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Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [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: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
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Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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2
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Noecker C, Turnbaugh PJ. Emerging tools and best practices for studying gut microbial community metabolism. Nat Metab 2024:10.1038/s42255-024-01074-z. [PMID: 38961185 DOI: 10.1038/s42255-024-01074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
The human gut microbiome vastly extends the set of metabolic reactions catalysed by our own cells, with far-reaching consequences for host health and disease. However, our knowledge of gut microbial metabolism relies on a handful of model organisms, limiting our ability to interpret and predict the metabolism of complex microbial communities. In this Perspective, we discuss emerging tools for analysing and modelling the metabolism of gut microorganisms and for linking microorganisms, pathways and metabolites at the ecosystem level, highlighting promising best practices for researchers. Continued progress in this area will also require infrastructure development to facilitate cross-disciplinary synthesis of scientific findings. Collectively, these efforts can enable a broader and deeper understanding of the workings of the gut ecosystem and open new possibilities for microbiome manipulation and therapy.
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Affiliation(s)
- Cecilia Noecker
- Department of Biological Sciences, Minnesota State University, Mankato, Mankato, MN, USA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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3
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Chen C, Yang H, Zhang K, Ye G, Luo H, Zou W. Revealing microbiota characteristics and predicting flavor-producing sub-communities in Nongxiangxing baijiu pit mud through metagenomic analysis and metabolic modeling. Food Res Int 2024; 188:114507. [PMID: 38823882 DOI: 10.1016/j.foodres.2024.114507] [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: 01/27/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The microorganisms of the pit mud (PM) of Nongxiangxing baijiu (NXXB) have an important role in the synthesis of flavor substances, and they determine attributes and quality of baijiu. Herein, we utilize metagenomics and genome-scale metabolic models (GSMMs) to investigate the microbial composition, metabolic functions in PM microbiota, as well as to identify microorganisms and communities linked to flavor compounds. Metagenomic data revealed that the most prevalent assembly of bacteria and archaea was Proteiniphilum, Caproicibacterium, Petrimonas, Lactobacillus, Clostridium, Aminobacterium, Syntrophomonas, Methanobacterium, Methanoculleus, and Methanosarcina. The important enzymes ofPMwere in bothGH and GT familymetabolism. A total of 38 high-quality metagenome-assembled genomes (MAGs) were obtained, including those at the family level (n = 13), genus level (n = 17), and species level (n = 8). GSMMs of the 38 MAGs were then constructed. From the GSMMs, individual and community capabilities respectively were predicted to be able to produce 111 metabolites and 598 metabolites. Twenty-three predicted metabolites were consistent with the metabonomics detected flavors and served as targets. Twelve sub-community of were screened by cross-feeding of 38 GSMMs. Of them, Methanobacterium, Sphaerochaeta, Muricomes intestini, Methanobacteriaceae, Synergistaceae, and Caloramator were core microorganisms for targets in each sub-community. Overall, this study of metagenomic and target-community screening could help our understanding of the metabolite-microbiome association and further bioregulation of baijiu.
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Affiliation(s)
- Cong Chen
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Kaizheng Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Guangbin Ye
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China
| | - Huibo Luo
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, Sichuan 644005, China
| | - Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644005, China; Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, Sichuan 644005, China.
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [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: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Kang J, Huang X, Li R, Zhang Y, Chen XX, Han BZ. Deciphering the core microbes and their interactions in spontaneous Baijiu fermentation: A comprehensive review. Food Res Int 2024; 188:114497. [PMID: 38823877 DOI: 10.1016/j.foodres.2024.114497] [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: 12/28/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The spontaneous Baijiu fermentation system harbors a complex microbiome that is highly dynamic in time and space and varies depending on the Jiuqu starters and environmental factors. The intricate microbiota presents in the fermentation environment is responsible for carrying out various reactions. These reactions necessitate the interaction among the core microbes to influence the community function, ultimately shaping the distinct Baijiu styles through the process of spontaneous fermentation. Numerous studies have been conducted to enhance our understanding of the diversity, succession, and function of microbial communities with the aim of improving fermentation manipulation. However, a comprehensive and critical assessment of the core microbes and their interaction remains one of the significant challenges in the Baijiu fermentation industry. This paper focuses on the fermentation properties of core microbes. We discuss the state of the art of microbial traceability, highlighting the crucial role of environmental and starter microbiota in the Baijiu brewing microbiome. Also, we discuss the various interactions between microbes in the Baijiu production system and propose a potential conceptual framework that involves constructing predictive network models to simplify and quantify microbial interactions using co-culture models. This approach offers effective strategies for understanding the core microbes and their interactions, thus beneficial for the management of microbiota and the regulation of interactions in Baijiu fermentation processes.
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Affiliation(s)
- Jiamu Kang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China; School of Food Science and Engineering, Hainan University, Haikou, China
| | - Xiaoning Huang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Rengshu Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Yuandi Zhang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Xiao-Xue Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China.
| | - Bei-Zhong Han
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China.
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Kim MS, Jeong DE, Jang JP, Jang JH, Choi SK. Mining biosynthetic gene clusters in Paenibacillus genomes to discover novel antibiotics. BMC Microbiol 2024; 24:226. [PMID: 38937695 PMCID: PMC11210098 DOI: 10.1186/s12866-024-03375-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied. RESULTS We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin. CONCLUSIONS This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.
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Grants
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
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Affiliation(s)
- Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea.
- Department of Applied Biological Engineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea.
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea.
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Nakai R, Kusada H, Sassa F, Makino A, Morigasaki S, Hayashi H, Takaya N, Tamaki H. Roseiterribacter gracilis gen. nov., sp. nov., a novel filterable alphaproteobacterium isolated from soil using a gel-filled microwell array device. PLoS One 2024; 19:e0304366. [PMID: 38857291 PMCID: PMC11164329 DOI: 10.1371/journal.pone.0304366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/11/2024] [Indexed: 06/12/2024] Open
Abstract
Our previous studies indicate the abundant and diverse presence of yet-to-be-cultured microorganisms in the micropore-filtered fractions of various environmental samples. Here, we isolated a novel bacterium (designated as strain TMPK1T) from a 0.45-μm-filtered soil suspension by using a gel-filled microwell array device comprising 900 microwells and characterized its phylogenetic and physiological features. This strain showed low 16S rRNA gene sequence identities (<91%) and low average nucleotide identity values (<70%) to the closest validly described species, and belonged to a novel-family-level lineage within the order Rhodospirillales of Alphaproteobacteria. Strain TMPK1T exhibited small cell sizes (0.08-0.23 μm3) and had a high cyclopropane fatty acid content (>13%), and these characteristics were differentiated from other Rhodospirillales bacteria. A comprehensive habitability search using amplicon datasets suggested that TMPK1T and its close relatives are mainly distributed in soil and plant-associated environments. Based on these results, we propose that strain TMPK1T represents a novel genus and species named Roseiterribacter gracilis gen. nov., sp. nov. (JCM 34627T = KCTC 82790T). We also propose Roseiterribacteraceae fam. nov. to accommodate the genus Roseiterribacter.
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Affiliation(s)
- Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Fumihiro Sassa
- Department of Electronics, Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan
| | - Ayaka Makino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Susumu Morigasaki
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hisayoshi Hayashi
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Naoki Takaya
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Katayama T, Nobu MK, Imachi H, Hosogi N, Meng XY, Morinaga K, Yoshioka H, Takahashi HA, Kamagata Y, Tamaki H. A Marine Group A isolate relies on other growing bacteria for cell wall formation. Nat Microbiol 2024:10.1038/s41564-024-01717-7. [PMID: 38831032 DOI: 10.1038/s41564-024-01717-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/29/2024] [Indexed: 06/05/2024]
Abstract
Most of Earth's prokaryotes live under energy limitation, yet the full breadth of strategies that enable survival under such conditions remain poorly understood. Here we report the isolation of a bacterial strain, IA91, belonging to the candidate phylum Marine Group A (SAR406 or 'Candidatus Marinimicrobia') that is unable to synthesize the central cell wall compound peptidoglycan itself. Using cultivation experiments and microscopy, we show that IA91 growth and cell shape depend on other bacteria, deriving peptidoglycan, energy and carbon from exogenous muropeptide cell wall fragments released from growing bacteria. Reliance on exogenous muropeptides is traceable to the phylum's ancestor, with evidence of vertical inheritance across several classes. This dependency may be widespread across bacteria (16 phyla) based on the absence of key peptidoglycan synthesis genes. These results suggest that uptake of exogenous cell wall components could be a relevant and potentially common survival strategy in energy-limited habitats like the deep biosphere.
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Affiliation(s)
- Taiki Katayama
- Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
| | - Masaru K Nobu
- Bioproduction Research Institute, AIST, Tsukuba, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiroyuki Imachi
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Naoki Hosogi
- EM Application Department, EM Business Unit, JEOL, Ltd., Akishima, Japan
| | | | - Kana Morinaga
- Bioproduction Research Institute, AIST, Tsukuba, Japan
| | - Hideyoshi Yoshioka
- Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hiroshi A Takahashi
- Research Institute of Earthquake and Volcano Geology, GSJ, AIST, Tsukuba, Japan
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Wang YC, Fu HM, Shen Y, Wang J, Wang N, Chen YP, Yan P. Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis. BIORESOURCE TECHNOLOGY 2024; 401:130740. [PMID: 38677385 DOI: 10.1016/j.biortech.2024.130740] [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: 01/29/2024] [Revised: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.
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Affiliation(s)
- Yi-Cheng Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Hui-Min Fu
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Nuo Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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Li Q, Liu C, Xie F, Lyu L, Zhang S, Li J. Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. isolated from coral tissue: proposal of two new families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38900566 DOI: 10.1099/ijsem.0.006427] [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] [Indexed: 06/21/2024] Open
Abstract
A genome-based polyphasic approach was used to determine the taxonomic status of two novel bacterial strains, SCSIO 12594T and SCSIO 12813T, isolated from tissues of a coral. Both strains were Gram-stain-negative and facultatively anaerobic. The genome sizes of strains SCSIO 12594T and SCSIO 12813T were 3.9 Mb and 4.1 Mb, respectively, and they possessed DNA G+C contents of 55.1 and 46.2 mol%, respectively . Both strains were found to be catalase- and oxidase-positive, while SCSIO 12594T also could hydrolyse starch. SCSIO 12594T was observed to grow at between 20 and 37 °C (optimally at 25 °C) and at a pH range from 6 to 7 and in the presence of 3-7 % (w/v) NaCl. The growth of SCSIO 12813T required seawater and occurred at 20-30 °C (optimum, 25 °C), pH 5-8 (optimum, pH 6-7) and in the presence of 3-3.7 % (w/v) NaCl. The results of 16S rRNA gene-based phylogenetic analysis indicated that SCSIO 12594T shared 92.97 % or less sequence similarity with its closest relatives Rhodobium gokarnense JA173T and other members of the order Hyphomicrobiales. The results of 16S rRNA sequences-based phylogenetic analysis of SCSIO 12813T indicated that Croceimicrobium hydrocarbonivorans A20-9T (89.34 %) was the most closely related species. SCSIO 12594T and SCSIO 12813T can be readily separated from their closest relatives, as indicated by the results of phylogenomic analysis, low average nucleotide indexes, average amino acid identity, digital DNA-DNA hybridisation (dDDH) similarities and associated phenotypic and chemical data. Consequently, the two coral isolates are considered to represent two novel genera and species for which the names Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. are proposed, the type strains are SCSIO 12594T (= JCM 35320T = GDMCC 1.3060T) and SCSIO 12813T (= JCM 35373T = GDMCC 1.3063T), respectively. In addition, two novel families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov are proposed to accommodate Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov., respectively.
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Affiliation(s)
- Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Cong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Feiyang Xie
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, PR China
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Mukherjee A, Singh BN, Kaur S, Sharma M, Ferreira de Araújo AS, Pereira APDA, Morya R, Puopolo G, Melo VMM, Verma JP. Unearthing the power of microbes as plant microbiome for sustainable agriculture. Microbiol Res 2024; 286:127780. [PMID: 38970905 DOI: 10.1016/j.micres.2024.127780] [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: 05/12/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/08/2024]
Abstract
In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.
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Affiliation(s)
- Arpan Mukherjee
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Bansh Narayan Singh
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Simranjit Kaur
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia; Crop Research Centre, Oak Park, Carlow, Ireland
| | - Minaxi Sharma
- CARAH ASBL, Rue Pal Pastur 11, Ath 7800, Belgium; China Beacons of Excellence Research and Innovation Institute (CBI), University of Nottingham Ningbo China, Ningbo 315000, China
| | | | | | - Raj Morya
- Department of Civil and Environmental engineering, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Gerardo Puopolo
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, San Michele all'Adige 38098, Italy; Research and Innovation center, Fondazione Edmund Mach, Via E. Mach 1, San Michelle all'Adige 38098, Italy
| | - Vânia Maria Maciel Melo
- Department of Biological Sciences, Faculty of Science, Federal University of Ceará, Pici, Fortaleza, Ceará 60020-181, Brazil
| | - Jay Prakash Verma
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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Wang Q, Chen Y, Chen Y, Lv J, Ding H, Huang J, Huang J, Huang Z, Yang B, Zhang W, Fang X. Improved cure rate of periprosthetic joint infection through targeted antibiotic therapy based on integrated pathogen diagnosis strategy. Front Cell Infect Microbiol 2024; 14:1388385. [PMID: 38836059 PMCID: PMC11148460 DOI: 10.3389/fcimb.2024.1388385] [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: 02/19/2024] [Accepted: 04/18/2024] [Indexed: 06/06/2024] Open
Abstract
Objectives This study aimed to determine whether combined of pathogen detection strategies, including specimen acquisition, culture conditions, and molecular diagnostics, can improve treatment outcomes in patients with periprosthetic joint infections (PJI). Methods This retrospective study included suspected PJI cases from three sequential stages at our institution: Stage A (July 2012 to June 2015), Stage B (July 2015 to June 2018), and Stage C (July 2018 to June 2021). Cases were categorized into PJI and aseptic failure (AF) groups based on European Bone and Joint Infection Society (EBJIS) criteria. Utilization of pathogen diagnostic strategies, pathogen detection rates, targeted antibiotic prescription rates, and treatment outcomes were analyzed and compared across the three stages. Results A total of 165 PJI cases and 38 AF cases were included in this study. With the progressive implementation of the three optimization approaches across stages A, B and C, pathogen detection rates exhibited a gradual increase (χ2 = 8.282, P=0.016). Similarly, utilization of targeted antibiotic therapy increased stepwise from 57.1% in Stage A, to 82.3% in Stage B, and to 84% in Stage C (χ2 = 9.515, P=0.009). The 2-year infection control rate exceeded 90% in both stages B and C, surpassing stage A (71.4%) (χ2 = 8.317, P=0.011). Combined application of all three optimized protocols yielded the highest sensitivity of 91.21% for pathogen detection, while retaining higher specificity of 92.11%. Conclusion The utilization of combined pathogen diagnostic strategies in PJI can increase pathogen detection rates, improve targeted antibiotic prescription, reduce the occurrence of antibiotic complications, and achieve better treatment outcomes.
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Affiliation(s)
- Qijin Wang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, The Affiliated Mindong Hospital of Fujian Medical University, Fuan, China
| | - Yongfa Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jianhua Lv
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Haiqi Ding
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jiagu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jiexin Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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13
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Wu R, Ji P, Hua Y, Li H, Zhang W, Wei Y. Research progress in isolation and identification of rumen probiotics. Front Cell Infect Microbiol 2024; 14:1411482. [PMID: 38836057 PMCID: PMC11148321 DOI: 10.3389/fcimb.2024.1411482] [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: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.
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Affiliation(s)
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | | | | | | | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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14
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Qi YL, Chen YT, Xie YG, Li YX, Rao YZ, Li MM, Xie QJ, Cao XR, Chen L, Qu YN, Yuan ZX, Xiao ZC, Lu L, Jiao JY, Shu WS, Li WJ, Hedlund BP, Hua ZS. Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes. Nat Commun 2024; 15:4066. [PMID: 38744885 PMCID: PMC11094006 DOI: 10.1038/s41467-024-48498-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.
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Affiliation(s)
- Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Jun Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Xing-Ru Cao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lei Chen
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhen-Xuan Yuan
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhi-Chao Xiao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.
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15
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Cui Z, Li Y, Jing X, Luan X, Liu N, Liu J, Meng Y, Xu J, Valentine DL. Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China's marginal seas. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133904. [PMID: 38422739 DOI: 10.1016/j.jhazmat.2024.133904] [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: 10/05/2023] [Revised: 01/30/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
The consumption of cycloalkanes is prevalent in low-temperature marine environments, likely influenced by psychrophilic microorganisms. Despite their significance, the primary active species responsible for marine cycloalkane degradation remain largely unidentified due to cultivation challenges. In this study, we provide compelling evidence indicating that the uncultured genus C1-B045 of Gammaproteobacteria is a pivotal participant in cycloalkane decomposition within China's marginal seas. Notably, the relative abundance of C1-B045 surged from 15.9% in the methylcyclohexane (MCH)-consuming starter culture to as high as 97.5% in MCH-utilizing extinction cultures following successive dilution-to-extinction and incubation cycles. We used stable isotope probing, Raman-activated gravity-driven encapsulation, and 16 S rRNA gene sequencing to link cycloalkane-metabolizing phenotype to genotype at the single-cell level. By annotating key enzymes (e.g., alkane monooxygenase, cyclohexanone monooxygenase, and 6-hexanolactone hydrolase) involved in MCH metabolism within C1-B045's representative metagenome-assembled genome, we developed a putative MCH degradation pathway.
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Affiliation(s)
- Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China.
| | - Yingchao Li
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100048, People's Republic of China
| | - Na Liu
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Jinyan Liu
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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16
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Li L, Zhang J, Jiao Z, Zhou X, Ren L, Wang M. Seamless Integration of Rapid Separation and Ultrasensitive Detection for Complex Biological Samples Using Multistage Annular Functionalized Carbon Nanotube Arrays. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312518. [PMID: 38354403 DOI: 10.1002/adma.202312518] [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: 11/21/2023] [Revised: 02/13/2024] [Indexed: 02/16/2024]
Abstract
Efficient separation, enrichment, and detection of bacteria in diverse media are pivotal for identifying bacterial diseases and their transmission pathways. However, conventional bacterial detection methods that split the separation and detection steps are plagued by prolonged processing times. Herein, a multistage annular functionalized carbon nanotube array device designed for the seamless integration of complex biological sample separation and multimarker detection is introduced. This device resorts to the supersmooth fluidity of the liquid sample in the carbon nanotubes interstice through rotation assistance, achieving the ability to quickly separate impurities and capture biomarkers (1 mL sample cost time of 2.5 s). Fluid dynamics simulations show that the reduction of near-surface hydrodynamic resistance drives the capture of bacteria and related biomarkers on the functionalized surface of carbon nanotube in sufficient time. When further assembled as an even detection device, it exhibited fast detection (<30 min), robust linear correlation (101-107 colony-forming units [CFU] mL-1, R2 = 0.997), ultrasensitivity (limit of detection = 1.7 CFU mL-1), and multitarget detection (Staphylococcus aureus, extracellular vesicles, and enterotoxin proteins). Collectively, the material and system offer an expanded platform for real-time diagnostics, enabling integrated rapid separation and detection of various disease biomarkers.
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Affiliation(s)
- Lihuang Li
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, P. R. China
| | - Jialing Zhang
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, P. R. China
| | - Zhengqi Jiao
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, P. R. China
| | - Xi Zhou
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, P. R. China
| | - Lei Ren
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, P. R. China
- State Key Lab of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, P. R. China
| | - Miao Wang
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, P. R. China
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17
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Ahmad T, Erum Ishaq S, Liang L, Hou J, Xie R, Dong Y, Yu T, Wang F. Description of the first cultured representative of "Candidatus Synoicihabitans" genus, isolated from deep-sea sediment of South China Sea. Syst Appl Microbiol 2024; 47:126490. [PMID: 38330528 DOI: 10.1016/j.syapm.2024.126490] [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: 12/23/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
In this study we describe the first cultured representative of Candidatus Synoicihabitans genus, a novel strain designated as LMO-M01T, isolated from deep-sea sediment of South China Sea. This bacterium is a facultative aerobe, Gram-negative, non-motile, and has a globular-shaped morphology, with light greenish, small, and circular colonies. Analysis of the 16S rRNA gene sequences of strain LMO-M01T showed less than 93% similarity to its closest cultured members. Furthermore, employing advanced phylogenomic methods such as comparative genome analysis, average nucleotide identity (ANI), average amino acids identity (AAI), and digital DNA-DNA hybridization (dDDH), placed this novel species within the candidatus genus Synoicihabitans of the family Opitutaceae, Phylum Verrucomicrobiota. The genomic analysis of strain LMO-M01T revealed 175 genes, encoding putative carbohydrate-active enzymes. This suggests its metabolic potential to degrade and utilize complex polysaccharides, indicating a significant role in carbon cycling and nutrient turnover in deep-sea sediment. In addition, the strain's physiological capacity to utilize diverse biopolymers such as lignin, xylan, starch, and agar as sole carbon source opens up possibilities for sustainable energy production and environmental remediation. Moreover, the genome sequence of this newly isolated strain has been identified across diverse ecosystems, including marine sediment, fresh water, coral, soil, plants, and activated sludge highlighting its ecological significance and adaptability to various environments. The recovery of strain LMO-M01T holds promise for taxonomical, ecological and biotechnological applications. Based on the polyphasic data, we propose that this ecologically important strain LMO-M01T represents a novel genus (previously Candidatus) within the family Opitutaceae of phylum Verrucomicrobiota, for which the name Synoicihabitans lomoniglobus gen. nov., sp. nov. was proposed. The type of strain is LMO-M01T (= CGMCC 1.61593T = KCTC 92913T).
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Affiliation(s)
- Tariq Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Sidra Erum Ishaq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Lewen Liang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jialin Hou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ruize Xie
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yijing Dong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Tiantian Yu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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18
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Huang Y, Hu H, Zhang T, Wang W, Liu W, Tang H. Meta-omics assisted microbial gene and strain resources mining in contaminant environment. Eng Life Sci 2024; 24:2300207. [PMID: 38708415 PMCID: PMC11065330 DOI: 10.1002/elsc.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 05/07/2024] Open
Abstract
Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.
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Affiliation(s)
- Yiqun Huang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Tingting Zhang
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Wenzhao Liu
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
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19
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Song HS, Kim YB, Kim JY, Roh SW, Whon TW. Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery. J Microbiol Biotechnol 2024; 34:757-764. [PMID: 38379289 DOI: 10.4014/jmb.2311.11024] [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: 11/17/2023] [Revised: 01/29/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024]
Abstract
Despite considerable advancements achieved using next-generation sequencing technologies in exploring microbial diversity, several species of the gut microbiome remain unknown. In this transformative era, culturomics has risen to prominence as a pivotal approach in unveiling realms of microbial diversity that were previously deemed inaccessible. Utilizing innovative strategies to optimize growth and culture medium composition, scientists have successfully cultured hard-to-cultivate microbes. This progress has fostered the discovery and understanding of elusive microbial entities, highlighting their essential role in human health and disease paradigms. In this review, we emphasize the importance of culturomics research on the gut microbiome and provide new theories and insights for expanding microbial diversity via the optimization of cultivation conditions.
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Affiliation(s)
- Hye Seon Song
- Division of Environmental Materials, Honam National Institute of Biological Resource (HNIBR), Mokpo 58762, Republic of Korea
| | - Yeon Bee Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Joon Yong Kim
- Microbiome Research Institute, LISCure Biosciences Inc., Gyeonggi-do 13486, Republic of Korea
| | - Seong Woon Roh
- Microbiome Research Institute, LISCure Biosciences Inc., Gyeonggi-do 13486, Republic of Korea
| | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
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Ji C, Guo J, Ma Y, Xu X, Zang T, Liu S, An Z, Yang M, He X, Zheng W. Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7586-7595. [PMID: 38530921 DOI: 10.1021/acs.jafc.3c08885] [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: 03/28/2024]
Abstract
Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.
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Affiliation(s)
- Chao Ji
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Junli Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Ying Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Xiangfu Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Tongyu Zang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Sentao Liu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Zhenzhen An
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Wenjie Zheng
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
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21
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Möller L, Vainshtein Y, Meyer B, Neidhardt J, Eren AM, Sohn K, Rabus R. Rich microbial and depolymerising diversity in Antarctic krill gut. Microbiol Spectr 2024; 12:e0403523. [PMID: 38466097 PMCID: PMC10986584 DOI: 10.1128/spectrum.04035-23] [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: 11/25/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.
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Affiliation(s)
- Lars Möller
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Yevhen Vainshtein
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Bettina Meyer
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- Biosciences, Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - John Neidhardt
- Department of Human Medicine, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - A. Murat Eren
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- HIFMB-MPG Bridging Group for Marine Genomics, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute (AWI), Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Kai Sohn
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Liu S, Zheng N, Wang J, Zhao S. Relationships among bacterial cell size, diversity, and taxonomy in rumen. Front Microbiol 2024; 15:1376994. [PMID: 38628864 PMCID: PMC11018980 DOI: 10.3389/fmicb.2024.1376994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction The rumen microbial community plays a crucial role in the digestion and metabolic processes of ruminants. Although sequencing-based studies have helped reveal the diversity and functions of bacteria in the rumen, their physiological and biochemical characteristics, as well as their dynamic regulation along the digestion process in the rumen, remain poorly understood. Addressing these gaps requires pure culture studies to demystify the intricate mechanisms at play. Bacteria exhibit morphological differentiation associated with different species. Based on the difference in size or shape of microorganisms, size fractionation by filters with various pore sizes can be used to separate them. Methods In this study, we used polyvinylidene difluoride filters with pore sizes of 300, 120, 80, 40, 20, 8, 6, 2.1, and 0.6 μm. Bacterial suspensions were successively passed through these filters for the analysis of microbial population distribution using 16S rRNA gene sequences. Results We found that bacteria from the different pore sizes were clustered into four branches (> 120 μm, 40-120 μm, 6-20 μm, 20-40 μm, and < 0.6 μm), indicating that size fractionation had effects on enriching specific groups but could not effectively separate dominant groups by cell size alone. The species of unclassified Flavobacterium, unclassified Chryseobacterium, unclassified Delftia, Methylotenera mobilis, unclassified Caulobacteraceae, unclassified Oligella, unclassified Sphingomonas, unclassified Stenotrophomonas, unclassified Shuttleworthia, unclassified Sutterella, unclassified Alphaproteobacteria, and unclassified SR1 can be efficiently enriched or separated by size fractionation. Discussion In this study, we investigated the diversity of sorted bacteria populations in the rumen for preliminary investigations of the relationship between the size and classification of rumen bacteria that have the potential to improve our ability to isolate and culture bacteria from the rumen in the future.
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Affiliation(s)
- Sijia Liu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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23
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Zhang Z, Zhang Q, Yang H, Cui L, Qian H. Mining strategies for isolating plastic-degrading microorganisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123572. [PMID: 38369095 DOI: 10.1016/j.envpol.2024.123572] [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: 12/27/2023] [Revised: 01/29/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Plastic waste is a growing global pollutant. Plastic degradation by microorganisms has captured attention as an earth-friendly tactic. Although the mechanisms of plastic degradation by bacteria, fungi, and algae have been explored over the past decade, a large knowledge gap still exists regarding the identification, sorting, and cultivation of efficient plastic degraders, primarily because of their uncultivability. Advances in sequencing techniques and bioinformatics have enabled the identification of microbial degraders and related enzymes and genes involved in plastic biodegradation. In this review, we provide an outline of the situation of plastic degradation and summarize the methods for effective microbial identification using multidisciplinary techniques such as multiomics, meta-analysis, and spectroscopy. This review introduces new strategies for controlling plastic pollution in an environmentally friendly manner. Using this information, highly efficient and colonizing plastic degraders can be mined via targeted sorting and cultivation. In addition, based on the recognized rules and plastic degraders, we can perform an in-depth analysis of the associated degradation mechanism, metabolic features, and interactions.
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Affiliation(s)
- Ziyao Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Huihui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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24
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Pan T, Su L, Zhang Y, Xu L, Chen Y. Advances in Bio-Optical Imaging Systems for Spatiotemporal Monitoring of Intestinal Bacteria. Mol Nutr Food Res 2024; 68:e2300760. [PMID: 38491399 DOI: 10.1002/mnfr.202300760] [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: 10/28/2023] [Revised: 01/26/2024] [Indexed: 03/18/2024]
Abstract
Vast and complex intestinal communities are regulated and balanced through interactions with their host organisms, and disruption of gut microbial balance can cause a variety of diseases. Studying the mechanisms of pathogenic intestinal flora in the host and early detection of bacterial translocation and colonization can guide clinical diagnosis, provide targeted treatments, and improve patient prognosis. The use of in vivo imaging techniques to track microorganisms in the intestine, and study structural and functional changes of both cells and proteins, may clarify the governing equilibrium between the flora and host. Despite the recent rapid development of in vivo imaging of intestinal microecology, determining the ideal methodology for clinical use remains a challenge. Advances in optics, computer technology, and molecular biology promise to expand the horizons of research and development, thereby providing exciting opportunities to study the spatio-temporal dynamics of gut microbiota and the origins of disease. Here, this study reviews the characteristics and problems associated with optical imaging techniques, including bioluminescence, conventional fluorescence, novel metabolic labeling methods, nanomaterials, intelligently activated imaging agents, and photoacoustic (PA) imaging. It hopes to provide a valuable theoretical basis for future bio-intelligent imaging of intestinal bacteria.
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Affiliation(s)
- Tongtong Pan
- Hepatology Diagnosis and Treatment Center, The First Affiliated Hospital of Wenzhou Medical University & Zhejiang Provincial Key Laboratory for Accurate Diagnosis and Treatment of Chronic Liver Diseases, Ouhai District, Wenzhou, Zhejiang, 325035, China
| | - Lihuang Su
- The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou, Zhejiang, 325035, China
| | - Yiying Zhang
- Alberta Institute, Wenzhou Medical University, Ouhai District, Wenzhou, Zhejiang, 325035, China
| | - Liang Xu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yongping Chen
- Hepatology Diagnosis and Treatment Center, The First Affiliated Hospital of Wenzhou Medical University & Zhejiang Provincial Key Laboratory for Accurate Diagnosis and Treatment of Chronic Liver Diseases, Ouhai District, Wenzhou, Zhejiang, 325035, China
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25
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Chen Z, Wu Y, Dolfing J, Zhuang S, Wang B, Li D, Huang S, Rittmann BE. Complex ammonium oxidation demands visualized resolution. Sci Bull (Beijing) 2024:S2095-9273(24)00210-X. [PMID: 38604937 DOI: 10.1016/j.scib.2024.03.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Zhihao Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China.
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle-upon-Tyne NE1 8QH, UK
| | - Shunyao Zhuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Dan Li
- College of Urban Construction, Nanjing Tech University, Nanjing 211816, China
| | - Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton NJ 08540, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe AZ 85287-5701, USA
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26
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Staskiewicz K, Dabrowska-Zawada M, Kozon L, Olszewska Z, Drewniak L, Kaminski TS. Droplet microfluidic system for high throughput and passive selection of bacteria producing biosurfactants. LAB ON A CHIP 2024; 24:1947-1956. [PMID: 38436364 DOI: 10.1039/d3lc00656e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Traditional methods for the enrichment of microorganisms rely on growth in a selective liquid medium or on an agar plate, followed by tedious characterization. Droplet microfluidic techniques have been recently used to cultivate microorganisms and preserve enriched bacterial taxonomic diversity. However, new methods are needed to select droplets comprising not only growing microorganisms but also those exhibiting specific properties, such as the production of value-added compounds. We describe here a droplet microfluidic screening technique for the functional selection of biosurfactant-producing microorganisms, which are of great interest in the bioremediation and biotechnology industries. Single bacterial cells are first encapsulated into picoliter droplets for clonal cultivation and then passively sorted at high throughput based on changes in interfacial tension in individual droplets. Our method expands droplet-based microbial enrichment with a novel approach that reduces the time and resources needed for the selection of surfactant-producing bacteria.
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Affiliation(s)
- Klaudia Staskiewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland.
- Dioscuri Centre for Physics and Chemistry of Bacteria, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Maria Dabrowska-Zawada
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland.
| | - Lukasz Kozon
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Zofia Olszewska
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Poland
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland.
| | - Tomasz S Kaminski
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland.
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Poland
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27
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Pan H, Wang J, Sun Z, Shi R, Ren Q. Resuscitation of baijiu pit mud bacteria based on Rpf protein of Umezawaea beigongshangensis. Arch Microbiol 2024; 206:184. [PMID: 38503937 DOI: 10.1007/s00203-024-03924-6] [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: 01/10/2024] [Revised: 02/23/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
The pit mud in the Baijiu fermentation cellar is an abundant microbial resource that is closely related to the quality of baijiu. However, many naturally existing species might be in a viable but nonculturable (VBNC) state, posing challenges to the isolation and application of functional species. Herein, a previously isolated strain from baijiu mash, Umezawaea beigongshangensis, was found to contain the rpf gene that encodes resuscitation promotion factor (Rpf). Therefore, the gene was cloned and heterologously expressed, and the recombinant protein (Ub-Rpf 2) was purified. Ub-Rpf 2 was found to significantly promote the growth of resuscitated VBNC state Corynebacterium beijingensis and Sphingomonas beigongshangensis. To determine the resuscitation effect of Ub-Rpf 2 on real ecological samples, the protein was supplemented in pit mud for enrichment culture. Results revealed that specific families and genera were enriched in abundance upon Ub-Rpf 2 incubation, including a new family of Symbiobacteraceae and culturable Symbiobacterium genus. Furthermore, 14 species belonging to 12 genera were obtained in Ub-Rpf 2 treated samples, including a suspected novel species. This study lays a foundation for applying Rpf from U. beigongshangensis to exploit microbial resources in baijiu pit mud.
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Affiliation(s)
- Hanxu Pan
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, China
| | - Jiaxuan Wang
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, China
| | - Zhanbin Sun
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, China
| | - Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Yunnan, China
| | - Qing Ren
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, China.
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28
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Geesink P, ter Horst J, Ettema TJG. More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities. FEMS Microbiol Ecol 2024; 100:fiae029. [PMID: 38444203 PMCID: PMC10950044 DOI: 10.1093/femsec/fiae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities.
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Affiliation(s)
- Patricia Geesink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jolanda ter Horst
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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29
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Yi X, Brandt KK, Xue S, Peng J, Wang Y, Li M, Deng Y, Duan G. Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China. ENVIRONMENTAL MICROBIOME 2024; 19:13. [PMID: 38429752 PMCID: PMC10908009 DOI: 10.1186/s40793-024-00555-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot springs. However, their presence in arable soils is relatively limited. In this study, we aimed to investigate the spatial distributions and diversity of Bathyarchaeia in paddy soils across eastern China, which is a major rice production region. The relative abundance of Bathyarchaeia among total archaea ranged from 3 to 68% in paddy soils, and Bathy-6 was the dominant subgroup among the Bathyarchaeia (70-80% of all sequences). Bathyarchaeia showed higher migration ability and wider niche width based on the neutral and null model simulations. Bathy-6 was primarily assembled by deterministic processes. Soil pH and C/N ratio were identified as key factors influencing the Bathyarchaeia composition, whereas C/N ratio and mean annual temperature influenced the relative abundance of Bathyarchaeia. Network analysis showed that specific Bathyarchaeia taxa occupied keystone positions in the archaeal community and co-occurred with some methanogenic archaea, including Methanosarcina and Methanobacteria, and ammonia-oxidizing archaea belonging to Nitrososphaeria. This study provides important insights into the biogeography and niche differentiation of Bathyarchaeia particularly in paddy soil ecosystems.
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Affiliation(s)
- Xingyun Yi
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Kristian Koefoed Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Sino-Danish Center (SDC), 101408, Beijing, China
| | - Shudan Xue
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jingjing Peng
- College of Resources and Environmental Sciences, China Agricultural University, 10093, Beijing, China
| | - Yifei Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, Guangdong, China
| | - Ye Deng
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Guilan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Zhang J, Liang Q, Mu D, Lian F, Gong Y, Ye M, Chen G, Ye Y, Du Z. Cultivating the uncultured: Harnessing the "sandwich agar plate" approach to isolate heme-dependent bacteria from marine sediment. MLIFE 2024; 3:143-155. [PMID: 38827516 PMCID: PMC11139205 DOI: 10.1002/mlf2.12093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/18/2023] [Accepted: 10/10/2023] [Indexed: 06/04/2024]
Abstract
In the classical microbial isolation technique, the isolation process inevitably destroys all microbial interactions and thus makes it difficult to culture the many microorganisms that rely on these interactions for survival. In this study, we designed a simple coculture technique named the "sandwich agar plate method," which maintains microbial interactions throughout the isolation and pure culture processes. The total yield of uncultured species in sandwich agar plates based on eight helper strains was almost 10-fold that of the control group. Many uncultured species displayed commensal lifestyles. Further study found that heme was the growth-promoting factor of some marine commensal bacteria. Subsequent genomic analysis revealed that heme auxotrophies were common in various biotopes and prevalent in many uncultured microbial taxa. Moreover, our study supported that the survival strategies of heme auxotrophy in different habitats varied considerably. These findings highlight that cocultivation based on the "sandwich agar plate method" could be developed and used to isolate more uncultured bacteria.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | | | - Da‐Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
- Shandong University‐Weihai Research Institute of Industrial TechnologyWeihaiChina
| | | | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Mengqi Ye
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Guan‐Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Yuqi Ye
- Marine CollegeShandong UniversityWeihaiChina
| | - Zong‐Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
- Shandong University‐Weihai Research Institute of Industrial TechnologyWeihaiChina
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Li J, Luo C, Cai X, Dai Y, Zhang D, Zhang G. Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC). ENVIRONMENT INTERNATIONAL 2024; 185:108555. [PMID: 38458119 DOI: 10.1016/j.envint.2024.108555] [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: 12/14/2023] [Revised: 01/28/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024]
Abstract
High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from 13C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from 13C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.
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Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xixi Cai
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang 110044, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Wei J, Luo J, Yang F, Dai W, Pan X, Luo M. Identification of commensal gut bacterial strains with lipogenic effects contributing to NAFLD in children. iScience 2024; 27:108861. [PMID: 38313052 PMCID: PMC10835367 DOI: 10.1016/j.isci.2024.108861] [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: 08/14/2023] [Revised: 11/07/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Gut microbiota is known to have a significant impact on nonalcoholic fatty liver disease (NAFLD), particularly in children with obesity. However, the specific functions of microbiota at the strain level in this population have not been fully elucidated. In this study, we successfully isolated and identified several commensal gut bacterial strains that were dominant in children with obesity and NAFLD. Among these, four novel isolates were found to have significant lipogenic effects in vitro. These strains exhibited a potential link to hepatocyte steatosis by regulating the expression of genes involved in lipid metabolism and inflammation. Moreover, a larger cohort analysis confirmed that these identified bacterial strains were enriched in the NAFLD group. The integrated analysis of these strains effectively distinguished NASH from NAFL. These four strains might serve as potential biomarkers in children with NAFLD. These findings provided new insights into the exploration of therapeutic targets for NAFLD.
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Affiliation(s)
- Jia Wei
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Jiayou Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Fei Yang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang 421001, Hunan, China
| | - Wen Dai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Xiongfeng Pan
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Miyang Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
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Dijamentiuk A, Mangavel C, Gapp C, Elfassy A, Revol-Junelles AM, Borges F. Serial cultures in invert emulsion and monophase systems for microbial community shaping and propagation. Microb Cell Fact 2024; 23:50. [PMID: 38355580 PMCID: PMC10865683 DOI: 10.1186/s12934-024-02322-3] [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: 12/14/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Microbial communities harbor important biotechnological potential in diverse domains, however, the engineering and propagation of such communities still face both knowledge and know-how gaps. More specifically, culturing tools are needed to propagate and shape microbial communities, to obtain desired properties, and to exploit them. Previous work suggested that micro-confinement and segregation of microorganisms using invert (water-in-oil, w/o) emulsion broth can shape communities during propagation, by alleviating biotic interactions and inducing physiological changes in cultured bacteria. The present work aimed at evaluating invert emulsion and simple broth monophasic cultures for the propagation and shaping of bacterial communities derived from raw milk in a serial propagation design. RESULTS The monophasic setup resulted in stable community structures during serial propagation, whereas the invert emulsion system resulted in only transiently stable structures. In addition, different communities with different taxonomic compositions could be obtained from a single inoculum. Furthermore, the implementation of invert emulsion systems has allowed for the enrichment of less abundant microorganisms and consequently facilitated their isolation on culture agar plates. CONCLUSIONS The monophasic system enables communities to be propagated in a stable manner, whereas the invert emulsion system allowed for the isolation of less abundant microorganisms and the generation of diverse taxonomic compositions from a single inoculum.
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Affiliation(s)
- Alexis Dijamentiuk
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France
| | - Cécile Mangavel
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France
| | - Chloé Gapp
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France
| | - Annelore Elfassy
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France
| | | | - Frédéric Borges
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France.
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Wang X, Deng Z, Gao J. Exploring the antibiotic potential of cultured 'unculturable' bacteria. Trends Microbiol 2024; 32:124-127. [PMID: 38102034 DOI: 10.1016/j.tim.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
In response to the severe global antibiotic resistance crisis, this forum delves into 'unculturable' bacteria, believed to be a promising source of novel antibiotics. We propose remarkable drug discovery strategies that leverage these bacteria's diversity, aspiring to transform resistance management. The urgent call for new antibiotics accentuates the essentiality of further research.
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Affiliation(s)
- Xiaozhao Wang
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jiangtao Gao
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Hu T, Chen J, Lin X, He W, Liang H, Wang M, Li W, Wu Z, Han M, Jin X, Kristiansen K, Xiao L, Zou Y. Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly. Sci Rep 2024; 14:1292. [PMID: 38221534 PMCID: PMC10788345 DOI: 10.1038/s41598-024-51725-0] [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: 08/11/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024] Open
Abstract
The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
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Affiliation(s)
- Tongyuan Hu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Xiaoqian Lin
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | - Hewei Liang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Wenxi Li
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
| | - Mo Han
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Karsten Kristiansen
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China.
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36
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Guo C, Wu JY. Pathogen Discovery in the Post-COVID Era. Pathogens 2024; 13:51. [PMID: 38251358 PMCID: PMC10821006 DOI: 10.3390/pathogens13010051] [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: 11/11/2023] [Revised: 12/22/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Pathogen discovery plays a crucial role in the fields of infectious diseases, clinical microbiology, and public health. During the past four years, the global response to the COVID-19 pandemic highlighted the importance of early and accurate identification of novel pathogens for effective management and prevention of outbreaks. The post-COVID era has ushered in a new phase of infectious disease research, marked by accelerated advancements in pathogen discovery. This review encapsulates the recent innovations and paradigm shifts that have reshaped the landscape of pathogen discovery in response to the COVID-19 pandemic. Primarily, we summarize the latest technology innovations, applications, and causation proving strategies that enable rapid and accurate pathogen discovery for both acute and historical infections. We also explored the significance and the latest trends and approaches being employed for effective implementation of pathogen discovery from various clinical and environmental samples. Furthermore, we emphasize the collaborative nature of the pandemic response, which has led to the establishment of global networks for pathogen discovery.
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Affiliation(s)
- Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Jian-Yong Wu
- School of Public Health, Xinjiang Medical University, Urumqi 830017, China
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Deutschmann IM, Delage E, Giner CR, Sebastián M, Poulain J, Arístegui J, Duarte CM, Acinas SG, Massana R, Gasol JM, Eveillard D, Chaffron S, Logares R. Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean. Nat Commun 2024; 15:126. [PMID: 38168083 PMCID: PMC10762198 DOI: 10.1038/s41467-023-44550-y] [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: 04/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.
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Affiliation(s)
| | - Erwan Delage
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | | | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | | | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Damien Eveillard
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Samuel Chaffron
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain.
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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Wang K, Li J, Gu X, Wang H, Li X, Peng Y, Wang Y. How to Provide Nitrite Robustly for Anaerobic Ammonium Oxidation in Mainstream Nitrogen Removal. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21503-21526. [PMID: 38096379 DOI: 10.1021/acs.est.3c05600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Innovation in decarbonizing wastewater treatment is urgent in response to global climate change. The practical implementation of anaerobic ammonium oxidation (anammox) treating domestic wastewater is the key to reconciling carbon-neutral management of wastewater treatment with sustainable development. Nitrite availability is the prerequisite of the anammox reaction, but how to achieve robust nitrite supply and accumulation for mainstream systems remains elusive. This work presents a state-of-the-art review on the recent advances in nitrite supply for mainstream anammox, paying special attention to available pathways (forward-going (from ammonium to nitrite) and backward-going (from nitrate to nitrite)), key controlling strategies, and physiological and ecological characteristics of functional microorganisms involved in nitrite supply. First, we comprehensively assessed the mainstream nitrite-oxidizing bacteria control methods, outlining that these technologies are transitioning to technologies possessing multiple selective pressures (such as intermittent aeration and membrane-aerated biological reactor), integrating side stream treatment (such as free ammonia/free nitrous acid suppression in recirculated sludge treatment), and maintaining high activity of ammonia-oxidizing bacteria and anammox bacteria for competing oxygen and nitrite with nitrite-oxidizing bacteria. We then highlight emerging strategies of nitrite supply, including the nitrite production driven by novel ammonia-oxidizing microbes (ammonia-oxidizing archaea and complete ammonia oxidation bacteria) and nitrate reduction pathways (partial denitrification and nitrate-dependent anaerobic methane oxidation). The resources requirement of different mainstream nitrite supply pathways is analyzed, and a hybrid nitrite supply pathway by combining partial nitrification and nitrate reduction is encouraged. Moreover, data-driven modeling of a mainstream nitrite supply process as well as proactive microbiome management is proposed in the hope of achieving mainstream nitrite supply in practical application. Finally, the existing challenges and further perspectives are highlighted, i.e., investigation of nitrite-supplying bacteria, the scaling-up of hybrid nitrite supply technologies from laboratory to practical implementation under real conditions, and the data-driven management for the stable performance of mainstream nitrite supply. The fundamental insights in this review aim to inspire and advance our understanding about how to provide nitrite robustly for mainstream anammox and shed light on important obstacles warranting further settlement.
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Affiliation(s)
- Kaichong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Jia Li
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Xin Gu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Xiang Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, P. R. China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
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Verhoeven MD, Nielsen PH, Dueholm MKD. Amplicon-guided isolation and cultivation of previously uncultured microbial species from activated sludge. Appl Environ Microbiol 2023; 89:e0115123. [PMID: 38051071 PMCID: PMC10734543 DOI: 10.1128/aem.01151-23] [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: 07/13/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Biological wastewater treatment relies on complex microbial communities that assimilate nutrients and break down pollutants in the wastewater. Knowledge about the physiology and metabolism of bacteria in wastewater treatment plants (WWTPs) may therefore be used to improve the efficacy and economy of wastewater treatment. Our current knowledge is largely based on 16S rRNA gene amplicon profiling, fluorescence in situ hybridization studies, and predictions based on metagenome-assembled genomes. Bacterial isolates are often required to validate genome-based predictions as they allow researchers to analyze a specific species without interference from other bacteria and with simple bulk measurements. Unfortunately, there are currently very few pure cultures representing the microbes commonly found in WWTPs. To address this, we introduce an isolation strategy that takes advantage of state-of-the-art microbial profiling techniques to uncover suitable growth conditions for key WWTP microbes. We furthermore demonstrate that this information can be used to isolate key organisms representing global WWTPs.
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Affiliation(s)
- Maarten D. Verhoeven
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per H. Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Morten K. D. Dueholm
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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Lo HY, Wink K, Nitz H, Kästner M, Belder D, Müller JA, Kaster AK. scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling. mSystems 2023; 8:e0099823. [PMID: 37982643 PMCID: PMC10734494 DOI: 10.1128/msystems.00998-23] [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: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.
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Affiliation(s)
- Hao-Yu Lo
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Konstantin Wink
- Institute for Analytical Chemistry, Leipzig University, Leipzig, Germany
| | - Henrike Nitz
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Detlev Belder
- Institute for Analytical Chemistry, Leipzig University, Leipzig, Germany
| | - Jochen A. Müller
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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Li M, Raza M, Song S, Hou L, Zhang ZF, Gao M, Huang JE, Liu F, Cai L. Application of culturomics in fungal isolation from mangrove sediments. MICROBIOME 2023; 11:272. [PMID: 38082427 PMCID: PMC10712113 DOI: 10.1186/s40168-023-01708-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 10/19/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Fungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them remain unknown to science. The description rate of fungi is very low, mainly due to the inability of most fungi to grow in artificial media, which could not provide a sufficiently similar environment to their natural habitats. Moreover, many species in nature are in a state of low metabolic activity which cannot readily proliferate without proper resuscitation. Previously developed culturomics techniques are mostly designed and applicable for bacteria, with few attempts for fungal isolation because of their significantly larger cell size and hyphal growth properties. RESULTS This study attempted to isolate previously uncultured and rare fungi from mangrove sediments using newly developed fungal enrichment culture method (FECM) and fungal isolation chips (FiChips). Comparison of fungal community composition at different enrichment stages showed that FECM had great influence on fungal community composition, with rare taxa increased significantly, thus improving the isolation efficiency of previously uncultured fungi. Similarly, in situ cultivation using FiChips has a significant advantage in detecting and culturing rare fungi, as compared to the conventional dilution plate method (DPM). In addition, based on morphological comparisons and phylogenetic analyses, we described and proposed 38 new ascomycetous taxa, including three new families, eight new genera, 25 new species, and two new combinations (presented in additional file 1). CONCLUSIONS Our study demonstrated that mangrove sediments harbor a high diversity of fungi, and our new isolation approaches (FECM and FiChips) presented a high efficiency in isolating hitherto uncultured fungi, which is potentially usable for fungal isolation in other similar environments. Video Abstract.
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Affiliation(s)
- Meng Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mubashar Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Integrated Pest Management On Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Shuang Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingwei Hou
- Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Zhi-Feng Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-En Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhou J, Wang J, Zhou Y, Liu K, Lu Y, Zhu L, Chen X. Microbial community structure and interactions between Aspergillus oryzae and bacteria in traditional solid-state fermentation of Jiangqu. Food Microbiol 2023; 116:104346. [PMID: 37689429 DOI: 10.1016/j.fm.2023.104346] [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: 11/17/2022] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 09/11/2023]
Abstract
Microbial interactions play an important role in the formation, stabilization and functional performance of natural microbial communities. However, little is known about how the microbes present interactions to build a stable natural microbial community. Here, we developed Jiangqu, the solid-state fermented starters of thick broad-bean sauce formed naturally in factory, as model microbial communities by characterizing its diversity of microbial communities and batch stability. The dominant microbial strains and their fungi-bacteria interactions during solid-state fermentation of Jiangqu were characterized. In all batches of Jiangqu, Aspergillus oryzae, Bacillus, Staphylococcus and Weissella dominated in the communities and such a community structure could almost reduplicate between batches. Direct adsorption and competition were identified as the main interactions between A. oryzae and dominant bacteria during solid-state fermentation, which were quite different from liquid co-cultivation of A. oryzae and dominant bacteria. These results will help us better understand the intrinsic mechanism in the formation and stabilization of microbial communities from traditional solid-state qu-making and fermentation.
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Affiliation(s)
- Jiawei Zhou
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jiayan Wang
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yuanlu Zhou
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Kaiqiang Liu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yuele Lu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Linjiang Zhu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Xiaolong Chen
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou, 310014, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
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Wang YW, Wang XH, Zhang J, Du ZJ, Mu DS. Cerina litoralis gen. nov., sp. nov., a novel potential polysaccharide degrading bacterium of the family Flavobacteriaceae, isolated from marine sediment. Antonie Van Leeuwenhoek 2023; 116:1447-1455. [PMID: 37899393 DOI: 10.1007/s10482-023-01888-z] [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: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023]
Abstract
The Gram-strain-negative, facultative anaerobic, chemoheterotrophic, short-rod-shaped, non-motile, forming yellow colonies strain, designated F89T, was isolated from marine sediment of Xiaoshi Island, Weihai. Strain F89T grew at 15-37 °C (optimally at 28 °C), at pH 6.0-8.5 (optimally at pH 7.0) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain F89T was related to the family Flavobacteriaceae. F89T had highest 16S rRNA gene sequence similarity to Maribacter cobaltidurans MCCC 1K03318T (93.3%). The predominant cellular fatty acids of F89T were iso-C15:0, iso-C15:0 G and Summed Feature 3. The main respiratory quinone of F89T was menaquinone 6 (MK-6), consistent with that observed for all related strains. The polar lipid profile of strain F89T contained phosphatidylethanolamine, two aminolipids and three unidentified polar lipids. The genomic DNA G + C content of strain F89T was 42.7%. Strain F89T encoded 121 glycoside hydrolases and was a potential polysaccharide degrading bacterium. Differential phenotypic and genotypic characteristics of the strain showed that F89T should be classified as a novel genus in Flavobacteriaceae, for which the name Cerina litoralis is proposed. The type strain is F89T (= MCCC 1H00510T = KCTC 92203T).
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Affiliation(s)
- Ya-Wei Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Xin-Hui Wang
- ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Jing Zhang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China.
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45
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Kost C, Patil KR, Friedman J, Garcia SL, Ralser M. Metabolic exchanges are ubiquitous in natural microbial communities. Nat Microbiol 2023; 8:2244-2252. [PMID: 37996708 DOI: 10.1038/s41564-023-01511-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 09/11/2023] [Indexed: 11/25/2023]
Abstract
Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.
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Affiliation(s)
- Christian Kost
- Osnabrück University, Department of Ecology, School of Biology/Chemistry, Osnabrück, Germany.
| | - Kiran Raosaheb Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany.
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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46
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Sondo M, Wonni I, Koïta K, Rimbault I, Barro M, Tollenaere C, Moulin L, Klonowska A. Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data. PLoS One 2023; 18:e0287084. [PMID: 38032916 PMCID: PMC10688718 DOI: 10.1371/journal.pone.0287084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.
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Affiliation(s)
- Moussa Sondo
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Kadidia Koïta
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Isabelle Rimbault
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Mariam Barro
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Charlotte Tollenaere
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Lionel Moulin
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Agnieszka Klonowska
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
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McAtamney A, Heaney C, Lizama-Chamu I, Sanchez LM. Reducing Mass Confusion over the Microbiome. Anal Chem 2023; 95:16775-16785. [PMID: 37934885 PMCID: PMC10841885 DOI: 10.1021/acs.analchem.3c02408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
As genetic tools continue to emerge and mature, more information is revealed about the identity and diversity of microbial community members. Genetic tools can also be used to make predictions about the chemistry that bacteria and fungi produce to function and communicate with one another and the host. Ongoing efforts to identify these products and link genetic information to microbiome chemistry rely on analytical tools. This tutorial highlights recent advancements in microbiome studies driven by techniques in mass spectrometry.
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Affiliation(s)
- Allyson McAtamney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Casey Heaney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Itzel Lizama-Chamu
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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Zhao Y, Huang F, Wang W, Gao R, Fan L, Wang A, Gao SH. Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165867. [PMID: 37516185 DOI: 10.1016/j.scitotenv.2023.165867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi, and protozoa, in urban water systems poses a significant risk to public health. The emergence of infectious waterborne diseases mediated by urban water systems has become one of the leading global causes of mortality. However, the detection and monitoring of these pathogenic microorganisms have been limited by the complexity and diversity in the environmental samples. Conventional methods were restricted by long assay time, high benchmarks of identification, and narrow application sceneries. Novel technologies, such as high-throughput sequencing technologies, enable potentially full-spectrum detection of trace pathogenic microorganisms in complex environmental matrices. This review discusses the current state of high-throughput sequencing technologies for identifying pathogenic microorganisms in urban water systems with a concise summary. Furthermore, future perspectives in pathogen research emphasize the need for detection methods with high accuracy and sensitivity, the establishment of precise detection standards and procedures, and the significance of bioinformatics software and platforms. We have compiled a list of pathogens analysis software/platforms/databases that boast robust engines and high accuracy for preference. We highlight the significance of analyses by combining targeted and non-targeted sequencing technologies, short and long reads technologies, sequencing technologies, and bioinformatic tools in pursuing upgraded biosafety in urban water systems.
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Affiliation(s)
- Yanmei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Fang Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wenxiu Wang
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Rui Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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Wang M, Zheng N, Li X, Zhao K, Xie BB. Enrichment Pretreatment Expands the Microbial Diversity Cultivated from Marine Sediments. Microorganisms 2023; 11:2771. [PMID: 38004782 PMCID: PMC10673404 DOI: 10.3390/microorganisms11112771] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The majority of the microbial diversity in nature has not been recovered through cultivation. Enrichment is a classical technique widely used in the selective cultivation of specific taxa. Whether enrichment is suitable for cultivation studies that aim to recover large numbers of species remains little explored. To address this issue, we evaluated the potential of enrichment pretreatment in the cultivation of bacteria from marine sediments. Upon obtaining and classifying a total of 943 pure cultures from chitin and cellulose enrichment pretreatment systems and a control system, our results showed that species obtained using enrichment pretreatment differed greatly from those without enrichment. Multiple enrichment media and different enrichment times increased the number of cultivated species in a sample. Amplicon sequencing showed that the increased relative abundance during pretreatment contributed greatly to bacterial cultivation. The testing of degradation abilities against chitin and cellulose and the whole-genome sequencing of representative strains suggested that microorganism-microorganism interactions play roles in the expanded diversity of cultivated bacteria. This study provides new insights into the abilities of enrichment in exploring cultivable diversity and mining microbial resources.
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Affiliation(s)
| | | | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.W.); (N.Z.); (X.L.); (K.Z.)
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50
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Zheng N, Hu W, Zhou X, Liu Y, Bartlam M, Wang Y. Influence of phycospheric bacterioplankton disruption or removal on algae growth and survival. ENVIRONMENTAL RESEARCH 2023; 237:117060. [PMID: 37659640 DOI: 10.1016/j.envres.2023.117060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/01/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Phycospheric bacteria play a crucial role in the survival of microalgae. However, the potential of using the growth regulation and community structure modulation of phycospheric bacteria to prevent the occurrence of blooms is yet to be verified. The phycospheric bacterioplankton of Cyclotella sp. can be categorized into HNA (high nucleic acid) bacteria and LNA (low nucleic acid) bacteria. 16S rRNA sequencing showed that the HNA bacteria exhibited higher α-diversity compared to the LNA bacteria, and the microbial community composition also exhibited variations. Metagenomic sequencing further indicated the distinct ecological functions between HNA and LNA bacteria. Furthermore, the study showcased the restorative capacity of the phycospheric bacterioplankton. Biomass analysis revealed that the recovery of phycospheric bacterioplankton positively influenced the microalgae growth, thus affirming the significance of phycospheric bacterioplankton to microalgae. The community structure of phycospheric bacterioplankton demonstrated a notable decrease in the abundance of restored LNA core bacteria. Additionally, the restored phycospheric bacterioplankton exhibited a more complex co-occurrence network structure, resulting in decreased resistance and sensitivity of microalgae to adverse environments. The presence of phycospheric bacterioplankton provides a protective shield for microalgae, and thus destabilizing or removing phycospheric bacterioplankton may effectively inhibit growth of microalgae.
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Affiliation(s)
- Ningning Zheng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Wei Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Xinzhu Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Yu Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, 300350, China.
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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