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Kuang Z, Li F, Duan Q, Tian C, Nevo E, Li K. Host diet shapes functionally differentiated gut microbiomes in sympatric speciation of blind mole rats in Upper Galilee, Israel. Front Microbiol 2022; 13:1062763. [PMID: 36458196 PMCID: PMC9707624 DOI: 10.3389/fmicb.2022.1062763] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
The gut microbiome is important for host nutrient metabolism and ecological adaptation. However, how the gut microbiome is affected by host phylogeny, ecology and diet during sympatric speciation remain unclear. Here, we compare and contrast the gut microbiome of two sympatric blind mole rat species and correlate them with their corresponding host phylogeny, ecology soil metagenomes, and diet to determine how these factors may influence their gut microbiome. Our results indicate that within the host microbiome there is no significant difference in community composition, but the functions between the two sympatric species populations vary significantly. No significant correlations were found between the gut microbiome differentiation and their corresponding ecological soil metagenomes and host phylogeny. Functional enrichment analysis suggests that the host diets may account for the functional divergence of the gut microbiome. Our results will help us understand how the gut microbiome changes with corresponding ecological dietary factors in sympatric speciation of blind subterranean mole rats.
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Affiliation(s)
- Zhuoran Kuang
- State Key Laboratory of Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Fang Li
- Department of Zoology, College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Qijiao Duan
- State Key Laboratory of Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Cuicui Tian
- Northwest Surveying and Planning Institute of National Forestry and Grassland Administration, Xi’an, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Kexin Li
- State Key Laboratory of Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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Mukherjee S, Kuang Z, Ghosh S, Detroja R, Carmi G, Tripathy S, Barash D, Frenkel-Morgenstern M, Nevo E, Li K. Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis. Biology 2022; 11:biology11081110. [PMID: 35892966 PMCID: PMC9331176 DOI: 10.3390/biology11081110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary The microevolutionary dynamics of soil bacteria under microclimatic differences are largely unexplored in contrast to our improving knowledge of their vast diversity. In this study, we performed a comparative metagenomic analysis of two sharply divergent rocks and soil types at the Evolution Plateau (EP) in eastern Upper Galilee, Israel. We have identified the significant differences in bacterial taxonomic diversity, functions, and patterns of RNA-based gene regulation between the bacteria from two different soil types. Furthermore, we have identified several species with a significant genetic divergence of the same species between the two soil types, highlighting the soil bacteria’s incipient sympatric speciation. Abstract Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.
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Affiliation(s)
- Sumit Mukherjee
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel;
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel;
- Correspondence: (S.M.); (K.L.)
| | - Zhuoran Kuang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
| | - Samrat Ghosh
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata 700054, India; (S.G.); (S.T.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201009, India
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Gon Carmi
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata 700054, India; (S.G.); (S.T.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201009, India
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel;
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel;
| | - Kexin Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
- Correspondence: (S.M.); (K.L.)
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Jiao H, Wang Q, Wang BJ, Li K, Lövy M, Nevo E, Li Q, Su W, Jiang P, Zhao H. Local adaptation of bitter taste and ecological speciation in a wild mammal. Mol Biol Evol 2021; 38:4562-4572. [PMID: 34240186 PMCID: PMC8476172 DOI: 10.1093/molbev/msab205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sensory systems are attractive evolutionary models to address how organisms adapt to local environments that can cause ecological speciation. However, tests of these evolutionary models have focused on visual, auditory, and olfactory senses. Here, we show local adaptation of bitter taste receptor genes in two neighboring populations of a wild mammal—the blind mole rat Spalax galili—that show ecological speciation in divergent soil environments. We found that basalt-type bitter receptors showed higher response intensity and sensitivity compared with chalk-type ones using both genetic and cell-based functional analyses. Such functional changes could help animals adapted to basalt soil select plants with less bitterness from diverse local foods, whereas a weaker reception to bitter taste may allow consumption of a greater range of plants for animals inhabiting chalk soil with a scarcity of food supply. Our study shows divergent selection on food resources through local adaptation of bitter receptors, and suggests that taste plays an important yet underappreciated role in speciation.
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Affiliation(s)
- Hengwu Jiao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qian Wang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Bing-Jun Wang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kexin Li
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 3498838, Israel.,State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Matěj Lövy
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, 37005, Czech Republic
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 3498838, Israel
| | - Qiyang Li
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenchuan Su
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peihua Jiang
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, 19104, USA
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Research Center for Ecology, College of Science, Tibet University, Lhasa, 850000, China
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Kang Y, Su J, Yao B, Wang C, Zhang D, Ji W. Interspecific skull variation at a small scale: The genus
Eospalax
exhibits functional morphological variations related to the exploitation of ecological niche. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Yukun Kang
- Key Laboratory of Grassland Ecosystem (Ministry of Education) College of Grassland Science Gansu Agricultural University Lanzhou China
- Gansu Agricultural University‐Massey University Research Centre for Grassland Biodiversity Gansu Agricultural University Lanzhou China
| | - Junhu Su
- Key Laboratory of Grassland Ecosystem (Ministry of Education) College of Grassland Science Gansu Agricultural University Lanzhou China
- Gansu Agricultural University‐Massey University Research Centre for Grassland Biodiversity Gansu Agricultural University Lanzhou China
| | - Baohui Yao
- Key Laboratory of Grassland Ecosystem (Ministry of Education) College of Grassland Science Gansu Agricultural University Lanzhou China
- Gansu Agricultural University‐Massey University Research Centre for Grassland Biodiversity Gansu Agricultural University Lanzhou China
| | - Chan Wang
- Key Laboratory of Grassland Ecosystem (Ministry of Education) College of Grassland Science Gansu Agricultural University Lanzhou China
- Gansu Agricultural University‐Massey University Research Centre for Grassland Biodiversity Gansu Agricultural University Lanzhou China
| | - Degang Zhang
- Key Laboratory of Grassland Ecosystem (Ministry of Education) College of Grassland Science Gansu Agricultural University Lanzhou China
- Gansu Agricultural University‐Massey University Research Centre for Grassland Biodiversity Gansu Agricultural University Lanzhou China
| | - Weihong Ji
- Gansu Agricultural University‐Massey University Research Centre for Grassland Biodiversity Gansu Agricultural University Lanzhou China
- Institute of Natural and Mathematical Sciences Massey University Auckland New Zealand
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