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Xiao Y, Zhou G, Qiu X, Liu F, Chen L, Zhang J. Biodiversity of network modules drives ecosystem functioning in biochar-amended paddy soil. Front Microbiol 2024; 15:1341251. [PMID: 38328424 PMCID: PMC10847562 DOI: 10.3389/fmicb.2024.1341251] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Introduction Soil microbes are central in governing soil multifunctionality and driving ecological processes. Despite biochar application has been reported to enhance soil biodiversity, its impacts on soil multifunctionality and the relationships between soil taxonomic biodiversity and ecosystem functioning remain controversial in paddy soil. Methods Herein, we characterized the biodiversity information on soil communities, including bacteria, fungi, protists, and nematodes, and tested their effects on twelve ecosystem metrics (including functions related to enzyme activities, nutrient provisioning, and element cycling) in biochar-amended paddy soil. Results The biochar amendment augmented soil multifunctionality by 20.1 and 35.7% in the early stage, while the effects were diminished in the late stage. Moreover, the soil microbial diversity and core modules were significantly correlated with soil multifunctionality. Discussion Our analysis revealed that not just soil microbial diversity, but specifically the biodiversity within the identified microbial modules, had a more pronounced impact on ecosystem functions. These modules, comprising diverse microbial taxa, especially protists, played key roles in driving ecosystem functioning in biochar-amended paddy soils. This highlights the importance of understanding the structure and interactions within microbial communities to fully comprehend the impact of biochar on soil ecosystem functioning in the agricultural ecosystem.
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Affiliation(s)
- Yu Xiao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guixiang Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiuwen Qiu
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Fangming Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Esmaili S, Langfelder P, Belgard TG, Vitale D, Azardaryany MK, Alipour Talesh G, Ramezani-Moghadam M, Ho V, Dvorkin D, Dervish S, Gloss BS, Grønbæk H, Liddle C, George J. Core liver homeostatic co-expression networks are preserved but respond to perturbations in an organism- and disease-specific manner. Cell Syst 2021; 12:432-445.e7. [PMID: 33957084 DOI: 10.1016/j.cels.2021.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/16/2020] [Accepted: 04/09/2021] [Indexed: 12/30/2022]
Abstract
Findings about chronic complex diseases are difficult to extrapolate from animal models to humans. We reason that organs may have core network modules that are preserved between species and are predictably altered when homeostasis is disrupted. To test this idea, we perturbed hepatic homeostasis in mice by dietary challenge and compared the liver transcriptome with that in human fatty liver disease and liver cancer. Co-expression module preservation analysis pointed to alterations in immune responses and metabolism (core modules) in both human and mouse datasets. The extent of derailment in core modules was predictive of survival in the cancer genome atlas (TCGA) liver cancer dataset. We identified module eigengene quantitative trait loci (module-eQTL) for these predictive co-expression modules, targeting of which may resolve homeostatic perturbations and improve patient outcomes. The framework presented can be used to understand homeostasis at systems levels in pre-clinical models and in humans. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Saeed Esmaili
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, NSW, Australia; Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Peter Langfelder
- The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, USA
| | | | - Daniele Vitale
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, NSW, Australia
| | - Mahmoud Karimi Azardaryany
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, NSW, Australia
| | - Ghazal Alipour Talesh
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, NSW, Australia
| | - Mehdi Ramezani-Moghadam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, NSW, Australia
| | - Vikki Ho
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, NSW, Australia
| | | | - Suat Dervish
- Westmead Research Hub, Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Brian S Gloss
- Westmead Research Hub, Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Henning Grønbæk
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Christopher Liddle
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, NSW, Australia
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, NSW, Australia.
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Abstract
BetaCore is a designed approximately 50-residue protein in which two BPTI-derived core modules, CM I and CM II, are connected by a 22-atom cross-link. At low temperature and pH 3, homo- and heteronuclear NMR data report a dominant folded ('f') conformation with well-dispersed chemical shifts, i, i+1 periodicity, numerous long-range NOEs, and slowed amide hydrogen isotope exchange patterns that is a four-stranded antiparallel beta-sheet with nonsymmetrical and specific association of CM I and CM II. BetaCore 'f' conformations undergo reversible, global, moderately cooperative, non-two-state thermal transitions to an equilibrium ensemble of unfolded 'u' conformations. There is a significant energy barrier between 'f' and 'u' conformations. This is the first designed four-stranded antiparallel beta-sheet that folds in water.
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Affiliation(s)
- Natàlia Carulla
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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