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Zhang H, Liu H, Han X. Traits-based approach: leveraging genome size in plant-microbe interactions. Trends Microbiol 2024; 32:333-341. [PMID: 37925351 DOI: 10.1016/j.tim.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
Trait-based approaches have gained growing interest in studying plant-microbe interactions. However, current traits normally considered (e.g., morphological, physiological, or chemical traits) are biased towards those showing large intraspecific variations, necessitating the identification of fewer plastic traits that differ between species. Here, we propose using genome size (the amount of DNA in the nucleus of a cell) as a suitable trait for studying plant-microbiome interactions due to its relatively stable nature, minimally affected by external environmental variations. Emerging evidence suggests that plant genome size affects the plant-associated microbial community, and tissue-specific environments select microbes based on their genome size. These findings pinpoint environmental selection in genome size as an emerging driver of plant-microbiome interactions, potentially impacting ecosystem functions and productivity.
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Affiliation(s)
- Haiyang Zhang
- College of Life Sciences, Hebei University, Baoding, China.
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2753, Australia
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Yu J, Lee JYY, Tang SN, Lee PKH. Niche differentiation in microbial communities with stable genomic traits over time in engineered systems. ISME J 2024; 18:wrae042. [PMID: 38470313 PMCID: PMC10987969 DOI: 10.1093/ismejo/wrae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/21/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Kowloon, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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Kumar V, Kashyap P, Kumar S, Thakur V, Kumar S, Singh D. Multiple Adaptive Strategies of Himalayan Iodobacter sp. PCH194 to High-Altitude Stresses. Front Microbiol 2022; 13:881873. [PMID: 35875582 PMCID: PMC9298515 DOI: 10.3389/fmicb.2022.881873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Bacterial adaption to the multiple stressed environments of high-altitude niches in the Himalayas is intriguing and is of considerable interest to biotechnologists. Previously, we studied the culturable and unculturable metagenome microbial diversity from glacial and kettle lakes in the Western Himalayas. In this study, we explored the adaptive strategies of a unique Himalayan eurypsychrophile Iodobacter sp. PCH194, which can synthesize polyhydroxybutyrate (PHB) and violacein pigment. Whole-genome sequencing and analysis of Iodobacter sp. PCH194 (4.58 Mb chromosome and three plasmids) revealed genetic traits associated with adaptive strategies for cold/freeze, nutritional fluctuation, defense against UV, acidic pH, and the kettle lake's competitive environment. Differential proteome analysis suggested the adaptive role of chaperones, ribonucleases, secretion systems, and antifreeze proteins under cold stress. Antifreeze activity inhibiting the ice recrystallization at −9°C demonstrated the bacterium's survival at subzero temperature. The bacterium stores carbon in the form of PHB under stress conditions responding to nutritional fluctuations. However, violacein pigment protects the cells from UV radiation. Concisely, genomic, proteomic, and physiological studies revealed the multiple adaptive strategies of Himalayan Iodobacter to survive the high-altitude stresses.
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Affiliation(s)
- Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Prakriti Kashyap
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Subhash Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
| | - Vikas Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
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Hu A, Ren M, Wang J. Microbial species performance responses to environmental changes: genomic traits and nutrient availability. Ecology 2021; 102:e03382. [PMID: 33942296 DOI: 10.1002/ecy.3382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/15/2021] [Accepted: 03/15/2021] [Indexed: 11/09/2022]
Abstract
How microbial species performance indicators, such as growth rate and carbon assimilation rate, respond to environmental changes is a challenging question, especially for complex communities. This limits our ability to understand how species performance responses to environmental changes (that is, species environmental responses) of microbes could be linked to genomic traits and nutrient availability. Based on stable isotope labeling of DNA, we propose a new approach with effect-size metrics to quantify the species environmental responses of microbes by comparing the species performance between defined control and treatment groups. The species performance within microbial communities of the natural or altered environments could be quantitatively determined with quantitative stable isotope probing (qSIP). We further apply this approach, namely effect-size qSIP, to measure species environmental responses upon carbon and nitrogen additions for soil bacteria on mountainsides and to understand their responses from the perspective of genomic traits. Towards high elevations, there is a stronger nitrogen limitation that is indicated by the higher aggregated responses, measured as community-weighted means, of bacterial growth rate upon nitrogen additions. The aggregated responses are further explained by genomic traits, which show higher percentages of significant Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues (KOs) and more diverse KEGG pathways under nutrient additions including nitrogen, and further improve the explanatory power of microbial environmental responses. Nitrogen-induced responses at the species level show the strongest associations with essential KOs for rare species, whereas carbon-induced responses show the strongest associations for dominant species. We conclude that, in addition to environmental determinants such as nitrogen limitation, genomic traits are extremely important for predicting microbial environmental responses at both the community and species levels. Taking advantage of this new approach at the species level, we reveal that rare and dominant species differentially respond to nutrient enrichment via their metabolic traits. The approach and findings can lead to a more holistic understanding of microbial environmental responses in natural habitats, which will be essential for predicting microbial community responses to global environmental changes.
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Affiliation(s)
- Ang Hu
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Minglei Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Pandit MK, White SM, Pocock MJO. The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis. New Phytol 2014; 203:697-703. [PMID: 24697788 DOI: 10.1111/nph.12799] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/05/2014] [Indexed: 05/28/2023]
Abstract
Understanding how species' traits relate to their status (e.g. invasiveness or rarity) is important because it can help to efficiently focus conservation and management effort and infer mechanisms affecting plant status. This is particularly important for invasiveness, in which proactive action is needed to restrict the establishment of potentially invasive plants. We tested the ability of genome size (DNA 1C-values) to explain invasiveness and compared it with cytogenetic traits (chromosome number and ploidy level). We considered 890 species from 62 genera, from across the angiosperm phylogeny and distributed from tropical to boreal latitudes. We show that invasiveness was negatively related to genome size and positively related to chromosome number (and ploidy level), yet there was a positive relationship between genome size and chromosome number; that is, our result was not caused by collinearity between the traits. Including both traits in explanatory models greatly increased the explanatory power of each. This demonstrates the potential unifying role that genome size, chromosome number and ploidy have as species' traits, despite the diverse impacts they have on plant physiology. It provides support for the continued cataloguing of cytogenetic traits and genome size of the world's flora.
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Affiliation(s)
- Maharaj K Pandit
- Department of Environmental Studies, Centre for Inter-disciplinary Studies of Mountain & Hill Environment, University of Delhi, Delhi, 110007, India
| | - Steven M White
- Centre for Ecology & Hydrology, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, Oxfordshire, OX1 3LB, UK
| | - Michael J O Pocock
- Centre for Ecology & Hydrology, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
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