal microbiota, leading to gut dysbiosis, and changes in receptor-mediated signaling pathways that alter the integrity and function of the gut intestinal tract. Arsenic, cadmium, and lead (heavy metals), influence the microbiome directly by altering different classes of bacteria, and subsequently driving inflammation through metabolite production and different signaling pathways (LPS/TLR4 or proteoglycan/TLR2 pathways). POPs can alter gut microbial composition either directly or indirectly depending on their ability to activate key signaling pathways within the intestine (e.g., PCB-126 and AHR). Nitrates and nitrites' effect on the gut and host may depend on their ability to be transformed to secondary and tertiary metabolites by gut bacteria. Future research should continue to support foundational research both in vitro, in vivo, and longitudinal population-based research to better identify opportunities for prevention, gain additional mechanistic insights into the complex interactions between environmental pollutants and the microbiome and support additional translational science.
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Affiliation(s)
- Menna Teffera
- Molecular and Environmental Toxicology, University of Wisconsin-Madison, Madison, WI, US; Biotechnology Center, University of Wisconsin-Madison, Madison, WI, US.
| | - Alex C Veith
- Department of Oncology, University of Wisconsin-Madison, Madison, WI, US.
| | - Sean Ronnekleiv-Kelly
- Molecular and Environmental Toxicology, University of Wisconsin-Madison, Madison, WI, US; Biotechnology Center, University of Wisconsin-Madison, Madison, WI, US; Department of Surgery, University of Wisconsin-Madison, Madison, WI, US.
| | - Christopher A Bradfield
- Molecular and Environmental Toxicology, University of Wisconsin-Madison, Madison, WI, US; Department of Surgery, University of Wisconsin-Madison, Madison, WI, US; Department of Oncology, University of Wisconsin-Madison, Madison, WI, US.
| | - Maria Nikodemova
- College of Public Health and Health Professionals, University of Florida, FL, US.
| | - Lisa Tussing-Humphreys
- Department of Kinesiology and Nutrition, University of Illinois-Chicago, Chicago, IL, US; University of Illinois Cancer Center, University of Illinois-Chicago, Chicago, IL, US.
| | - Kristen Malecki
- Molecular and Environmental Toxicology, University of Wisconsin-Madison, Madison, WI, US; Biotechnology Center, University of Wisconsin-Madison, Madison, WI, US; University of Illinois Cancer Center, University of Illinois-Chicago, Chicago, IL, US; Environmental Occupational Health Sciences, University of Illinois-Chicago, Chicago, IL, US.
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Zhu H, Gong L, Wang R, Shao Z. The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis. Microorganisms 2024; 12:326. [PMID: 38399729 PMCID: PMC10892627 DOI: 10.3390/microorganisms12020326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Pyrene is a pollutant in the environment and affects the health of living organisms. It is important to understand microbial-mediated pyrene resistance and the related molecular mechanisms due to its toxicity and biodegradability. Due to the unclear response mechanisms of bacteria to PAHs, this study detected the transcriptional changes in Escherichia coli under different pyrene concentrations using transcriptome sequencing technology. Global transcriptome analysis showed that the number of differentially expressed genes (DEGs) in multiple metabolic pathways increased with increasing concentrations of pyrene. In addition, the effects and toxicity of pyrene on Escherichia coli mainly included the up-regulation and inhibition of genes related to carbohydrate metabolism, membrane transport, sulfate reduction, various oxidoreductases, and multidrug efflux pumps. Moreover, we also constructed an association network between significantly differentially expressed sRNAs and key genes and determined the regulatory relationship and key genes of Escherichia coli under pyrene stress. Our study utilized pyrene as an exogenous stress substance to investigate the possible pathways of the bacterial stress response. In addition, this study provides a reference for other related research and serves as a foundation for future research.
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Affiliation(s)
- Han Zhu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Ruicheng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China (R.W.)
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China
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4
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Hu P, Sharaby Y, Gu J, Radian A, Lang‐Yona N. Environmental processes and health implications potentially mediated by dust-borne bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13222. [PMID: 38151778 PMCID: PMC10866058 DOI: 10.1111/1758-2229.13222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023]
Abstract
Understanding microbial migration and survival mechanisms in dust events (DEs) can elucidate genetic and metabolic exchange between environments and help predict the atmospheric pathways of ecological and health-related microbial stressors. Dust-borne microbial communities have been previously characterized, but the impact and interactions between potentially active bacteria within transported communities remain limited. Here, we analysed samples collected during DEs in Israel, using amplicon sequencing of the 16S rRNA genes and transcripts. Different air trajectories and wind speeds were associated not only with the genomic microbial community composition variations but also with specific 16S rRNA bacterial transcripts. Potentially active dust-borne bacteria exhibited positive interactions, including carbon and nitrogen cycling, biotransformation of heavy metals, degradation of organic compounds, biofilm formation, and the presence of pathogenic taxa. This study provides insights into the potential interactive relationships and survival strategies of microorganisms within the extreme dust environment.
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Affiliation(s)
- Pengfei Hu
- Civil and Environmental EngineeringTechnion—Israel Institute of TechnologyHaifaIsrael
- Environmental Science and Engineering Research GroupGuangdong Technion—Israel Institute of TechnologyShantouGuangdongChina
| | - Yehonatan Sharaby
- Civil and Environmental EngineeringTechnion—Israel Institute of TechnologyHaifaIsrael
- Present address:
Department of Biology and EnvironmentUniversity of HaifaOranimTivonIsrael
| | - Ji‐Dong Gu
- Environmental Science and Engineering Research GroupGuangdong Technion—Israel Institute of TechnologyShantouGuangdongChina
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy ConversionGuangdong Technion—Israel Institute of TechnologyShantouGuangdongChina
| | - Adi Radian
- Civil and Environmental EngineeringTechnion—Israel Institute of TechnologyHaifaIsrael
| | - Naama Lang‐Yona
- Civil and Environmental EngineeringTechnion—Israel Institute of TechnologyHaifaIsrael
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Chen L, Wang C, Su J. Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis. Microorganisms 2023; 11:2401. [PMID: 37894061 PMCID: PMC10609351 DOI: 10.3390/microorganisms11102401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Glucose is an important carbon source for microbial growth, and its content in infertile soils is essential for the growth of bacteria. Since the mechanism of oligotrophic bacterium adaptation in barren soils is unclear, this research employed RNA-seq technology to examine the impact of glucose concentration on the oligotrophic bacterium B. subtilis BS-G1 in soil affected by desertification. A global transcriptome analysis (RNA-Seq) revealed that the significantly differentially expressed genes (DEGs) histidine metabolism, glutamate synthesis, the HIF-1 signaling pathway, sporulation, and the TCA cycle pathway of B. subtilis BS-G1 were significantly enriched with a 0.015 g/L glucose concentration (L group), compared to a 10 g/L glucose concentration (H group). The DEGs amino acid system, two-component system, metal ion transport, and nitrogen metabolism system of B. subtilis BS-G1 were significantly enriched in the 5 g/L glucose concentration (M group), compared with the H group. In addition, the present study identified the regulation pattern and key genes under a low-glucose environment (7 mRNAs and 16 sRNAs). This study primarily investigates the variances in the regulatory pathways of the oligotrophic B. subtilis BS-G1, which holds substantial importance in comprehending the mechanism underlying the limited sugar tolerance of oligotrophic bacteria.
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Affiliation(s)
- Liping Chen
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Chenglong Wang
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jianyu Su
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
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Thacharodi A, Hassan S, Singh T, Mandal R, Chinnadurai J, Khan HA, Hussain MA, Brindhadevi K, Pugazhendhi A. Bioremediation of polycyclic aromatic hydrocarbons: An updated microbiological review. CHEMOSPHERE 2023; 328:138498. [PMID: 36996919 DOI: 10.1016/j.chemosphere.2023.138498] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/08/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
A class of organic priority pollutants known as PAHs is of critical public health and environmental concern due to its carcinogenic properties as well as its genotoxic, mutagenic, and cytotoxic properties. Research to eliminate PAHs from the environment has increased significantly due to awareness about their negative effects on the environment and human health. Various environmental factors, including nutrients, microorganisms present and their abundance, and the nature and chemical properties of the PAH affect the biodegradation of PAHs. A large spectrum of bacteria, fungi, and algae have ability to degrade PAHs with the biodegradation capacity of bacteria and fungi receiving the most attention. A considerable amount of research has been conducted in the last few decades on analyzing microbial communities for their genomic organization, enzymatic and biochemical properties capable of degrading PAH. While it is true that PAH degrading microorganisms offer potential for recovering damaged ecosystems in a cost-efficient way, new advances are needed to make these microbes more robust and successful at eliminating toxic chemicals. By optimizing some factors like adsorption, bioavailability and mass transfer of PAHs, microorganisms in their natural habitat could be greatly improved to biodegrade PAHs. This review aims to comprehensively discuss the latest findings and address the current wealth of knowledge in the microbial bioremediation of PAHs. Additionally, recent breakthroughs in PAH degradation are discussed in order to facilitate a broader understanding of the bioremediation of PAHs in the environment.
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Affiliation(s)
- Aswin Thacharodi
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Saqib Hassan
- Division of Non-Communicable Diseases, Indian Council of Medical Research (ICMR), New Delhi, 110029, India; Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Tripti Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, 201309, India
| | - Ramkrishna Mandal
- Department of Chemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Jeganathan Chinnadurai
- Department of Research and Development, Dr. Thacharodi's Laboratories, No. 24, 5th Cross, Thanthaiperiyar Nagar, Ellapillaichavadi, Puducherry, 605005, India
| | - Hilal Ahmad Khan
- Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Mir Ashiq Hussain
- Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Kathirvel Brindhadevi
- Center for Transdisciplinary Research (CFTR), Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Arivalagan Pugazhendhi
- School of Engineering, Lebanese American University, Byblos, Lebanon; University Centre for Research & Development, Department of Civil Engineering, Chandigarh University, Mohali,140103, India.
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7
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Liu SJ. Special Issue "Biodegradation and Environmental Microbiomes": Editorial. Microorganisms 2023; 11:1253. [PMID: 37317227 DOI: 10.3390/microorganisms11051253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
The Earth is unique, and we as human beings rely on its air, water, and land [...].
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Affiliation(s)
- Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Global Meta-analysis of Urine Microbiome: Colonization of Polycyclic Aromatic Hydrocarbon-degrading Bacteria Among Bladder Cancer Patients. Eur Urol Oncol 2023; 6:190-203. [PMID: 36868921 DOI: 10.1016/j.euo.2023.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/28/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023]
Abstract
BACKGROUND The application of next-generation sequencing techniques has enabled characterization of urinary tract microbiome. Although many studies have demonstrated associations between the human microbiome and bladder cancer (BC), these have not always reported consistent results, thereby necessitating cross-study comparisons. Thus, the fundamental questions remain how we can utilize this knowledge. OBJECTIVE The aim of our study was to examine the disease-associated changes in urine microbiome communities globally utilizing a machine learning algorithm. DESIGN, SETTING, AND PARTICIPANTS Raw FASTQ files were downloaded for the three published studies in urinary microbiome in BC patients, in addition to our own prospectively collected cohort. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Demultiplexing and classification were performed using the QIIME 2020.8 platform. De novo operational taxonomic units were clustered using the uCLUST algorithm and defined by 97% sequence similarity and classified at the phylum level against the Silva RNA sequence database. The metadata available from the three studies included were used to evaluate the differential abundance between BC patients and controls via a random-effect meta-analysis using the metagen R function. A machine learning analysis was performed using the SIAMCAT R package. RESULTS AND LIMITATIONS Our study includes 129 BC urine and 60 healthy control samples across four different countries. We identified a total of 97/548 genera to be differentially abundant in the BC urine microbiome compared with that of healthy patients. Overall, while the differences in diversity metrics were clustered around the country of origin (Kruskal-Wallis, p < 0.001), collection methodology was a driver of microbiome composition. When assessing dataset from China, Hungary, and Croatia, data demonstrated no discrimination capacity to distinguish between BC patients and healthy adults (area under the curve [AUC] 0.577). However, inclusion of samples with catheterized urine improved the diagnostic accuracy of prediction for BC to AUC 0.995, with precision-recall AUC = 0.994. Through elimination of contaminants associated with the collection methodology among all cohorts, our study identified increased abundance of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria Sphingomonas, Acinetobacter, Micrococcus, Pseudomonas, and Ralstonia to be consistently present in BC patients. CONCLUSIONS The microbiota of the BC population may be a reflection of PAH exposure from smoking, environmental pollutants, and ingestion. Presence of PAHs in the urine of BC patients may allow for a unique metabolic niche and provide necessary metabolic resources where other bacteria are not able to flourish. Furthermore, we found that while compositional differences are associated with geography more than with disease, many are driven by the collection methodology. PATIENT SUMMARY The goal of our study was to compare the urine microbiome of bladder cancer patients with that of healthy controls and evaluate any potential bacteria that may be more likely to be found in patients with bladder cancer. Our study is unique as it evaluates this across multiple countries, to find a common pattern. After we removed some of the contamination, we were able to localize several key bacteria that are more likely to be found in the urine of bladder cancer patients. These bacteria all share their ability to break down tobacco carcinogens.
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Wang J, Zhao S, Xu S, Zhao W, Zhang X, Lei Y, Zhai H, Huang Z. Co-inoculation of antagonistic Bacillus velezensis FH-1 and Brevundimonas diminuta NYM3 promotes rice growth by regulating the structure and nitrification function of rhizosphere microbiome. Front Microbiol 2023; 14:1101773. [PMID: 36846752 PMCID: PMC9948033 DOI: 10.3389/fmicb.2023.1101773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023] Open
Abstract
Microbial inoculation with plant growth-promoting microorganisms (PGPMs) is one of the most promising technologies to solve the current global challenges. Co-inoculants is more efficient and stable than mono-inoculants. However, the growth promoting mechanism of co-inoculants in complex soil system is still poorly understood. In this study, the effects on rice, soil and the microbiome of the mono-inoculant Bacillus velezensis FH-1 (F) and Brevundimonas diminuta NYM3 (N) and the co-inoculant FN obtained in previous works were compared. Correlation analysis and PLS-PM were used to explore the primary mechanism of different inoculants promoting rice growth. We hypothesized that inoculants promoted plant growth (i) by themselves, (ii) by improving soil nutrient availability or (iii) by regulating the rhizosphere microbiome in complex soil system. We also assumed that different inoculants had different ways of promoting plant growth. The results showed that FN significantly promoted rice growth and nitrogen absorption and slightly increased soil total nitrogen and microbial network complexity compared with F, N and the control (CK). B. velezensis FH-1 and B. diminuta NYM3 interfered with each other's colonization in FN. FN increased the complexity of the microbial network compared to F and N. The bacterial community of FN was quite different from CK and N, while the fungal community was not significantly different from other treatments. The species and functions enriched or inhibited by FN are part of F. The correlation analysis and PLS-PM results showed that inoculants (F/N/FN) promoted the growth of rice mainly by regulating the rhizosphere microbiome rather than by themselves or by improving soil nutrient availability. Co-inoculant FN promotes rice growth specifically by enhancing microbial nitrification function through enriching related species compared with F or N. This may provide theoretical guidance for the construction and application of co-inoculants in the future.
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Affiliation(s)
- Jingjing Wang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China,*Correspondence: Jingjing Wang, ✉
| | - Siqi Zhao
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Song Xu
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wei Zhao
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoxia Zhang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yu Lei
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China,Core Facility, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Huanhuan Zhai
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China,Core Facility, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiyong Huang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China,Zhiyong Huang, ✉
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Wang P, Liu J, Han S, Wang Y, Duan Y, Liu T, Hou L, Zhang Z, Li L, Lin Y. Polyethylene mulching film degrading bacteria within the plastisphere: Co-culture of plastic degrading strains screened by bacterial community succession. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130045. [PMID: 36162306 DOI: 10.1016/j.jhazmat.2022.130045] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
As an ecological niche close to the polymer, microorganisms in the plastisphere possess the advantage of degrading plastics. This study aims to investigate the bacterial community succession and obtain degrading bacteria in the plastisphere, as well as identify the most efficient degradation combination by co-culture of multiple strains. The findings demonstrate the alpha-diversity indices of the plastisphere bacterial community are significantly lower, and the community structure is regularly and significantly altered. With the time of culture, the plastisphere community composition alters regularly, and the hydrocarbon-degrading genera become the core members. Functional prediction of community reveals the potential for Xenobiotics Biodegradation and Metabolism of plastisphere, and the apparent variations detections of polyethylene mulching film (PMF) indicating the PMF degrading ability of plastisphere. Besides, three PMF-degrading bacterial strains, Rhodopseudomonas sp. P1 (P), Rhodanobacter sp. Rs (R) and Microbacterium sp. M1 (M), are screened for co-culture with PMF degrading strain Bacillus aryabhattai 5-3 (B). By considering bacterial growth, biofilm adhesion, and apparent degradation of different samples, RB (R. sp. Rs + B. aryabhattai 5-3) is ultimately selected as the best PMF degradation combination. This study provides a new possibility for plastisphere-related research from the perspective of mitigating plastic pollution on agricultural land.
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Affiliation(s)
- Peiyuan Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jiaxi Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Siqi Han
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yufan Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yifan Duan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Tingting Liu
- College of Science, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Lijun Hou
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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Liu H, Liu S, Liu H, Liu M, Yin X, Lu P, Hong Q, Liu A, Wan R, Fang S. Revealing the driving synergistic degradation mechanism of Rhodococcus sp. B2 on the bioremediation of pretilachlor-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159086. [PMID: 36179826 DOI: 10.1016/j.scitotenv.2022.159086] [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: 07/06/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
The pretilachlor has been widely used worldwide and has contaminated the environment for many years. The environmental fate of pretilachlor and its residues removal from the contaminated environment have attracted great concern. Reportedly, pretilachlor could partly be transformed to HECDEPA by Rhodococcus sp. B2. However, the effects of pretilachlor on soil bacterial communities and its complete metabolic pathway remain unknown. Herein, we investigated the mechanism of driving synergistic degradation of pretilachlor by strain B2 in the soil. The results revealed that pretilachlor showed a negative effect on bacterial communities and caused significant variations in the community structure. Strain B2 showed the ability to remediate the pretilachlor-contaminated soils and network analysis revealed that it may drive the enrichment of potential pretilachlor-degrading bacteria from the soil. The soil pretilachlor degradation may be facilitated by the members of the keystone families Comamonadaceae, Caulobacteraceae, Rhodospirillaceae, Chitinophagaceae, and Sphingomonadaceae. Meanwhile, Sphingomonas sp. M6, a member of the Sphingomonadaceae family, has been isolated from the strain B2 inoculation sample soil. The co-culture, comprising strain M6 and B2, could synergistic degrade pretilachlor within 30 h, which is the highest degradation rate. Strain M6 could completely degrade the HECDEPA via CDEPA and DEA. In the soil, a comparable pretilachlor degradation pathway may exist. This study suggested that strain B2 had the potential to drive the remediation of pretilachlor-contaminated soils.
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Affiliation(s)
- Hongming Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China.
| | - Shiyan Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Huijun Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Mengna Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Xiaye Yin
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Peng Lu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Qing Hong
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Aimin Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Rui Wan
- School of Ecology and Environment, Anhui Normal University, South of Jiuhua Road, Wuhu, Anhui 241002, China.
| | - Shangping Fang
- School of Anesthesiology, Wannan Medical College, Wuhu, Anhui, China
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Núñez-Montero K, Rojas-Villalta D, Barrientos L. Antarctic Sphingomonas sp. So64.6b showed evolutive divergence within its genus, including new biosynthetic gene clusters. Front Microbiol 2022; 13:1007225. [DOI: 10.3389/fmicb.2022.1007225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022] Open
Abstract
IntroductionThe antibiotic crisis is a major human health problem. Bioprospecting screenings suggest that proteobacteria and other extremophile microorganisms have biosynthetic potential for the production novel antimicrobial compounds. An Antarctic Sphingomonas strain (So64.6b) previously showed interesting antibiotic activity and elicitation response, then a relationship between environmental adaptations and its biosynthetic potential was hypothesized. We aimed to determine the genomic characteristics in So64.6b strain related to evolutive traits for the adaptation to the Antarctic environment that could lead to its diversity of potentially novel antibiotic metabolites.MethodsThe complete genome sequence of the Antarctic strain was obtained and mined for Biosynthetic Gene Clusters (BGCs) and other unique genes related to adaptation to extreme environments. Comparative genome analysis based on multi-locus phylogenomics, BGC phylogeny, and pangenomics were conducted within the closest genus, aiming to determine the taxonomic affiliation and differential characteristics of the Antarctic strain.Results and discussionThe Antarctic strain So64.6b showed a closest identity with Sphingomonas alpina, however containing a significant genomic difference of ortholog cluster related to degradation multiple pollutants. Strain So64.6b had a total of six BGC, which were predicted with low to no similarity with other reported clusters; three were associated with potential novel antibiotic compounds using ARTS tool. Phylogenetic and synteny analysis of a common BGC showed great diversity between Sphingomonas genus but grouping in clades according to similar isolation environments, suggesting an evolution of BGCs that could be linked to the specific ecosystems. Comparative genomic analysis also showed that Sphingomonas species isolated from extreme environments had the greatest number of predicted BGCs and a higher percentage of genetic content devoted to BGCs than the isolates from mesophilic environments. In addition, some extreme-exclusive clusters were found related to oxidative and thermal stress adaptations, while pangenome analysis showed unique resistance genes on the Antarctic strain included in genetic islands. Altogether, our results showed the unique genetic content on Antarctic strain Sphingomonas sp. So64.6, −a probable new species of this genetically divergent genus–, which could have potentially novel antibiotic compounds acquired to cope with Antarctic poly-extreme conditions.
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Draft Genome Sequence of Endophytic Sphingomonas faeni Strain ALB2, Isolated from the Leaf of a Cold-Desert Medicinal Plant. Microbiol Resour Announc 2022; 11:e0068722. [PMID: 36227099 PMCID: PMC9671012 DOI: 10.1128/mra.00687-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A leaf endophyte, Sphingomonas faeni strain ALB2, was isolated from a high-altitude medicinal plant, Arnebia euchorma. The draft genome sequence of the bacterium comprised 4,720,245 bp and contained 4,233 protein-coding genes, with a GC content of 65.66%. The bacterium harbored numerous biotechnology-relevant genes in its genome.
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