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Wani AK, Qadir F, Elboughdiri N, Rahayu F, Saefudin, Pranowo D, Martasari C, Kosmiatin M, Suhara C, Sudaryono T, Prayogo Y, Yadav KK, Muzammil K, Eltayeb LB, Alreshidi MA, Singh R. Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health. Biotechnol Adv 2025; 82:108580. [PMID: 40246210 DOI: 10.1016/j.biotechadv.2025.108580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Revised: 03/19/2025] [Accepted: 04/13/2025] [Indexed: 04/19/2025]
Abstract
Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India.
| | - Fayzan Qadir
- Department of Civil Engineering, Engineering & Technology, Jamia Millia Islamia-Jamia Nagar, New Delhi 110025, India
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il 81441, Saudi Arabia
| | - Farida Rahayu
- Research Center for Genetic Engineering, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Saefudin
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Dibyo Pranowo
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Chaireni Martasari
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Mia Kosmiatin
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Cece Suhara
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Tri Sudaryono
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Yusmani Prayogo
- Food Crops Research Center, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Krishna Kumar Yadav
- Department of VLSI Microelectronics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai -602105, Tamil Nadu, India; Environmental and Atmospheric Sciences Research Group, Scientific Research Center, Al-Ayen University, Nasiriyah, Thi-Qar, Iraq
| | - Khursheed Muzammil
- Department of Public Health, College of Applied Medical Sciences, Khamis Mushait, King Khalid University, Abha 62561, Saudi Arabia
| | - Lienda Bashier Eltayeb
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin AbdulAziz University- Al-Kharj, 11942 Riyadh, Saudi Arabia
| | - Maha Awjan Alreshidi
- Department of Chemistry, College of Science, University of Ha'il, Ha'il 81441, Saudi Arabia
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India
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Kracmarova-Farren M, Alexova E, Kodatova A, Mercl F, Szakova J, Tlustos P, Demnerova K, Stiborova H. Biochar-induced changes in soil microbial communities: a comparison of two feedstocks and pyrolysis temperatures. ENVIRONMENTAL MICROBIOME 2024; 19:87. [PMID: 39516989 PMCID: PMC11549753 DOI: 10.1186/s40793-024-00631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 10/24/2024] [Indexed: 11/16/2024]
Abstract
BACKGROUND The application of a biochar in agronomical soil offers a dual benefit of improving soil quality and sustainable waste recycling. However, utilizing new organic waste sources requires exploring the biochar's production conditions and application parameters. Woodchips (W) and bone-meat residues (BM) after mechanical deboning from a poultry slaughterhouse were subjected to pyrolysis at 300 °C and 500 °C and applied to cambisol and luvisol soils at ratios of 2% and 5% (w/w). RESULTS Initially, the impact of these biochar amendments on soil prokaryotes was studied over the course of one year. The influence of biochar variants was further studied on prokaryotes and fungi living in the soil, rhizosphere, and roots of Triticum aestivum L., as well as on soil enzymatic activity. Feedstock type, pyrolysis temperature, application dose, and soil type all played significant roles in shaping both soil and endophytic microbial communities. BM treated at a lower pyrolysis temperature of 300 °C increased the relative abundance of Pseudomonadota while causing a substantial decrease in soil microbial diversity. Conversely, BM prepared at 500 °C favored the growth of microbes known for their involvement in various nutrient cycles. The W biochar, especially when pyrolysed at 500 °C, notably affected microbial communities, particularly in acidic cambisol compared to luvisol. In cambisol, biochar treatments had a significant impact on prokaryotic root endophytes of T. aestivum L. Additionally, variations in prokaryotic community structure of the rhizosphere depended on the increasing distance from the root system (2, 4, and 6 mm). The BM biochar enhanced the activity of acid phosphatase, whereas the W biochar increased the activity of enzymes involved in the carbon cycle (β-glucosidase, β-xylosidase, and β-N-acetylglucosaminidase). CONCLUSIONS These results collectively suggest, that under appropriate production conditions, biochar can exert a positive influence on soil microorganisms, with their response closely tied to the biochar feedstock composition. Such insights are crucial for optimizing biochar application in agricultural practices to enhance soil health.
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Affiliation(s)
- Martina Kracmarova-Farren
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, Prague 6, 166 28, Czech Republic
| | - Eliska Alexova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, Prague 6, 166 28, Czech Republic
| | - Anezka Kodatova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, Prague 6, 166 28, Czech Republic
| | - Filip Mercl
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague - Suchdol, 165 21, Czech Republic
| | - Jirina Szakova
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague - Suchdol, 165 21, Czech Republic
| | - Pavel Tlustos
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague - Suchdol, 165 21, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, Prague 6, 166 28, Czech Republic
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague - Suchdol, 165 21, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, Prague 6, 166 28, Czech Republic.
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Shu S, Shi Y, Wang Z, Zhao Y, Fan B. Comprehensive agricultural ecological effects of aeration on regenerated liquid fertilizer of mini flush toilet. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174234. [PMID: 38917901 DOI: 10.1016/j.scitotenv.2024.174234] [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: 03/12/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
The high concentration of organic waste liquid obtained from the mini flush pipeline discharge technology based on source separation has the potential for fertilizer utilization. However, there are concerns about the risk of secondary pollution. This study proposes the idea of aeration treatment for regenerated liquid fertilizers to induce beneficial changes in their material composition and properties. Initially, this study compares the characteristic changes in nitrogen transformation of liquid fertilizer through aeration treatment. Subsequently, it examines the effects of different types of liquid fertilizers on soil properties, plant physiology, and soil microbial communities. Finally, we elucidate the flow and distribution of nitrogen in soil, plants, and nitrogen-containing gas emissions in agricultural ecosystems through material flow accounting. The study found that aeration treatment can reduce the ammonia nitrogen ratio while increasing the proportions of nitrite nitrogen and nitrate nitrogen. The regenerated liquid fertilizer through aeration treatment not only significantly increased the chlorophyll, protein, and polysaccharide content of vegetable leaves (P < 0.05) but also reduced nitrate accumulation. Moreover, it can reduce the risk of soil nitrate nitrogen leaching and increase the diversity of soil bacterial communities, enhancing the ecological functions of bacteria involved in carbon and nitrogen cycling. Material flow accounting indicated that aeration treatment for liquid fertilizer could reduce gaseous nitrogen loss by 50.0 %, improve the nitrogen utilization efficiency of vegetables by 95.5 %, and enhance soil nitrogen retention by 11.4 %. Overall, the results show that aeration treatment can improve the agricultural utilization of liquid fertilizer and reduce the risk of secondary pollution, providing preliminary decision-making support for optimizing resource treatment strategies for mini-flush toilet fecal waste to realize the agricultural cycle.
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Affiliation(s)
- Shangyi Shu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunpeng Shi
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zixiao Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yubing Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bin Fan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Chen Z, Liu Z, Song C. Agricultural fertilization near marshes impacts the potential for greenhouse gas emissions from wetland ecosystems by modifying microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172400. [PMID: 38631634 DOI: 10.1016/j.scitotenv.2024.172400] [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: 11/15/2023] [Revised: 03/15/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Ensuring agricultural security and preserving the health of wetland ecosystems are crucial concerns facing northeast China. However, the adverse effects of environmental pollution, especially nitrogen (N), caused by prolonged agricultural development on the health of marsh wetlands cannot be systematically recognized. To address this issue, an 18-year trial with four different levels of N application was carried out in a typical area of the Northeast region: 0, 6, 12, and 24 gN·m-2·a-1 (referred to as CK, N6, N12, and N24, respectively) to investigate changes in wetland ecological functioning. The results showed that long-term N input significantly enhanced soil N availability. High-level of N addition (N24) significantly reduced soil bacterial richness in October, while fungal diversity was significantly higher in June than in October for both control and N6 treatments. The main environmental factors affecting microorganisms in June were TN, NH4+, and EC, while bacterial and fungal communities were influenced by TN and Leaf Area Index (LAI), respectively, in October. It was found that the AN16S gene was significantly higher in June than in October, indicating that summer is the critical time for N removal in the wetland. N addition significantly reduced the abundance of the NIFH gene and decreased the N fixation potential of the wetland. In June, low and medium levels of N inputs promoted denitrification processes in the wetland and elevated the wetland N2O emission potential. The abundance of NARG, NIRK, and NOSZ genes decreased significantly in October compared to June, indicating a decrease in the wetland N2O emission potential. Additionally, it was observed that soil methanotrophs were positively affected by NH4+ and TN in October, thereby reducing the wetland CH4 emission potential. Our research provides a systematic understanding of the impact of agricultural N pollution on marsh wetlands, which can inform strategies to protect wetland health.
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Affiliation(s)
- Zhenbo Chen
- Faculty of Infrastructure Engineering, Dalian University of Technology, Dalian 116023, China
| | - Zhihong Liu
- Faculty of Infrastructure Engineering, Dalian University of Technology, Dalian 116023, China.
| | - Changchun Song
- Faculty of Infrastructure Engineering, Dalian University of Technology, Dalian 116023, China.
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Bel Mokhtar N, Asimakis E, Galiatsatos I, Maurady A, Stathopoulou P, Tsiamis G. Development of MetaXplore: An Interactive Tool for Targeted Metagenomic Analysis. Curr Issues Mol Biol 2024; 46:4803-4814. [PMID: 38785557 PMCID: PMC11120546 DOI: 10.3390/cimb46050289] [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: 04/15/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Over the last decades, the analysis of complex microbial communities by high-throughput sequencing of marker gene amplicons has become routine work for many research groups. However, the main challenges faced by scientists who want to make use of the generated sequencing datasets are the lack of expertise to select a suitable pipeline and the need for bioinformatics or programming skills to apply it. Here, we present MetaXplore, an interactive, user-friendly platform that enables the discovery and visualization of amplicon sequencing data. Currently, it provides a set of well-documented choices for downstream analysis, including alpha and beta diversity analysis, taxonomic composition, differential abundance analysis, identification of the core microbiome within a population, and biomarker analysis. These features are presented in a user-friendly format that facilitates easy customization and the generation of publication-quality graphics. MetaXplore is implemented entirely in the R language using the Shiny framework. It can be easily used locally on any system with R installed, including Windows, Mac OS, and most Linux distributions, or remotely via a web server without bioinformatic expertise. It can also be used as a framework for advanced users who can modify and expand the tool.
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Affiliation(s)
- Naima Bel Mokhtar
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, 30100 Agrinio, Greece; (N.B.M.); (E.A.); (I.G.); (P.S.)
| | - Elias Asimakis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, 30100 Agrinio, Greece; (N.B.M.); (E.A.); (I.G.); (P.S.)
| | - Ioannis Galiatsatos
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, 30100 Agrinio, Greece; (N.B.M.); (E.A.); (I.G.); (P.S.)
| | - Amal Maurady
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaâdi University, Tanger 93000, Morocco;
| | - Panagiota Stathopoulou
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, 30100 Agrinio, Greece; (N.B.M.); (E.A.); (I.G.); (P.S.)
| | - George Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, 30100 Agrinio, Greece; (N.B.M.); (E.A.); (I.G.); (P.S.)
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Branysova T, Petru N, Lopez Marin MA, Solcova M, Demnerova K, Stiborova H. Uncovering the microbial diversity of Czech Republic archives: A study of metabolically active airborne microbes. Heliyon 2024; 10:e27930. [PMID: 38560214 PMCID: PMC10981025 DOI: 10.1016/j.heliyon.2024.e27930] [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: 11/29/2023] [Revised: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Despite the diligent efforts of libraries, archives, and similar institutions to preserve cultural monuments, biodeterioration continues to pose a significant threat to these objects. One of the main sources of microorganisms responsible for the biodeterioration process is the presence of airborne microorganisms. Therefore, this research aims to monitor and compare outcomes of both culture-dependent (utilising various cultivation strategies) and culture-independent approaches (RNA-based sequencing) to identifying metabolically active airborne microorganisms in archives in the Czech Republic. Through this study, several species that have the potential to pose risks to both cultural heritage objects and the health of institution employees were found. Additionally, the efficacy of different cultivation media was demonstrated to be varied across archive rooms, highlighting the necessity of employing multiple cultivation media for comprehensive analyses. Of noteworthy importance, the resuscitating-promoting factor (Rpf) proved to be a pivotal tool, increasing bacterial culturability by up to 30% when synergistically employed Reasoner's 2A agar (R2A) and R2A + Rpf media. Next, the study emphasises the importance of integrating both culture-dependent and culture-independent approaches. The overlap between genera identified by the culture-dependent approach and those identified also by the culture-independent approach varied from 33% to surpassing 94%, with the maximum alignment exceeding 94% in only one case. Our results highlight the importance of actively monitoring and assessing levels of microbial air contamination in archives to prevent further deterioration of cultural heritage objects and to promote improved conditions for employees in archives and similar institutions.
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Affiliation(s)
- Tereza Branysova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Nicole Petru
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Marco A. Lopez Marin
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Milada Solcova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
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Zhang M, Xiong J, Zhou L, Li J, Fan J, Li X, Zhang T, Yin Z, Yin H, Liu X, Meng D. Community ecological study on the reduction of soil antimony bioavailability by SRB-based remediation technologies. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132256. [PMID: 37567138 DOI: 10.1016/j.jhazmat.2023.132256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Sulfate-reducing bacteria (SRB) were effective in stabilizing Sb. However, the influence of electron donors and acceptors during SRB remediation, as well as the ecological principles involved, remained unclear. In this study, Desulfovibrio desulfuricans ATCC 7757 was utilized to stabilize soil Sb within microcosm. Humic acid (HA) or sodium sulfate (Na2SO4) were employed to enhance SRB capacity. The SRB+HA treatment exhibited the highest Sb stabilization rate, achieving 58.40%. Bacterial community analysis revealed that SRB altered soil bacterial diversity, community composition, and assembly processes, with homogeneous selection as the predominant assembly processes. When HA and Na2SO4 significantly modified the stimulated microbial community succession trajectories, shaped the taxonomic composition and interactions of the bacterial community, they showed converse effect in shaping bacterial community which were both helpful for promoting dissimilatory sulfate reduction. Na2SO4 facilitated SRB-mediated anaerobic reduction and promoted interactions between SRB and bacteria involved in nitrogen and sulfur cycling. The HA stimulated electron generation and storage, and enhanced the interactions between SRB and bacteria possessing heavy metal tolerance or carbohydrate degradation capabilities.
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Affiliation(s)
- Min Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Jing Xiong
- Hunan urban and Rural Environmental Construction Co., Ltd, Changsha 410118, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing 101148, China
| | - Jingjing Li
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian 361000, China
| | - Jianqiang Fan
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian 361000, China
| | - Xing Li
- Hunan HIKEE Environmental Technology CO., LTD, Changsha 410221, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Hunan urban and Rural Environmental Construction Co., Ltd, Changsha 410118, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhuzhong Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China.
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Branysova T, Limpouch O, Durovic M, Demnerova K, Stiborova H. Bacterial Diversity on Historical Audio-Visual Materials and in the Atmosphere of Czech Depositories. Microbiol Spectr 2023; 11:e0117623. [PMID: 37428069 PMCID: PMC10434117 DOI: 10.1128/spectrum.01176-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/23/2023] [Indexed: 07/11/2023] Open
Abstract
Microbial contamination in cultural heritage storage facilities is undoubtedly still a huge problem and leads to the biodeterioration of historical objects and thus the loss of information for future generations. Most studies focus on fungi that colonize materials, which are the primary agents of biodeterioration. However, bacteria also play crucial roles in this process. Therefore, this study focuses on identifying bacteria that colonize audio-visual materials and those present in the air in the archives of the Czech Republic. For our purposes, the Illumina MiSeq amplicon sequencing method was used. Using this method, 18 bacterial genera with an abundance of higher than 1% were identified on audio-visual materials and in the air. We also evaluated some factors that were assumed to possibly influence the composition of bacterial communities on audio-visual materials, of which locality was shown to be significant. Locality also explained most of the variability in bacterial community structure. Furthermore, an association between genera colonizing materials and genera present in the air was demonstrated, and indicator genera were evaluated for each locality. IMPORTANCE The existing literature on microbial contamination of audio-visual materials has predominantly used culture-based methods to evaluate contamination and has overlooked the potential impact of environmental factors and material composition on microbial communities. Furthermore, previous studies have mainly focused on contamination by microscopic fungi, neglecting other potentially harmful microorganisms. To address these gaps in knowledge, our study is the first to provide a comprehensive analysis of bacterial communities present on historical audio-visual materials. Our statistical analyses demonstrate the critical importance of including air analysis in such studies, as airborne microorganisms can significantly contribute to the contamination of these materials. The insights gained from this study are not only valuable in developing effective preventive measures to mitigate contamination but also valuable in identifying targeted disinfection methods for specific types of microorganisms. Overall, our findings highlight the need for a more holistic approach to understanding microbial contamination in cultural heritage materials.
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Affiliation(s)
- Tereza Branysova
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Ondrej Limpouch
- Faculty of Chemical Technology, Department of Chemical Technology of Monument Conservation, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Michal Durovic
- Faculty of Chemical Technology, Department of Chemical Technology of Monument Conservation, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Katerina Demnerova
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Hana Stiborova
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Prague, Czech Republic
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Zheng W, Zheng X, Wu Y, Lv S, Ge C, Wang X, Wang Q, Cui J, Ren N, Chen Y. Diversity Temporal-Spatial Dynamics of Potato Rhizosphere Ciliates and Contribution to Nitrogen- and Carbon-Derived Nutrition in North-East China. PLANTS (BASEL, SWITZERLAND) 2023; 12:2260. [PMID: 37375886 DOI: 10.3390/plants12122260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023]
Abstract
Ciliates are an important component of the rhizosphere microorganism community, but their nutritional contribution to plants has not been fully revealed. In this paper, we investigated the rhizosphere ciliate community of potatoes during six growth stages, illustrated the spatial-temporal dynamics of composition and diversity, and analyzed the correlation between soil physicochemical properties. The contributions of ciliates to the carbon- and nitrogen-derived nutrition of potatoes were calculated. Fifteen species of ciliates were identified, with higher diversity in the top soil, which increased as the potatoes grew, while they were more abundant in the deep soil, and the number decreased as the potatoes grew. The highest number of species of ciliates appeared in July (seedling stage). Among the five core species of ciliates, Colpoda sp. was the dominant species in all six growth stages. Multiple physicochemical properties affected the rhizosphere ciliate community, with ammonium nitrogen (NH4+-N) and the soil water content (SWC) greatly influencing ciliate abundance. The key correlation factors of ciliates diversity were NH4+-N, available phosphorus (AP), and soil organic matter (SOM). The annual average contribution rates of carbon and nitrogen by rhizosphere ciliates to potatoes were 30.57% and 23.31%, respectively, with the highest C/N contribution rates reaching 94.36% and 72.29% in the seedling stage. This study established a method for estimating the contributions of carbon and nitrogen by ciliates to crops and found that ciliates could be potential organic fertilizer organisms. These results might be used to improve water and nitrogen management in potato cultivation and promote ecological agriculture.
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Affiliation(s)
- Weibin Zheng
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xiaodan Zheng
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yuqing Wu
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Shaoyang Lv
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Chang Ge
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xiang Wang
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Qiuhong Wang
- Crop Academy, Heilongjiang University, Harbin 150080, China
| | - Jingjing Cui
- Crop Academy, Heilongjiang University, Harbin 150080, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Ying Chen
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
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Ma Y, Wang D, Guo X, Zhu YG, Delgado-Baquerizo M, Chu H. Root stoichiometry explains wheat endophytes and their link with crop production after four decades of fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157407. [PMID: 35850352 DOI: 10.1016/j.scitotenv.2022.157407] [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: 05/01/2022] [Revised: 06/24/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Fertilization can impact root endophytic microbiomes and food production. However, the impacts of decades of continued fertilization on root microbiomes, and their link with ongoing crop production, remain poorly understood. Here, we used a four decade-long fertilization experiment, including contrasting types of organic and inorganic fertilization, to investigate the effects of long-term fertilization on multi-kingdom root endophytic microbiomes, including keystone species (modules within microbial networks), and their indirect associations with the production of wheat, which is one of the most important crops worldwide. We found that long-term inorganic (nitrogen, phosphorus, potassium (NPK)) and organic (NPK with straw (NPKS) and NPK with cow manure (NPKM)) fertilization had significant impacts on the community composition of endophytic arbuscular mycorrhizal fungi (AMF), bacteria, and non-mycorrhizal fungi. In addition, compared with NPK fertilization, NPKS and NPKM amendments significantly decreased the microbial network complexity, which was associated with changes in the root iron content. Finally, we identified an important subset of keystone root endophyte species within the microbial network (Module #2), which was positively correlated with wheat yield, and affected by changes in root carbon to phosphorus ratio. This study provides evidence that long-term fertilization can affect keystone root endophytic species in the root microbiome, with implications for food security in an over-fertilized world.
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Affiliation(s)
- Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Daozhong Wang
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei 230031, China
| | - Xisheng Guo
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei 230031, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012 Sevilla, Spain; Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013 Sevilla, Spain.
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Kracmarova M, Uhlik O, Strejcek M, Szakova J, Cerny J, Balik J, Tlustos P, Kohout P, Demnerova K, Stiborova H. Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic. ENVIRONMENTAL MICROBIOME 2022; 17:13. [PMID: 35346385 PMCID: PMC8962459 DOI: 10.1186/s40793-022-00406-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/08/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial community structure in four different locations with three soil types. Since 1996, manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and NPK (NPK; 330 kg N/ha) fertilizers were periodically applied to the soils classified as chernozem, luvisol and cambisol, which are among the most abundant or fertile soils used for agricultural purposes in the world. In these soils, potato (Solanum tuberosum L.), winter wheat (Triticum aestivum L.), and spring barley (Hordeum vulgare L.) were rotated every three years. RESULTS Soil chemistry, which was significantly associated with location, fertilization, crop rotation, and the interaction of fertilization and location, was the dominant driver of soil microbial communities, both prokaryotic and fungal. A direct effect of long-term crop rotation and fertilization on the structure of their communities was confirmed, although there was no evidence of their influence on microbial diversity. Fungal and bacterial communities responded differently to fertilization treatments; prokaryotic communities were only significantly different from the control soil (CF) in soils treated with MF and SF3x, while fungal communities differed across all treatments. Indicator genera were identified for different treatments. These taxa were either specific for their decomposition activities or fungal plant pathogens. Sequential rotation of the three crops restricted the growth of several of the indicator plant pathogens. CONCLUSIONS Long-term fertilization and crop rotation significantly altered microbial community structure in the soil. While fertilization affected soil microorganisms mainly through changes in nutrient profile, crop rotations lead to the attraction and repulsion of specific plant pathogens. Such changes in soil microbial communities need to be considered when planning soil management.
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Affiliation(s)
- Martina Kracmarova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Jirina Szakova
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jindrich Cerny
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jiri Balik
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Pavel Tlustos
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Videnska 1083, 142 20, Praha 4, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Vinicna 5, 128 44, Praha 2, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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12
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Special Issue: Microorganisms and Plant Nutrition. Microorganisms 2021; 9:microorganisms9122571. [PMID: 34946172 PMCID: PMC8703746 DOI: 10.3390/microorganisms9122571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022] Open
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Factors Influencing the Fungal Diversity on Audio-Visual Materials. Microorganisms 2021; 9:microorganisms9122497. [PMID: 34946099 PMCID: PMC8709410 DOI: 10.3390/microorganisms9122497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 01/04/2023] Open
Abstract
The biodeterioration of audio–visual materials is a huge problem, as it can cause incalculable losses. To preserve these cultural heritage objects for future generations, it is necessary to determine the main agents of biodeterioration. This study focuses on identifying fungi, both from the air and smears from photographs and cinematographic films that differ in the type of carrier and binder, using high-throughput sequencing approaches. The alpha diversity measures of communities present on all types of carriers were compared, and a significant difference between cellulose acetate and baryta paper was observed. Next, the locality, type of carrier, and audio–visual material seem to affect the structure of fungal communities. Additionally, a link between the occurrence of the most abundant classes and species on audio–visual materials and air contamination in the archives was proven. In both cases, the most abundant classes were Agariomycetes, Dothideomycetes, and Eurotiomycetes, and approximately half of the 50 most abundant species detected on the audio–visual materials and in the air were identical.
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Beltran-Garcia MJ, Martínez-Rodríguez A, Olmos-Arriaga I, Valdes-Salas B, Di Mascio P, White JF. Nitrogen fertilization and stress factors drive shifts in microbial diversity in soils and plants. Symbiosis 2021. [DOI: 10.1007/s13199-021-00787-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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