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Wang X, Li J, Wang D, Sun C, Zhang X, Zhao J, Teng J, Wang Q. Unveiling microplastic's role in nitrogen cycling: Metagenomic insights from estuarine sediment microcosms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124591. [PMID: 39043311 DOI: 10.1016/j.envpol.2024.124591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/30/2024] [Accepted: 07/20/2024] [Indexed: 07/25/2024]
Abstract
Marine microplastics (MPs) pollution, with rivers as a major source, leads to MPs accumulation in estuarine sediments, which are also nitrogen cycling hotspots. However, the impact of MPs on nitrogen cycling in estuarine sediments has rarely been documented. In this study, we conducted microcosm experiment to investigate the effects of commonly encountered polyethylene (PE) and polystyrene (PS) MPs, with two MPs concentrations (0.3% and 3% wet sediment weight) based on environmental concentration considerations and dose-response effects, on sediment dissolved oxygen (DO) diffusion capacity and microbial communities using microelectrode system and metagenomic analysis respectively. The results indicated that high concentrations of PE-MPs inhibited DO diffusion during the mid-phase of the experiment, an effect that dissipated in the later stages. Metagenomic analysis revealed that MP treatments reduced the relative abundance of dominant microbial colonies in the sediments. The PCoA results demonstrated that MPs altered the microbial community structure, particularly evident under high concentration PE-MPs treatments. Functional analysis related to the nitrogen cycle suggested that PS-MPs promoted the nitrification, denitrification, and DNRA processes, but inhibited the ANRA process, while PE-MPs had an inhibitory effect on the nitrate reduction process and the ANRA process. Additionally, the high concentration of PE-MPs treatment significantly stimulated the abundance of genus (Bacillus) by 34.1% and genes (lip, pnbA) by 100-187.5% associated with plastic degradation, respectively. Overall, in terms of microbial community structure and the abundance of nitrogen cycling functional genes, PE- and PS- MPs exhibit both similarities and differences in their impact on nitrogen cycling. Our findings highlight the complexity of MP effects on nitrogen cycling in estuarine sediments and high concentrations of PE-MP stimulated plastic-degrading genus and genes.
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Affiliation(s)
- Xiaodan Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Jiasen Li
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Dongyu Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Chaofan Sun
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Xiaoli Zhang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China
| | - Jianmin Zhao
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Jia Teng
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Qing Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China.
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Flinkstrom Z, Bryson S, Candry P, Winkler MKH. Metagenomic clustering links specific metabolic functions to globally relevant ecosystems. mSystems 2024:e0057324. [PMID: 38980052 DOI: 10.1128/msystems.00573-24] [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: 04/22/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024] Open
Abstract
Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome's functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute's Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data. IMPORTANCE Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome's metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.
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Affiliation(s)
- Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | | | - Pieter Candry
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
- Laboratory of Systems & Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Mari-Karoliina H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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Wu Z, Li M, Qu L, Zhang C, Xie W. Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary. MICROBIOME 2024; 12:115. [PMID: 38918820 PMCID: PMC11200988 DOI: 10.1186/s40168-024-01817-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 04/17/2024] [Indexed: 06/27/2024]
Abstract
BACKGROUND Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the "salt-in" strategy, involving inorganic ion uptake, or the "salt-out" strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem. RESULTS Here, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline-specific to low-, intermediate-, or high-salinity-based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the "inorganic ion transport and metabolism" COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the "salt-in" strategy, three to the "salt-out" strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K+ transporter related to the "salt-in" strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla. CONCLUSIONS We demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the "salt-in" strategy mediated by Trk-type K+ transporters for microorganisms thriving under osmotic stress in the short residence-time estuary. Video Abstract.
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Affiliation(s)
- Ziheng Wu
- School of Marine Sciences, Sun Yat-Sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Minchun Li
- School of Marine Sciences, Sun Yat-Sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Liping Qu
- School of Marine Sciences, Sun Yat-Sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-Sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China.
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Abulfaraj AA, Shami AY, Alotaibi NM, Alomran MM, Aloufi AS, Al-Andal A, AlHamdan NR, Alshehrei FM, Sefrji FO, Alsaadi KH, Abuauf HW, Alshareef SA, Jalal RS. Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum. AMB Express 2024; 14:27. [PMID: 38381255 PMCID: PMC10881953 DOI: 10.1186/s13568-024-01678-4] [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: 12/22/2023] [Accepted: 01/28/2024] [Indexed: 02/22/2024] Open
Abstract
The operative mechanisms and advantageous synergies existing between the rhizobiome and the wild plant species Abutilon fruticosum were studied. Within the purview of this scientific study, the reservoir of genes in the rhizobiome, encoding the most highly enriched enzymes, was dominantly constituted by members of phylum Thaumarchaeota within the archaeal kingdom, phylum Proteobacteria within the bacterial kingdom, and the phylum Streptophyta within the eukaryotic kingdom. The ensemble of enzymes encoded through plant exudation exhibited affiliations with 15 crosstalking KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways. The ultimate goal underlying root exudation, as surmised from the present investigation, was the biosynthesis of saccharides, amino acids, and nucleic acids, which are imperative for the sustenance, propagation, or reproduction of microbial consortia. The symbiotic companionship existing between the wild plant and its associated rhizobiome amplifies the resilience of the microbial community against adverse abiotic stresses, achieved through the orchestration of ABA (abscisic acid) signaling and its cascading downstream effects. Emergent from the process of exudation are pivotal bioactive compounds including ATP, D-ribose, pyruvate, glucose, glutamine, and thiamine diphosphate. In conclusion, we hypothesize that future efforts to enhance the growth and productivity of commercially important crop plants under both favorable and unfavorable environmental conditions may focus on manipulating plant rhizobiomes.
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Affiliation(s)
- Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia.
| | - Ashwag Y Shami
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nahaa M Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Maryam M Alomran
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Abeer S Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Abeer Al-Andal
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Fatimah M Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, P.O. Box 7388, Makkah 21955, Saudi Arabia
| | - Fatmah O Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - Khloud H Alsaadi
- Department of Biological Science, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Haneen W Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 24381, Saudi Arabia
| | - Sahar A Alshareef
- Department of Biological Science, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21921, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biological Science, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia.
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Rui Y, Qiu G. Analysis of Antibiotic Resistance Genes in Water Reservoirs and Related Wastewater from Animal Farms in Central China. Microorganisms 2024; 12:396. [PMID: 38399800 PMCID: PMC10893252 DOI: 10.3390/microorganisms12020396] [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: 01/16/2024] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide evidence for the transmission mechanisms of drug resistance genes, in order to reveal the spread of drug resistance genes in wastewater from intensive farms in Central China to urban reservoirs that serve as drinking water sources and provide preliminary data for the treatment of wastewater from animal farms to reduce the threat to human beings. DNA extraction and metagenomic sequencing were performed on eight groups of samples collected from four water reservoirs and four related wastewaters from animal farms in Central China. Metagenomic sequencing showed that the top 20 AROs with the highest abundance were vanT_gene, vanY_gene, adeF, qacG, Mtub_rpsL_STR, vanY_gene_, vanW_gene, Mtub_murA_FOF, vanY_gene, vanH_gene, FosG, rsmA, qacJ, RbpA, vanW_gene, aadA6, vanY_gene, sul4, sul1, and InuF. The resistance genes mentioned above belong to the following categories of drug resistance mechanisms: antibiotic target replacement, antibiotic target protection, antibiotic inactivation, and antibiotic efflux. The resistomes that match the top 20 genes are Streptococcus agalactiae and Streptococcus anginosus; Enterococcus faecalis; Enterococcus faecium; Actinomyces viscosus and Bacillus cereus. Enterococcus faecium; Clostridium tetani; Streptococcus agalactiae and Streptococcus anginosus; Streptococcus agalactiae and Streptococcus anginosus; Acinetobacter baumannii, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Corynebacterium jeikeium, Corynebacterium urealyticum, Mycobacterium kansasii, Mycobacterium tuberculosis, Schaalia odontolytica, and Trueperella pyogenes; Mycobacterium avium and Mycobacterium tuberculosis; Aeromonas caviae, Enterobacter hormaechei, Vibrio cholerae, Vibrio metoecus, Vibrio parahaemolyticus, and Vibrio vulnificus; Pseudomonas aeruginosa and Pseudomonas fluorescens; Staphylococcus aureus and Staphylococcus equorum; M. avium, Achromobacter xylosoxidans, and Acinetobacter baumannii; Sphingobium yanoikuyae, Acinetobacter indicus, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, and Providencia stuartii. Unreported drug resistance genes and drug-resistant bacteria in Central China were identified in 2023. In the transmission path of drug resistance genes, the transmission path from aquaculture wastewater to human drinking water sources cannot be ignored. For the sake of human health and ecological balance, the treatment of aquaculture wastewater needs to be further strengthened, and the effective blocking of drug resistance gene transmission needs to be considered.
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Affiliation(s)
- Yapei Rui
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang 464000, China;
| | - Gang Qiu
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang 464000, China;
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Chang H, Gu C, Wang M, Chang Z, Zhou J, Yue M, Chen J, Qin X, Feng Z. Integrating shotgun metagenomics and metabolomics to elucidate the dynamics of microbial communities and metabolites in fine flavor cocoa fermentation in Hainan. Food Res Int 2024; 177:113849. [PMID: 38225124 DOI: 10.1016/j.foodres.2023.113849] [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: 09/13/2023] [Revised: 11/06/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024]
Abstract
The aim of this study was to investigate the dynamic profile of microorganisms and metabolites in Hainan Trinitario cocoa during a six-day spontaneous box fermentation process. Shotgun metagenomic and metabolomic approaches were employed for this investigation. The potential metabolic functions of microorganisms in cocoa fermentation were revealed through a joint analysis of microbes, functional genes, and metabolites. During the anaerobic fermentation phase, Hanseniaspora emerged as the most prevalent yeast genus, implicated in pectin decomposition and potentially involved in glycolysis and starch and sucrose metabolism. Tatumella, possessing potential for pyruvate kinase, and Fructobacillus with a preference for fructose, constituted the primary bacteria during the pre-turning fermentation stage. Upon the introduction of oxygen into the fermentation mass, acetic acid bacteria ascended to dominant within the microflora. The exponential proliferation of Acetobacter resulted in a decline in taxonomic richness and abundance. Moreover, the identification of novel species within the Komagataeibacter genus suggests that Hainan cocoa may serve as a valuable reservoir for the discovery of unique cocoa fermentation bacteria. The KEGG annotation of metabolites and enzymes also highlighted the significant involvement of phenylalanine metabolism in cocoa fermentation. This research will offer a new perspective for the selection of starter strains and the formulation of mixed starter cultures.
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Affiliation(s)
- Haode Chang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Chunhe Gu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Mengrui Wang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Ziqing Chang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Junping Zhou
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Mingzhe Yue
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Junxia Chen
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiaowei Qin
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China.
| | - Zhen Feng
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China.
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Song L, Feng Z, Zhou Q, Wu X, Zhang L, Sun Y, Li R, Chen H, Yang F, Yu Y. Metagenomic analysis of healthy and diseased peri-implant microbiome under different periodontal conditions: a cross-sectional study. BMC Oral Health 2024; 24:105. [PMID: 38233815 PMCID: PMC10795403 DOI: 10.1186/s12903-023-03442-9] [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: 02/05/2023] [Accepted: 09/21/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Peri-implantitis is a polybacterial infection that can lead to the failure of dental implant rehabilitation. This study aimed to profile the microbiome of the peri-implant plaque and estimate the effect of periodontitis on it among 40 Chinese participants with dental implant prostheses and presenting with varying peri-implant and periodontal health states. METHODS Submucosal plaque samples were collected from four distinct clinical categories based on both their implant and periodontal health status at sampling point. Clinical examinations of dental implant and remaining teeth were carried out. Metagenomic analysis was then performed. RESULTS The microbiome of the peri-implantitis sites differed from that of healthy implant sites, both taxonomically and functionally. Moreover, the predominant species in peri-implantitis sites were slightly affected by the presence of periodontitis. T. forsythia, P. gingivalis, T. denticola, and P. endodontalis were consistently associated with peri-implantitis and inflammatory clinical parameters regardless of the presence of periodontitis. Prevotella spp. and P. endodontalis showed significant differences in the peri-implantitis cohorts under different periodontal conditions. The most distinguishing function between diseased and healthy implants is related to flagellar assembly, which plays an important role in epithelial cell invasion. CONCLUSIONS The composition of the peri-implant microbiome varied in the diseased and healthy states of implants and is affected by individual periodontal conditions. Based on their correlations with clinical parameters, certain species are associated with disease and healthy implants. Flagellar assembly may play a vital role in the process of peri-implantitis.
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Affiliation(s)
- Liang Song
- Department of Stomatology, Shanghai Fifth People's Hospital, Fudan University, 801 Heqing Road, Shanghai, 200240, China
| | - Ziying Feng
- Department of Stomatology, Shanghai Fifth People's Hospital, Fudan University, 801 Heqing Road, Shanghai, 200240, China
| | - Qianrong Zhou
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Xingwen Wu
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Limin Zhang
- Department of Stomatology, Shanghai Fifth People's Hospital, Fudan University, 801 Heqing Road, Shanghai, 200240, China
| | - Yang Sun
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Ruixue Li
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Huijuan Chen
- Department of Stomatology, Shanghai Fifth People's Hospital, Fudan University, 801 Heqing Road, Shanghai, 200240, China
| | - Fei Yang
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Youcheng Yu
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
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Onwusereaka CO, Jalaludin J, Oluchi SE, Poh Choo VC. New generation sequencing: molecular approaches for the detection and monitoring of bioaerosols in an indoor environment: a systematic review. REVIEWS ON ENVIRONMENTAL HEALTH 2024; 0:reveh-2023-0004. [PMID: 38214730 DOI: 10.1515/reveh-2023-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024]
Abstract
INTRODUCTION The exposure of occupants to indoor air pollutants has increased in recent decades. The aim of this review is to discuss an overview of new approaches that are used to study fungal aerosols. Thus, this motivation was to compensate the gaps caused by the use of only traditional approaches in the study of fungal exposure. CONTENT The search involved various databases such as; Science Direct, PubMed, SAGE, Springer Link, EBCOHOST, MEDLINE, CINAHL, Cochrane library, Web of Science and Wiley Online Library. It was limited to full text research articles that reported the use of non-viable method in assessing bioaerosol, written in English Language, full text publications and published from year 2015-2022. SUMMARY AND OUTLOOK A total of 15 articles met the inclusion criteria and was included in this review. The use of next-generation sequencing, which is more commonly referred to as high-throughput sequencing (HTS) or molecular methods in microbial studies is based on the detection of genetic material of organisms present in a given sample. Applying these methods to different environments permitted the identification of the microorganisms present, and a better comprehension of the environmental impacts and ecological roles of microbial communities. Based on the reviewed articles, there is evidence that dust samples harbour a high diversity of human-associated bacteria and fungi. Molecular methods such as next generation sequencing are reliable tools for identifying and tracking the bacterial and fungal diversity in dust samples using 18S metagenomics approach.
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Affiliation(s)
- Cynthia Oluchi Onwusereaka
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Selangor, Malaysia
| | - Juliana Jalaludin
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Selangor, Malaysia
| | - Sampson Emilia Oluchi
- Department of Community Health, Faculty of Medicine and Health Science, Universiti Putra Malaysia Serdang, Selangor, Malaysia
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Solomon W, Janda T, Molnár Z. Unveiling the significance of rhizosphere: Implications for plant growth, stress response, and sustainable agriculture. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108290. [PMID: 38150841 DOI: 10.1016/j.plaphy.2023.108290] [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: 08/14/2023] [Revised: 12/11/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
In the rhizosphere, the activities within all processes and functions are primarily influenced by plant roots, microorganisms present in the rhizosphere, and the interactions between roots and microorganisms. The rhizosphere, a dynamic zone surrounding the roots, provides an ideal environment for a diverse microbial community, which significantly shapes plant growth and development. Microbial activity in the rhizosphere can promote plant growth by increasing nutrient availability, influencing plant hormonal signaling, and repelling or outcompeting pathogenic microbial strains. Understanding the associations between plant roots and soil microorganisms has the potential to revolutionize crop yields, improve productivity, minimize reliance on chemical fertilizers, and promote sustainable plant growth technologies. The rhizosphere microbiome could play a vital role in the next green revolution and contribute to sustainable and eco-friendly agriculture. However, there are still knowledge gaps concerning plant root-environment interactions, particularly regarding roots and microorganisms. Advances in metabolomics have helped to understand the chemical communication between plants and soil biota, yet challenges persist. This article provides an overview of the latest advancements in comprehending the communication and interplay between plant roots and microbes, which have been shown to impact crucial factors such as plant growth, gene expression, nutrient absorption, pest and disease resistance, and the alleviation of abiotic stress. By improving these aspects, sustainable agriculture practices can be implemented to increase the overall productivity of plant ecosystems.
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Affiliation(s)
- Wogene Solomon
- Department of Plant Science, Albert Kazmer Faculty of Mosonmagyarovar, Széchenyi István University, Hungary.
| | - Tibor Janda
- Agricultural Institute Centre for Agricultural Research, Martonvásár, Hungary
| | - Zoltán Molnár
- Department of Plant Science, Albert Kazmer Faculty of Mosonmagyarovar, Széchenyi István University, Hungary
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Song S, Morales Moreira Z, Briggs AL, Zhang XC, Diener AC, Haney CH. PSKR1 balances the plant growth-defence trade-off in the rhizosphere microbiome. NATURE PLANTS 2023; 9:2071-2084. [PMID: 37973937 DOI: 10.1038/s41477-023-01539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Abstract
Microbiota benefit their hosts by improving nutrient uptake and pathogen protection. How host immunity restricts microbiota while avoiding autoimmunity is poorly understood. Here we show that the Arabidopsis phytosulfokine receptor 1 (pskr1) mutant displays autoimmunity (plant stunting, defence-gene expression and reduced rhizosphere bacterial growth) in response to growth-promoting Pseudomonas fluorescens. Microbiome profiling and microbiota colonization showed that PSKR1-mediated reduction in bacterial growth and stunting is largely specific to Pseudomonas. Transcriptional profiling demonstrated that PSKR1 regulates the growth-defence trade-off during Pseudomonas colonization: PSKR1 upregulates plant photosynthesis and root growth but suppresses salicylic-acid-mediated defences. Genetic epistasis experiments showed that pskr1 stunting and restriction of bacterial growth are salicylic acid dependent. Finally, we showed that Pseudomonas, but not other bacteria, induces PSKR1 expression in roots, suggesting that Pseudomonas might manipulate plant signalling to promote its colonization. Our data demonstrate a genetic mechanism to coordinate beneficial functions of the microbiome while preventing autoimmunity.
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Affiliation(s)
- Siyu Song
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zayda Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Annika L Briggs
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xue-Cheng Zhang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Andrew C Diener
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Biological Sciences, The University of Pittsburgh, Pittsburgh, PA, USA.
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11
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Igo M, Xu L, Krishna A, Stewart S, Xu L, Li Z, Weaver JL, Stone H, Sacks L, Bensman T, Florian J, Rouse R, Han X. A metagenomic analysis for combination therapy of multiple classes of antibiotics on the prevention of the spread of antibiotic-resistant genes. Gut Microbes 2023; 15:2271150. [PMID: 37908118 PMCID: PMC10621307 DOI: 10.1080/19490976.2023.2271150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023] Open
Abstract
Antibiotics used systemically to treat infections may have off-target effects on the gut microbiome, potentially resulting in the emergence of drug-resistant bacteria or selection of pathogenic species. These organisms may present a risk to the host and spread to the environment with a risk of transmission in the community. To investigate the risk of emergent antibiotic resistance in the gut microbiome following systemic treatment with antibiotics, this metagenomic analysis project used next-generation sequencing, a custom-built metagenomics pipeline, and differential abundance analysis to study the effect of antibiotics (ampicillin, ciprofloxacin, and fosfomycin) in monotherapy and different combinations at high and low doses, to determine the effect on resistome and taxonomic composition in the gut of Balb/c mice. The results showed that low-dose monotherapy treatments showed little change in microbiome composition but did show an increase in expression of many antibiotic-resistant genes (ARGs) posttreatment. Dual combination treatments allowed the emergence of some conditionally pathogenic bacteria and some increase in the abundance of ARGs despite a general decrease in microbiota diversity. Triple combination treatment was the most successful in inhibiting emergence of relevant opportunistic pathogens and completely suppressed all ARGs after 72 h of treatment. The relative abundances of mobile genetic elements that can enhance transmission of antibiotic resistance either decreased or remained the same for combination therapy while increasing for low-dose monotherapy. Combination therapy prevented the emergence of ARGs and decreased bacterial diversity, while low-dose monotherapy treatment increased ARGs and did not greatly change bacterial diversity.
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Affiliation(s)
- Matthew Igo
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Lei Xu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ashok Krishna
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Sharron Stewart
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Lin Xu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - James L. Weaver
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Heather Stone
- Office of Medical Policy, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Leonard Sacks
- Office of Medical Policy, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Timothy Bensman
- Division of Infectious Disease Pharmacology, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Jeffry Florian
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Rodney Rouse
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
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12
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Shivaram KB, Bhatt P, Verma MS, Clase K, Simsek H. Bacteriophage-based biosensors for detection of pathogenic microbes in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165859. [PMID: 37516175 DOI: 10.1016/j.scitotenv.2023.165859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Wastewater is discarded from several sources, including industry, livestock, fertilizer application, and municipal waste. If the disposed of wastewater has not been treated and processed before discharge to the environment, pathogenic microorganisms and toxic chemicals are accumulated in the disposal area and transported into the surface waters. The presence of harmful microbes is responsible for thousands of human deaths related to water-born contamination every year. To be able to take the necessary step and quick action against the possible presence of harmful microorganisms and substances, there is a need to improve the effective speed of identification and treatment of these problems. Biosensors are such devices that can give quantitative information within a short period of time. There have been several biosensors developed to measure certain parameters and microorganisms. The discovered biosensors can be utilized for the detection of axenic and mixed microbial strains from the wastewaters. Biosensors can further be developed for specific conditions and environments with an in-depth understanding of microbial organization and interaction within that community. In this regard, bacteriophage-based biosensors have become a possibility to identify specific live bacteria in an infected environment. This paper has investigated the current scenario of microbial community analysis and biosensor development in identifying the presence of pathogenic microorganisms.
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Affiliation(s)
- Karthik Basthi Shivaram
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Mohit S Verma
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Kari Clase
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Halis Simsek
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA.
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13
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Fang K, Yang AL, Li YX, Zeng ZY, Wang RF, Li T, Zhao ZW, Zhang HB. Native plants change the endophyte assembly and growth of an invasive plant in response to climatic factors. Appl Environ Microbiol 2023; 89:e0109323. [PMID: 37815356 PMCID: PMC10617555 DOI: 10.1128/aem.01093-23] [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: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 10/11/2023] Open
Abstract
Climate change, microbial endophytes, and local plants can affect the establishment and expansion of invasive species, yet no study has been performed to assess these interactions. Using a growth chamber, we integrated the belowground (rhizosphere soils) and aboveground (mixture of mature leaf and leaf litter) microbiota into an experimental framework to evaluate the impacts of four native plants acting as microbial inoculation sources on endophyte assembly and growth of the invasive plant Ageratina adenophora in response to drought stress and temperature change. We found that fungal and bacterial enrichment in the leaves and roots of A. adenophora exhibited distinct patterns in response to climatic factors. Many fungi were enriched in roots in response to high temperature and drought stress; in contrast, many bacteria were enriched in leaves in response to low temperature and drought stress. Inoculation of microbiota from phylogenetically close native plant species (i.e., Asteraceae Artemisia atrovirens) causes the recipient plant A. adenophora (Asteraceae) to enrich dominant microbial species from inoculation sources, which commonly results in a lower dissimilar endophytic microbiota and thus produces more negative growth effects when compared to non-Asteraceae inoculations. Drought, microbial inoculation source, and temperature directly impacted the growth of A. adenophora. Both drought and inoculation also indirectly impacted the growth of A. adenophora by changing the root endophytic fungal assembly. Our data indicate that native plant identity can greatly impact the endophyte assembly and host growth of invasive plants, which is regulated by drought and temperature.IMPORTANCEThere has been increasing interest in the interactions between global changes and plant invasions; however, it remains to quantify the role of microbial endophytes in plant invasion with a consideration of their variation in the root vs leaf of hosts, as well as the linkages between microbial inoculations, such as native plant species, and climatic factors, such as temperature and drought. Our study found that local plants acting as microbial inoculants can impact fungal and bacterial enrichment in the leaves and roots of the invasive plant Ageratina adenophora and thus produce distinct growth effects in response to climatic factors; endophyte-mediated invasion of A. adenophora is expected to operate more effectively under favorable moisture. Our study is important for understanding the interactions between climate change, microbial endophytes, and local plant identity in the establishment and expansion of invasive species.
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Affiliation(s)
- Kai Fang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ai-Ling Yang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yu-Xuan Li
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Zhao-Ying Zeng
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Rui-Fang Wang
- College of Agriculture and Forestry, Puer University, Puer, Yunnan, China
| | - Tao Li
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Zhi-Wei Zhao
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
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14
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Simister RL, Iulianella Phillips BP, Wickham AP, Cayer EM, Hart CJR, Winterburn PA, Crowe SA. DNA sequencing, microbial indicators, and the discovery of buried kimberlites. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:387. [PMID: 38665197 PMCID: PMC11041713 DOI: 10.1038/s43247-023-01020-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 09/19/2023] [Indexed: 04/28/2024]
Abstract
Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.
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Affiliation(s)
- Rachel L. Simister
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Bianca P. Iulianella Phillips
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Andrew P. Wickham
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Erika M. Cayer
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Craig J. R. Hart
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Peter A. Winterburn
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Sean A. Crowe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
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15
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Châtillon E, Cébron A, Rigal F, Cagnon C, Lorgeoux C, Faure P, Duran R, Cravo-Laureau C. Functional redundancy in response to runoff input upholds microbial community in hydrocarbon-contaminated land-sea continuum. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122330. [PMID: 37572846 DOI: 10.1016/j.envpol.2023.122330] [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: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/05/2023] [Indexed: 08/14/2023]
Abstract
An experimental approach mimicking the land-sea continuum in microcosms was developed in order to determine the effect of the terrigenous inputs by soil runoff on the microbial functional potential in hydrocarbon (HC) contaminated marine coastal sediment. We hypothesized that the coalescent event increases the functional potential of microbial communities in marine coastal sediments, influencing the fate of HC in marine coastal ecosystems. The microbial functional potential including the HC degradation ability was assessed by DNA-array to compare the sediment receiving or not terrigenous inputs. The removal of HC and the functional gene richness in sediment was unchanged with the terrigenous inputs. However, the gene variants (GVs) composition was modified indicating functional redundancy. In addition, functional indicators including GVs related to sulfite reduction, denitrification and polyaromatic degradation were identified in higher proportion in sediment receiving terrigenous inputs. The terrigenous inputs modified the functional co-occurrence networks, showing a reorganization of the GVs associations with an increase of the network complexity. Different keystone GVs ensuring similar functions were identified in networks with or without terrigenous inputs, further confirming functional redundancy. We argue that functional redundancy maintains the structure of microbial community in hydrocarbon-contaminated land-sea continuum mixing zone. Our results provide helpful functional information for the monitoring and management of coastal environment affected by human land-based activities.
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Affiliation(s)
- Elise Châtillon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, GeoRessources, F-54000, Nancy, France
| | - François Rigal
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Pierre Faure
- Université de Lorraine, CNRS, LIEC, F-54000, Nancy, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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16
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Lim Y, Yang SJ, Kang I, Cho JC. Metagenomic data from surface seawater of the east coast of South Korea. Sci Data 2023; 10:647. [PMID: 37737276 PMCID: PMC10517112 DOI: 10.1038/s41597-023-02556-7] [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: 06/14/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
The East Sea, also known as the Sea of Japan, is a marginal sea located in the western Pacific Ocean, displaying comparable characteristics to Earth's oceans, thereby meriting its recognition as a "miniature ocean". The East Sea exhibits a range of annually-recurring biogeochemical features in accordance with seasonal fluctuations, such as phytoplankton blooms during the spring and autumn seasons. Despite ongoing monitoring efforts focused on water quality and physicochemical parameters, the investigation of prokaryotic assemblages in the East Sea, encompassing seasonal variations, has been infrequently pursued. Here, we present a monthly time-series metagenomic dataset spanning a one-year period in 2009, obtained from surface (10 m) seawater samples collected off the coast of the East Sea. The dataset encompasses 12 metagenomes, amounting 195 Gbp, with 14.73-22.52 Gbp per sample. This dataset is accompanied by concurrently measured physicochemical parameters. Our anticipation is that these metagenomes will facilitate extensive investigations aimed at elucidating various aspects of the marine microbial ecosystems in the East Sea.
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Affiliation(s)
- Yeonjung Lim
- Center for Molecular and Cell Biology, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea
| | - Seung-Jo Yang
- CJ Bioscience, Inc., Sejong-daero 14, Seoul, 04527, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
- Department of Biological Sciences and Bioengineering, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
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17
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Liu J, Xu H, Wang Z, Liu J, Gong X. Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae). Microorganisms 2023; 11:2364. [PMID: 37764208 PMCID: PMC10537169 DOI: 10.3390/microorganisms11092364] [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: 08/20/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes.
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Affiliation(s)
- Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Xu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Zhaochun Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
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18
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Sanz-Sáez I, Sánchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós-Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME COMMUNICATIONS 2023; 3:92. [PMID: 37660234 PMCID: PMC10475052 DOI: 10.1038/s43705-023-00290-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/04/2023]
Abstract
Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2-0.8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
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Affiliation(s)
- Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering; The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Eric Karsenti
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016, Paris, France
- Directors' Research European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Susana Agustí
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
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Goffredi SK, Panossian B, Brzechffa C, Field N, King C, Moggioli G, Rouse GW, Martín-Durán JM, Henry LM. A dynamic epibiont community associated with the bone-eating polychaete genus Osedax. mBio 2023; 14:e0314022. [PMID: 37382438 PMCID: PMC10470745 DOI: 10.1128/mbio.03140-22] [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: 11/08/2022] [Accepted: 05/08/2023] [Indexed: 06/30/2023] Open
Abstract
Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of Osedax, which change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of Osedax, which comprise 67% of the bacterial community on the trunk, appear initially dominated by the genus Arcobacter (at early time points <24 mo), the Sulfurospirillum at intermediate stages (~50 mo), and the Sulfurimonas at later stages (>140 mo) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests potential for a transition from heterotrophy to autotrophy and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free-living relatives, the Osedax epibiont genomes were enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein (ELP) domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms. IMPORTANCE Symbiotic associations are widespread in nature and we can expect to find them in every type of ecological niche. In the last twenty years, the myriad of functions, interactions and species comprising microbe-host associations has fueled a surge of interest and appreciation for symbiosis. During this 14-year study, we reveal a dynamic population of bacterial epibionts, integrated into the epidermis of 7 species of a deep-sea worm group that feeds exclusively on the remains of marine mammals. The bacterial genomes provide clues of a long evolutionary history with these enigmatic worms. On the host surface, they exchange genes and appear to undergo ecological succession, as the whale carcass habitat degrades over time, similar to what is observed for some free-living communities. These, and other annelid worms are important keystone species for diverse deep-sea environments, yet the role of attached external bacteria in supporting host health has received relatively little attention.
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Affiliation(s)
- Shana K. Goffredi
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Balig Panossian
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Camille Brzechffa
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Naomi Field
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Chad King
- Monterey Bay National Marine Sanctuary, Monterey, California, USA
| | - Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg W. Rouse
- Scripps Oceanography, University of California, La Jolla, California, USA
| | - José M. Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Lee M. Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
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20
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Qu H, Long Y, Wang X, Wang K, Chen L, Yang Y, Chen L. Diversity and Abundance of Bacterial and Fungal Communities Inhabiting Camellia sinensis Leaf, Rhizospheric Soil, and Gut of Agriophara rhombata. Microorganisms 2023; 11:2188. [PMID: 37764032 PMCID: PMC10536862 DOI: 10.3390/microorganisms11092188] [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: 06/26/2023] [Revised: 08/16/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
Agriophara rhombata is a tea leaf moth that is considered one of the most destructive pests of Camellia sinensis (tea plant). Several recent studies have shown that many insects acquire part of the microbiome from their host and soil, but the pattern and diversity of their microbiome have not been clearly demonstrated. The present study aimed to investigate the bacterial and fungal communities present in the rhizospheric soil and leaf of tea plant compared to the gut of tea moth at different developmental stages (larvae, pupae, adult female and male) using Illumina MiSeq technology. Alpha diversity (Shannon index) showed higher (p < 0.05) bacterial and fungal diversity in soil samples than in leaf and tea moth larvae, pupae, and adult gut samples. However, during different developmental stages of tea moth, bacterial and fungal diversity did not differ (p > 0.05) between larvae, pupae, female, and male guts. Beta diversity also revealed more distinct bacterial and fungal communities in soil and leaf samples compared with tea moth gut samples, which had a more similar microbiome. Furthermore, Proteobacteria, Firmicutes, and Tenericutes were detected as the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most abundant fungal phyla among all groups, but their relative abundance was comparatively higher (p < 0.05) in soil and leaf samples compared to tea moth gut samples. Similarly, Klebsiella, Streptophyta, and Enterococcus were the top three bacterial genera, while Candida, Aureobasidium, and Strelitziana were the top three fungal genera, and their relative abundance varied significantly (p < 0.05) among all groups. The KEGG analysis also revealed significantly higher (p < 0.5) enrichment of the functional pathways of bacterial communities in soil and leaf samples than in tea moth gut samples. Our study concluded that the bacterial and fungal communities of soil and tea leaves were more diverse and were significantly different from the tea moth gut microbiome at different developmental stages. Our findings contribute to our understanding of the gut microbiota of the tea moth and its potential application in the development of pest management techniques.
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Affiliation(s)
- Hao Qu
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650000, China
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - Yaqin Long
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650000, China
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - Xuesong Wang
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650000, China
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - Kaibo Wang
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650000, China
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - Long Chen
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650000, China
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - Yunqiu Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230000, China
| | - Linbo Chen
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650000, China
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
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Alshehri WA, Abulfaraj AA, Alqahtani MD, Alomran MM, Alotaibi NM, Alwutayd K, Aloufi AS, Alshehrei FM, Alabbosh KF, Alshareef SA, Ashy RA, Refai MY, Jalal RS. Abundant resistome determinants in rhizosphere soil of the wild plant Abutilon fruticosum. AMB Express 2023; 13:92. [PMID: 37646836 PMCID: PMC10469157 DOI: 10.1186/s13568-023-01597-w] [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: 05/30/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
A metagenomic whole genome shotgun sequencing approach was used for rhizospheric soil micribiome of the wild plant Abutilon fruticosum in order to detect antibiotic resistance genes (ARGs) along with their antibiotic resistance mechanisms and to detect potential risk of these ARGs to human health upon transfer to clinical isolates. The study emphasized the potential risk to human health of such human pathogenic or commensal bacteria, being transferred via food chain or horizontally transferred to human clinical isolates. The top highly abundant rhizospheric soil non-redundant ARGs that are prevalent in bacterial human pathogens or colonizers (commensal) included mtrA, soxR, vanRO, golS, rbpA, kdpE, rpoB2, arr-1, efrA and ileS genes. Human pathogenic/colonizer bacteria existing in this soil rhizosphere included members of genera Mycobacterium, Vibrio, Klebsiella, Stenotrophomonas, Pseudomonas, Nocardia, Salmonella, Escherichia, Citrobacter, Serratia, Shigella, Cronobacter and Bifidobacterium. These bacteria belong to phyla Actinobacteria and Proteobacteria. The most highly abundant resistance mechanisms included antibiotic efflux pump, antibiotic target alteration, antibiotic target protection and antibiotic inactivation. antimicrobial resistance (AMR) families of the resistance mechanism of antibiotic efflux pump included resistance-nodulation-cell division (RND) antibiotic efflux pump (for mtrA, soxR and golS genes), major facilitator superfamily (MFS) antibiotic efflux pump (for soxR gene), the two-component regulatory kdpDE system (for kdpE gene) and ATP-binding cassette (ABC) antibiotic efflux pump (for efrA gene). AMR families of the resistance mechanism of antibiotic target alteration included glycopeptide resistance gene cluster (for vanRO gene), rifamycin-resistant beta-subunit of RNA polymerase (for rpoB2 gene) and antibiotic-resistant isoleucyl-tRNA synthetase (for ileS gene). AMR families of the resistance mechanism of antibiotic target protection included bacterial RNA polymerase-binding protein (for RbpA gene), while those of the resistance mechanism of antibiotic inactivation included rifampin ADP-ribosyltransferase (for arr-1 gene). Better agricultural and food transport practices are required especially for edible plant parts or those used in folkloric medicine.
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Affiliation(s)
- Wafa A Alshehri
- Department of Biology, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia
| | - Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, 21911, Rabigh, Saudi Arabia
| | - Mashael D Alqahtani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Maryam M Alomran
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Nahaa M Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Khairiah Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Abeer S Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Fatimah M Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, P.O. Box 7388, 21955, Makkah, Saudi Arabia
| | - Khulood F Alabbosh
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Sahar A Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, 21921, Jeddah, Saudi Arabia
| | - Ruba A Ashy
- Department of Biology, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia
| | - Mohammed Y Refai
- Department of Biochemistry, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biology, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia.
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Kim H, Hong JS, Yun PY, Hwang KG, Kim KS, Lee HJ, Park KU. Exploration of the interplay between spatially distinct microbial habitats through comparative analysis. J Oral Microbiol 2023; 15:2229693. [PMID: 37396300 PMCID: PMC10308874 DOI: 10.1080/20002297.2023.2229693] [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: 04/10/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023] Open
Abstract
Objectives The oral microbiome is closely associated with systemic diseases, indicating the presence of bacteremia and inflammatory mediators in the systemic circulation. Our research aims to investigate the relationship between the oral microbiome and other microbial habitats. Methods We analyzed 180 specimens from 36 patients, including saliva, buccal swab, plaque, stool, and blood samples from a healthy group (Non_PD, n = 18) and a periodontitis group (PD, n = 18). The final analysis included 147 specimens, with varying sample sizes for each group. Metagenomic analysis was performed using prokaryotic 16S rRNA on the MiSeq platform (Illumina). Results PD saliva showed significant richness differences (P's < 0.05), similar to plaque. Buccal swabs had slight variations. Microbial network analysis revealed altered microbial interactions in the PD group, with decreased interactions in saliva and buccal swabs, and increased interactions in plaque. In our analysis of nine specimens where all paired habitat samples could be analyzed, microorganisms linked to oral periodontitis were found in sterile blood samples, resembling the oral cavity's composition. Conclusions Microbiome differences should consider overall microbial-environment interactions, alongside diversity and richness. Our data cautiously suggest that disease-related changes in the salivary microbiome may be reflected in blood specimens through the oral-blood axis.
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Affiliation(s)
- Hyunji Kim
- Department of Laboratory Medicine, Seoul National University Bundang Hospital and Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin-Sil Hong
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Pil-Young Yun
- Department of Oral and Maxillofacial Surgery, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Dentistry and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Kyung-Gyun Hwang
- Division of Oral and Maxillofacial Surgery, Department of Dentistry, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital and Seoul National University College of Medicine, Seoul, Republic of Korea
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Jiang J, Hu X, Ji X, Chen H. High throughput sequencing technology facility research of genomic modification crop cultivation influencing soil microbe. FRONTIERS IN PLANT SCIENCE 2023; 14:1208111. [PMID: 37324715 PMCID: PMC10264764 DOI: 10.3389/fpls.2023.1208111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023]
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Takahashi M, Saccò M, Kestel JH, Nester G, Campbell MA, van der Heyde M, Heydenrych MJ, Juszkiewicz DJ, Nevill P, Dawkins KL, Bessey C, Fernandes K, Miller H, Power M, Mousavi-Derazmahalleh M, Newton JP, White NE, Richards ZT, Allentoft ME. Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162322. [PMID: 36801404 DOI: 10.1016/j.scitotenv.2023.162322] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.
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Affiliation(s)
- Miwa Takahashi
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia.
| | - Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia.
| | - Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mieke van der Heyde
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew J Heydenrych
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Jarman Laboratory, Indian Ocean Marine Research Centre, School of Biological Sciences, University of Western Australia, Australia
| | - David J Juszkiewicz
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Kathryn L Dawkins
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Cindy Bessey
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Joshua P Newton
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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Wang Q, Wang D, Agathokleous E, Cheng C, Shang B, Feng Z. Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone. Appl Environ Microbiol 2023; 89:e0018023. [PMID: 37022183 PMCID: PMC10132097 DOI: 10.1128/aem.00180-23] [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: 02/04/2023] [Accepted: 03/04/2023] [Indexed: 04/07/2023] Open
Abstract
Ethylenediurea (EDU) can effectively mitigate the crop yield loss caused by ozone (O3), a major, phytotoxic air pollutant. However, the relevant mechanisms are poorly understood, and the effect of EDU on soil ecosystems has not been comprehensively examined. In this study, a hybrid rice variety (Shenyou 63) was cultivated under ambient O3 and sprayed with 450 ppm EDU or water every 10 days. Real time quantitative polymerase chain reaction (RT-qPCR) showed that EDU had no significant effect on the microbial abundance in either rhizospheric or bulk soils. By applying both metagenomic sequencing and the direct assembly of nitrogen (N)-cycling genes, EDU was found to decrease the abundance of functional genes related to nitrification and denitrification processes. Moreover, EDU increased the abundance of genes involved in N-fixing. Although the abundance of some functional genes did not change significantly, nonmetric multidimensional scaling (NMDS) and a principal coordinates analysis (PCoA) suggested that the microbial community structure involved in N cycling was altered by EDU. The relative abundances of nifH-and norB-harboring microbial genera in the rhizosphere responded differently to EDU, suggesting the existence of functional redundancy, which may play a key role in sustaining microbially mediated N-cycling under ambient O3. IMPORTANCE Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. Due to its sensitivity to environmental changes, the microbial community can be used as an indicator to assess the environmental impacts of agricultural practices on soil quality. This study aimed to unravel the effects of EDU spray on the abundance, community structure, and ecological functions of microbial communities in the rhizosphere of rice plants. Our study provides a deep insight into the impact of EDU spray on microbial-mediated N cycling and the structure of N-cycling microbial communities. Our findings help to elucidate the mode of action of EDU in alleviating O3 stress in crops from the perspective of regulating the structure and function of the rhizospheric soil microbial community.
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Affiliation(s)
- Qi Wang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Dan Wang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Evgenios Agathokleous
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Cheng Cheng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Bo Shang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
| | - Zhaozhong Feng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, Jiangsu, China
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26
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Liu Y, Wang M, Li W, Gao Y, Li H, Cao N, Hao W, Zhao L. Differences in gut microbiota and its metabolic function among different fasting plasma glucose groups in Mongolian population of China. BMC Microbiol 2023; 23:102. [PMID: 37060052 PMCID: PMC10105465 DOI: 10.1186/s12866-023-02852-7] [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: 06/23/2022] [Accepted: 04/05/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Many studies reported the association between gut microbiota and type 2 diabetes mellitus (T2D), but it is still unclear which bacterial genus plays a key role and how the metabolic function of gut microbiota changes in the occurrence and development of T2D. Besides, there is a high diabetic prevalence in Mongolian population, which may be partly affected by their high calorie diet. This study identified the main bacterial genus influencing T2D in Mongolian population, and analyzed the changes of metabolic function of gut microbiome. The association between dietary factors and the relative abundance of main bacterial genus and its metabolic function was also studied. METHODS Dietary surveys and gut microbiota test were performed on 24 Mongolian volunteers that were divided into T2D (6 cases), PRET2D (6 cases) and Control group (12 cases) according to fasting plasma glucose (FPG) values. The relative abundance and metabolic function of gut microbiome from their fecal samples were measured by metagenomic analysis. Statistic method was used to evaluate the association between dietary factors and the relative abundance of the main bacterial genus or its metabolic function. RESULTS This study found that the Clostridium genus may be one of the key bacterial genera affecting the process of T2D. First, the relative abundance of Clostridium genus was significantly different among the three groups. Second, there was a higher relative abundance of metabolic enzymes of gut bacteria in PRET2D and T2D group than that in Control group. Third, a strong correlation between Clostridium genus and many metabolic enzymes was uncovered, many of which may be produced by the Clostridium. Last, carotene intake daily was negatively correlated with the Clostridium but positively correlated with tagaturonate reductase catalyzing interconversions of pentose and glucuronate. CONCLUSIONS The gut Clostridium genus may play an important role in the development of T2D and it could be a potential biomarker for T2D in Mongolian population. Meanwhile, the metabolic function of gut bacteria has changed during the early stage of T2D and the changes in carbohydrate, amino acid, lipid or energy metabolism of Clostridium genus may play a critical role. In addition, the carotene intake may affect reproduction and metabolic function of Clostridium genus.
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Affiliation(s)
- Yanchao Liu
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
- Laboratory for Molecular Epidemiology in Chronic Diseases, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Mingxiao Wang
- Cspc Zhongqi Pharmaceutical Technology (Shijiazhuang) Co., Ltd, Shijiazhuang, Hebei Province, 050035, China
| | - Wuyuntana Li
- Laboratory for Molecular Epidemiology in Chronic Diseases, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Yumin Gao
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Hailing Li
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Ning Cao
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Wenli Hao
- Laboratory for Molecular Epidemiology in Chronic Diseases, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China
| | - Lingyan Zhao
- Department of Epidemiology, School of Public Health, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China.
- Laboratory for Molecular Epidemiology in Chronic Diseases, Inner Mongolia Medical University, Inner Mongolia Autonomous Region, Hohhot, 010110, China.
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Shrestha H, Yao T, Qiao Z, Muchero W, Hettich RL, Chen JG, Abraham PE. Lectin Receptor-like Kinase Signaling during Engineered Ectomycorrhiza Colonization. Cells 2023; 12:cells12071082. [PMID: 37048154 PMCID: PMC10093077 DOI: 10.3390/cells12071082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Mutualistic association can improve a plant’s health and productivity. G-type lectin receptor-like kinase (PtLecRLK1) is a susceptibility factor in Populus trichocarpa that permits root colonization by a beneficial fungus, Laccaria bicolor. Engineering PtLecRLK1 also permits L. bicolor root colonization in non-host plants similar to Populus trichocarpa. The intracellular signaling reprogramed by PtLecRLK1 upon recognition of L. bicolor to allow for the development and maintenance of symbiosis is yet to be determined. In this study, phosphoproteomics was utilized to identify phosphorylation-based relevant signaling pathways associated with PtLecRLK1 recognition of L. bicolor in transgenic switchgrass roots. Our finding shows that PtLecRLK1 in transgenic plants modifies the chitin-triggered plant defense and MAPK signaling along with a significant adjustment in phytohormone signaling, ROS balance, endocytosis, cytoskeleton movement, and proteasomal degradation in order to facilitate the establishment and maintenance of L. bicolor colonization. Moreover, protein–protein interaction data implicate a cGMP-dependent protein kinase as a potential substrate of PtLecRLK1.
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Affiliation(s)
- Him Shrestha
- Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zhenzhen Qiao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert L. Hettich
- Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul E. Abraham
- Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Mejia MP, Rojas CA, Curd E, Renshaw MA, Edalati K, Shih B, Vincent N, Lin M, Nguyen PH, Wayne R, Jessup K, Parker SS. Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site. MICROBIAL ECOLOGY 2023; 85:998-1012. [PMID: 35802172 PMCID: PMC10156844 DOI: 10.1007/s00248-022-02061-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/21/2022] [Indexed: 05/04/2023]
Abstract
Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.
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Affiliation(s)
- Maura Palacios Mejia
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Connie A Rojas
- Ecology, Evolution, and Behavior Program, Michigan State University, Lansing, MI, USA
| | - Emily Curd
- Natural Science, Landmark College, Putney, VT, USA
| | - Mark A Renshaw
- Cherokee Federal, USGS Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Kiumars Edalati
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Beverly Shih
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nitin Vincent
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Meixi Lin
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peggy H Nguyen
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert Wayne
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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Schaedel M, Ishii S, Wang H, Venterea R, Paul B, Mutimura M, Grossman J. Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks. PLoS One 2023; 18:e0281442. [PMID: 36787300 PMCID: PMC9928094 DOI: 10.1371/journal.pone.0281442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Microbial nitrogen (N) cycling pathways are largely responsible for producing forms of N that are available for plant uptake or lost from the system as gas or leachate. The temporal dynamics of microbial N pathways in tropical agroecosystems are not well defined, even though they are critical to understanding the potential impact of soil conservation strategies. We aimed to 1) characterize temporal changes in functional gene associations across a seasonal gradient, 2) identify keystone genes that play a central role in connecting N cycle functions, and 3) detect gene co-occurrences that remained stable over time. Soil samples (n = 335) were collected from two replicated field trials in Rwanda between September 2020 and March 2021. We found high variability among N-cycle gene relationships and network properties that was driven more by sampling timepoint than by location. Two nitrification gene targets, hydroxylamine oxidoreductase and nitrite oxidoreductase, co-occurred across all timepoints, indicating that they may be ideal year-round targets to limit nitrification in rainfed agricultural soils. We also found that gene keystoneness varied across time, suggesting that management practices to enhance N-cycle functions such as the application of nitrification inhibitors could be adapted to seasonal conditions. Our results mark an important first step in employing gene networks to infer function in soil biogeochemical cycles, using a tropical seasonal gradient as a model system.
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Affiliation(s)
- Marie Schaedel
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States of America
- * E-mail:
| | - Satoshi Ishii
- Department of Soil, Water, & Climate, University of Minnesota, St. Paul, MN, United States of America
- BioTechnology Institute, St Paul, MN, United States of America
| | - Hao Wang
- Department of Soil, Water, & Climate, University of Minnesota, St. Paul, MN, United States of America
| | - Rodney Venterea
- Department of Soil, Water, & Climate, University of Minnesota, St. Paul, MN, United States of America
- USDA-ARS, Soil & Water Management Research Unit, St. Paul, MN, United States of America
| | - Birthe Paul
- Tropical Forages Program, International Center for Tropical Agriculture, Nairobi, Kenya
| | - Mupenzi Mutimura
- Department of Animal Production, Rwanda Agriculture Board, Kigali, Rwanda
| | - Julie Grossman
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States of America
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Uzun M, Koziaeva V, Dziuba M, Alekseeva L, Krutkina M, Sukhacheva M, Baslerov R, Grouzdev D. Recovery and genome reconstruction of novel magnetotactic Elusimicrobiota from bog soil. THE ISME JOURNAL 2023; 17:204-214. [PMID: 36302955 PMCID: PMC9859788 DOI: 10.1038/s41396-022-01339-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 01/22/2023]
Abstract
Studying the minor part of the uncultivated microbial majority ("rare biosphere") is difficult even with modern culture-independent techniques. The enormity of microbial diversity creates particular challenges for investigating low-abundance microbial populations in soils. Strategies for selective sample enrichment to reduce community complexity can aid in studying the rare biosphere. Magnetotactic bacteria, apart from being a minor part of the microbial community, are also found in poorly studied bacterial phyla and certainly belong to a rare biosphere. The presence of intracellular magnetic crystals within magnetotactic bacteria allows for their significant enrichment using magnetic separation techniques for studies using a metagenomic approach. This work investigated the microbial diversity of a black bog soil and its magnetically enriched fraction. The poorly studied phylum representatives in the magnetic fraction were enriched compared to the original soil community. Two new magnetotactic species, Candidatus Liberimonas magnetica DUR002 and Candidatus Obscuribacterium magneticum DUR003, belonging to different classes of the relatively little-studied phylum Elusimicrobiota, were proposed. Their genomes contain clusters of magnetosome genes that differ from the previously described ones by the absence of genes encoding magnetochrome-containing proteins and the presence of unique Elusimicrobiota-specific genes, termed mae. The predicted obligately fermentative metabolism in DUR002 and lack of flagellar motility in the magnetotactic Elusimicrobiota broadens our understanding of the lifestyles of magnetotactic bacteria and raises new questions about the evolutionary advantages of magnetotaxis. The findings presented here increase our understanding of magnetotactic bacteria, soil microbial communities, and the rare biosphere.
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Affiliation(s)
- Maria Uzun
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Veronika Koziaeva
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marina Dziuba
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Lolita Alekseeva
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Marina Sukhacheva
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Roman Baslerov
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Denis Grouzdev
- SciBear OU, Tallinn, Estonia.
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.
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Zhang Z, Han P, Zheng Y, Jiao S, Dong H, Liang X, Gao D, Niu Y, Yin G, Liu M, Hou L. Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone. MICROBIAL ECOLOGY 2023; 85:383-399. [PMID: 35298685 DOI: 10.1007/s00248-022-01996-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.
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Affiliation(s)
- Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Yuhui Niu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
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Jeon Y, Baranwal P, Li L, Piezer K, Seo Y. Review: Current understanding on biological filtration for the removal of microcystins. CHEMOSPHERE 2023; 313:137160. [PMID: 36356807 DOI: 10.1016/j.chemosphere.2022.137160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/10/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Harmful algal blooms (HABs) have become a global problem not only in aquatic habitats but also in public health and safety due to the production of cyanotoxins as their secondary metabolites. Among the various identified cyanotoxin groups, microcystins (MCs) are one of the most prevalent cyanotoxin detected during HABs. Different strategies including advanced physical and chemical treatment processes have been developed to mitigate the threat of cyanotoxins in water utilities, but these have revealed certain limitations in terms of high operational costs, low removal efficacy, and harmful by-products formation. Recently, biological filtration systems (BFS) have gained attention for safe drinking water production as they can treat various natural organic matter (NOM) and emerging contaminants through a highly efficient and environmentally sustainable process. However, limited attention has been given to understand the current research progress, research challenges, and knowledge gaps for the successful implementation of BFS for MC removal. Therefore, in this review, currently identified MC biodegradation pathways and MC-degrading microorganisms with their degradation rates are summarized, which may be pivotal for studying bioaugmented BFS to enhance the MC removal during HABs. Moreover, both laboratory and field studies on BFS for MC removal are reviewed, followed by a discussion of current challenges and future research needs for the practical application of BFS.
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Affiliation(s)
- Youchul Jeon
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States
| | - Parul Baranwal
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States
| | - Lei Li
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States
| | - Kayla Piezer
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States; Department of Chemical Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, 43606, United States
| | - Youngwoo Seo
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States; Department of Chemical Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, 43606, United States.
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Metagenomic insights into bacterial communities and functional genes associated with texture characteristics of Kazakh artisanal fermented milk Ayran in Xinjiang, China. Food Res Int 2023; 164:112414. [PMID: 36737993 DOI: 10.1016/j.foodres.2022.112414] [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: 08/29/2022] [Revised: 11/28/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022]
Abstract
The complex microflora of traditional fermented milk is crucial to milk coagulation mainly through acid and protease production; however, it is still unclear which microbes and proteases significantly influence the texture of Ayran, a Kazakh artisanal fermented milk in Xinjiang, China. In this study, fifty-nine samples of Ayran were collected and investigated on texture properties. Finally, six Ayran samples with different texture features were screened out, and the taxonomic and functional attributes of their microbiota were characterized by metagenomics. The results showed that the hardness of the fermented milk in Yili Kazakh Autonomous Prefecture was significantly higher than that in other pasture areas. Lactobacillus and Lactococcus were the core genera that affected the coagulation quality of milk. Furthermore, we found that the proline iminopeptidase pip (EC 3.4.11.5) gene of Lactobacillus helveticus and Limosilactobacillus fermentum and the dipeptidase E pepE (EC 3.4.13.21) gene of Lactococcus lactis were most associated with the coagulation quality of fermented milk. Furthermore, positive correlations were observed among the hardness of fermented milk, the activity of the proteases, and the corresponding functional gene expressions.
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In-situ observations of an intact natural whale fall in Palmer deep, Western Antarctic Peninsula. Polar Biol 2023. [DOI: 10.1007/s00300-022-03109-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
AbstractWhale carcasses on the seafloor support unique, ephemeral communities of organisms, and ‘natural’ whale fall sites are infrequently encountered, especially in polar regions. During a manned submersible dive in early 2017, we discovered the skeleton of an Antarctic minke whale (Balaenoptera bonaerensis) at 963 m in Palmer Deep, in the Western Antarctic Peninsula. The site was filmed in HD for approximately two hours, enabling visual identification of representatives from at least eight phyla, although physical sampling was not possible. The remains appeared to be in the late ‘enrichment–opportunistic’ phase (although some mobile scavengers were still present and some sulfonic activity had already commenced), with polychaetes of the order Aciculata, and family Ampharetidae, plus several amphipod species, most abundant. Novel eusirid amphipod and rhodaliid siphonophore taxa were also present. The observed faunal distribution suggests patterns consistent with reports from other Antarctic whale falls (both experimental and natural). This discovery represents the highest-latitude natural whale fall reported to date.
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Böttner L, Malacrinò A, Schulze Gronover C, van Deenen N, Müller B, Xu S, Gershenzon J, Prüfer D, Huber M. Natural rubber reduces herbivory and alters the microbiome below ground. THE NEW PHYTOLOGIST 2023. [PMID: 36597727 DOI: 10.1111/nph.18709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Laticifers are hypothesized to mediate both plant-herbivore and plant-microbe interactions. However, there is little evidence for this dual function. We investigated whether the major constituent of natural rubber, cis-1,4-polyisoprene, a phylogenetically widespread and economically important latex polymer, alters plant resistance and the root microbiome of the Russian dandelion (Taraxacum koksaghyz) under attack of a root herbivore, the larva of the May cockchafer (Melolontha melolontha). Rubber-depleted transgenic plants lost more shoot and root biomass upon herbivory than normal rubber content near-isogenic lines. Melolontha melolontha preferred to feed on artificial diet supplemented with rubber-depleted rather than normal rubber content latex. Likewise, adding purified cis-1,4-polyisoprene in ecologically relevant concentrations to diet deterred larval feeding and reduced larval weight gain. Metagenomics and metabarcoding revealed that abolishing biosynthesis of natural rubber alters the structure but not the diversity of the rhizosphere and root microbiota (ecto- and endophytes) and that these changes depended on M. melolontha damage. However, the assumption that rubber reduces microbial colonization or pathogen load is contradicted by four lines of evidence. Taken together, our data demonstrate that natural rubber biosynthesis reduces herbivory and alters the plant microbiota, which highlights the role of plant-specialized metabolites and secretory structures in shaping multitrophic interactions.
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Affiliation(s)
- Laura Böttner
- Institute of Plant Biology and Biotechnology, University of Münster, D-48143, Münster, Germany
- Institute for Evolution and Biodiversity, University of Münster, D-48149, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, D-55128, Mainz, Germany
| | - Antonino Malacrinò
- Institute for Evolution and Biodiversity, University of Münster, D-48149, Münster, Germany
- Department of Agriculture, Università degli Studi Mediterranea di Reggio Calabria, I-89122, Reggio Calabria, Italy
| | - Christian Schulze Gronover
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, D-48143, Münster, Germany
| | - Nicole van Deenen
- Institute of Plant Biology and Biotechnology, University of Münster, D-48143, Münster, Germany
| | - Boje Müller
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, D-48143, Münster, Germany
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, D-48149, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, D-55128, Mainz, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Dirk Prüfer
- Institute of Plant Biology and Biotechnology, University of Münster, D-48143, Münster, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, D-48143, Münster, Germany
| | - Meret Huber
- Institute of Plant Biology and Biotechnology, University of Münster, D-48143, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, D-55128, Mainz, Germany
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Wu C, Yi H, Hu Y, Luo D, Tang Z, Wen X, Zhang Y, Tang M, Zhang L, Wu S, Chen M. Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis. Front Cell Infect Microbiol 2023; 13:1127916. [PMID: 37187470 PMCID: PMC10178494 DOI: 10.3389/fcimb.2023.1127916] [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: 12/20/2022] [Accepted: 03/13/2023] [Indexed: 05/17/2023] Open
Abstract
Objective To determine the effects of second-line anti-tuberculosis (TB) drugs on the composition and functions of intestinal microbiota in patients with rifampicin-resistant TB (RR-TB). Methods In this cross-sectional study, stool samples and relevant clinical information were collected from patients with RR-TB admitted to the Drug-resistant Specialty Department at Hunan Chest Hospital (Hunan Institute For Tuberculosis Control). The composition and functions of intestinal microbiota were analyzed using metagenomic sequencing and bioinformatics methods. Results Altered structural composition of the intestinal microbiota was found when patients from the control, intensive phase treatment, and continuation phase treatment groups were compared (P<0.05). Second-line anti-TB treatment resulted in a decrease in the relative abundance of species, such as Prevotella copri, compared with control treatment. However, the relative abundance of Escherichia coli, Salmonella enterica, and 11 other conditionally pathogenic species increased significantly in the intensive phase treatment group. Based on differential functional analysis, some metabolism-related functions, such as the biosynthesises of phenylalanine, tyrosine, and tryptophan, were significantly inhibited during second-line anti-TB drug treatment, while other functions, such as phenylalanine metabolism, were significantly promoted during the intensive phase of treatment. Conclusion Second-line anti-TB drug treatment caused changes in the structural composition of the intestinal microbiota in patients with RR-TB. In particular, this treatment induced a significant increase in the relative abundance of 11 conditionally pathogenic species, including Escherichia coli. Functional analysis revealed significantly decreased biosynthesises of phenylalanine, tyrosine, and tryptophan and significantly increased phenylalanine metabolism.
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Affiliation(s)
- Chunli Wu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Hengzhong Yi
- 6th Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
- *Correspondence: Hengzhong Yi,
| | - Yanmei Hu
- 6th Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
| | - Danlin Luo
- 6th Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
| | - Zhigang Tang
- 6th Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
| | - Xinmin Wen
- 6th Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
| | - Yong Zhang
- 6th Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
| | - Mi Tang
- 6th Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
| | - Lizhi Zhang
- Orthopedics and integration Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
| | - Shu Wu
- 6th Medical Department, Hunan Province Chest Hospital, Changsha, Hunan, China
| | - Mengshi Chen
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
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Reineke W, Schlömann M. Microbial Communities: Structural and Functional Analyses with Molecular Biological Approach. Environ Microbiol 2023. [DOI: 10.1007/978-3-662-66547-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Zhang Y, Li X, Hu A, Wang L. Effects of Hericium erinaceus Hedgehog mushroom on the endophytic microbial community of the host plant. J Basic Microbiol 2023; 63:92-103. [PMID: 36316246 DOI: 10.1002/jobm.202200476] [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: 08/03/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 01/03/2023]
Abstract
Hedgehog mushroom is a Hericium erinaceus associated with fagaceae and pinaceae trees in the northern hemisphere. It is still unknown whether this symbiotic relationship will affect the endophytic microbial community of the host plants. In this study, the endophytic microbial communities of different Quercus aliena tissues (root, stem, and leaf) with or without H. erinaceus partner were analyzed by bar-coded pyrosequencing. About 29,000 clean reads were obtained per sample representing 28 phyla of bacteria and 6 phyla of fungi. A total of 26,838 operational taxonomic units (OTUs) of bacteria and 4323 OTUs of fungi were observed at a 97% similarity level. Three bacterial phyla, Proteobacteria, Cyanobacteria and Bacteroidetes, and fungal phylum Ascomycota were dominant in all tissues. The relative abundance of these dominant communities showed significantly differences between Q. aliena tissues with or without H. erinaceus. Bacterial genus Pseudomonas and fungal genus Cryptosporiopsis were species-rich in Q. aliena root infected by H. erinaceus hyphae. This study demonstrated that the endophytic microbial community structure and dominant species varied in Q. aliena mycorrhized with H. erinaceus.
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Affiliation(s)
- Yizhe Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xinwei Li
- Luohe Medical College, Luohe, Henan, China
| | - Anxin Hu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Landi Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Pavlidou E, Fasoulas A, Mantzorou M, Giaginis C. Clinical Evidence on the Potential Beneficial Effects of Probiotics and Prebiotics in Cardiovascular Disease. Int J Mol Sci 2022; 23:ijms232415898. [PMID: 36555535 PMCID: PMC9779729 DOI: 10.3390/ijms232415898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
The 'gut microbiome'-the hundreds of trillions of bacteria in the human gastrointestinal tract-serves several functions. The gut microbiome includes all the microorganisms, bacteria, viruses, protozoa, and fungi in the gastrointestinal tract and their genetic material. It helps digest indigestible foods and produces nutrients. Through the metabolism of sugars and proteins, it helps the intestinal barrier, the immune system, and metabolism. Some bacteria, such as those in the gut microbiome, cause disease, but others are essential to our health. These "good" microbes protect us from pathogens. Numerous studies have linked an unhealthy gut microbiome to obesity, insulin resistance, depression, and cardiometabolic risk factors. To maximize probiotic benefits in each case, knowledge of probiotic bacterial strains and how to consume them should be increased. This study aims to examine the benefits of probiotic and prebiotic organisms on cardiovascular health, specifically on heart disease, coronary heart disease, stroke, and hypertension. To complete the research, a literature review was conducted by gathering clinical studies and data. The clinical evidence demonstrates the beneficial effect of probiotics and prebiotic microorganisms on the gut microbiome, which has multiple benefits for overall health and especially for cardiovascular diseases.
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40
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Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice. Genes (Basel) 2022; 13:genes13122280. [PMID: 36553546 PMCID: PMC9777648 DOI: 10.3390/genes13122280] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/09/2022] Open
Abstract
The study of microorganisms is a field of great interest due to their environmental (e.g., soil contamination) and biomedical (e.g., parasitic diseases, autism) importance. The advent of revolutionary next-generation sequencing techniques, and their application to the hypervariable regions of the 16S, 18S or 23S ribosomal subunits, have allowed the research of a large variety of organisms more in-depth, including bacteria, archaea, eukaryotes and fungi. Additionally, together with the development of analysis software, the creation of specific databases (e.g., SILVA or RDP) has boosted the enormous growth of these studies. As the cost of sequencing per sample has continuously decreased, new protocols have also emerged, such as shotgun sequencing, which allows the profiling of all taxonomic domains in a sample. The sequencing of hypervariable regions and shotgun sequencing are technologies that enable the taxonomic classification of microorganisms from the DNA present in microbial communities. However, they are not capable of measuring what is actively expressed. Conversely, we advocate that metatranscriptomics is a "new" technology that makes the identification of the mRNAs of a microbial community possible, quantifying gene expression levels and active biological pathways. Furthermore, it can be also used to characterise symbiotic interactions between the host and its microbiome. In this manuscript, we examine the three technologies above, and discuss the implementation of different software and databases, which greatly impact the obtaining of reliable results. Finally, we have developed two easy-to-use pipelines leveraging Nextflow technology. These aim to provide everything required for an average user to perform a metagenomic analysis of marker genes with QIMME2 and a metatranscriptomic study using Kraken2/Bracken.
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41
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Analysis of Gut Microbial Communities and Resistance Genes in Pigs and Chickens in Central China. Animals (Basel) 2022; 12:ani12233404. [PMID: 36496925 PMCID: PMC9736826 DOI: 10.3390/ani12233404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND Basic data concerning the gut microbiota of the main animal husbandry breeds (pigs and chickens) are scarce in China. The dynamics of gut microbiota (pigs and chickens) in China and antibiotic resistance genes carried by microorganisms in the natural environment are unknown. METHODS Free range and factory-farmed Gushi chickens and Huainan pigs were divided into eight groups. Faecal samples were collected from each group, and the metagenomic sequencing method was used to detect each group of samples. RESULTS The resistance genes showed the following trend, from high to low relative abundance: tetW was the highest, followed by tetW/N/W, then lnuA; and others from high to low were mdtB, lnuC, ANT6-la, ErmB, mdtC, ErmQ, tetBP, vatE, evgS, acrB, cpxA, mefA, Escherichia coli-ampC, tetL, yojl, AcrF and mdtA. All groups administered enrofloxacin and oregano oil did not develop a drug-resistant phenotype during the 5-day treatment period, as grouped in this trial. In 2022, after Announcement No. 194 of the Ministry of Agriculture and Rural Affairs in China, the antimicrobial resistance (AMR) trend declined, but it did not fundamentally change, presumably due to the impact of environmental pollution caused by the long-term use of antimicrobials.
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Meslier V, Quinquis B, Da Silva K, Plaza Oñate F, Pons N, Roume H, Podar M, Almeida M. Benchmarking second and third-generation sequencing platforms for microbial metagenomics. Sci Data 2022; 9:694. [PMID: 36369227 PMCID: PMC9652401 DOI: 10.1038/s41597-022-01762-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.
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Affiliation(s)
- Victoria Meslier
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France
| | - Benoit Quinquis
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France
| | - Kévin Da Silva
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France
| | | | - Nicolas Pons
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France
| | - Hugo Roume
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Mathieu Almeida
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France.
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McDaniel EA, van Steenbrugge JJM, Noguera DR, McMahon KD, Raaijmakers JM, Medema MH, Oyserman BO. TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome. ISME COMMUNICATIONS 2022; 2:111. [PMID: 37938301 PMCID: PMC9723799 DOI: 10.1038/s43705-022-00189-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2023]
Abstract
A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.
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Affiliation(s)
- E A McDaniel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
| | - J J M van Steenbrugge
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands.
- Microbial Ecology, Netherlands Institute of Ecological Research, Wageningen, The Netherlands.
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.
| | - D R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - K D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - J M Raaijmakers
- Microbial Ecology, Netherlands Institute of Ecological Research, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - M H Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - B O Oyserman
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands.
- Microbial Ecology, Netherlands Institute of Ecological Research, Wageningen, The Netherlands.
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44
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Kawa D, Brady SM. Root cell types as an interface for biotic interactions. TRENDS IN PLANT SCIENCE 2022; 27:1173-1186. [PMID: 35792025 DOI: 10.1016/j.tplants.2022.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 05/27/2023]
Abstract
Root responses to environmental stresses show a high level of cell type and developmental stage specificity. Interactions with beneficial and pathogenic organisms - including microbes and parasites - elicit a set of transcriptional responses unique to each root cell type, often dependent on their differentiation state. Localized changes to the cell wall and to the integrity of root cell types can serve as a physical barrier for a range of pests. Conversely, certain microorganisms weaken existing barriers within root cell types. Interactions with microorganisms vary between roots of different developmental origins and cellular architectures. Here we provide an overview of the molecular, architectural, and structural properties of root cell types crucial to both maintaining beneficial interactions and protecting from pathogens.
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Affiliation(s)
- Dorota Kawa
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA.
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA.
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45
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Jiang MZ, Zhu HZ, Zhou N, Liu C, Jiang CY, Wang Y, Liu SJ. Droplet microfluidics-based high-throughput bacterial cultivation for validation of taxon pairs in microbial co-occurrence networks. Sci Rep 2022; 12:18145. [PMID: 36307549 PMCID: PMC9616874 DOI: 10.1038/s41598-022-23000-7] [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: 05/26/2022] [Accepted: 10/21/2022] [Indexed: 12/31/2022] Open
Abstract
Co-occurrence networks inferred from the abundance data of microbial communities are widely applied to predict microbial interactions. However, the high workloads of bacterial isolation and the complexity of the networks themselves constrained experimental demonstrations of the predicted microbial associations and interactions. Here, we integrate droplet microfluidics and bar-coding logistics for high-throughput bacterial isolation and cultivation from environmental samples, and experimentally investigate the relationships between taxon pairs inferred from microbial co-occurrence networks. We collected Potamogeton perfoliatus plants (including roots) and associated sediments from Beijing Olympic Park wetland. Droplets of series diluted homogenates of wetland samples were inoculated into 126 96-well plates containing R2A and TSB media. After 10 days of cultivation, 65 plates with > 30% wells showed microbial growth were selected for the inference of microbial co-occurrence networks. We cultivated 129 bacterial isolates belonging to 15 species that could represent the zero-level OTUs (Zotus) in the inferred co-occurrence networks. The co-cultivations of bacterial isolates corresponding to the prevalent Zotus pairs in networks were performed on agar plates and in broth. Results suggested that positively associated Zotu pairs in the co-occurrence network implied complicated relations including neutralism, competition, and mutualism, depending on bacterial isolate combination and cultivation time.
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Affiliation(s)
- Min-Zhi Jiang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China
| | - Hai-Zhen Zhu
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Nan Zhou
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Chang Liu
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Cheng-Ying Jiang
- grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Yulin Wang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China
| | - Shuang-Jiang Liu
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China ,grid.9227.e0000000119573309State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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46
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Brown DC, Aggarwal N, Turner RJ. Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36190831 DOI: 10.1099/mic.0.001248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
As sequencing technology improves and the cost of metagenome sequencing decreases, the number of sequenced environments increases. These metagenomes provide a wealth of data in the form of annotated and unannotated genes. The role of multidrug resistance efflux pumps (MDREPs) is the removal of antibiotics, biocides and toxic metabolites created during aromatic hydrocarbon metabolism. Due to their naturally occurring role in hydrocarbon metabolism and their role in biocide tolerance, MDREP genes are of particular importance for the protection of pipeline assets. However, the heterogeneity of MDREP genes creates a challenge during annotation and detection. Here we use a selection of primers designed to target MDREPs in six pure species and apply them to publicly available metagenomes associated with oil and gas environments. Using in silico PCR with relaxed primer binding conditions we probed the metagenomes of a shale reservoir, a heavy oil tailings pond, a civil wastewater treatment, two marine sediments exposed to hydrocarbons following the Deepwater Horizon oil spill and a non-exposed marine sediment to assess the presence and abundance of MDREP genes. Through relaxed primer binding conditions during in silico PCR, the prevalence of MDREPs was determined. The percentage of nucleotide sequences identified by the MDREP primers was partially augmented by exposure to hydrocarbons in marine sediment and in shale reservoir compared to hydrocarbon-free marine sediments while tailings ponds and wastewater had the highest percentages. We believe this approach lays the groundwork for a supervised method of identifying poorly conserved genes within metagenomes.
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47
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Cui N, Faure G, Singh A, Macrae R, Zhang F. Microfluidic Enrichment and Computational Analysis of Rare Sequences from Mixed Genomic Samples for Metagenomic Mining. CRISPR J 2022; 5:677-684. [PMID: 36206017 PMCID: PMC9595627 DOI: 10.1089/crispr.2022.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Many powerful molecular biology tools have their origins in natural systems, including restriction modification enzymes and the CRISPR effectors, Cas9, Cas12, and Cas13. Heightened interest in these systems has led to mining of genomic and metagenomic data to identify new orthologs of these proteins, new types of CRISPR systems, and uncharacterized natural systems with novel mechanisms. To accelerate metagenomic mining, we developed a high-throughput, low-cost droplet microfluidic-based method for enrichment of rare sequences in a mixed starting population. Using a computational pipeline, we then searched in the enriched data for the presence of CRISPR-Cas systems, identifying a previously unknown CRISPR-Cas system. Our approach enables researchers to efficiently mine metagenomic samples for sequences of interest, greatly accelerating the search for nature's treasures.
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Affiliation(s)
- Naiwen Cui
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guihem Faure
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ankita Singh
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rhiannon Macrae
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Address correspondence to: Feng Zhang, PhD, Broad Institute of MIT and Harvard, 75 Ames St. Cambridge, MA 02142, USA,
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Shami AY, Abulfaraj AA, Refai MY, Barqawi AA, Binothman N, Tashkandi MA, Baeissa HM, Baz L, Abuauf HW, Ashy RA, Jalal RS. Abundant antibiotic resistance genes in rhizobiome of the human edible Moringa oleifera medicinal plant. Front Microbiol 2022; 13:990169. [PMID: 36187977 PMCID: PMC9524394 DOI: 10.3389/fmicb.2022.990169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022] Open
Abstract
Moringa oleifera (or the miracle tree) is a wild plant species widely grown for its seed pods and leaves, and is used in traditional herbal medicine. The metagenomic whole genome shotgun sequencing (mWGS) approach was used to characterize antibiotic resistance genes (ARGs) of the rhizobiomes of this wild plant and surrounding bulk soil microbiomes and to figure out the chance and consequences for highly abundant ARGs, e.g., mtrA, golS, soxR, oleC, novA, kdpE, vanRO, parY, and rbpA, to horizontally transfer to human gut pathogens via mobile genetic elements (MGEs). The results indicated that abundance of these ARGs, except for golS, was higher in rhizosphere of M. oleifera than that in bulk soil microbiome with no signs of emerging new soil ARGs in either soil type. The most highly abundant metabolic processes of the most abundant ARGs were previously detected in members of phyla Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and Firmicutes. These processes refer to three resistance mechanisms namely antibiotic efflux pump, antibiotic target alteration and antibiotic target protection. Antibiotic efflux mechanism included resistance-nodulation-cell division (RND), ATP-binding cassette (ABC), and major facilitator superfamily (MFS) antibiotics pumps as well as the two-component regulatory kdpDE system. Antibiotic target alteration included glycopeptide resistance gene cluster (vanRO), aminocoumarin resistance parY, and aminocoumarin self-resistance parY. While, antibiotic target protection mechanism included RbpA bacterial RNA polymerase (rpoB)-binding protein. The study supports the claim of the possible horizontal transfer of these ARGs to human gut and emergence of new multidrug resistant clinical isolates. Thus, careful agricultural practices are required especially for plants used in circles of human nutrition industry or in traditional medicine.
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Affiliation(s)
- Ashwag Y. Shami
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science and Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aminah A. Barqawi
- Department of Chemistry, Al-Leith University College, Umm Al Qura University, Makkah, Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hanadi M. Baeissa
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science—King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- *Correspondence: Rewaa S. Jalal,
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Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity. BIOLOGY 2022; 11:biology11091297. [PMID: 36138776 PMCID: PMC9495823 DOI: 10.3390/biology11091297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance. Abstract The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
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Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:ijms23179834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
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