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Zhang J, Zhang F, Dong Z, Zhang W, Sun T, Chen L. Response and acclimation of cyanobacteria to acidification: A comprehensive review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173978. [PMID: 38897479 DOI: 10.1016/j.scitotenv.2024.173978] [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: 04/17/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Cyanobacteria, as vital components of aquatic ecosystems, face increasing challenges due to acidification driven by various anthropogenic and natural factors. Understanding how cyanobacteria adapt and respond to acidification is crucial for predicting their ecological dynamics and potential impacts on ecosystem health. This comprehensive review synthesizes current knowledge on the acclimation mechanisms and responses of cyanobacteria to acidification stress. Detailly, ecological roles of cyanobacteria were firstly briefly concluded, followed by the effects of acidification on aquatic ecosystems and cyanobacteria. Then the review focuses on the physiological, biochemical, and molecular strategies employed by cyanobacteria to cope with acidification stress, highlighting key adaptive mechanisms and their ecological implications. Finally, a summary of strategies to enhance acid resistance in cyanobacteria and future directions was discussed. Utilizing omics data and machine learning technology to build a cyanobacterial acid regulatory network allows for predicting the impact of acidification on cyanobacteria and inferring its broader effects on ecosystems. Additionally, acquiring acid-tolerant chassis cells of cyanobacteria through innovative techniques facilitates the advancement of environmentally friendly production of acidic chemicals. By synthesizing empirical evidence and theoretical frameworks, this review aims to elucidate the complex interplay between cyanobacteria and acidification stressors, providing insights for future research directions and ecosystem management strategies.
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Affiliation(s)
- Jie Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Fenfang Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Zhengxin Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China..
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China.
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2
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Gu S, Wu S, Zeng W, Deng Y, Luo G, Li P, Yang Y, Wang Z, Hu Q, Tan L. High-elevation-induced decrease in soil pH weakens ecosystem multifunctionality by influencing soil microbiomes. ENVIRONMENTAL RESEARCH 2024; 257:119330. [PMID: 38830394 DOI: 10.1016/j.envres.2024.119330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/05/2024]
Abstract
Plant environmental stress response has become a global research hotspot, yet there is a lack of clear understanding regarding the mechanisms that maintain microbial diversity and their ecosystem services under environmental stress. In our research, we examined the effects of moderate elevation on the rhizosphere soil characteristics, microbial community composition, and ecosystem multifunctionality (EMF) within agricultural systems. Our findings revealed a notable negative correlation between EMF and elevation, indicating a decline in multifunctionality at higher elevations. Additionally, our analysis across bacterial and protistan communities showed a general decrease in microbial richness with increasing elevation. Using random forest models, pH was identified as the key environmental stressor influencing microbial communities. Furthermore, we found that microbial community diversity is negatively correlated with stability by mediating complexity. Interestingly, while pH was found to affect the complexity within bacterial networks, it did not significantly impact the ecosystem stability along the elevation gradients. Using a Binary-State Speciation and Extinction (BiSSE) model to explore the evolutionary dynamics, we found that Generalists had higher speciation rates and lower extinction rates compared to specialists, resulting in a skewed distribution towards higher net diversification for generalists under increasing environmental stress. Moreover, structural equation modeling (SEM) analysis highlighted a negative correlation between environmental stress and community diversity, but showed a positive correlation between environmental stress and degree of cooperation & competition. These interactions under environmental stress indirectly increased community stability and decreased multifunctionality. Our comprehensive study offers valuable insights into the intricate relationship among environmental factors, microbial communities, and ecosystem functions, especially in the context of varying elevation gradients. These findings contribute significantly to our understanding of how environmental stressors affect microbial diversity and ecosystem services, providing a foundation for future ecological research and management strategies in similar contexts.
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Affiliation(s)
- Songsong Gu
- Hunan Agricultural University, Changsha, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shaolong Wu
- Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Weiai Zeng
- Changsha Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Gongwen Luo
- Hunan Agricultural University, Changsha, China
| | - Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | | | | | - Qiulong Hu
- Hunan Agricultural University, Changsha, China.
| | - Lin Tan
- Hunan Agricultural University, Changsha, China.
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3
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Li Y, Zhu D, Niu L, Zhang W, Wang L, Zhang H, Zou S, Zhou C. Carbon-fixing bacteria in diverse groundwaters of karst area: Distribution patterns, ecological interactions, and driving factors. WATER RESEARCH 2024; 261:121979. [PMID: 38941678 DOI: 10.1016/j.watres.2024.121979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024]
Abstract
The biological carbon pump in karst areas is of great significance for maintaining the effectiveness of karst carbon sinks. However, the spatial distribution and carbon-fixing potential of microorganisms in different aquifers within karst areas remain poorly understood. In this study, the distribution patterns, ecological roles, and environmental drivers of microbiota associated with CO2 fixation were investigated in karst groundwater (KW), porous groundwater (PW), fractured groundwater (FW), and surface water (SW) within a typical karst watershed, located in Guilin, southwest China. KW, PW, and FW displayed the similar community structure and indicative carbon-fixing bacteria composition, which were dominated by chemoautotrophic bacteria compared to SW. Higher abundances of indicative carbon-fixing bacteria and carbon-fixing genes, as well as richer proportions of microbial-derived DOC, indicated the more significant microbial carbon-fixing potential in KW and PW. At the profile of KW, a carbon-fixing hotspot was discovered at the depths of 0-50 m. Correlation analysis between carbon-fixing bacteria and DOC revealed that the chemoautotrophic process driven by nitrogen and sulfur oxidation predominated the microbial carbon fixation in groundwater. Co-occurrence network analysis demonstrated that carbon-fixing bacteria exhibited cooperation with other bacterial taxa in KW, while competition was the dominant interaction in PW. Moreover, carbon-fixing bacteria was found to lead bacterial assembly more deterministic in KW. The analysis of environmental factors and microbial diversity illustrated that inorganic carbon and redox state drove community variations across groundwaters. Structural equation model (SEM) further confirmed that ORP was the primary factor influencing the carbon fixation potential. This study provides a new insight into biological carbon fixation in karst aquatic systems, which holds significance in the accurate assessment of karst carbon sinks.
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Affiliation(s)
- Yi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China.
| | - Danni Zhu
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Shengzhang Zou
- Key Laboratory of Karst Dynamics, MNR&GZAR, Institute of Karst Geology, CAGS, Guilin 541004, China; Guangxi Karst Resources and Environment Research Center of Engineering Technology, Guilin 541004, China
| | - Changsong Zhou
- Key Laboratory of Karst Dynamics, MNR&GZAR, Institute of Karst Geology, CAGS, Guilin 541004, China; Guangxi Karst Resources and Environment Research Center of Engineering Technology, Guilin 541004, China
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4
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Forni D, Pozzoli U, Mozzi A, Cagliani R, Sironi M. Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures. NAR Genom Bioinform 2024; 6:lqae088. [PMID: 39071851 PMCID: PMC11282364 DOI: 10.1093/nargab/lqae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/17/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024] Open
Abstract
Dinucleotide biases have been widely investigated in the genomes of eukaryotes and viruses, but not in bacteria. We assembled a dataset of bacterial genomes (>15 000), which are representative of the genetic diversity in the kingdom Eubacteria, and we analyzed dinucleotide biases in relation to different traits. We found that TpA dinucleotides are the most depleted and that CpG dinucleotides show the widest dispersion. The abundances of both dinucleotides vary with genomic G + C content and show a very strong phylogenetic signal. After accounting for G + C content and phylogenetic inertia, we analyzed different bacterial lifestyle traits. We found that temperature preferences associate with the abundance of CpG dinucleotides, with thermophiles/hyperthemophiles being particularly depleted. Conversely, the TpA dinucleotide displays a bias that only depends on genomic G + C composition. Using predictions of intrinsic cyclizability we also show that CpG depletion may associate with higher DNA bendability in both thermophiles/hyperthermophiles and mesophiles, and that the former are predicted to have significantly more flexible genomes than the latter. We suggest that higher bendability is advantageous at high temperatures because it facilitates DNA positive supercoiling and that, through modulation of DNA mechanical properties, local or global CpG depletion controls genome organization, most likely not only in bacteria.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
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Gao SM, Wang P, Li Q, Shu WS, Tang LY, Lin ZL, Li JT, Huang LN. Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135478. [PMID: 39137550 DOI: 10.1016/j.jhazmat.2024.135478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/28/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.
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Affiliation(s)
- Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Pandeng Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Ling-Yun Tang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhi-Liang Lin
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China.
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6
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Iglesias A, Martínez L, Torrent D, Porcar M. The microwave bacteriome: biodiversity of domestic and laboratory microwave ovens. Front Microbiol 2024; 15:1395751. [PMID: 39176272 PMCID: PMC11338789 DOI: 10.3389/fmicb.2024.1395751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/19/2024] [Indexed: 08/24/2024] Open
Abstract
Microwaves have become an essential part of the modern kitchen, but their potential as a reservoir for bacterial colonization and the microbial composition within them remain largely unexplored. In this study, we investigated the bacterial communities in microwave ovens and compared the microbial composition of domestic microwaves, microwaves used in shared large spaces, and laboratory microwaves, using next-generation sequencing and culturing techniques. The microwave oven bacterial population was dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, similar to the bacterial composition of human skin. Comparison with other environments revealed that the bacterial composition of domestic microwaves was similar to that of kitchen surfaces, whereas laboratory microwaves had a higher abundance of taxa known for their ability to withstand microwave radiation, high temperatures and desiccation. These results suggest that different selective pressures, such as human contact, nutrient availability and radiation levels, may explain the differences observed between domestic and laboratory microwaves. Overall, this study provides valuable insights into microwave ovens bacterial communities and their potential biotechnological applications.
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Affiliation(s)
- Alba Iglesias
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Lorena Martínez
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | | | - Manuel Porcar
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
- Darwin Bioprospecting Excellence S.L., Valencia, Spain
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7
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Rappaport HB, Oliverio AM. Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life. Genome Biol Evol 2024; 16:evae160. [PMID: 39101574 PMCID: PMC11299111 DOI: 10.1093/gbe/evae160] [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] [Accepted: 07/15/2024] [Indexed: 08/06/2024] Open
Abstract
From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.
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Affiliation(s)
- H B Rappaport
- Department of Biology, Syracuse University, Syracuse, NY, USA
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8
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Xu H, Ji M, Xu D, Liu Y. Computer-aided mining of a psychrophilic cellobiose 2-epimerase from the Qinghai-Tibet Plateau gene catalogue. Int J Biol Macromol 2024; 277:134202. [PMID: 39089546 DOI: 10.1016/j.ijbiomac.2024.134202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Cellobiose 2-epimerase (CE) catalyzes the conversion of the lactose into its high-value derivatives, epilactose and lactulose, which has great prospects in food applications. In this study, CE sequences from the Qinghai-Tibet Plateau gene catalogue, we screened these for structural flexibility through molecular dynamics simulation to identify potential psychrophilic CE candidates. One such psychrophilic CE we termed psyCE demonstrated exceptional epimerization activity, achieving an optimum activity of 122.2 ± 1.6 U/mg. Its kinetic parameters (Kcat and Km) for epimerization activity were 219.9 ± 5.6 s-1 and 261.9 ± 18.1 mM, respectively, representing the highest Kcat recorded among known cold-active CEs. Notably, this is the first report of a psychrophilic CE. The psyCE can effectively produce epilactose at 8 °C, converting 20.3 % of 200 mM lactose into epilactose within four hours. These findings suggest that psyCE is highly suitable for cryogenic food processing, and glaciers may serve as a valuable repository of psychrophilic enzymes.
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Affiliation(s)
- Hu Xu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; College of Ecology, Lanzhou University, Lanzhou 730000, China; CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; College of Ecology, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
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9
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Qiu Z, He S, Lian CA, Qiao X, Zhang Q, Yao C, Mu R, Wang L, Cao XA, Yan Y, Yu K. Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments. NPJ Biofilms Microbiomes 2024; 10:62. [PMID: 39069527 DOI: 10.1038/s41522-024-00537-1] [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: 01/03/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of microbial communities remain largely underexplored. This study investigated the characteristics of microbial communities on rare and abundant taxa in alkaline lake sediments in west and northwest China. We observed that abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences. The assembly process of abundant taxa was influenced by dispersal limitation, whilst rare taxa were predominantly driven by heterogeneous selection. Network analysis indicated that rare taxa as core species for community interactions and community stability. Rare taxa exhibited higher speciation and transition rate than abundant taxa, serving as a genetic reservoir and potential candidates to become abundance taxa, highlighting their crucial role in maintaining microbial diversity. These insights underscore the significant influence of rare taxa on ecosystem biodiversity and stability in alkaline lakes.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Shuhang He
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Qing Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Ciqin Yao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Li Wang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Xiao-Ai Cao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yan Yan
- State Key Laboratory of Isotope Geochemistry, CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China.
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10
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Wang Y, Liu J, Yi Y, Zhu L, Liu M, Zhang Z, Xie Q, Jiang L. Insights into the synthesis, engineering, and functions of microbial pigments in Deinococcus bacteria. Front Microbiol 2024; 15:1447785. [PMID: 39119139 PMCID: PMC11306087 DOI: 10.3389/fmicb.2024.1447785] [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: 06/12/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
The ability of Deinococcus bacteria to survive in harsh environments, such as high radiation, extreme temperature, and dryness, is mainly attributed to the generation of unique pigments, especially carotenoids. Although the limited number of natural pigments produced by these bacteria restricts their industrial potential, metabolic engineering and synthetic biology can significantly increase pigment yield and expand their application prospects. In this study, we review the properties, biosynthetic pathways, and functions of key enzymes and genes related to these pigments and explore strategies for improving pigment production through gene editing and optimization of culture conditions. Additionally, studies have highlighted the unique role of these pigments in antioxidant activity and radiation resistance, particularly emphasizing the critical functions of deinoxanthin in D. radiodurans. In the future, Deinococcus bacterial pigments will have broad application prospects in the food industry, drug production, and space exploration, where they can serve as radiation indicators and natural antioxidants to protect astronauts' health during long-term space flights.
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Affiliation(s)
- Yuxian Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Jiayu Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yuanyang Yi
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, China
- College of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, China
| | - Minghui Liu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Zhidong Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, China
| | - Qiong Xie
- China Astronaut Research and Training Center, Beijing, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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11
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de Lorenzo V, Pérez-Pantoja D, Nikel PI. Pseudomonas putida KT2440: the long journey of a soil-dweller to become a synthetic biology chassis. J Bacteriol 2024; 206:e0013624. [PMID: 38975763 PMCID: PMC11270871 DOI: 10.1128/jb.00136-24] [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] [Indexed: 07/09/2024] Open
Abstract
Although members of the genus Pseudomonas share specific morphological, metabolic, and genomic traits, the diversity of niches and lifestyles adopted by the family members is vast. One species of the group, Pseudomonas putida, thrives as a colonizer of plant roots and frequently inhabits soils polluted with various types of chemical waste. Owing to a combination of historical contingencies and inherent qualities, a particular strain, P. putida KT2440, emerged time ago as an archetype of an environmental microorganism amenable to recombinant DNA technologies, which was also capable of catabolizing chemical pollutants. Later, the same bacterium progressed as a reliable platform for programming traits and activities in various biotechnological applications. This article summarizes the stepwise upgrading of P. putida KT2440 from being a system for fundamental studies on the biodegradation of aromatic compounds (especially when harboring the TOL plasmid pWW0) to its adoption as a chassis of choice in metabolic engineering and synthetic biology. Although there are remaining uncertainties about the taxonomic classification of KT2440, advanced genome editing capabilities allow us to tailor its genetic makeup to meet specific needs. This makes its traditional categorization somewhat less important, while also increasing the strain's overall value for contemporary industrial and environmental uses.
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Affiliation(s)
- Victor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Danilo Pérez-Pantoja
- Instituto Universitario de Investigación y Desarrollo Tecnológico, Universidad Tecnológica Metropolitana (UTEM), Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Systems Environmental Microbiology Group, Kgs. Lyngby, Denmark
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12
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Jiang Y, Zhang Z, Jiang J, Zhu F, Guo X, Jia P, Li H, Liu Z, Huang S, Zhang Y, Xue S. Enhancement of nitrogen on core taxa recruitment by Penicillium oxalicum stimulated microbially-driven soil formation in bauxite residue. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134647. [PMID: 38762986 DOI: 10.1016/j.jhazmat.2024.134647] [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: 02/26/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Microbially-driven soil formation process is an emerging technology for the ecological rehabilitation of alkaline tailings. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. Herein, a 1-year field-scale experiment was applied to demonstrate the effect of nitrogen input on the structure and function of the microbiome in alkaline bauxite residue. Results showed that the contents of nutrient components were increased with Penicillium oxalicum (P. oxalicum) incorporation, as indicated by the increasing of carbon and nitrogen mineralization and enzyme metabolic efficiency. Specifically, the increasing enzyme metabolic efficiency was associated with nitrogen input, which shaped the microbial nutrient acquisition strategy. Subsequently, we evidenced that P. oxalicum played a significant role in shaping the assemblages of core bacterial taxa and influencing ecological functioning through intra- and cross-kingdom network analysis. Furthermore, a recruitment experiment indicated that nitrogen enhanced the enrichment of core microbiota (Nitrosomonas, Bacillus, Pseudomonas, and Saccharomyces) and may provide benefits to fungal community bio-diversity and microbial network stability. Collectively, these results demonstrated nitrogen-based coexistence patterns among P. oxalicum and microbiome and revealed P. oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. It will aid in promoting soil formation and ecological rehabilitation of bauxite residue. ENVIRONMENT IMPLICATION: Bauxite residue is a highly alkaline solid waste generated during the Bayer process for producing alumina. Attempting to transform bauxite residue into a stable soil-like substrate using low-cost microbial resources is a highly promising engineering. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. In this study, we evidenced the nitrogen-based coexistence patterns among Penicillium oxalicum and microbiome and revealed Penicillium oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. This study can improve the understanding of core microbes' assemblies that affect the microbiome physiological traits in soil formation processes.
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Affiliation(s)
- Yifan Jiang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Ziying Zhang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Jun Jiang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Feng Zhu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Xuyao Guo
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Pu Jia
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hongzhe Li
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhongkai Liu
- Zhengzhou Non-ferrous Metals Research Institute Co., Ltd of Chalco, Zhengzhou 450000, China
| | - Shiwei Huang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Yufei Zhang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Shengguo Xue
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
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13
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Belkin P, Nechaeva Y, Blinov S, Vaganov S, Perevoshchikov R, Plotnikova E. Sediment microbial communities of a technogenic saline-alkaline reservoir. Heliyon 2024; 10:e33640. [PMID: 39071596 PMCID: PMC11283119 DOI: 10.1016/j.heliyon.2024.e33640] [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: 01/25/2023] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/30/2024] Open
Abstract
Various natural saline and alkaline habitats have recently been widely investigated, but knowledge of anthropogenic habitats with more complex environmental conditions is still lacking. This research looks at the structure of microbial communities in 18 bottom sediment samples from a technogenic water body with saline and alkaline composition. The core samples were collected from 2 columns in the western and eastern parts of an artificial water body at the Verkhnekamskoe Salt Deposit (Russia). The microbial community structure was studied using high-throughput 16S rRNA gene sequencing. The bottom sediment composition (salinity, pH, and toxic element content) varies greatly with depth and laterally throughout the study area. The study found a considerable difference in bacterial community diversity between the 2 columns, but no considerable difference was found between the communities at various depths of the studied layers. Proteobacteria, Firmicutes, and Actinobacteria, which are common in both natural and artificial saline and alkaline environments, make up the majority of the bacteria found in the samples. Studies have shown that salinity and total alkalinity are the key factors influencing the formation of microbial communities. Ralstonia and Pseudomonas were the two most common genera in the sediment samples. These two genera are known for having high metabolic flexibility, which means they can survive in extreme environments and use a variety of carbon compounds as energy sources. The study also found that Ralstonia is indicator bacteria in samples with the highest concentrations of toxic elements compared to the other samples. A relatively high microbial diversity was discovered in the studied anthropogenic water reservoir despite the extreme alkaline and saline conditions, but it is considerably lower than that found in natural, less alkaline habitats. This research offers insight into the mechanisms behind microbial community formation in complex anthropogenic environments and covers key factors in microbial community distribution.
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Affiliation(s)
- Pavel Belkin
- Natural Science Institute, Perm State University, 614068, Bukireva st. 15, Perm, Russia
| | - Yulia Nechaeva
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Аcademy of Sciences, 614081, Goleva st. 13, Perm, Russia
| | - Sergey Blinov
- Natural Science Institute, Perm State University, 614068, Bukireva st. 15, Perm, Russia
| | - Sergey Vaganov
- Natural Science Institute, Perm State University, 614068, Bukireva st. 15, Perm, Russia
| | - Roman Perevoshchikov
- Natural Science Institute, Perm State University, 614068, Bukireva st. 15, Perm, Russia
| | - Elena Plotnikova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Аcademy of Sciences, 614081, Goleva st. 13, Perm, Russia
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14
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Wang N, Ding D, Zhang H, Ding X, Zhang D, Yao C, Fan X, Ding R, Wang H, Jiang T. Anthropogenic activity shapes the assemble and co-occurrence pattern of microbial communities in fishing harbors around the Bohai Economic Circle. ENVIRONMENTAL RESEARCH 2024; 259:119563. [PMID: 38971358 DOI: 10.1016/j.envres.2024.119563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
This study aimed to elucidate the effects of coastal environmental stress on the composition of sediment bacterial communities and their cooccurrence patterns in fishing harbors around the Bohai Economic Circle, China. Compared with the natural sea area, fishing harbors contained higher levels of organic pollution (organic pollution index = 0.12±0.026) and considerably reduced bacterial richness and evenness. The distributions of sediment microbial communities clustered along the pollutant concentration gradients across fishing harbors. Betaproteobacteria dominated (76%) organically polluted fishing harbors, which were mostly disturbed by anthropogenic activities. However, the harbors also revealed the absence of numerous pathogenic (Coxiella and Legionella) and photosynthetic (Synechococcus and Leptolyngbya) bacteria. Abundant genera, including Thiobacillus and Arenimonas, exhibited a positive correlation with total phosphorus and a negative correlation with total nitrogen in sediments. Meanwhile, Sulfurovum, Psychrobacter, and Woeseia showed the opposite trend. Pollutant accumulation and anthropogenic activities caused the decrease in the sediment microbial diversity and dispersal ability and promoted convergent evolution. Severely polluted harbors with simplified cooccurrence networks revealed the presence of destabilized microbial communities. In addition, the modularity of bacterial networks decreased with organic pollution. Our results provide important insights into the adjustment mechanism of microbial communities to community organization and functions under environmental pollution stress. Overall, this study enhanced our understanding of how microbial communities in coastal sediments adapted and survived amidst anthropogenic activities like oily effluent discharges from large ships, wash water, domestic sewage, garbage, and fisheries wastes. It also examined their resilience to future contamination.
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Affiliation(s)
- Nan Wang
- School of Ocean, Yantai University, Yantai 264005, China
| | - Dongsheng Ding
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Huihui Zhang
- School of Ocean, Yantai University, Yantai 264005, China
| | - Xiaokun Ding
- School of Ocean, Yantai University, Yantai 264005, China
| | - Di Zhang
- School of Ocean, Yantai University, Yantai 264005, China
| | - Chenghao Yao
- Shandong Hongxin Environmental Protection Technology Co., Ltd
| | - Xiao Fan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - RenYe Ding
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Tao Jiang
- School of Ocean, Yantai University, Yantai 264005, China.
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15
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Yi Y, Liang L, de Jong A, Kuipers OP. A systematic comparison of natural product potential, with an emphasis on RiPPs, by mining of bacteria of three large ecosystems. Genomics 2024; 116:110880. [PMID: 38857812 DOI: 10.1016/j.ygeno.2024.110880] [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: 01/08/2024] [Revised: 04/22/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria. We demonstrate the utility of public dataset collections for revealing the different secondary metabolite biosynthetic potentials among these different living environments. We show that there is a higher occurrence of RiPPs in terrestrial systems, while in marine systems, we found relatively more terpene-, NRP-, and PK encoding gene clusters. Among the many new biosynthetic gene clusters (BGCs) identified, we analyzed various Nif-11-like and nitrile hydratase leader peptide (NHLP) containing gene clusters that would merit further study, including promising products, such as mersacidin-, LAP- and proteusin analogs. This research highlights the significance of public datasets in elucidating the biosynthetic potential of microbes in different living environments and underscores the wide bioengineering opportunities within the RiPP family.
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Affiliation(s)
- Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | | | - Anne de Jong
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands.
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16
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Saravanakumar S, Prabakaran NN, Ashokkumar R, Jamuna S. Unlocking the Gut's Treasure: Lipase-Producing Bacillus subtilis Probiotic from the Intestine of Microstomus kitt (Lemon sole). Appl Biochem Biotechnol 2024; 196:4273-4286. [PMID: 37943408 DOI: 10.1007/s12010-023-04749-7] [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] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
The main objective of this research was to identify potential probiotic candidates belonging to the Bacillus species that could demonstrate tolerance to bile salt and acidic conditions. The study focused on isolating Bacillus strains from the intestine of marine fish-Microstomus kitt. The isolation process involved the use of selective MRS media through the pour plate method. After 24 h, one particular isolate was identified based on its morphological and biochemical traits as Bacillus species. To confirm the identity, molecular characterization of the 16S RNA from the isolated strain was performed, and the sequence analysis verified it as Bacillus subtilis strain ACL_BS 001. With the molecular confirmation, the next step was to assess the probiotic characteristics of this B. subtilis strain. Various tests were conducted to evaluate its acid/pH tolerance, NaCl tolerance, and bile salt tolerance. The results indicated that B. subtilis exhibited high viability percentages even under acidic pH, in the presence of 1.5% bile salt, and at high salt concentrations. Subsequently, we investigated the strain's ability to produce lipase, an important enzyme with potential industrial applications. B. subtilis was grown in MRS agar amended with olive oil as a lipase substrate. After incubation, the presence of lipase activity was confirmed, and the enzymatic assay revealed a significant lipase enzyme activity of 100.23 µmoles/ml of the sample. In conclusion, the study successfully isolated and identified B. subtilis from the intestine of Microstomus kitt, and the strain exhibited promising probiotic characteristics, including resistance to bile salt and acidic conditions. Furthermore, the strain was found to produce lipase, which opens up possibilities for future research focusing on isolating and purifying the lipase from this potential probiotic B. subtilis strain.
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Affiliation(s)
| | | | - Rathinavel Ashokkumar
- Centre for Laboratory Animal Technology and Animal Research, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.
| | - S Jamuna
- Affyclone Laboratories Pvt Ltd, Chrompet, Chennai, Tamil Nadu, 600044, India.
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17
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Gu X, Sun W, Hu Z. Natural products from untapped sources as a potent reserve against antimicrobial resistance crisis. Chin J Nat Med 2024; 22:577-579. [PMID: 39059826 DOI: 10.1016/s1875-5364(24)60610-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 07/28/2024]
Affiliation(s)
- Xiaoxia Gu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weiguang Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Zhengxi Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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18
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Hassan S, Mushtaq M, Ganiee SA, Zaman M, Yaseen A, Shah AJ, Ganai BA. Microbial oases in the ice: A state-of-the-art review on cryoconite holes as diversity hotspots and their scientific connotations. ENVIRONMENTAL RESEARCH 2024; 252:118963. [PMID: 38640991 DOI: 10.1016/j.envres.2024.118963] [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: 12/09/2023] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Cryoconite holes, small meltwater pools on the surface of glaciers and ice sheets, represent extremely cold ecosystems teeming with diverse microbial life. Cryoconite holes exhibit greater susceptibility to the impacts of climate change, underlining the imperative nature of investigating microbial communities as an essential module of polar and alpine ecosystem monitoring efforts. Microbes in cryoconite holes play a critical role in nutrient cycling and can produce bioactive compounds, holding promise for industrial and pharmaceutical innovation. Understanding microbial diversity in these delicate ecosystems is essential for effective conservation strategies. Therefore, this review discusses the microbial diversity in these extreme environments, aiming to unveil the complexity of their microbial communities. The current study envisages that cryoconite holes as distinctive ecosystems encompass a multitude of taxonomically diverse and functionally adaptable microorganisms that exhibit a rich microbial diversity and possess intricate ecological functions. By investigating microbial diversity and ecological functions of cryoconite holes, this study aims to contribute valuable insights into the broader field of environmental microbiology and enhance further understanding of these ecosystems. This review seeks to provide a holistic overview regarding the formation, evolution, characterization, and molecular adaptations of cryoconite holes. Furthermore, future research directions and challenges underlining the need for long-term monitoring, and ethical considerations in preserving these pristine environments are also provided. Addressing these challenges and resolutely pursuing future research directions promises to enrich our comprehension of microbial diversity within cryoconite holes, revealing the broader ecological and biogeochemical implications. The inferences derived from the present study will provide researchers, ecologists, and policymakers with a profound understanding of the significance and utility of cryoconite holes in unveiling the microbial diversity and its potential applications.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Misba Mushtaq
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Shahid Ahmad Ganiee
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Muzafar Zaman
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Aarif Yaseen
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Abdul Jalil Shah
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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19
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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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20
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Liu M, Xu N, Chen B, Zhang Z, Chen X, Zhu Y, Hong W, Wang T, Zhang Q, Ye Y, Lu T, Qian H. Effects of different assembly strategies on gene annotation in activated sludge. ENVIRONMENTAL RESEARCH 2024; 252:119116. [PMID: 38734289 DOI: 10.1016/j.envres.2024.119116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments.
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Affiliation(s)
- Meng Liu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Xinyu Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yuke Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yangqing Ye
- College of Mechanical Engineering, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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21
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Zhang Z, Zhao H, Zhu R, Cheng S, Yu Y, Xiang L, Xiang Z, Guo Z, Wang Y. Characterization and correlation analysis of microbial flora and flavor profile of stinky acid, a Chinese traditional fermented condiment. Food Chem X 2024; 22:101311. [PMID: 38559445 PMCID: PMC10978482 DOI: 10.1016/j.fochx.2024.101311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
To explore the microbial diversity and flavor profiles of stinky acid, we utilized high-throughput sequencing, culture-based techniques, and bionic E-sensory technologies. The results revealed a significant correlation between the acidity levels of stinky acid and the richness of its microbial community. Ten core bacterial genera and three core fungal genera exhibited ubiquity across all stinky acid samples. Through E-nose analysis, it was found that sulfides constituted the principal odor compounds responsible for stinky acid's distinct aroma. Further insights arose from the correlation analysis, indicating the potential contribution of Debaryomyces yeast to the sour taste profile. Meanwhile, three genera-Rhizopus and Thermoascus and Companilactobacillus-were identified as contributors to aromatic constituents. Interestingly, the findings indicated that Rhizopus and Thermoascus could reduce the intensity of the pungent odor of stinky acid. In summary, this investigation's outcomes offer new insights into the complex bacterial diversity of stinky acid.
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Affiliation(s)
- Zhendong Zhang
- School of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyu, Guizhou Province, China
| | - Huijun Zhao
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei Province, China
- Xiangyang Lactic Acid Bacteria Biotechnology and Engineering Key Laboratory, Hubei University of Arts and Science, Xiangyang, Hubei Province, China
| | - Renzhi Zhu
- School of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyu, Guizhou Province, China
| | - Shaojing Cheng
- School of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyu, Guizhou Province, China
| | - Yuanqi Yu
- School of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyu, Guizhou Province, China
| | - Lan Xiang
- School of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyu, Guizhou Province, China
| | - Zhipan Xiang
- School of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyu, Guizhou Province, China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei Province, China
- Xiangyang Lactic Acid Bacteria Biotechnology and Engineering Key Laboratory, Hubei University of Arts and Science, Xiangyang, Hubei Province, China
| | - Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei Province, China
- Xiangyang Lactic Acid Bacteria Biotechnology and Engineering Key Laboratory, Hubei University of Arts and Science, Xiangyang, Hubei Province, China
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22
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Rowe L, Dowd SE, Davidson K, Kovarik C, VanAken M, Jarabek A, Taylor C. Comparing microbial populations from diverse hydrothermal features in Yellowstone National Park: hot springs and mud volcanoes. Front Microbiol 2024; 15:1409664. [PMID: 38993494 PMCID: PMC11236564 DOI: 10.3389/fmicb.2024.1409664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Geothermal features, such as hot springs and mud volcanoes, host diverse microbial life, including many extremophile organisms. The physicochemical parameters of the geothermal feature, such as temperature, pH, and heavy metal concentration, can influence the alpha and beta diversity of microbial life in these environments, as can spatiotemporal differences between sites and sampling. In this study, water and sediment samples were collected and analyzed from eight geothermal sites at Yellowstone National Park, including six hot springs, a mud volcano, and an acidic lake within the same week in July 2019, and these geothermal sites varied greatly in their temperature, pH, and chemical composition. All samples were processed and analyzed with the same methodology and taxonomic profiles and alpha and beta diversity metrics determined with 16S rRNA sequencing. These microbial diversity results were then analyzed with respect to pH, temperature, and chemical composition of the geothermal features. Results indicated that predominant microbial species varied greatly depending on the physicochemical composition of the geothermal site, with decreases in pH and increases in dissolved heavy metals in the water corresponding to decreases in alpha diversity, especially in the sediment samples. Similarly, sites with acidic pH values had more similar microbial populations (beta diversity) to one another than to relatively neutral or alkaline pH geothermal sites. This study suggests that pH and/or heavy metal concentration is a more important driver for microbial diversity and population profile than the temperature for these sites and is also the first reported microbial diversity study for multiple geothermal sites in Yellowstone National Park, including the relatively new mud volcano Black Dragon's Caldron, which erupted in 1948.
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Affiliation(s)
- Laura Rowe
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, United States
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Scot E. Dowd
- Molecular Research LP (MR DNA Lab), Shallowater, TX, United States
| | - Kelly Davidson
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Claire Kovarik
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Michayla VanAken
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Alyssa Jarabek
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Churro Taylor
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, United States
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23
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Wang C, Fan Y, Wang C, Tang J, Qiu Y, Xu K, Ding Y, Liu Y, Ying Y, Wang H. Discovery of Prenyltransferase-Guided Hydroxyphenylacetic Acid Derivatives from Marine Fungus Penicillium sp. W21C371. Mar Drugs 2024; 22:296. [PMID: 39057405 PMCID: PMC11278016 DOI: 10.3390/md22070296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Traditional isolation methods often lead to the rediscovery of known natural products. In contrast, genome mining strategies are considered effective for the continual discovery of new natural products. In this study, we discovered a unique prenyltransferase (PT) through genome mining, capable of catalyzing the transfer of a prenyl group to an aromatic nucleus to form C-C or C-O bonds. A pair of new hydroxyphenylacetic acid derivative enantiomers with prenyl units, (±)-peniprenydiol A (1), along with 16 known compounds (2-17), were isolated from a marine fungus, Penicillium sp. W21C371. The separation of 1 using chiral HPLC led to the isolation of the enantiomers 1a and 1b. Their structures were established on the basis of extensive spectroscopic analysis, including 1D, 2D NMR and HRESIMS. The absolute configurations of the new compounds were determined by a modified Mosher method. A plausible biosynthetic pathway for 1 was deduced, facilitated by PT catalysis. In the in vitro assay, 2 and 3 showed promising inhibitory activity against Escherichia coli β-glucuronidase (EcGUS), with IC50 values of 44.60 ± 0.84 μM and 21.60 ± 0.76 μM, respectively, compared to the positive control, D-saccharic acid 1,4-lactone hydrate (DSL). This study demonstrates the advantages of genome mining in the rational acquisition of new natural products.
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Affiliation(s)
- Cancan Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ye Fan
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jing Tang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yixian Qiu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Keren Xu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yingjia Ding
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ying Liu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Youmin Ying
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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24
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Buschi E, Dell’Anno A, Tangherlini M, Candela M, Rampelli S, Turroni S, Palladino G, Esposito E, Martire ML, Musco L, Stefanni S, Munari C, Fiori J, Danovaro R, Corinaldesi C. Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome. SCIENCE ADVANCES 2024; 10:eadk9117. [PMID: 38905343 PMCID: PMC11192080 DOI: 10.1126/sciadv.adk9117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.
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Affiliation(s)
- Emanuela Buschi
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luigi Musco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica “Anton Dohrn,” Villa Comunale, Napoli, Italy
| | - Cristina Munari
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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25
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Zhang Q, Pu Q, Hao Z, Liu J, Zhang K, Meng B, Feng X. Warming inhibits Hg II methylation but stimulates methylmercury demethylation in paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172832. [PMID: 38688367 DOI: 10.1016/j.scitotenv.2024.172832] [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: 01/13/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Inorganic mercury (HgII) can be transformed into neurotoxic methylmercury (MeHg) by microorganisms in paddy soils, and the subsequent accumulation in rice grains poses an exposure risk for human health. Warming as an important manifestation of climate change, changes the composition and structure of microbial communities, and regulates the biogeochemical cycles of Hg in natural environments. However, the response of specific HgII methylation/demethylation to the changes in microbial communities caused by warming remain unclear. Here, nationwide sampling of rice paddy soils and a temperature-adjusted incubation experiment coupled with isotope labeling technique (202HgII and Me198Hg) were conducted to investigate the effects of temperature on HgII methylation, MeHg demethylation, and microbial mechanisms in paddy soils along Hg gradients. We showed that increasing temperature significantly inhibited HgII methylation but promoted MeHg demethylation. The reduction in the relative abundance of Hg-methylating microorganisms and increase in the relative abundance of MeHg-demethylating microorganisms are the likely reasons. Consequently, the net Hg methylation production potential in rice paddy soils was largely inhibited under the increasing temperature. Collectively, our findings offer insights into the decrease in net MeHg production potential associated with increasing temperature and highlight the need for further evaluation of climate change for its potential effect on Hg transformation in Hg-sensitive ecosystems.
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Affiliation(s)
- Qianshuo Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Pu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Zhengdong Hao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Kun Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Meng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
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26
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Li Y, Yu T, Feng X, Zhao B, Chen H, Yang H, Chen X, Zhang XH, Anderson HR, Burns NZ, Zeng F, Tao L, Zeng Z. Biosynthesis of GMGT lipids by a radical SAM enzyme associated with anaerobic archaea and oxygen-deficient environments. Nat Commun 2024; 15:5256. [PMID: 38898040 PMCID: PMC11186832 DOI: 10.1038/s41467-024-49650-x] [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: 01/18/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024] Open
Abstract
Archaea possess characteristic membrane-spanning lipids that are thought to contribute to the adaptation to extreme environments. However, the biosynthesis of these lipids is poorly understood. Here, we identify a radical S-adenosyl-L-methionine (SAM) enzyme that synthesizes glycerol monoalkyl glycerol tetraethers (GMGTs). The enzyme, which we name GMGT synthase (Gms), catalyzes the formation of a C(sp3)-C(sp3) linkage between the two isoprenoid chains of glycerol dialkyl glycerol tetraethers (GDGTs). This conclusion is supported by heterologous expression of gene gms from a GMGT-producing species in a methanogen, as well as demonstration of in vitro activity using purified Gms enzyme. Additionally, we show that genes encoding putative Gms homologs are present in obligate anaerobic archaea and in metagenomes obtained from oxygen-deficient environments, and appear to be absent in metagenomes from oxic settings.
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Affiliation(s)
- Yanan Li
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
| | - Ting Yu
- Department of Systems Biology and Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - Xi Feng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Bo Zhao
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huahui Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huan Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | | | - Noah Z Burns
- Department of Chemistry, Stanford University, Stanford, USA
| | - Fuxing Zeng
- Department of Systems Biology and Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
| | - Lizhi Tao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China.
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.
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27
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Ninck S, Klaus T, Kochetkova TV, Esser SP, Sewald L, Kaschani F, Bräsen C, Probst AJ, Kublanov IV, Siebers B, Kaiser M. Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities. ENVIRONMENTAL MICROBIOME 2024; 19:36. [PMID: 38831353 PMCID: PMC11145796 DOI: 10.1186/s40793-024-00577-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging. RESULTS Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. CONCLUSIONS By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.
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Affiliation(s)
- Sabrina Ninck
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
| | - Thomas Klaus
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Sarah P Esser
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Leonard Sewald
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
- Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
- Centre of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany.
| | - Markus Kaiser
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
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28
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Rubin-Blum M, Makovsky Y, Rahav E, Belkin N, Antler G, Sisma-Ventura G, Herut B. Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106497. [PMID: 38631226 DOI: 10.1016/j.marenvres.2024.106497] [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: 01/14/2024] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 04/19/2024]
Abstract
Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.
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Affiliation(s)
- Maxim Rubin-Blum
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel; The Department of Marine Biology, Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
| | - Yizhaq Makovsky
- The Dr. Moses Strauss Department of Marine Geosciences, Charney School of Marine Sciences , University of Haifa, Haifa, Israel; The Hatter Department of Marine Technologies, Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eyal Rahav
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Natalia Belkin
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Gilad Antler
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; The Interuniversity Institute for Marine Sciences, Eilat, Israel
| | - Guy Sisma-Ventura
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Barak Herut
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel; The Dr. Moses Strauss Department of Marine Geosciences, Charney School of Marine Sciences , University of Haifa, Haifa, Israel
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29
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Borsodi AK. Taxonomic diversity of extremophilic prokaryotes adapted to special environmental parameters in Hungary: a review. Biol Futur 2024; 75:183-192. [PMID: 38753295 DOI: 10.1007/s42977-024-00224-4] [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: 01/17/2024] [Accepted: 04/26/2024] [Indexed: 06/18/2024]
Abstract
The taxonomic and metabolic diversity of prokaryotes and their adaptability to extreme environmental parameters have allowed extremophiles to find their optimal living conditions under extreme conditions for one or more environmental parameters. Natural habitats abundant in extremophilic microorganisms are relatively rare in Hungary. Nevertheless, alkaliphiles and halophiles can flourish in shallow alkaline lakes (soda pans) and saline (solonetz) soils, where extreme weather conditions favor the development of unique bacterial communities. In addition, the hot springs and thermal wells that supply spas and thermal baths and provide water for energy use are suitable colonization sites for thermophiles and hyperthermophiles. Polyextremophiles, adapted to multiple extreme circumstances, can be found in the aphotic, nutrient-poor and radioactive hypogenic caves of the Buda Thermal Karst, among others. The present article reviews the organization, taxonomic composition, and potential role of different extremophilic bacterial communities in local biogeochemical cycles, based on the most recent studies on extremophiles in Hungary.
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Affiliation(s)
- Andrea K Borsodi
- Department of Microbiology, Institute of Biology, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary.
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30
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Wang Y, Li L, Li Q, Hu Y, Li W, Wu Z, Huang H, Lv Z, Liu W, Cao R, Zhao G, Wang F, Zhang G. MASH-Ocean 1.0: Interactive platform for investigating microbial diversity, function, and biogeography with marine metagenomic data. IMETA 2024; 3:e201. [PMID: 38898978 PMCID: PMC11183159 DOI: 10.1002/imt2.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/21/2024]
Abstract
A large number of oceanic metagenomic data and environmental metadata have been published. However, most studies focused on limited ecosystems using different analysis tools, making it challenging to integrate these data into robust results and comprehensive global understanding of marine microbiome. Here, we constructed a systematic and quantitative analysis platform, the Microbiome Atlas/Sino-Hydrosphere for Ocean Ecosystem (MASH-Ocean: https://www.biosino.org/mash-ocean/), by integrating global marine metagenomic data and a unified data processing flow. MASH-Ocean 1.0 comprises 2147 metagenomic samples with five analysis modules: sample view, diversity, function, biogeography, and interaction network. This platform provides convenient and stable support for researchers in microbiology, environmental science, and biogeochemistry, to ensure the integration of omics data generated from hydrosphere ecosystems, to bridge the gap between elusive omics data and biological, ecological, and geological discovery, ultimately to foster the formation of a comprehensive atlas for aquatic environments.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Liuyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Qiang Li
- National Genomics Data Center & Bio‐Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghaiChina
| | - Yaoxun Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Wenjie Li
- Shanghai Southgene Technology Co., Ltd.ShanghaiChina
| | - Zhile Wu
- Shanghai Southgene Technology Co., Ltd.ShanghaiChina
| | - Hungchia Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhenbo Lv
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Wan Liu
- National Genomics Data Center & Bio‐Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghaiChina
| | - Ruifang Cao
- National Genomics Data Center & Bio‐Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghaiChina
| | - Guoping Zhao
- National Genomics Data Center & Bio‐Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghaiChina
- Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life SciencesFudan UniversityShanghaiChina
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
| | - Guoqing Zhang
- National Genomics Data Center & Bio‐Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghaiChina
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31
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Klimek D, Herold M, Calusinska M. Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes. BMC Genomics 2024; 25:523. [PMID: 38802741 PMCID: PMC11131199 DOI: 10.1186/s12864-024-10413-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: 01/26/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Members of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given the abundance and diversity of carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Here, we present a comprehensive comparative analysis of all available planctomycetotal genome representatives and detail encoded carbohydrolytic potential across phylogenetic groups and different habitats. RESULTS Our in-depth characterisation of the available planctomycetotal genomic resources increases our knowledge of the carbohydrolytic capacities of Planctomycetota. We show that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families and that many members encode a versatile enzymatic machinery towards complex carbohydrate degradation, including lignocellulose. We highlight members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to the Phycisphaerales order could represent an interesting source of novel lytic polysaccharide monooxygenases to boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors encode CAZymes targeting algal polysaccharides - this opens new perspectives for algal biomass valorisation in biogas processes. CONCLUSIONS Our study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.
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Affiliation(s)
- Dominika Klimek
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg.
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, 2 Avenue de l'Université, Esch-sur-Alzette, L-4365, Luxembourg.
| | - Malte Herold
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg
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Brauer VS, Voskuhl L, Mohammadian S, Pannekens M, Haque S, Meckenstock RU. Imprints of ecological processes in the taxonomic core community: an analysis of naturally replicated microbial communities enclosed in oil. FEMS Microbiol Ecol 2024; 100:fiae074. [PMID: 38734895 PMCID: PMC11110866 DOI: 10.1093/femsec/fiae074] [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: 09/08/2023] [Revised: 03/02/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
It is widely assumed that a taxonomic core community emerges among microbial communities from similar habitats because similar environments select for the same taxa bearing the same traits. Yet, a core community itself is no indicator of selection because it may also arise from dispersal and neutral drift, i.e. by chance. Here, we hypothesize that a core community produced by either selection or chance processes should be distinguishable. While dispersal and drift should produce core communities with similar relative taxon abundances, especially when the proportional core community, i.e. the sum of the relative abundances of the core taxa, is large, selection may produce variable relative abundances. We analyzed the core community of 16S rRNA gene sequences of 193 microbial communities occurring in tiny water droplets enclosed in heavy oil from the Pitch Lake, Trinidad and Tobago. These communities revealed highly variable relative abundances along with a large proportional core community (68.0 ± 19.9%). A dispersal-drift null model predicted a negative relationship of proportional core community and compositional variability along a range of dispersal probabilities and was largely inconsistent with the observed data, suggesting a major role of selection for shaping the water droplet communities in the Pitch Lake.
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Affiliation(s)
- Verena S Brauer
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, 45141 Essen, Germany
| | - Lisa Voskuhl
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Sadjad Mohammadian
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Mark Pannekens
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
- IWW Water Center, 45476 Mülheim an der Ruhr, Germany
| | - Shirin Haque
- Department of Physics, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Rainer U Meckenstock
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, 45141 Essen, Germany
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Zhang Y, Zhou Q, Gao C, Lu Y, Sheng Y, Xiao M, Yun Y, Selvaraj JN, Zhang X, Li Y, Yu X. Endophytic bacteria for Cd remediation in rice: Unraveling the Cd tolerance mechanisms of Cupriavidus metallidurans CML2. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133846. [PMID: 38412644 DOI: 10.1016/j.jhazmat.2024.133846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/30/2024] [Accepted: 02/18/2024] [Indexed: 02/29/2024]
Abstract
The utility of endophytic bacteria in Cadmium (Cd) remediation has gained significant attention due to their ability to alleviate metal-induced stress and enhance plant growth. Here, we investigate C. metallidurans CML2, an endophytic bacterial strain prevalent in rice, showing resilience against 2400 mg/L of Cd(II). We conducted an in-depth integrated morphological and transcriptomic analysis illustrating the multifarious mechanisms CML2 employs to combat Cd, including the formation of biofilm and CdO nanoparticles, upregulation of genes involved in periplasmic immobilization, and the utilization of RND efflux pumps to extract excess Cd ions. Beyond Cd, CML2 exhibited robust tolerance to an array of heavy metals, including Mn2+, Se4+, Ni2+, Cu2+, and Hg2+, demonstrating effective Cd(II) removal capacity. Furthermore, CML2 has exhibited plant growth-promoting properties through the production of indole-3-acetic acid (IAA) at 0.93 mg/L, soluble phosphorus compounds at 1.11 mg/L, and siderophores at 22.67%. Supportively, pot experiments indicated an increase in root lengths and a decrease in Cd bioaccumulation in rice seedlings inoculated with CML2, consequently reducing Cd translocation rates from 43% to 31%. These findings not only contribute to the understanding of Cd resistance mechanisms in C. metallidurans, but also underscore CML2's promising application in Cd remediation within rice farming ecosystems.
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Affiliation(s)
- Yuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Qi Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Chang Gao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yue Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yang Sheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Ming Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jonathan Nimal Selvaraj
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Xianhua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yadong Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China.
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She Z, Wang J, Pan X, Ma D, Gao Y, Wang S, Chuai X, Mu Y, Yue Z. Multi-omics insights into biogeochemical responses to organic matter addition in an acidic pit lake: Implications for bioremediation. WATER RESEARCH 2024; 254:121404. [PMID: 38442608 DOI: 10.1016/j.watres.2024.121404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/30/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Acidic pit lakes (APLs) emerge as reservoirs of acid mine drainage in flooded open-pit mines, representing extreme ecosystems and environmental challenges worldwide. The bioremediation of these oligotrophic waters necessitates the addition of organic matter, but the biogeochemical response of APLs to exogenous organic matter remains inadequately comprehended. This study delves into the biogeochemical impacts and remediation effects of digestate-derived organic matter within an APL, employing a multi-omics approach encompassing geochemical analyses, amplicon and metagenome sequencing, and ultra-high resolution mass spectrometry. The results indicated that digestate addition first stimulated fungal proliferation, particularly Ascomycetes and Basidiomycetes, which generated organic acids through lignocellulosic hydrolysis and fermentation. These simple compounds further supported heterotrophic growth, including Acidiphilium, Acidithrix, and Clostridium, thereby facilitating nitrate, iron, and sulfate reduction linked with acidity consumption. Nutrients derived from digestate also promoted the macroscopic development of acidophilic algae. Notably, the increased sulfate reduction-related genes primarily originated from assimilatory metabolism, thus connecting sulfate decrease to organosulfur increase. Assimilatory and dissimilatory sulfate reduction collectively contributed to sulfate removal and metal fixation. These findings yield multi-omics insights into APL biogeochemical responses to organic matter addition, enhancing the understanding of carbon-centered biogeochemical cycling in extreme ecosystems and guiding organic amendment-based bioremediation in oligotrophic polluted environments.
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Affiliation(s)
- Zhixiang She
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China.
| | - Xin Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Ding Ma
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yijun Gao
- Luohe Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Hefei, Anhui 230009, China
| | - Shaoping Wang
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Ma'anshan, Anhui 243000, China
| | - Xin Chuai
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Ma'anshan, Anhui 243000, China
| | - Yang Mu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China.
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35
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Jeilu O, Alexandersson E, Johansson E, Simachew A, Gessesse A. A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation. Sci Rep 2024; 14:10012. [PMID: 38693138 PMCID: PMC11063200 DOI: 10.1038/s41598-024-60645-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: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.
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Affiliation(s)
- Oliyad Jeilu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden.
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia.
| | - Erik Alexandersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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36
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Yang L, Fan W, Xu Y. Qu-omics elucidates the formation and spatio-temporal differentiation mechanism underlying the microecology of high temperature Daqu. Food Chem 2024; 438:137988. [PMID: 37979262 DOI: 10.1016/j.foodchem.2023.137988] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Even if fermented in the same qu-room, Daqu will form various microecologies. A gradual differentiation of microbial population niches was observed within different qu-layers, manifesting as variations in the abundance of dominant microorganisms including Bacillus, Saccharopolyspora, Weissella, Kroppenstedtia, Thermoascus, Thermomyces, Saccharomycopsis, and Rasamsonia. Moreover, distinctions were observed in the functional expression of microorganisms, including Aspergillus, Virgibacillus, Oceanobacillus, and Neurospora. The community in middle layer Daqu exhibited characteristics of high compactness and niche diversity, which facilitated efficient substrate utilization. During the initial phase, the upper Daqu community demonstrated heightened activity. However, in the middle and lower layers, fungi and bacteria respectively exhibited greater functional expression. The key environmental factors regulating the assembly of communities in the upper and middle layers were pH and temperature, respectively, and the lower was moisture and acidity. Notably, deterministic assembly exerted a stronger influence on fungi.
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Affiliation(s)
- Liang Yang
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China; Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, China
| | - Wenlai Fan
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China.
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China.
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37
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Leung PM, Grinter R, Tudor-Matthew E, Lingford JP, Jimenez L, Lee HC, Milton M, Hanchapola I, Tanuwidjaya E, Kropp A, Peach HA, Carere CR, Stott MB, Schittenhelm RB, Greening C. Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures. Nat Commun 2024; 15:3219. [PMID: 38622143 PMCID: PMC11018855 DOI: 10.1038/s41467-024-47324-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.
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Affiliation(s)
- Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Eve Tudor-Matthew
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James P Lingford
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Luis Jimenez
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Han-Chung Lee
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Michael Milton
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Iresha Hanchapola
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Erwin Tanuwidjaya
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hanna A Peach
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
| | - Carlo R Carere
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Matthew B Stott
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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Zhang J, Zhang H, Luo S, Ye L, Wang C, Wang X, Tian C, Sun Y. Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress. Microorganisms 2024; 12:790. [PMID: 38674734 PMCID: PMC11052302 DOI: 10.3390/microorganisms12040790] [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: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.
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Affiliation(s)
- Jianfeng Zhang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Hengfei Zhang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Shouyang Luo
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Libo Ye
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Changji Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Xiaonan Wang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
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Li R, Jiao H, Sun B, Song M, Yan G, Bai Z, Wang J, Zhuang X, Hu Q. Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics. Microorganisms 2024; 12:683. [PMID: 38674627 PMCID: PMC11052110 DOI: 10.3390/microorganisms12040683] [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: 03/03/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity's critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere.
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Affiliation(s)
- Rui Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou 256606, China;
| | - Haihua Jiao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- Department of Biological Sciences and Technology, Changzhi University, Changzhi 046011, China
| | - Bo Sun
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Manjiao Song
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaojun Yan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiancheng Wang
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou 256606, China;
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Hu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Xiongan Innovation Institute, Xiongan New Area, Baoding 071000, China
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Stratigaki M, Armirotti A, Ottonello G, Manente S, Traviglia A. Fungal and bacterial species richness in biodeteriorated seventeenth century Venetian manuscripts. Sci Rep 2024; 14:7003. [PMID: 38523163 PMCID: PMC10961312 DOI: 10.1038/s41598-024-57228-2] [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] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
Historical paper documents are susceptible to complex degradation processes, including biodeterioration, which can progressively compromise their aesthetic and structural integrity. This study analyses seventeenth century handwritten historical letters stored at the Correr Museum Library in Venice, Italy, exhibiting pronounced signs of biodeterioration. The techniques used encompassed traditional colony isolation on agar plates and proteomics analyses, employing nanoscale liquid chromatography coupled with high-resolution mass spectrometry (nano-LC-MS). Fluorescence microscopy was used for the first time in the historical paper biodeterioration context to supplement the conventional stereoscopic, optical, and scanning electron microscopic imaging techniques. This method enables the visualisation of microorganisms beyond and beneath the paper's surface through their natural intrinsic autofluorescence in a non-invasive and non-destructive way. The results demonstrate a diverse, complex, and abundant microbiota composed of coexisting fungal and bacterial species (Ascomycota, Mucoromycota, Basidiomycota, Proteobacteria, and Actinobacteria), along with mite carcasses, insects, parasites, and possibly protists. Furthermore, this study reveals certain species that were not previously documented in the biodeterioration of historical paper, including human pathogens, such as Histoplasma capsulatum, Brucella, Candida albicans, and species of Aspergillus (A. flavus, A. fumigatus, A. oryzae, A. terreus, A. niger) known to cause infections or produce mycotoxins, posing substantial risk to both artefacts and humans.
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Affiliation(s)
- Maria Stratigaki
- Center for Cultural Heritage Technology (CCHT), Istituto Italiano di Tecnologia, Via Torino 155, 30172, Venice, Italy.
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Giuliana Ottonello
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Sabrina Manente
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy
| | - Arianna Traviglia
- Center for Cultural Heritage Technology (CCHT), Istituto Italiano di Tecnologia, Via Torino 155, 30172, Venice, Italy
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Ma C, Liu S, Koslicki D. MetagenomicKG: a knowledge graph for metagenomic applications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585056. [PMID: 38559251 PMCID: PMC10980061 DOI: 10.1101/2024.03.14.585056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Motivation The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities and their interrelations into a cohesive network. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored. Results We present MetagenomicKG, a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information from widely used databases, and further links these with established biomedical knowledge graphs to expand biological connections. Through several use cases, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction. Availability and Implementation The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available at Github: https://github.com/KoslickiLab/MetagenomicKG. We also host a Neo4j instance: http://mkg.cse.psu.edu:7474 for accessing and querying this graph.
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Affiliation(s)
- Chunyu Ma
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, Pennsylvania, USA
| | - Shaopeng Liu
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, Pennsylvania, USA
| | - David Koslicki
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, Pennsylvania, USA
- Department of Computer Science and Engineering, Pennsylvania State University, State College, Pennsylvania, USA
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, Pennsylvania, USA
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Ma L, Banda JF, Wang Y, Yang Q, Zhao L, Hao C, Dong H. Metagenomic insight into the acidophilic functional communities driving elemental geochemical cycles in an acid mine drainage lake. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133070. [PMID: 38278071 DOI: 10.1016/j.jhazmat.2023.133070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/06/2023] [Accepted: 11/21/2023] [Indexed: 01/28/2024]
Abstract
Acidophiles play a key role in the generation, evolution and attenuation of acid mine drainage (AMD), which is characterized by strong acidity (pH<3.5) and high metal concentrations. In this study, the seasonal changes of acidophilic communities and their roles in elemental cycling in an AMD lake (pH∼3.0) in China were analyzed through metagenomics. The results showed eukaryotic algae thrived in the lake, and Coccomyxa was dominant in January (38.1%) and May (33.9%), while Chlorella in July (9.5%). The extensive growth of Chlamydomonas in December (22.7%) resulted in an ultrahigh chlorophyll a concentration (587 μg/L), providing abundant organic carbon for the ecosystem. In addition, the iron-oxidizing and nitrogen-fixing bacterium Ferrovum contributed to carbon fixation. Ammonia oxidation likely occurred in the acidic lake, as was revealed by archaea Ca. Nitrosotalea. To gain a competitive advantage in the nutrient-poor environment, some acidophiles exhibited facultative characteristics, e.g. the most abundant bacterium Acidiphilium utilized both organic and inorganic carbon, and obtained energy from organic matter, inorganic sulfur, and sunlight simultaneously. It was suggested that sunlight, rather than chemical energy of reduced iron-sulfur was the major driver of elemental cycling in the AMD lake. The results are beneficial to the development of bioremediation strategies for AMD.
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Affiliation(s)
- Linqiang Ma
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Joseph Frazer Banda
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Yikai Wang
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Qingwei Yang
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Linting Zhao
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Chunbo Hao
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China.
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
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Huang D, Xia R, Chen C, Liao J, Chen L, Wang D, Alvarez PJJ, Yu P. Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends Microbiol 2024:S0966-842X(24)00042-8. [PMID: 38433027 DOI: 10.1016/j.tim.2024.02.002] [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: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rong Xia
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengyi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Linxing Chen
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dongsheng Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China.
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Zhang T, Zhang D, Lyu Z, Zhang J, Wu X, Yu Y. Effects of extreme precipitation on bacterial communities and bioaerosol composition: Dispersion in urban outdoor environments and health risks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123406. [PMID: 38244904 DOI: 10.1016/j.envpol.2024.123406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/22/2024]
Abstract
Concerns about contaminants dispersed by seasonal precipitation have grown due to their potential hazards to outdoor environments and human health. However, studies on the crucial environmental factors influencing dispersion changes in bacterial communities are limited. This research adopted four-season in situ monitoring and sequencing techniques to examine the regional distribution profiles of bioaerosols, bacterial communities, and risks associated with extreme snowfall versus rainfall events in two monsoon cities. In the early-hours of winter snowfall, airborne cultivable bioaerosol concentrations were 4.1 times higher than the reference exposure limit (500 CFU/m3). The concentration of ambient particles (2.5 μm) exceeded 24,910 particles/L (97 μg/m3), positively correlating with the prevalence of cultivable bioaerosols. These bioaerosols contained cultivable bacterial species such as pathogenic Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, and Escherichia coli. Bioaerosol concentrations increased by 53.0% during 50-mm snow extremes. Taxonomic analysis revealed that Pseudomonas, Staphylococcus, and Veillonella were the most abundant bacterial taxa in the initial snowmelt samples during winter precipitation. However, their abundance decreased by 87.6% as snowing continued (24 h). Reduced water base cation concentration also led to a 1.15-fold increase in the Shannon index, indicating a similar yet heightened bacterial diversity. Seasonally, Pedobacter and Massilia showed higher relative abundance (25% and 18%, respectively), presenting increased bacterial transmission to the soil. Furthermore, Pseudomonas was identified in 60% of spring snowstorm samples, suggesting long-distance dispersal of pathogenic bacteria. When these atmospheric aerosol particles carrying biological entities (0.65-1.1 μm) penetrated human alveoli, the calculated hazard ratio was 0.55, which as observed in inhalation exposures. Consequently, this study underscores the risk of seasonal precipitation-enhanced ambient bacterial transmission.
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Affiliation(s)
- Ting Zhang
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Dingqiang Zhang
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Zhonghang Lyu
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Jitao Zhang
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Xian Wu
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Yingxin Yu
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
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Bernacchi A, Semenzato G, di Mascolo M, Amata S, Bechini A, Berti F, Calonico C, Catania V, Emiliani G, Esposito A, Greco C, Mocali S, Mucci N, Padula A, Piccionello AP, Nasanbat B, Davaakhuu G, Bazarragchaa M, Riga F, Augugliaro C, Puglia AM, Zaccaroni M, Renato F. Antibacterial activity of Arthrobacter strains isolated from Great Gobi A Strictly Protected Area, Mongolia. AIMS Microbiol 2024; 10:161-186. [PMID: 38525036 PMCID: PMC10955175 DOI: 10.3934/microbiol.2024009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/26/2024] Open
Abstract
Desert soil hosts many microorganisms, whose activities are essential from an ecological viewpoint. Moreover, they are of great anthropic interest. The knowledge of extreme environments microbiomes may be beneficial for agriculture, technology, and human health. In this study, 11 Arthrobacter strains from topsoil samples collected from the Great Gobi A Strictly Protected Area in the Gobi Desert, were characterized by a combination of different techniques. The phylogenetic analysis, performed using their 16S rDNA sequences and the most similar Arthrobacter sequences found in databases, revealed that most of them were close to A. crystallopoietes, while others joined a sister group to the clade formed by A. humicola, A. pascens, and A. oryzae. The resistance of each strain to different antibiotics, heavy-metals, and NaCl was also tested as well as the inhibitory potential against human pathogens (i.e., Burkholderia ssp., Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus ssp.) via cross-streaking, to check the production of metabolites with antimicrobial activity. Data obtained revealed that all strains were resistant to heavy metals and were able to strongly interfere with the growth of many of the human pathogens tested. The volatile organic compounds (VOCs) profile of the 11 Arthrobacter strains was also analyzed. A total of 16 different metabolites were found, some of which were already known for having an inhibitory action against different Gram-positive and Gram-negative bacteria. Isolate MS-3A13, producing the highest quantity of VOCs, is the most efficient against Burkholderia cepacia complex (Bcc), K. pneumoniae, and coagulase-negative Staphylococci (CoNS) strains. This work highlights the importance of understanding microbial populations' phenotypical characteristics and dynamics in extreme environments to uncover the antimicrobial potential of new species and strains.
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Affiliation(s)
- Alberto Bernacchi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Manuel di Mascolo
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Sara Amata
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed.17, 90128, Palermo, Italy
| | - Angela Bechini
- Department of Health Sciences, University of Florence, viale G.B. Morgagni, 48, 50134 Firenze, Italy
| | - Fabiola Berti
- Department of Health Sciences, University of Florence, viale G.B. Morgagni, 48, 50134 Firenze, Italy
| | - Carmela Calonico
- Department of Health Sciences, University of Florence, viale G.B. Morgagni, 48, 50134 Firenze, Italy
| | - Valentina Catania
- Department of Earth and Sea Science (DiSTeM), University of Palermo, Viale delle Scienze Blg. 16, Palermo, 90128, Italy
| | - Giovanni Emiliani
- Institute for Sustainable Plant Protection (IPSP)—National Research Council (CNR), Via Madonna del Piano 10, Sesto Fiorentino 50019 Florence, Italy
| | - Antonia Esposito
- Council for Agricultural and Economics Research (CREA) – Agriculture and Environment, Via di Lanciola 12/A, Cascine del Riccio, 50125, Florence, Italy
| | - Claudia Greco
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, via Ca' Fornacetta, 9, 40064 Ozzano dell'Emilia Bologna, Italy
| | - Stefano Mocali
- Council for Agricultural and Economics Research (CREA) – Agriculture and Environment, Via di Lanciola 12/A, Cascine del Riccio, 50125, Florence, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, via Ca' Fornacetta, 9, 40064 Ozzano dell'Emilia Bologna, Italy
| | - Anna Padula
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, via Ca' Fornacetta, 9, 40064 Ozzano dell'Emilia Bologna, Italy
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed.17, 90128, Palermo, Italy
| | - Battogtokh Nasanbat
- Institute of Biology, Mongolian Academy of Sciences, Peace Avenue-54B, Bayanzurkh District, Ulaanbaatar-13330, Mongolia
| | - Gantulga Davaakhuu
- Institute of Biology, Mongolian Academy of Sciences, Peace Avenue-54B, Bayanzurkh District, Ulaanbaatar-13330, Mongolia
| | | | - Francesco Riga
- Italian Institute for Envioronmental Protection and Research, via Vitalino Brancati, 48, 00144, Roma, Italy
| | - Claudio Augugliaro
- Wildlife Initiative, Bayangol, 6th Khoroo, Micro District 10, Ulaanbaatar, 210349, Mongolia
| | | | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Fani Renato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
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Zhang M, Zhao B, Yan Y, Cheng Z, Li Z, Han L, Sun Y, Zheng Y, Xia Y. Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169203. [PMID: 38086476 DOI: 10.1016/j.scitotenv.2023.169203] [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: 10/11/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d-1 and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.
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Affiliation(s)
- Miao Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuxi Yan
- School of Environment, Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zengyi Li
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Long Han
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuqin Sun
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Zheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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Wu Y, Zhou S, Li Y, Niu L, Wang L. Climate and local environment co-mediate the taxonomic and functional diversity of bacteria and archaea in the Qinghai-Tibet Plateau rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168968. [PMID: 38042190 DOI: 10.1016/j.scitotenv.2023.168968] [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: 10/08/2023] [Revised: 11/18/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Understanding the environmental response patterns of riverine microbiota is essential for predicting the potential impact of future environmental change on river ecosystems. Vulnerable plateau ecosystems are particularly sensitive to climate and local environmental changes, however, the environmental response patterns of the taxonomic and functional diversity of riverine microbiota remain unclear. Here, we conducted a systematic investigation of the taxonomic and functional diversity of bacteria and archaea from riparian soils, sediments, and water across the elevation of 1800- 4800 m in the Qinghai-Tibet Plateau rivers. We found that within the elevation range of 1800 to 3800 m, riparian soils and sediments exhibited similarities and stabilities in microbial taxonomic and functional diversity, and water microbiomes were more sensitive with great fluctuations in microbial diversity. Beyond the elevation of 3800 m, microbial diversity declined across all riverine matrixes. Local environmental conditions can influence the sensitivity of microbiomes to climate change. The combination of critical climate and local environmental factors, including total nitrogen, total organic carbon, as well as climate variables associated with temperature and precipitation, provided better explanations for microbial diversity than single-factor analyses. Under the extremely adverse scenario of high greenhouse gas emission concentrations (SSP585), we anticipate that by the end of this century, the bacterial, archaeal, and microbial functional diversity across the river network of the Yangtze and Yellow source basin would potentially change by -16.9- 5.2 %, -16.1- 5.7 %, and -9.3- 6.4 %, respectively. Overall, climate and local environments jointly shaped the microbial diversity in plateau river ecosystems, and water microbiomes would provide early signs of environmental changes. Our study provides effective theoretical foundations for the conservation of river biodiversity and functional stability under environmental changes.
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Affiliation(s)
- Yunyu Wu
- College of Hydrology and Water Resources, Hohai University, Nanjing 210024, PR China
| | - Shubu Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China
| | - Yi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing 210024, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210024, PR China.
| | - Linqiong Wang
- College of Oceanography, Hohai University, Nanjing 210024, PR China
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Zhang Y, Qiu X, Luo J, Li H, How SW, Wu D, He J, Cheng Z, Gao Y, Lu H. A review of the phosphorus removal of polyphosphate-accumulating organisms in natural and engineered systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169103. [PMID: 38065508 DOI: 10.1016/j.scitotenv.2023.169103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/13/2023] [Accepted: 12/02/2023] [Indexed: 01/18/2024]
Abstract
Increasing eutrophication has led to a continuous deterioration of many aquatic ecosystems. Polyphosphate-accumulating organisms (PAOs) can provide insight into the human response to this challenge, as they initiate enhanced biological phosphorus removal (EBPR) through cyclical anaerobic phosphorus release and aerobic phosphorus uptake. Although the limiting environmental factors for PAO growth and phosphorus removal have been widely discussed, there remains a gap in the knowledge surrounding the differences in the type and phosphorus removal efficiencies of natural and engineered PAO systems. Furthermore, due to the limitations of PAOs in conventional wastewater treatment environments, there is an urgent need to find functional PAOs in extreme environments for better wastewater treatment. Therefore, it is necessary to explore the effects of extreme conditions on the phosphorus removal efficiency of PAOs as well as the types, sources, and characteristics of PAOs. In this paper, we summarize the response mechanisms of PAOs, denitrifying polyphosphate-accumulating organisms (D-PAOs), aerobic denitrifying polyphosphate-accumulating organisms (AD-PAOs), and sulfur-related PAOs (S-PAOs). The mechanism of nitrogen and phosphorus removal in PAOs is related to the coupling cycles of carbon, nitrogen, phosphorus, and sulfur. The genera of PAOs differ in natural and engineered systems, but PAOs have more diversity in aquatic environments and soils. Recent studies on the impact of several parameters (e.g., temperature, carbon source, pH, and dissolved oxygen) and extracellular polymer substances on the phosphorus removal efficiency of PAOs in natural and engineered systems are further discussed. Most of the PAOs screened under extreme conditions still had high phosphorus removal efficiencies (>80.0 %). These results provide a reference for searching for PAOs with different adaptations to achieve better wastewater treatment.
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Affiliation(s)
- Yan Zhang
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Xiaoqing Qiu
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Jiahao Luo
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Huishi Li
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Seow-Wah How
- Centre for Environmental and Energy Research, Ghent University Global Campus, Incheon 21985, Republic of Korea; Department of Green Chemistry and Technology, Ghent University, Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Ghent B9000, Belgium
| | - Di Wu
- Centre for Environmental and Energy Research, Ghent University Global Campus, Incheon 21985, Republic of Korea; Department of Green Chemistry and Technology, Ghent University, Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Ghent B9000, Belgium
| | - Juhua He
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Zihang Cheng
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Yunan Gao
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China.
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Malas J, Russo DC, Bollengier O, Malaska MJ, Lopes RMC, Kenig F, Meyer-Dombard DR. Biological functions at high pressure: transcriptome response of Shewanella oneidensis MR-1 to hydrostatic pressure relevant to Titan and other icy ocean worlds. Front Microbiol 2024; 15:1293928. [PMID: 38414766 PMCID: PMC10896736 DOI: 10.3389/fmicb.2024.1293928] [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: 09/13/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
High hydrostatic pressure (HHP) is a key driver of life's evolution and diversification on Earth. Icy moons such as Titan, Europa, and Enceladus harbor potentially habitable high-pressure environments within their subsurface oceans. Titan, in particular, is modeled to have subsurface ocean pressures ≥ 150 MPa, which are above the highest pressures known to support life on Earth in natural ecosystems. Piezophiles are organisms that grow optimally at pressures higher than atmospheric (0.1 MPa) pressure and have specialized adaptations to the physical constraints of high-pressure environments - up to ~110 MPa at Challenger Deep, the highest pressure deep-sea habitat explored. While non-piezophilic microorganisms have been shown to survive short exposures at Titan relevant pressures, the mechanisms of their survival under such conditions remain largely unelucidated. To better understand these mechanisms, we have conducted a study of gene expression for Shewanella oneidensis MR-1 using a high-pressure experimental culturing system. MR-1 was subjected to short-term (15 min) and long-term (2 h) HHP of 158 MPa, a value consistent with pressures expected near the top of Titan's subsurface ocean. We show that MR-1 is metabolically active in situ at HHP and is capable of viable growth following 2 h exposure to 158 MPa, with minimal pressure training beforehand. We further find that MR-1 regulates 264 genes in response to short-term HHP, the majority of which are upregulated. Adaptations include upregulation of the genes argA, argB, argC, and argF involved in arginine biosynthesis and regulation of genes involved in membrane reconfiguration. MR-1 also utilizes stress response adaptations common to other environmental extremes such as genes encoding for the cold-shock protein CspG and antioxidant defense related genes. This study suggests Titan's ocean pressures may not limit life, as microorganisms could employ adaptations akin to those demonstrated by terrestrial organisms.
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Affiliation(s)
- Judy Malas
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL, United States
| | - Daniel C. Russo
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL, United States
| | - Olivier Bollengier
- Nantes Université, Univ Angers, Le Mans Université, CNRS, Laboratoire de Planétologie et Géosciences, LPG UMR 6112, Nantes, France
| | - Michael J. Malaska
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Rosaly M. C. Lopes
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Fabien Kenig
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL, United States
| | - D'Arcy R. Meyer-Dombard
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL, United States
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50
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Esposito A, Del Duca S, Vitali F, Bigiotti G, Mocali S, Semenzato G, Papini A, Santini G, Mucci N, Padula A, Greco C, Nasanbat B, Davaakhuu G, Bazarragchaa M, Riga F, Augugliaro C, Cecchi L, Fani R, Zaccaroni M. The Great Gobi A Strictly Protected Area: Characterization of Soil Bacterial Communities from Four Oases. Microorganisms 2024; 12:320. [PMID: 38399724 PMCID: PMC10891509 DOI: 10.3390/microorganisms12020320] [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: 12/31/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Understanding how microbial communities survive in extreme environmental pressure is critical for interpreting ecological patterns and microbial diversity. Great Gobi A Strictly Protected Area represents an intriguing model for studying the bacterial community since it is a protected and intact wild area of the Mongolian desert. In this work, the composition of a bacterial community of the soil from four oases was characterized by extracting total DNA and sequencing through the Illumina NovaSeq platform. In addition, the soil's chemical and physical properties were determined, and their influence on shaping the microbial communities was evaluated. The results showed a high variability of bacterial composition among oases. Moreover, combining specific chemical and physical parameters significantly shapes the bacterial community among oases. Data obtained suggested that the oases were highly variable in physiochemical parameters and bacterial communities despite the similar extreme climate conditions. Moreover, core functional microbiome were constituted by aerobic chemoheterotrophy and chemoheterotrophy, mainly contributed by the most abundant bacteria, such as Actinobacteriota, Pseudomonadota, and Firmicutes. This result supposes a metabolic flexibility for sustaining life in deserts. Furthermore, as the inhabitants of the extreme regions are likely to produce new chemical compounds, isolation of key taxa is thus encouraged.
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Affiliation(s)
- Antonia Esposito
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Sara Del Duca
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
| | - Francesco Vitali
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
| | - Gaia Bigiotti
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
| | - Stefano Mocali
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Alessio Papini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Giacomo Santini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.); (C.G.)
| | - Anna Padula
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.); (C.G.)
| | - Claudia Greco
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.); (C.G.)
| | - Battogtokh Nasanbat
- Institute of Biology, Mongolian Academy of Sciences, Peace Avenue-54B, Bayanzurkh District, Ulaanbaatar 13330, Mongolia; (B.N.); (G.D.)
| | - Gantulga Davaakhuu
- Institute of Biology, Mongolian Academy of Sciences, Peace Avenue-54B, Bayanzurkh District, Ulaanbaatar 13330, Mongolia; (B.N.); (G.D.)
| | - Munkhtsetseg Bazarragchaa
- Department of Molecular Biology and Genetics, School of Bio-Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia;
| | - Francesco Riga
- Italian Institute for Environmental Protection and Research (ISPRA), Via Brancati 48, 00144 Rome, Italy;
| | | | - Lorenzo Cecchi
- Natural History Museum, Botanical Collections “Filippo Parlatore”—Via Giorgio la Pira 4, 50121 Florence, Italy;
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
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