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Li F, Sun A, Jiao X, Yu DT, Ren P, Wu BX, He P, Bi L, He JZ, Hu HW. Nitrogenous fertilizer plays a more important role than cultivars in shaping sorghum-associated microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173831. [PMID: 38866152 DOI: 10.1016/j.scitotenv.2024.173831] [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: 04/02/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
The plant microbiome plays a crucial role in facilitating plant growth through enhancing nutrient cycling, acquisition and transport, as well as alleviating stresses induced by nutrient limitations. Despite its significance, the relative importance of common agronomic practices, such as nitrogenous fertilizer, in shaping the plant microbiome across different cultivars remains unclear. This study investigated the dynamics of bacterial and fungal communities in leaf, root, rhizosphere, and bulk soil in response to nitrogenous fertilizer across ten sorghum varieties, using 16S rRNA and ITS gene amplicon sequencing, respectively. Our results revealed that nitrogen addition had a greater impact on sorghum-associated microbial communities compared to cultivar. Nitrogen addition significantly reduced bacterial diversity in all compartments except for the root endophytes. However, N addition significantly increased fungal diversity in both rhizosphere and bulk soils, while significantly reducing fungal diversity in the root endophytes. Furthermore, N addition significantly altered the community composition of bacteria and fungi in all four compartments, while cultivars only affected the community composition of root endosphere bacteria and fungi. Network analysis revealed that fertilization significantly reduced microbial network complexity and increased fungal-related network complexity. Collectively, this study provides empirical evidence that sorghum-associated microbiomes are predominantly shaped by nitrogenous fertilizer rather than by cultivars, suggesting that consistent application of nitrogenous fertilizer will ultimately alter plant-associated microbiomes regardless of cultivar selection.
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Affiliation(s)
- Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaoyan Jiao
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Dan-Ting Yu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China.
| | - Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Bing-Xue Wu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Peng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Li Bi
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Gong J, Wang C, Wang J, Yang Y, Kong X, Liu J, Tang M, Lou H, Wen Z, Yang S, Yi Y. Integrative study of transcriptome and microbiome to reveal the response of Rhododendron decorum to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116536. [PMID: 38833983 DOI: 10.1016/j.ecoenv.2024.116536] [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: 01/31/2024] [Revised: 04/06/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
The anomalies of cadmium (Cd) in karst region pose a severe threat to plant growth and development. In this study, the responses of Rhododendron decorum to Cd stress were investigated at physiological, molecular, and endophytic microbial levels, and the potential correlation among these responses was assessed. The Cd stress impeded R. decorum growth and led to an increase in malondialdehyde (MDA) and hydrogen peroxide (H2O2) levels, as well as enhanced superoxide dismutase (SOD) and catalase (CAT) activities. Meanwhile, Cd stress increased the Cd (up to 80 times compared to the control), sodium (Na), aluminum (Al), and zinc (Zn) contents, while decreased the magnesium (Mg) and manganese (Mn) contents in R. decorum leaves. Transcriptome suggested that Cd significantly regulated the pathways including "protein repair", "hormone-mediated signaling pathway", and "ATP-binding cassette (ABC) transporters". Additionally, q-PCR analysis showed that Cd stress significantly up-regulated the expressions of ABCB19-like and pleiotropic drug resistance, while down-regulated the expressions of indole-3-acetic acid-amido synthetase and cytokinin dehydrogenase. The Cd stress influenced the composition of endophytic microbial communities in R. decorum leaves and enhanced the interspecific bacterial associations. Furthermore, the bacterial genera Achromobacter, Aureimonas and fungal genus Vishniacozyma exhibited a high degree of connectivity with other nodes in networks constructed by the metal element contents, differentially expressed genes (DEGs), and microbial communities, respectively. These findings provide a comprehensive insight into the response of R. decorum to Cd-induced stress, which might facilitate the breeding of the Cd-tolerant R. decorum.
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Affiliation(s)
- Jiyi Gong
- College of Water Sciences, Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing Normal University, Beijing 100875, China; Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Chao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Jianfeng Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Yang Yang
- Gansu Yasheng Agricultural Research Institute Co., Ltd., Lanzhou 730010, China
| | - Xin Kong
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Jie Liu
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Ming Tang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Hezhen Lou
- College of Water Sciences, Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing Normal University, Beijing 100875, China
| | - Zhirui Wen
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Shengtian Yang
- College of Water Sciences, Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing Normal University, Beijing 100875, China.
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China.
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3
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Wu F, Chen Z, Xu X, Xue X, Zhang Y, Sui N. Halotolerant Bacillus sp. strain RA coordinates myo-inositol metabolism to confer salt tolerance to tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38967265 DOI: 10.1111/jipb.13733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
Soil salinity is a worldwide problem threatening crop yields. Some plant growth-promoting rhizobacteria (PGPR) could survive in high salt environment and assist plant adaptation to stress. Nevertheless, the genomic and metabolic features, as well as the regulatory mechanisms promoting salt tolerance in plants by these bacteria remain largely unknown. In the current work, a novel halotolerant PGPR strain, namely, Bacillus sp. strain RA can enhance tomato tolerance to salt stress. Comparative genomic analysis of strain RA with its closely related species indicated a high level of evolutionary plasticity exhibited by strain-specific genes and evolutionary constraints driven by purifying selection, which facilitated its genomic adaptation to salt-affected soils. The transcriptome further showed that strain RA could tolerate salt stress by balancing energy metabolism via the reprogramming of biosynthetic pathways. Plants exude a plethora of metabolites that can strongly influence plant fitness. The accumulation of myo-inositol in leaves under salt stress was observed, leading to the promotion of plant growth triggered by Bacillus sp. strain RA. Importantly, myo-inositol serves as a selective force in the assembly of the phyllosphere microbiome and the recruitment of plant-beneficial species. It promotes destabilizing properties in phyllosphere bacterial co-occurrence networks, but not in fungal networks. Furthermore, interdomain interactions between bacteria and fungi were strengthened by myo-inositol in response to salt stress. This work highlights the genetic adaptation of RA to salt-affected soils and its ability to impact phyllosphere microorganisms through the adjustment of myo-inositol metabolites, thereby imparting enduring resistance against salt stress in tomato.
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Affiliation(s)
- Fenghui Wu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zengting Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, No. 2 Kangyang Road, Dongying, 257000, China
| | - Xiaotong Xu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, No. 2 Kangyang Road, Dongying, 257000, China
| | - Xin Xue
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Yanling Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
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Zhang S, Hu W, Zhang J, Yu G, Liu Y, Kong Z, Wu L. Long-term cultivation reduces soil carbon storage by altering microbial network complexity and metabolism activity in macroaggregates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172788. [PMID: 38677431 DOI: 10.1016/j.scitotenv.2024.172788] [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: 01/24/2024] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Cultivation alters soil aggregation, microbial compositions and the potential for carbon sequestration in cropland soils. However, the specific effects of long-term cultivation and the underlying mechanisms on soil organic carbon (SOC) storage at different aggregate sizes remain poorly understood. We characterized the dynamics of SOC storage in macroaggregates (>0.25 mm) and microaggregates (<0.25 mm) across four paddy soils successively cultivated for 60, 100, 125, and 150 years. Microbial community compositions, network patterns, enzyme activities and carbon use efficiency (CUE) were examined to elucidate the underlying microbial pathways governing SOC storage. The results showed that prolonged cultivation led to an average reduction of 45 % in SOC storage, particularly in macroaggregates. Partial least squares path modeling revealed that shifts in microorganisms in macroaggregates explained almost 80 % of the variation in SOC storage. Specifically, variations in fungal composition and decreased complexity of microbial interaction networks were strongly correlated with SOC storage. Fungal community and microbial interactions also indirectly affected SOC storage by positively correlating with extracellular enzyme activity. Moreover, bacterial composition indirectly regulated SOC storage by positively correlating with carbon use efficiency. Our findings indicated that the macroaggregate-associated microbial interactions and the metabolism activities had significant implications for SOC sequestration in paddy fields. We suggest that implementation of management practices targeted at improvement of these microbial attributes could enhance agroecosystems sustainability.
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Affiliation(s)
- Shan Zhang
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Wanjin Hu
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Jinting Zhang
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Guanjun Yu
- Jiangxi Poyang Lake Nanji Wetland National Nature Reserve Authority, Nanchang 330038, China
| | - Yizhen Liu
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China.
| | - Zhaoyu Kong
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Lan Wu
- School of Life Sciences, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China.
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5
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Meng L, Liang L, Shi Y, Yin H, Li L, Xiao J, Huang N, Zhao A, Xia Y, Hou J. Biofilms in plastisphere from freshwater wetlands: Biofilm formation, bacterial community assembly, and biogeochemical cycles. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134930. [PMID: 38901258 DOI: 10.1016/j.jhazmat.2024.134930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/10/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
Microorganisms can colonize to the surface of microplastics (MPs) to form biofilms, termed "plastisphere", which could significantly change their physiochemical properties and ecological roles. However, the biofilm characteristics and the deep mechanisms (interaction, assembly, and biogeochemical cycles) underlying plastisphere in wetlands currently lack a comprehensive perspective. In this study, in situ biofilm formation experiments were performed in a park with different types of wetlands to examine the plastisphere by extrinsic addition of PVC MPs in summer and winter, respectively. Results from the spectroscopic and microscopic analyses revealed that biofilms attached to the MPs in constructed forest wetlands contained the most abundant biomass and extracellular polymeric substances. Meanwhile, data from the high-throughput sequencing showed lower diversity in plastisphere compared with soil bacterial communities. Network analysis suggested a simple and unstable co-occurrence pattern in plastisphere, and the null model indicated increased deterministic process of heterogeneous selection for its community assembly. Based on the quantification of biogeochemical cycling genes by high-throughput qPCR, the relative abundances of genes involving in carbon degradation, carbon fixation, and denitrification were significantly higher in plastisphere than those of soil communities. This study greatly enhanced our understanding of biofilm formation and ecological effects of MPs in freshwater wetlands.
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Affiliation(s)
- Liang Meng
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China; Key Laboratory of Environment Remediation and Ecological Health, Zhejiang University, Ministry of Education, Hangzhou 310058, China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai 201722, China
| | - Longrui Liang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yansong Shi
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Haitao Yin
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Li Li
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiamu Xiao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Nannan Huang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Angang Zhao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yangrongchang Xia
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jingwen Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China.
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Li C, Shao X, Zhang S, Wang Y, Jin K, Yang P, Lu X, Fan X, Wang Y. scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network. Cell Rep Med 2024; 5:101568. [PMID: 38754419 PMCID: PMC11228399 DOI: 10.1016/j.xcrm.2024.101568] [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: 05/05/2023] [Revised: 12/27/2023] [Accepted: 04/21/2024] [Indexed: 05/18/2024]
Abstract
Cells respond divergently to drugs due to the heterogeneity among cell populations. Thus, it is crucial to identify drug-responsive cell populations in order to accurately elucidate the mechanism of drug action, which is still a great challenge. Here, we address this problem with scRank, which employs a target-perturbed gene regulatory network to rank drug-responsive cell populations via in silico drug perturbations using untreated single-cell transcriptomic data. We benchmark scRank on simulated and real datasets, which shows the superior performance of scRank over existing methods. When applied to medulloblastoma and major depressive disorder datasets, scRank identifies drug-responsive cell types that are consistent with the literature. Moreover, scRank accurately uncovers the macrophage subpopulation responsive to tanshinone IIA and its potential targets in myocardial infarction, with experimental validation. In conclusion, scRank enables the inference of drug-responsive cell types using untreated single-cell data, thus providing insights into the cellular-level impacts of therapeutic interventions.
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Affiliation(s)
- Chengyu Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China.
| | - Shujing Zhang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Yingchao Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Kaiyu Jin
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China
| | - Penghui Yang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China
| | - Xiaoyan Lu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China; Jinhua Institute of Zhejiang University, Jinhua 321299, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
| | - Yi Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China.
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Gai X, Xing W, Chen G. Divergent responses of rhizosphere soil phosphorus fractions and biological features of Salix psammophila to fertilization strategies under cadmium contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172554. [PMID: 38657824 DOI: 10.1016/j.scitotenv.2024.172554] [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: 01/18/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Soil oligotrophy in areas heavily contaminated with heavy metals poses a significant challenge to vegetation establishment and phytoremediation processes. Phosphorus (P) cycling plays a critical role in global biogeochemical cycles, but there is limited understanding of its response to varying fertilization strategies and its correlation with phytoremediation effectiveness. This study primarily investigated the effects of various fertilization strategies, including nitrogen (N, 300 mg·kg-1), P (100 mg·kg-1), NP (combined N and P at 300 mg·kg-1 and 100 mg·kg-1, respectively), and HP (high P, 300 mg·kg-1) application, on rhizosphere soil P fractions and P-solubilizing microbial community (harboring phoD and phoC genes, respectively) of Salix psammophila under cadmium contamination. Application of NP significantly enhanced plant growth and cadmium accumulation, whereas HP inhibited cadmium bioaccumulation but promoted its translocation. Compared to untreated soil, N application promoted P cycling, leading to increases of 141.9 %, 60.4 %, and 10.3 % in Resin-Pi, diluted HCl-Pi, and conc.HCl-Pi, respectively. P application decreased organic phosphorus (Po) fractions by 24.4 % - 225.8 %, but N incorporation mitigated the declining trend in Po and augmented alkaline phosphatase activity. Fertilization strategies significantly regulated phoC- or phoD-harboring bacterial community structure, but their differential nutrient demands resulted in distinct responses. The phoD-harboring bacteria exhibited higher diversity and network complexity, with numerous biomarkers and fertilizer-sensitive OTUs discovered across treatments. Structural equation modeling (SEM) analysis indicated that phytoremediation efficiency was directly affected by Pi fractions, and phoD-harboring bacteria exhibited stronger associations with Pi fractions than phoC-harboring bacteria. In conclusion, our results reveal potential pathways through which fertilization strategies influence phytoremediation by affecting the structure of P-solubilizing microbial community. Furthermore, our study emphasizes the importance of combined N and P application in promoting Cd accumulation in plants, with high P levels appearing as an ideal fertilization strategy for phytoremediation targeting the harvest of aboveground biomass.
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Affiliation(s)
- Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China
| | - Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, PR China.
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8
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Mes W, Lücker S, Jetten MSM, Siepel H, Gorissen M, van Kessel MAHJ. Feeding strategy and feed protein level affect the gut microbiota of common carp (Cyprinus carpio). ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13262. [PMID: 38725141 PMCID: PMC11082430 DOI: 10.1111/1758-2229.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Common carp (Cyprinus carpio) were fed food with different protein concentrations following different feeding regimes, which were previously shown to affect growth, nitrogen excretion and amino acid catabolism. 16S rRNA gene amplicon sequencing was performed to investigate the gut microbiota of these fish. Lower dietary protein content increased microbial richness, while the combination of demand feeding and dietary protein content affected the composition of the gut microbiota. Hepatic glutamate dehydrogenase (GDH) activity was correlated to the composition of the gut microbiota in all dietary treatments. We found that demand-fed carp fed a diet containing 39% protein had a significantly higher abundance of Beijerinckiaceae compared to other dietary groups. Network analysis identified this family and two Rhizobiales families as hubs in the microbial association network. In demand-fed carp, the microbial association network had significantly fewer connections than in batch-fed carp. In contrast to the large effects of the feeding regime and protein content of the food on growth and nitrogen metabolism, it had only limited effects on gut microbiota composition. However, correlations between gut microbiota composition and liver GDH activity showed that host physiology and gut microbiota are connected, which warrants functional studies into the role of the gut microbiota in fish physiology.
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Affiliation(s)
- Wouter Mes
- Department of Microbiology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
- Department of Plant and Animal Biology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Henk Siepel
- Department of Plant and Animal Biology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Marnix Gorissen
- Department of Plant and Animal Biology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
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9
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Kochel B. Negative feedback systems for modelling NF-κB transcription factor oscillatory activity. Transcription 2024:1-32. [PMID: 38739365 DOI: 10.1080/21541264.2024.2331887] [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: 10/27/2023] [Accepted: 03/13/2024] [Indexed: 05/14/2024] Open
Abstract
Low-dimensional negative feedback systems (NFSs) were developed within a signal flow model to describe the oscillatory activities of NF-κB caused by interactions with its inhibitor IκBα. The NFSs were established as 3rd- and 4th-order linear systems containing unperturbed and perturbed negative feedback (NF) loops with constant or time-varying NF strengths and a feed-forward loop. NF-related analytical solutions to the NFSs representing the time courses of NF-κB and IκBα were determined and their exact mathematical relationship was found. The NFS's parameters were determined to fit the experimental time courses of NF-κB in TNF-α-stimulated embryonic fibroblasts, rela-/- embryonic fibroblasts reconstituted with RelA, C9L cells, GFP-p65 knock-in embryonic fibroblasts and embryogenic fibroblasts lacking Iκβ and IκBε, LPS-stimulated IC-21 macrophages treated or not with DCPA, and anti-IgM-stimulated DT40 B-lymphocytes. The unperturbed and perturbed NFSs describing the above biosystems generated isochronous and non-isochronous solutions, depending on a constant or time-varying NF strength, respectively. The oscillation period of the NF-coupled solutions, the phase difference between them and the time delays in the appearance of cytoplasmic IκBα after stimulation of NF-κB were determined. A significant divergence between the IκBα solutions to the NFSs and the IκBα experimental courses led to a rejection of the NF coupling between NF-κB and IκBα in the above biosystems. It was shown that neither the linearity nor the low dimensionality of the NFSs altered the NF relationship and the divergence between the IκBα solutions to the NFS and IκBα experimental time courses. Although the NF relationship between IκBα and NF-κB was not confirmed in all the experimental data analyzed, delayed negative feedback was found in some cases.
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Affiliation(s)
- Bonawentura Kochel
- Immunotherapy Central Europe, Wroclaw Medical University, Wrocław, Poland
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10
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Cao T, Shi M, Zhang J, Ji H, Wang X, Sun J, Chen Z, Li Q, Song X. Nitrogen fertilization practices alter microbial communities driven by clonal integration in Moso bamboo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171581. [PMID: 38461973 DOI: 10.1016/j.scitotenv.2024.171581] [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: 01/11/2024] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Nitrogen (N) fertilization is crucial for maintaining plant productivity. Clonal plants can share resources between connected ramets through clonal integration influencing microbial communities and regulating soil biogeochemical cycling, especially in the rhizosphere. However, the effect of various N fertilization practices on microbial communities in the rhizosphere of clonal ramets remain unknown. In this study, clonal fragments of Moso bamboo (Phyllostachys edulis), consisting of a parent ramet, an offspring ramet, and an interconnecting rhizome, were established in the field. NH4NO3 solution was applied to the parent, offspring ramets or rhizomes to investigate the effect of fertilization practices on the structure and function of rhizosphere microbial communities. The differences in N availability, microbial biomass and community composition, and abundance of nitrifying genes among rhizosphere soils of ramets gradually decreased during the rapid growth of Moso bamboo, irrespective of fertilization practice. The soil N availability variation, particularly in NO3-, caused by fertilization practices altered the rhizosphere microbial community. Soil N availability and stable microbial biomass N in parent fertilization were the highest, being 9.0 % and 18.7 %, as well as 60.8 % and 90.4 % higher than rhizome and offspring fertilizations, respectively. The microbial network nodes and links in rhizome fertilization were 1.8 and 7.5 times higher than in parent and offspring fertilization, respectively. However, the diversity of bacterial community and abundance of nitrifying and denitrifying genes were the highest in offspring fertilization among three practices, which may be associated with increased N loss. Collectively, the rhizosphere microbial community characteristics depended on fertilization practices by altering the clonal integration of N in Moso bamboo. Parent and rhizome fertilization were favorable for N retention in plant-soil system and resulted in more stable microbial functions than offspring fertilization. Our findings provide new insights into precision fertilization for the sustainable Moso bamboo forest management.
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Affiliation(s)
- Tingting Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Man Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Junbo Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Hangxiang Ji
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jilei Sun
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhenxiong Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Quan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinzhang Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China.
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11
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Li J, Zheng Q, Liu J, Pei S, Yang Z, Chen R, Ma L, Niu J, Tian T. Bacterial-fungal interactions and response to heavy metal contamination of soil in agricultural areas. Front Microbiol 2024; 15:1395154. [PMID: 38800759 PMCID: PMC11116572 DOI: 10.3389/fmicb.2024.1395154] [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: 03/03/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Long-term heavy metal contamination of soil affects the structure and function of microbial communities. The aim of our study was to investigate the effect of soil heavy metal contamination on microorganisms and the impact of different heavy metal pollution levels on the microbial interactions. Methods We collected soil samples and determined soil properties. Microbial diversity was analyzed in two groups of samples using high-throughput sequencing technology. Additionally, we constructed microbial networks to analyze microbial interactions. Results The pollution load index (PLI) < 1 indicates that the area is not polluted. 1 < PLI < 2 represents moderate pollution. PLI was 1.05 and 0.14 for the heavy metal contaminated area and the uncontaminated area, respectively. Cd, Hg, Pb, Zn, and Cu were identified as the major contaminants in the contaminated area, with the contamination factors were 30.35, 11.26, 5.46, 5.19, and 2.46, respectively. The diversities and compositions of the bacterial community varied significantly between the two groups. Compared to the uncontaminated area, the co-occurrence network between bacterial and fungal species in the contaminated area was more complex. The keystone taxa of the co-occurrence network in the contaminated area were more than those in the uncontaminated area and were completely different from it. Discussion Heavy metal concentrations played a crucial role in shaping the difference in microbial community compositions. Microorganisms adapt to long-term and moderate levels of heavy metal contamination through enhanced interactions. Bacteria resistant to heavy metal concentrations may play an important role in soils contaminated with moderate levels of heavy metals over long periods of time.
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Affiliation(s)
- Jia Li
- School of Public Health, Lanzhou University, Lanzhou, Gansu, China
| | - Qiwen Zheng
- School of Public Health, Lanzhou University, Lanzhou, Gansu, China
| | - Jiangyun Liu
- School of Public Health, Lanzhou University, Lanzhou, Gansu, China
| | - Shuwei Pei
- School of Public Health, Lanzhou University, Lanzhou, Gansu, China
| | - Zhen Yang
- Lanzhou Maternal and Child Health Care Hospital, Lanzhou, Gansu, China
| | - Rentong Chen
- School of Public Health, Lanzhou University, Lanzhou, Gansu, China
| | - Li Ma
- School of Public Health, Lanzhou University, Lanzhou, Gansu, China
| | - Jingping Niu
- School of Public Health, Lanzhou University, Lanzhou, Gansu, China
| | - Tian Tian
- School of Public Health, Lanzhou University, Lanzhou, Gansu, China
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Zhang M, Zhou Y, Cui X, Zhu L. The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis. Microorganisms 2024; 12:713. [PMID: 38674657 PMCID: PMC11051890 DOI: 10.3390/microorganisms12040713] [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: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
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Affiliation(s)
| | | | | | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210098, China; (M.Z.); (Y.Z.); (X.C.)
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Lopez-Moreno A, Cerk K, Rodrigo L, Suarez A, Aguilera M, Ruiz-Rodriguez A. Bisphenol A exposure affects specific gut taxa and drives microbiota dynamics in childhood obesity. mSystems 2024; 9:e0095723. [PMID: 38426791 PMCID: PMC10949422 DOI: 10.1128/msystems.00957-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/15/2024] [Indexed: 03/02/2024] Open
Abstract
Cumulative xenobiotic exposure has an environmental and human health impact which is currently assessed under the One Health approach. Bisphenol A (BPA) exposure and its potential link with childhood obesity that has parallelly increased during the last decades deserve special attention. It stands during prenatal or early life and could trigger comorbidities and non-communicable diseases along life. Accumulation in the nature of synthetic chemicals supports the "environmental obesogen" hypothesis, such as BPA. This estrogen-mimicking xenobiotic has shown endocrine disruptive and obesogenic effects accompanied by gut microbiota misbalance that is not yet well elucidated. This study aimed to investigate specific microbiota taxa isolated and selected by direct BPA exposure and reveal its role on the overall children microbiota community and dynamics, driving toward specific obesity dysbiosis. A total of 333 BPA-resistant isolated species obtained through culturing after several exposure conditions were evaluated for their role and interplay with the global microbial community. The selected BPA-cultured taxa biomarkers showed a significant impact on alpha diversity. Specifically, Clostridium and Romboutsia were positively associated promoting the richness of microbiota communities, while Intestinibacter, Escherichia-Shigella, Bifidobacterium, and Lactobacillus were negatively associated. Microbial community dynamics and networks analyses showed differences according to the study groups. The normal-weight children group exhibited a more enriched, structured, and connected taxa network compared to overweight and obese groups, which could represent a more resilient community to xenobiotic substances. In this sense, subnetwork analysis generated with the BPA-cultured genera showed a correlation between taxa connectivity and more diverse potential enzymatic BPA degradation capacities.IMPORTANCEOur findings indicate how gut microbiota taxa with the capacity to grow in BPA were differentially represented within differential body mass index children study groups and how these taxa affected the overall dynamics toward patterns of diversity generally recognized in dysbiosis. Community network and subnetwork analyses corroborated the better connectedness and stability profiles for normal-weight group compared to the overweight and obese groups.
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Affiliation(s)
- Ana Lopez-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- />Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Klara Cerk
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, United Kingdom
| | - Lourdes Rodrigo
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
| | - Antonio Suarez
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Campus of Cartuja, University of Granada, Granada, Spain
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- />Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Alicia Ruiz-Rodriguez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Campus of Cartuja, University of Granada, Granada, Spain
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14
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Yue H, Sun X, Wang T, Zhang A, Han D, Wei G, Song W, Shu D. Host genotype-specific rhizosphere fungus enhances drought resistance in wheat. MICROBIOME 2024; 12:44. [PMID: 38433268 PMCID: PMC10910722 DOI: 10.1186/s40168-024-01770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses. RESULTS Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum). CONCLUSIONS Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.
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Affiliation(s)
- Hong Yue
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuming Sun
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Wang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ali Zhang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dejun Han
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
| | - Weining Song
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Duntao Shu
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
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15
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Zhao P, Gao G, Ding G, Zhang Y, Ren Y. Fungal complexity and stability across afforestation areas in changing desert environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169398. [PMID: 38114026 DOI: 10.1016/j.scitotenv.2023.169398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
The great achievements in combating desertification are attributed to large-scale afforestation, yet we lack verification of how the stability of the fungal community changes in afforestation areas in desert environments. Here, we present the fungal network structure from different niches (root and bulk soil) of plantations of Mongolian pine, a crucial species for afforestation introduced widely in desertification regions. We assessed changes in community complexity and stability of root-associated fungi (RAF) and soil fungi (SF) among different introduction sites: the Hulunbuir Desert (HB), the Horqin Desert (HQ) and the Mu Us Desert (MU). To illuminate the complexity and stability of the fungal network, the differences in topological properties, fungal function, and vegetation and environmental factors between introduction sites were fully considered. We showed that (1) the SF networks had more nodes and edges than the RAF networks. There was a lower ratio of negative:positive cohesion of RAF networks in HB and MU. For SF but not for RAF, across the three introduction sites, a higher modularity and ratio of negative:positive cohesion indicated higher stability. (2) Ectomycorrhizal (EcM) fungi were the dominant functional group in the RAF network (especially in HQ), and were only significantly correlated with vegetation factor. There was a higher relative abundance and number of OTUs of saprophytic fungi in the SF network and they showed positive correlations with soil nutrients. (3) RAF and SF network complexity and stability showed different responses to environmental and vegetation variables. The key determinant of the complexity and stability of the SF networks in Mongolian pine plantations was soil nutrients, followed by climate conditions. The composition and structure of the RAF community was closely related to host plants. Therefore, clarifying the complexity and stability of fungal communities in afforestation areas in changing desert environments is helpful for understanding the interactions between the environment, plants and fungi.
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Affiliation(s)
- Peishan Zhao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Guanglei Gao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China.
| | - Guodong Ding
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Ying Zhang
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yue Ren
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
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Khatri-Chhetri U, Banerjee S, Thompson KA, Quideau SA, Boyce MS, Bork EW, Carlyle CN. Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169353. [PMID: 38104847 DOI: 10.1016/j.scitotenv.2023.169353] [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: 01/18/2023] [Revised: 05/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.
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Affiliation(s)
- Upama Khatri-Chhetri
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Karen A Thompson
- Trent School of Environment, Trent University, Peterborough, ON K9L 0G2, Canada
| | - Sylvie A Quideau
- Department of Renewable Resources, Earth Science Building University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Mark S Boyce
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Edward W Bork
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Cameron N Carlyle
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Zhang S, Liu S, Liu H, Li H, Luo J, Zhang A, Ding Y, Ren T, Chen W. Stochastic Assembly Increases the Complexity and Stability of Shrimp Gut Microbiota During Aquaculture Progression. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:92-102. [PMID: 38165637 DOI: 10.1007/s10126-023-10279-4] [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: 10/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
The gut microbiota of aquaculture species contributes to their food metabolism and regulates their health, which has been shown to vary during aquaculture progression of their hosts. However, limited research has examined the outcomes and mechanisms of these changes in the gut microbiota of hosts. Here, Kuruma shrimps from the beginning, middle, and late stages of aquaculture progression (about a time duration of 2 months between each stage) were collected and variations in the gut microbiota of Kuruma shrimp during the whole aquaculture process were examined. High-throughput sequencing demonstrated increases in the diversity and richness of the shrimp gut microbiota with aquaculture progression. In addition, the gut microbiota composition differed among cultural stages, with enrichment of Firmicutes, RF39, and Megamonas and a reduction in Proteobacteria in the mid-stage. Notably, only very few taxa were persistent in the shrimp gut microbiota during the whole aquaculture progression, while the number of taxa that specific to the end of aquaculture was high. Network analysis revealed increasing complexity of the shrimp gut microbiota during aquaculture progression. Moreover, the shrimp gut microbiota became significantly more stable towards the end of aquaculture. According to the results of neutral community model, contribution of stochastic processes for shaping the shrimp gut microbiota was elevated along the aquaculture progression. This study showed substantial variations in shrimp gut microbiota during aquaculture progression and explored the underlying mechanisms regulating these changes.
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Affiliation(s)
- Saisai Zhang
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Shuang Liu
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Hongwei Liu
- Dalian Ocean University, Dalian Liaoning, 116023, China
| | - Hui Li
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Jun Luo
- Dalian Sun Asia Tourism Holding Co. Ltd., Dalian, Liaoning, 116023, China
| | - Aili Zhang
- Dalian Ocean School, Dalian, Liaoning, 116023, China
| | - Yinpeng Ding
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Tongjun Ren
- Dalian Ocean University, Dalian Liaoning, 116023, China
| | - Wenbo Chen
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China.
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Zhang B, Xi Y, Huang Y, Zhang Y, Guo F, Yang H. Integration of single-nucleus RNA sequencing and network disturbance to elucidate crosstalk between multicomponent drugs and trigeminal ganglia cells in migraine. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117286. [PMID: 37838292 DOI: 10.1016/j.jep.2023.117286] [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: 08/02/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Migraine is caused by hyperactivity of the trigeminovascular system, where trigeminal ganglia (TG) plays an important role. TG is composed of multiple neuronal and non-neuronal cell types, which is related to "neuro-inflammation-vascular" disorder in migraine. Tou Tong Ning capsule (TTNC), a CFDA-approved traditional Chinese medicine for treating migraine, has the characteristics of "multicomponents, multitargets, multipathways". AIM OF THE STUDY To clarify the mechanism of TTNC and elucidate crosstalk between multicomponent drugs and neuronal and non-neuronal functions and cells in migraine. MATERIALS AND METHODS We integrated single-nucleus RNA sequencing and a quantitative evaluation algorithm of the disturbance of multitarget drugs on the disease network and explored the specific pathology of migraine and corresponding compounds. A cerebrovascular smooth muscle spasmolytic activity experiment was carried out to verify the results of the bioinformatics analysis. RESULTS TTNC exhibited its regulation activities in neuronal and non-neuronal aspects based on drugs attack to four subnetworks and cell specific networks, which explored the MoA of TTNC in comprehensive and refined perspectives. Compared to neuronal regulation, TTNC showed more significant attack score on non-neuronal biological function (smooth muscle and vessel). And TTNC compound clusters C1, C6 and C7, targeting non-neuronal function and cells, had larger group area than C10, C4 and C6 for neuronal function and cell, which implied that TTNC may mainly regulate the non-neuronal function, e.g., vessel smooth muscle contraction. Contraction of cerebrovascular smooth muscle of mice ex vivo confirmed the vasodilation activity of TTNC and active compounds from C1, C6, C9 (Emodin, Luteolin and Levistilide A). Literature mining confirmed the vasospasmodolytic activity and neuroprotective effect of TTNC. CONCLUSIONS The study found that TTNC may primarily alleviate non-neuronal functional disorders in migraine by relaxing cerebral vascular smooth muscle cell spasm to alleviate migraine. Integrating single-nucleus RNA sequencing data and network disturbance tools provides a new strategy for the pharmacological mechanism of multicomponent drugs through cell subtyping.
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Affiliation(s)
- Bo Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yujie Xi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China; Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Huang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Feifei Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Hongjun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China; Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China; China Academy of Chinese Medical Sciences, Beijing, China.
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19
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Liang J, Wei C, Song X, Wang R, Shi H, Tan J, Cheng D, Wang W, Wang X. Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum. ENVIRONMENTAL MICROBIOME 2024; 19:6. [PMID: 38229154 DOI: 10.1186/s40793-024-00548-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Beneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. Nonetheless, the dynamics of microbiome assembly and defense mechanisms during pathogen invasion remain largely unknown. In this study, we aimed to investigate the diversity and assembly of microbial communities within four niches (bulk soils, rhizosphere, rhizoplane, and endosphere) under the influence of the bacterial plant pathogen Ralstonia solanacearum. RESULTS Our results revealed that healthy tobacco plants exhibited more diverse community compositions and more robust co-occurrence networks in root-associated niches compared to diseased tobacco plants. Stochastic processes (dispersal limitation and drift), rather than determinism, dominated the assembly processes, with a higher impact of drift observed in diseased plants than in healthy ones. Furthermore, during the invasion of R. solanacearum, the abundance of Fusarium genera, a known potential pathogen of Fusarium wilt, significantly increased in diseased plants. Moreover, the response strategies of the microbiomes to pathogens in diseased and healthy plants diverged. Diseased microbiomes recruited beneficial microbial taxa, such as Streptomyces and Bacilli, to mount defenses against pathogens, with an increased presence of microbial taxa negatively correlated with the pathogen. Conversely, the potential defense strategies varied across niches in healthy plants, with significant enrichments of functional genes related to biofilm formation in the rhizoplane and antibiotic biosynthesis in the endosphere. CONCLUSION Our study revealed the varied community composition and assembly mechanism of microbial communities between healthy and diseased tobacco plants along the soil-root continuum, providing new insights into niche-specific defense mechanisms against pathogen invasions. These findings may underscore the potential utilization of different functional prebiotics to enhance plants' ability to fend off pathogens.
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Affiliation(s)
- Jinchang Liang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
| | - Chengjian Wei
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
- College of Agriculture, Guangxi University, 530004, Nanning, China
| | - Xueru Song
- Engineering Center for Biological Control of Diseases and Pests in Tobacco Industry, 653100, Yuxi, China
| | - Rui Wang
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Heli Shi
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Jun Tan
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Dejie Cheng
- College of Agriculture, Guangxi University, 530004, Nanning, China
| | - Wenjing Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
| | - Xiaoqiang Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
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20
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Maurice K, Bourceret A, Youssef S, Boivin S, Laurent-Webb L, Damasio C, Boukcim H, Selosse MA, Ducousso M. Anthropic disturbances impact the soil microbial network structure and stability to a greater extent than natural disturbances in an arid ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167969. [PMID: 37914121 DOI: 10.1016/j.scitotenv.2023.167969] [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: 08/16/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Growing pressure from climate change and agricultural land use is destabilizing soil microbial community interactions. Yet little is known about microbial community resistance and adaptation to disturbances over time. This hampers our ability to determine the recovery latency of microbial interactions after disturbances, with fundamental implications for ecosystem functioning and conservation measures. Here we examined the response of bacterial and fungal community networks in the rhizosphere of Haloxylon salicornicum (Moq.) Bunge ex Boiss. over the course of soil disturbances resulting from a history of different hydric constraints involving flooding-drought successions. An anthropic disturbance related to past agricultural use, with frequent successions of flooding and drought, was compared to a natural disturbance, i.e., an evaporation basin, with yearly flooding-drought successions. The anthropic disturbance resulted in a specific microbial network topology characterized by lower modularity and stability, reflecting the legacy of past agricultural use on soil microbiome. In contrast, the natural disturbance resulted in a network topology and stability close to those of natural environments despite the lower alpha diversity, and a different community composition compared to that of the other sites. These results highlighted the temporality in the response of the microbial community structure to disturbance, where long-term adaptation to flooding-drought successions lead to a higher stability than disturbances occurring over a shorter timescale.
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Affiliation(s)
- Kenji Maurice
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France.
| | - Amélia Bourceret
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France
| | - Sami Youssef
- Department of Research and Development, VALORHIZ, 1900, Boulevard de la Lironde, PSIII, Parc Scientifique Agropolis, F34980 Montferrier sur Lez, France
| | - Stéphane Boivin
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
| | - Liam Laurent-Webb
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France
| | - Coraline Damasio
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
| | - Hassan Boukcim
- Department of Research and Development, VALORHIZ, 1900, Boulevard de la Lironde, PSIII, Parc Scientifique Agropolis, F34980 Montferrier sur Lez, France; ASARI, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid Ben Guerir, 43150, Morocco
| | - Marc-André Selosse
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France; Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland; Institut Universitaire de France, Paris, France
| | - Marc Ducousso
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
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21
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Li K, Xu L, Bai X, Zhang G, Zhang M, Huang Y. Differential fungal assemblages and functions between the plastisphere of biodegradable and conventional microplastics in farmland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167478. [PMID: 37804989 DOI: 10.1016/j.scitotenv.2023.167478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023]
Abstract
The heterogeneity of plastisphere and soil can lead to variation in microbiome, potentially impacting soil functions. Current studies of the plastisphere have mainly focused on bacterial communities, and fungal communities are poorly understood. Biodegradable and conventional microplastics may recruit specific microbial taxa due to their different biodegradability. Herein, we collected polyethylene (PE) and polybutylene adipate terephthalate/polylactide (PBAT/PLA) microplastics in farmland (Hebei, China) and characterized the fungal community in PE and PBAT/PLA plastisphere. Results from high-throughput sequencing showed significantly lower alpha diversity and distinct composition of fungal community in PBAT/PLA plastisphere compared to PE plastisphere. Additionally, the PBAT/PLA plastisphere demonstrated a significant enrichment of fungal taxa with potential plastic-degrading capability such as Nectriaceae, Pleosporaceae and Didymellaceae. The stochasticity of drift (28.7-43.5 %) and dispersal limitation (38.6-39.4 %) were dominant in the assembly of PE and PBAT/PLA plastisphere fungal community. Higher stable and more complex network in PBAT/PLA plastispheres were observed as compared to PE plastisphere. Besides, the total relative abundance of plant and animal pathogens were higher in PBAT/PLA plastisphere than that in PE plastisphere, suggesting that biodegradable microplastics may pose a higher threat to soil health. This study contributes to our understanding of the characteristics of plastisphere fungal communities in soil environments and the associated risks to terrestrial ecosystems resulting from microplastic accumulation.
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Affiliation(s)
- Kang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Libo Xu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xinyi Bai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Guangbao Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Mengjun Zhang
- Marine Institute for Bioresources and Environment, Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Marine Institute for Bioresources and Environment, Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China.
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22
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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23
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Wang JF, Huang JW, Cai ZX, Li QS, Sun YY, Zhou HZ, Zhu H, Song XS, Wu HM. Differential Nitrous oxide emission and microbiota succession in constructed wetlands induced by nitrogen forms. ENVIRONMENT INTERNATIONAL 2024; 183:108369. [PMID: 38070437 DOI: 10.1016/j.envint.2023.108369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/26/2023] [Accepted: 12/03/2023] [Indexed: 01/25/2024]
Abstract
Nitrous oxide (N2O) emission during the sewage treatment process is a serious environmental issue that requires attention. However, the N2O emission in constructed wetlands (CWs) as affected by different nitrogen forms in influents remain largely unknown. This study investigated the N2O emission profiles driven by microorganisms in CWs when exposed to two typical nitrogen sources (NH4+-N or NO3--N) along with different carbon source supply (COD/N ratios: 3, 6, and 9). The results showed that CWs receiving NO3--N caused a slight increase in total nitrogen removal (by up to 11.8 %). This increase was accomplished by an enrichment of key bacteria groups, including denitrifiers, dissimilatory nitrate reducers, and assimilatory nitrate reducers, which enhanced the stability of microbial interaction. Additionally, it led to a greater abundance of denitrification genes (e.g., nirK, norB, norC, and nosZ) as inferred from the database. Consequently, this led to a gradual increase in N2O emission from 66.51 to 486.77 ug-N/(m2·h) as the COD/N ratio increased in CWs. Conversely, in CWs receiving NH4+-N, an increasing influent COD/N ratio had a negative impact on nitrogen biotransformation. This resulted in fluctuating trend of N2O emissions, which decreased initially, followed by an increase at later stage (with values of 122.87, 44.00, and 148.59 ug-N/(m2·h)). Furthermore, NH4+-N in the aquatic improved the nitrogen uptake by plants and promoted the production of more root exudates. As a result, it adjusted the nitrogen-transforming function, ultimately reducing N2O emissions in CWs. This study highlights the divergence in microbiota succession and nitrogen transformation in CWs induced by nitrogen form and COD/N ratio, contributing to a better understanding of the microbial mechanisms of N2O emission in CWs with NH4+-N or NO3--N at different COD/N ratios.
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Affiliation(s)
- Jun-Feng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jia-Wei Huang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ze-Xiang Cai
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Qu-Sheng Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yun-Yun Sun
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Huan-Zhan Zhou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hui Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Xin-Shan Song
- State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, College of Environmental Science and Engineering, Donghua University, Shanghai 201600, China
| | - Hai-Ming Wu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China.
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24
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Ren S, Zhang L, Tang X, Fan C, Zhao Y, Cheng Q, Zhang Y. Plant Secondary Compounds Promote White Adipose Tissue Browning via Modulation of the Gut Microbiota in Small Mammals. Int J Mol Sci 2023; 24:17420. [PMID: 38139249 PMCID: PMC10743627 DOI: 10.3390/ijms242417420] [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] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The browning of white adipose tissue (WAT) is a promising area of research for treating metabolic disorders and obesity in the future. However, studies on plant secondary compounds promoting WAT browning are limited. Herein, we explored the effects of swainsonine (SW) on gut microbiota and WAT browning in captive pikas. SW inhibited body mass gain, increased brown adipose tissue (BAT) mass, and induced WAT browning in pikas. The 16S rDNA sequencing revealed a significant reduction in the alpha diversity and altered community structure of the gut microbiota in captive pikas. However, the addition of SW to the diet significantly increased the alpha diversity of gut microbiota and the relative abundance of Akkermansia, Prevotella, and unclassified_f__Lachnospiraceae, along with the complexity of the microbial co-occurrence network structure, which decreased in the guts of captive pikas. Functional profiles showed that SW significantly decreased the relative abundances of energy metabolism, lipid metabolism, and glycan biosynthesis and metabolism, which were enriched in captive pikas. Furthermore, SW decreased deterministic processes of gut microbiota assembly in July and increased them in November. Finally, the genera Prevotella and unclassified_f__Prevotellaceae were positively correlated with BAT mass. Our results highlighted that plant secondary compounds promote WAT browning by modulating the gut microbiota in small mammals.
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Affiliation(s)
- Shien Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
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25
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Guan X, Zhao Z, Jiang J, Fu L, Liu J, Pan Y, Gao S, Wang B, Chen Z, Wang X, Sun H, Jiang B, Dong Y, Zhou Z. Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:545-556. [PMID: 37537784 PMCID: PMC10667648 DOI: 10.1111/1758-2229.13188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.
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Affiliation(s)
- Xiaoyan Guan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Jingwei Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Lei Fu
- Dalian Salt Chemical Group Co., LtdDalianLiaoningPeople's Republic of China
| | - Jiaojiao Liu
- Dalian Salt Chemical Group Co., LtdDalianLiaoningPeople's Republic of China
| | - Yongjia Pan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Shan Gao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Bai Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zhong Chen
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Xuda Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Hongjuan Sun
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Bing Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Ying Dong
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
| | - Zunchun Zhou
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic AnimalsLiaoning Ocean and Fisheries Science Research InstituteDalianLiaoningPeople's Republic of China
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Xu CCY, Lemoine J, Albert A, Whirter ÉM, Barrett RDH. Community assembly of the human piercing microbiome. Proc Biol Sci 2023; 290:20231174. [PMID: 38018103 PMCID: PMC10685111 DOI: 10.1098/rspb.2023.1174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
Predicting how biological communities respond to disturbance requires understanding the forces that govern their assembly. We propose using human skin piercings as a model system for studying community assembly after rapid environmental change. Local skin sterilization provides a 'clean slate' within the novel ecological niche created by the piercing. Stochastic assembly processes can dominate skin microbiomes due to the influence of environmental exposure on local dispersal, but deterministic processes might play a greater role within occluded skin piercings if piercing habitats impose strong selection pressures on colonizing species. Here we explore the human ear-piercing microbiome and demonstrate that community assembly is predominantly stochastic but becomes significantly more deterministic with time, producing increasingly diverse and ecologically complex communities. We also observed changes in two dominant and medically relevant antagonists (Cutibacterium acnes and Staphylococcus epidermidis), consistent with competitive exclusion induced by a transition from sebaceous to moist environments. By exploiting this common yet uniquely human practice, we show that skin piercings are not just culturally significant but also represent ecosystem engineering on the human body. The novel habitats and communities that skin piercings produce may provide general insights into biological responses to environmental disturbances with implications for both ecosystem and human health.
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Affiliation(s)
- Charles C. Y. Xu
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0C4
- Department of Biology, McGill University, Montreal, Quebec, Canada H3A 1B1
| | - Juliette Lemoine
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0C4
- Department of Biology, McGill University, Montreal, Quebec, Canada H3A 1B1
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Avery Albert
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0C4
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada H9X 3V9
- Trottier Space Institute, McGill University, Montreal, Quebec, Canada H3A 2A7
| | | | - Rowan D. H. Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0C4
- Department of Biology, McGill University, Montreal, Quebec, Canada H3A 1B1
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Zhao X, Meng T, Jin S, Ren K, Cai Z, Cai B, Li S. The Salinity Survival Strategy of Chenopodium quinoa: Investigating Microbial Community Shifts and Nitrogen Cycling in Saline Soils. Microorganisms 2023; 11:2829. [PMID: 38137973 PMCID: PMC10745458 DOI: 10.3390/microorganisms11122829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/07/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Quinoa is extensively cultivated for its nutritional value, and its exceptional capacity to endure elevated salt levels presents a promising resolution to the agricultural quandaries posed by salinity stress. However, limited research has been dedicated to elucidating the correlation between alterations in the salinity soil microbial community and nitrogen transformations. To scrutinize the underlying mechanisms behind quinoa's salt tolerance, we assessed the changes in microbial community structure and the abundance of nitrogen transformation genes across three distinct salinity thresholds (1 g·kg-1, 3 g·kg-1, and 6 g·kg-1) at two distinct time points (35 and 70 days). The results showed the positive effect of quinoa on the soil microbial community structure, including changes in key populations and its regulatory role in soil nitrogen cycling under salt stress. Choroflexi, Acidobacteriota, and Myxococcota were inhibited by increased salinity, while the relative abundance of Bacteroidota increased. Proteobacteria and Actinobacteria showed relatively stable abundances across time and salinity levels. Quinoa possesses the ability to synthesize or modify the composition of keystone species or promote the establishment of highly complex microbial networks (modularity index > 0.4) to cope with fluctuations in external salt stress environments. Furthermore, quinoa exhibited nitrogen (N) cycling by downregulating denitrification genes (nirS, nosZ), upregulating nitrification genes (Archaeal amoA (AOA), Bacterial amoA (AOB)), and stabilizing nitrogen fixation genes (nifH) to absorb nitrate-nitrogen (NO3-_N). This study paves the way for future research on regulating quinoa, promoting soil microbial communities, and nitrogen transformation in saline environments.
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Affiliation(s)
- Xuli Zhao
- College of Agricultural Science and Engineering, Hohai University, No. 8 Focheng West Road, Nanjing 211100, China
| | - Tianzhu Meng
- College of Agricultural Science and Engineering, Hohai University, No. 8 Focheng West Road, Nanjing 211100, China
| | - Shenghan Jin
- College of Agricultural Science and Engineering, Hohai University, No. 8 Focheng West Road, Nanjing 211100, China
| | - Kaixing Ren
- College of Agricultural Science and Engineering, Hohai University, No. 8 Focheng West Road, Nanjing 211100, China
| | - Zhe Cai
- College of Agricultural Science and Engineering, Hohai University, No. 8 Focheng West Road, Nanjing 211100, China
| | - Bo Cai
- College of Agricultural Science and Engineering, Hohai University, No. 8 Focheng West Road, Nanjing 211100, China
| | - Saibao Li
- College of Water Resources and Civil Engineering, Tibet Agricultural and Animal Husbandry University, No. 8 Xueyuan Road, Linzhi 860000, China
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Malyutina A, Tang J, Amiryousefi A. Resolving network clusters disparity based on dissimilarity measurements with nonmetric analysis of variance. iScience 2023; 26:108354. [PMID: 38026214 PMCID: PMC10663764 DOI: 10.1016/j.isci.2023.108354] [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: 10/26/2022] [Revised: 06/22/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Classic ANOVA (cA) tests the explanatory power of a partitioning on a set of objects. More fit for clusters proximity analysis, nonparametric ANOVA (npA) extends to a case where instead of the object values themselves, their mutual distances are available. However, extending the cA applicability, the metric conditions in npA are limiting. Based on the central limit theorem (CLT), here we introduce nonmetric ANOVA (nmA) that by relaxing the metric properties between objects, allows an ANOVA-like statistical testing of a network clusters disparity. We present a parametric test statistic which under the null hypothesis of no differences between the competing clusters means, follows an exact F-distribution. We apply our method on three diverse biological examples, discuss its parallel performance, and note the specific use of each method tailored by the inherent data properties. The R code is provided at github.com/AmiryousefiLab/nmANOVA.
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Affiliation(s)
- Alina Malyutina
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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Ma Q, Li Q, Wang J, Parales RE, Li L, Ruan Z. Exposure to three herbicide mixtures influenced maize root-associated microbial community structure, function and the network complexity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122393. [PMID: 37595734 DOI: 10.1016/j.envpol.2023.122393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Herbicide mixtures are a new and effective agricultural strategy for managing suppress weed resistance and have been widely used in controlling weeding growth in maize fields. However, the potential ecotoxicological impact of these mixtures on the microbial community structure and function within various root-associated niches, remains inadequately understood. Here, the effects of nicosulfuron, mesotrione and atrazine on soil enzyme activity and microbial community structure and function were investigated when applied alone and in combination. The findings indicated that herbicide mixtures exhibit a prolonged half-life compared to single herbicides. Ecological niches are the major factor influencing the structure and functions of the microbial community, with the rhizosphere exhibiting a more intensive response to herbicide stress. Herbicides significantly inhibited the activities of soil functional enzymes, including dehydrogenase, urease and sucrose in the short-term. Single herbicide did not drastically influence the alpha or beta diversity of the soil bacterial community, but herbicide mixtures significantly increased the richness of the fungal community. Meanwhile, the key functional microbial populations, such as Pseudomonas and Enterobacteriaceae, were significantly altered by herbicide stress. Both individual and combined use of the three herbicides reduced the complexity and stability of the bacterial network but increased the interspecific cooperations of fungal community in the rhizosphere. Moreover, by quantification of residual herbicide concentrations in the soil, we showed that the degradation period of the herbicide mixture was longer than that of single herbicides. Herbicide mixtures increased the contents of NO3--N and NH4+-N in the soil in the short-term. Overall, our study provided a comprehensive insight into the response of maize root-associated microbial communities to herbicide mixtures and facilitated the assessment of the ecological risks posed by herbicide mixtures to the agricultural environment from an agricultural sustainability perspective.
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Affiliation(s)
- Qingyun Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China; State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Qingqing Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jie Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; College of Life Science, Xinjiang Normal University, Urumqi, 830046, PR China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China
| | - Zhiyong Ruan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
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Guo Y, Zhang D, Qi W. Bacterial diversity of herbal rhizospheric soils in Ordos desert steppes under different degradation gradients. PeerJ 2023; 11:e16289. [PMID: 37927778 PMCID: PMC10625353 DOI: 10.7717/peerj.16289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/22/2023] [Indexed: 11/07/2023] Open
Abstract
Objectives This study explored the effects of different degradation gradients on bacterial diversity in the rhizospheric soils of herb plants. Methods The alpha diversity, species composition and correlations of bacterial communities in the rhizospheric soils of herb plants were studied using metagenomics 16SrDNA gene high-throughput sequencing. Results The diversity of bacterial communities in the rhizospheric soils of herb plants differed during the degradation of desert steppes. An analysis of bacterial community alpha diversity indices showed the bacterial diversity and species evenness of rhizospheric soils were best in moderately degraded desert steppes. Among all samples, a total of 43 phyla, 133 classes, 261 orders, 421 families, 802 genera and 1,129 species were detected. At the phylum level, the predominant bacterial phyla were: Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Bacteroidetes. At the genus level, the predominant bacterial genera were: RB41, Sphingomonas, WD2101_soil_group_unclassified, Pseudomonas and Actinomyces. The relative abundance of unknown genera was very large, which deserves further research. At the phylum and genus levels, the species abundance levels under slight and moderate degradation were significantly higher than those under extreme degradation. Correlation network diagrams showed there were many nodes in both slightly deteriorated and moderately deteriorated soils, and the node proportions were large and mostly positively correlated. These results indicate the bacterial communities in rhizospheric soils under slight or moderate deterioration are relatively stable. The rhizospheric soil microbes of desert steppes can form a stable network structure, allowing them to adequately respond to environmental conditions. Conclusions The bacterial communities in the rhizospheric soils of herb plants differ between different degradation gradients. The species number, abundance and diversity of bacterial communities in rhizospheric soils are not directly correlated with degree of degradation. The abundance, species diversity and species abundance of bacterial communities in the rhizospheric soils of moderately degraded desert steppes are the highest and most stable. The soil bacterial diversity is lowest in severely degraded desert steppes.
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Affiliation(s)
- Yuefeng Guo
- College of Desert Control Science and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, Asia, China
| | - Dan Zhang
- College of Desert Control Science and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, Asia, China
| | - Wei Qi
- Inner Mongolia Autonomous Region Water Conservancy Development Center, Hohot, Inner Mongolia, Asia, China
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Zheng Y, Cao X, Zhou Y, Li Z, Yang Y, Zhao D, Li Y, Xu Z, Zhang CS. Effect of planting salt-tolerant legumes on coastal saline soil nutrient availability and microbial communities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118574. [PMID: 37423189 DOI: 10.1016/j.jenvman.2023.118574] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 07/11/2023]
Abstract
Soil salinization is a serious global environmental problem affecting sustainable development of agriculture. Legumes are excellent candidates for the phytoremediation of saline soils; however, how soil microbes mediate the amelioration of coastal saline ecosystems is unknown. In this study, two salt-tolerant legumes, Glycine soja and Sesbania cannabina were planted in coastal saline soil for three years. Soil nutrient availability and microbiota structure (including bacteria, fungi, and diazotrophs) were compared between the phytoremediated soils and control soil (barren land). Planting legumes reduced soil salinity, and increased total carbon, total nitrogen, and NO3--N contents. Among the soil microbiota, some nitrogen-fixing bacteria (e.g., Azotobacter) were enriched in legumes, which were probably responsible for soil nitrogen accumulation. The complexity of the bacterial, fungal, and diazotrophic networks increased significantly from the control to the phytoremediated soils, suggesting that the soil microbial community formed closer ecological interactions during remediation. Furthermore, the dominant microbial functions were chemoheterotrophy (24.75%) and aerobic chemoheterotrophy (21.97%) involved in the carbon cycle, followed by nitrification (13.68%) and aerobic ammonia oxidation (13.34%) involved in the nitrogen cycle. Overall, our findings suggested that G. soja and S. cannabina legumes were suitable for ameliorating saline soils as they decreased soil salinity and increased soil nutrient content, with microorganisms especially nitrogen-fixing bacteria, playing an important role in this remediation process.
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Affiliation(s)
- Yanfen Zheng
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Xuwen Cao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266200, China
| | - Yanan Zhou
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhe Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yanzhe Yang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Donglin Zhao
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Zongchang Xu
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China.
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China.
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Ozen M, Lopez CF. Data-driven structural analysis of small cell lung cancer transcription factor network suggests potential subtype regulators and transition pathways. NPJ Syst Biol Appl 2023; 9:55. [PMID: 37907529 PMCID: PMC10618210 DOI: 10.1038/s41540-023-00316-2] [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: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive disease and challenging to treat due to its mixture of transcriptional subtypes and subtype transitions. Transcription factor (TF) networks have been the focus of studies to identify SCLC subtype regulators via systems approaches. Yet, their structures, which can provide clues on subtype drivers and transitions, are barely investigated. Here, we analyze the structure of an SCLC TF network by using graph theory concepts and identify its structurally important components responsible for complex signal processing, called hubs. We show that the hubs of the network are regulators of different SCLC subtypes by analyzing first the unbiased network structure and then integrating RNA-seq data as weights assigned to each interaction. Data-driven analysis emphasizes MYC as a hub, consistent with recent reports. Furthermore, we hypothesize that the pathways connecting functionally distinct hubs may control subtype transitions and test this hypothesis via network simulations on a candidate pathway and observe subtype transition. Overall, structural analyses of complex networks can identify their functionally important components and pathways driving the network dynamics. Such analyses can be an initial step for generating hypotheses and can guide the discovery of target pathways whose perturbation may change the network dynamics phenotypically.
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Affiliation(s)
- Mustafa Ozen
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling Group, SI3, Altos Labs, Redwood City, CA, USA
| | - Carlos F Lopez
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Multiscale Modeling Group, SI3, Altos Labs, Redwood City, CA, USA.
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Liu Q, Li G, Baladandayuthapani V. Pan-Cancer Drug Response Prediction Using Integrative Principal Component Regression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560366. [PMID: 37873111 PMCID: PMC10592913 DOI: 10.1101/2023.10.03.560366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The pursuit of precision oncology heavily relies on large-scale genomic and pharmacological data garnered from preclinical cancer model systems such as cell lines. While cell lines are instrumental in understanding the interplay between genomic programs and drug response, it well-established that they are not fully representative of patient tumors. Development of integrative methods that can systematically assess the commonalities between patient tumors and cell-lines can help bridge this gap. To this end, we introduce the Integrative Principal Component Regression (iPCR) model which uncovers both joint and model-specific structured variations in the genomic data of cell lines and patient tumors through matrix decompositions. The extracted joint variation is then used to predict patient drug responses based on the pharmacological data from preclinical models. Moreover, the interpretability of our model allows for the identification of key driver genes and pathways associated with the treatment-specific response in patients across multiple cancers. We demonstrate that the outputs of the iPCR model can assist in inferring both model-specific and shared co-expression networks between cell lines and patients. We show that iPCR performs favorably compared to competing approaches in predicting patient drug responses, in both simulation studies and real-world applications, in addition to identifying key genomic drivers of cancer drug responses.
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Wang X, Zhao Z, Jiang J, Mi R, Guan X, Dong Y, Li S, Chen Z, Gao S, Wang B, Xiao Y, Pan Y, Zhou Z. Temporal stability and assembly mechanisms of gut microbiota in sea cucumbers response to nanoplastics treatment. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115407. [PMID: 37639828 DOI: 10.1016/j.ecoenv.2023.115407] [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: 06/22/2023] [Revised: 08/13/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Aquaculture provides essential food for humans, and the health of farmed species is particularly important for the aquaculture industry. Aquaculture environment could be a sink of plastic debris (PDs) due to the enclosed character and heavy use of plastics. Gut microbiota of aquaculture species could respond to the exogenous pollutants and regulate the health of hosts. Here, variations in gut microbiota of Apostichopus japonicus induced by the ingested nanoplastics (NPs) were investigated by a lab experiment. We selected a NPs concentration gradient of 100 mg/kg and 500 mg/kg to simulate microplastic pollution to A. japonicus, and the significant differences in gut microbiota composition after 21 days of NP exposure were evaluated. According to the high-throughput sequencing from time series samples, a decrease of diversity in gut microbiota of A. japonicus with dietary NPs was observed. In addition, the gut microbiota compositions of sea cucumbers with and without NPs exposure were also distinct, expressing as enrichment of Bacteroidota while reducement of Proteobacteria under NPs stresses. Combined the results of network analysis, the less complexity and stability of gut microbiota in sea cucumbers with dietary NPs were proved. Based on the neutral community model, the ingested NPs elevated the contribution of stochastic processes for the gut microbiota assembly in sea cucumbers. Our study showed that substantial variations in gut microbiota of A. japonicus under NPs stresses, and also explored the underlying mechanisms regulating these changes. This research would offer new meaningful insights into the toxicity of NPs on sea cucumbers, contributing a solid fundament to improve the health of sea cucumbers under NPs stresses.
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Affiliation(s)
- Xuda Wang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zelong Zhao
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Rui Mi
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Ying Dong
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shilei Li
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zhong Chen
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shan Gao
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bai Wang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yao Xiao
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yongjia Pan
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
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Li Y, Zhang SW, Xie MY, Zhang T. PhenoDriver: interpretable framework for studying personalized phenotype-associated driver genes in breast cancer. Brief Bioinform 2023; 24:bbad291. [PMID: 37738403 DOI: 10.1093/bib/bbad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 09/24/2023] Open
Abstract
Identifying personalized cancer driver genes and further revealing their oncogenic mechanisms is critical for understanding the mechanisms of cell transformation and aiding clinical diagnosis. Almost all existing methods primarily focus on identifying driver genes at the cohort or individual level but fail to further uncover their underlying oncogenic mechanisms. To fill this gap, we present an interpretable framework, PhenoDriver, to identify personalized cancer driver genes, elucidate their roles in cancer development and uncover the association between driver genes and clinical phenotypic alterations. By analyzing 988 breast cancer patients, we demonstrate the outstanding performance of PhenoDriver in identifying breast cancer driver genes at the cohort level compared to other state-of-the-art methods. Otherwise, our PhenoDriver can also effectively identify driver genes with both recurrent and rare mutations in individual patients. We further explore and reveal the oncogenic mechanisms of some known and unknown breast cancer driver genes (e.g. TP53, MAP3K1, HTT, etc.) identified by PhenoDriver, and construct their subnetworks for regulating clinical abnormal phenotypes. Notably, most of our findings are consistent with existing biological knowledge. Based on the personalized driver profiles, we discover two existing and one unreported breast cancer subtypes and uncover their molecular mechanisms. These results intensify our understanding for breast cancer mechanisms, guide therapeutic decisions and assist in the development of targeted anticancer therapies.
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Affiliation(s)
- Yan Li
- School of Automation from Northwestern Polytechnical University, China
| | - Shao-Wu Zhang
- School of Automation from Northwestern Polytechnical University, China
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, China
| | - Ming-Yu Xie
- School of Automation from Northwestern Polytechnical University, China
| | - Tong Zhang
- School of Automation from Northwestern Polytechnical University, China
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36
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Li W, Xiao Y. Microplastics increase soil microbial network complexity and trigger diversity-driven community assembly. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122095. [PMID: 37385357 DOI: 10.1016/j.envpol.2023.122095] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
The widespread existence of microplastics (MPs) in soil has been extensively demonstrated, and their presence would ineluctably change soil physicochemical properties and microbial community composition. However, there is limited understanding of how MPs affect soil microbial assembly. In this study, three different polymer types of MPs, i.e., high-density polyethylene (HDPE), polystyrene (PS), and polylactic acid (PLA), with the same particle size (100 μm) and dose (2%) were applied under the planted and unplanted condition, Pennisetum alopecuroides was chosen as a model species. Plant growth parameters, soil physicochemical properties, and microbial communities (including bacteria and eukaryotes) were determined. The assembly and the co-occurrence network of microbial communities were analyzed. Results revealed that the effect of MPs on soil physicochemical properties was type-dependent and could influenced by the presence of P . alopecuroides. MPs could enrich bacterial genera related to nitrogen cycle and some pathogens of eukaryotes. The presence of MPs changed bacterial and eukaryotic community assembly, in which diversity drove the deterministic/stochastic assembly processes. MPs addition increased the complexity of bacterial network, while had a minor effect on eukaryotic network. The inhibition of MPs on P . alopecuroides growth decayed over time, HDPE MPs was more harmful to P . alopecuroides growth than PS and PLA MPs. Our findings enormously improved our comprehensions of MPs-induced ecological impacts and interactions of soil bacterial and eukaryotic communities .
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Affiliation(s)
- Wanlin Li
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yan Xiao
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China.
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37
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Liu W, Cui X, Wang X, Shen C, Ji L, Zhang M, Wong MH, Zhang J, Shan S. Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere. mSystems 2023; 8:e0019823. [PMID: 37382454 PMCID: PMC10469604 DOI: 10.1128/msystems.00198-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/18/2023] [Indexed: 06/30/2023] Open
Abstract
Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.
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Affiliation(s)
- Wenbo Liu
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xin Cui
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xinhai Wang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing, China
| | - Cheng Shen
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Lingfei Ji
- Department of Biology, University of York, Wentworth Way, York, United Kingdom
| | - Min Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Ming Hung Wong
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
- Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
| | - Jin Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
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Barker-Clarke R, Weaver DT, Scott JG. Graph 'texture' features as novel metrics that can summarize complex biological graphs. Phys Med Biol 2023; 68:174001. [PMID: 37385267 PMCID: PMC10598684 DOI: 10.1088/1361-6560/ace305] [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: 11/29/2022] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/01/2023]
Abstract
Objective.Image texture features, such as those derived by Haralicket al, are a powerful metric for image classification and are used across fields including cancer research. Our aim is to demonstrate how analogous texture features can be derived for graphs and networks. We also aim to illustrate how these new metrics summarize graphs, may aid comparative graph studies, may help classify biological graphs, and might assist in detecting dysregulation in cancer.Approach.We generate the first analogies of image texture for graphs and networks. Co-occurrence matrices for graphs are generated by summing over all pairs of neighboring nodes in the graph. We generate metrics for fitness landscapes, gene co-expression and regulatory networks, and protein interaction networks. To assess metric sensitivity we varied discretization parameters and noise. To examine these metrics in the cancer context we compare metrics for both simulated and publicly available experimental gene expression and build random forest classifiers for cancer cell lineage.Main results.Our novel graph 'texture' features are shown to be informative of graph structure and node label distributions. The metrics are sensitive to discretization parameters and noise in node labels. We demonstrate that graph texture features vary across different biological graph topologies and node labelings. We show how our texture metrics can be used to classify cell line expression by lineage, demonstrating classifiers with 82% and 89% accuracy.Significance.New metrics provide opportunities for better comparative analyzes and new models for classification. Our texture features are novel second-order graph features for networks or graphs with ordered node labels. In the complex cancer informatics setting, evolutionary analyses and drug response prediction are two examples where new network science approaches like this may prove fruitful.
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Affiliation(s)
- R Barker-Clarke
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland, OH 44195, United States of America
| | - D T Weaver
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland, OH 44195, United States of America
- School of Medicine, Case Western Reserve University, Cleveland, OH 44195, United States of America
| | - J G Scott
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland, OH 44195, United States of America
- School of Medicine, Case Western Reserve University, Cleveland, OH 44195, United States of America
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Chen Q, Li D, Luo N, Yang J. Differences in Juniperus przewalskii Rhizosphere Microbiomes across Age Classes: Community Diversity and Assembly. Microorganisms 2023; 11:2094. [PMID: 37630654 PMCID: PMC10458523 DOI: 10.3390/microorganisms11082094] [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: 07/27/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Evidence shows that biotic and abiotic factors have apparent diversity at different forest ages, leading to changes in rhizosphere microbiomes. However, the difference in diversity, co-occurrence pattern, and assembly of the rhizosphere microbial community among the different forest ages is still unclear. A total of 24 Juniperus przewalskii rhizosphere soil samples were selected from four representative age classes, using diameter at breast height (DBH) as a proxy for tree age (age class I: 5 < DBH ≤ 12.5 cm, age class II: 12.5 < DBH ≤ 22.5 cm, age class III: 22.5 < DBH ≤ 32.5 cm, and age class IV: DBH > 32.5 cm), and analyzed the structural characteristics of the soil microbial community by high-throughput amplicon sequencing. With the increase in age class, the microbial community α-diversity and β-diversity had an increased trend. The bacterial Shannon index in class II and class III were markedly higher than in class I. From class I to class IV, the relative abundances of dominant phyla such as Actinobacteria and Ascomycota decreased, and the relative abundances of Proteobacteria and Basidiomycota increased in contrast. The complexity and association stability of the bacteria and fungi community network structure increase with forest age. Stochastic processes mediated the assembly of soil bacterial communities, while deterministic processes played a more significant role in the assembly of fungal communities. In addition, the relative importance of deterministic components in the microbial community increased significantly with age class. Random forests suggested that soil pH, plant Shannon-Wiener index (H), and Pielou's evenness index (J) were the most important driving factors of bacterial and fungal community assembly. Overall, these results provide information useful for understanding the generation and maintenance mechanisms of rhizosphere microbial communities across age classes.
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Affiliation(s)
| | - Dengwu Li
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (Q.C.); (N.L.); (J.Y.)
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40
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Lv J, Liu G, Ju Y, Sun B, Huang H, Sun Y. Integrating multi-source drug information to cluster drug-drug interaction network. Comput Biol Med 2023; 162:107088. [PMID: 37263154 DOI: 10.1016/j.compbiomed.2023.107088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/10/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023]
Abstract
Characterizing drug-drug interactions is important to improve efficacy and/or slow down the evolution of antimicrobial resistance. Experimental methods are both time-consuming and laborious for characterizing drug-drug interactions. In recent years, many computational methods have been proposed to explore drug-drug interactions. However, these methods failed to effectively integrate multi-source drug information. In this study, we propose a similarity matrix fusion (SMF) method to integrate four drug information (i.e., structural similarity, pharmaceutical similarity, phenotypic similarity and therapeutic similarity). SMF combined with t-distributed stochastic neighbor embedding (t-SNE) and hierarchical clustering algorithm can effectively identify drug groups and group-group interactions are almost monochromatic (purely synergetic or purely antagonistic). To evaluate clustering quality (i.e., monochromaticity), two measures (edge purity and edge normalized mutual information) are proposed, and SMF showed the best performance. In addition, clustered drug-drug interaction network can also be used to predict new drug-drug interactions (accuracy = 0.741). Overall, SMF provides a comprehensive view to understand drug groups and group-group interactions.
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Affiliation(s)
- Ji Lv
- College of Computer Science and Technology, Jilin University, Changchun, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Guixia Liu
- College of Computer Science and Technology, Jilin University, Changchun, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China.
| | - Yuan Ju
- Sichuan University Library, Sichuan University, Chengdu, China
| | - Binwen Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Houhou Huang
- College of Chemistry, Jilin University, Changchun, China
| | - Ying Sun
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
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41
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Wei X, Fu T, He G, Zhong Z, Yang M, Lou F, He T. Types of vegetables shape composition, diversity, and co-occurrence networks of soil bacteria and fungi in karst areas of southwest China. BMC Microbiol 2023; 23:194. [PMID: 37468849 PMCID: PMC10354930 DOI: 10.1186/s12866-023-02929-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Microorganisms are of significant importance in soil. Yet their association with specific vegetable types remains poorly comprehended. This study investigates the composition of bacterial and fungal communities in soil by employing high-throughput sequencing of 16 S rRNA genes and ITS rRNA genes while considering the cultivation of diverse vegetable varieties. RESULTS The findings indicate that the presence of cultivated vegetables influenced the bacterial and fungal communities leading to discernible alterations when compared to uncultivated soil. In particular, the soil of leafy vegetables (such as cabbage and kale) exhibited higher bacterial α-diversity than melon and fruit vegetable (such as cucumber and tomato), while fungal α-diversity showed an inverse pattern. The prevailing bacterial phyla in both leafy vegetable and melon and fruit vegetable soils were Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. In leafy vegetable soil, dominant fungal phyla included Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota whereas in melon and fruit vegetable soil. Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota held prominence. Notably, the relative abundance of Ascomycota was lower in leafy vegetable soil compared to melon and fruit vegetable soil. Moreover, leafy vegetable soil exhibited a more complex and stable co-occurrence network in comparison to melon and fruit vegetable soil. CONCLUSION The findings enhance our understanding of how cultivated soil bacteria and fungi respond to human disturbance, thereby providing a valuable theoretical basis for soil health in degraded karst areas of southwest China.
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Affiliation(s)
- Xiaoliao Wei
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Tianling Fu
- Institute of New Rural Development, Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, PR China
| | - Guandi He
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Zhuoyan Zhong
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Fei Lou
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Tengbing He
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China.
- Institute of New Rural Development, Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, PR China.
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42
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Nair NU, Greninger P, Zhang X, Friedman AA, Amzallag A, Cortez E, Sahu AD, Lee JS, Dastur A, Egan RK, Murchie E, Ceribelli M, Crowther GS, Beck E, McClanaghan J, Klump-Thomas C, Boisvert JL, Damon LJ, Wilson KM, Ho J, Tam A, McKnight C, Michael S, Itkin Z, Garnett MJ, Engelman JA, Haber DA, Thomas CJ, Ruppin E, Benes CH. A landscape of response to drug combinations in non-small cell lung cancer. Nat Commun 2023; 14:3830. [PMID: 37380628 PMCID: PMC10307832 DOI: 10.1038/s41467-023-39528-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
Combination of anti-cancer drugs is broadly seen as way to overcome the often-limited efficacy of single agents. The design and testing of combinations are however very challenging. Here we present a uniquely large dataset screening over 5000 targeted agent combinations across 81 non-small cell lung cancer cell lines. Our analysis reveals a profound heterogeneity of response across the tumor models. Notably, combinations very rarely result in a strong gain in efficacy over the range of response observable with single agents. Importantly, gain of activity over single agents is more often seen when co-targeting functionally proximal genes, offering a strategy for designing more efficient combinations. Because combinatorial effect is strongly context specific, tumor specificity should be achievable. The resource provided, together with an additional validation screen sheds light on major challenges and opportunities in building efficacious combinations against cancer and provides an opportunity for training computational models for synergy prediction.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xiaohu Zhang
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Adam A Friedman
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eliane Cortez
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Avinash Das Sahu
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Joo Sang Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Anahita Dastur
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Regina K Egan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ellen Murchie
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Erin Beck
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | | | | | | | - Leah J Damon
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jeffrey Ho
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela Tam
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sam Michael
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Zina Itkin
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Mathew J Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | | | - Daniel A Haber
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD, 20850, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Ji C, Huang J, Zhang X, Yang G, Xing S, Fu W, Hao Z, Chen B, Zhang X. Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163244. [PMID: 37004770 DOI: 10.1016/j.scitotenv.2023.163244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.
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Affiliation(s)
- Chuning Ji
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Jiu Huang
- School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Xuemeng Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; RDFZ Chaoyang School, Beijing 100028, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Shi A, Hu Y, Zhang X, Zhou D, Xu J, Rensing C, Zhang L, Xing S, Ni W, Yang W. Biochar loaded with bacteria enhanced Cd/Zn phytoextraction by facilitating plant growth and shaping rhizospheric microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121559. [PMID: 37023890 DOI: 10.1016/j.envpol.2023.121559] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/22/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Biochar and metal-tolerant bacteria have been widely used in the remediation of heavy metal contaminated soil. However, the synergistic effect of biochar-functional microbes on phytoextraction by hyperaccumulators remains unclear. In this study, the heavy metal-tolerant strain Burkholderia contaminans ZCC was selected and loaded on biochar to produce biochar-resistant bacterial material (BM), and the effects of BM on Cd/Zn phytoextraction by Sedum alfredii Hance and rhizospheric microbial community were explored. The results showed that, BM application significantly enhanced the Cd and Zn accumulation of S. alfredii by 230.13% and 381.27%, respectively. Meanwhile, BM alleviated metal toxicity of S. alfredii by reducing oxidative damage and increasing chlorophyll and antioxidant enzyme activity. High-throughput sequencing revealed that BM significantly improved soil bacterial and fungal diversity, and increased the abundance of genera with plant growth promoting and metal solubilizing functions such as Gemmatimonas, Dyella and Pseudarthrobacter. Co-occurrence network analysis showed that BM significantly increased the complexity of the rhizospheric bacterial and fungal network. Structural equation model analysis revealed that soil chemistry property, enzyme activity and microbial diversity contributed directly or indirectly to Cd and Zn extraction by S. alfredii. Overall, our results suggested that biochar- B. contaminans ZCC was able to enhance the growth and Cd/Zn accumulation by S. alfredii. This study enhanced our understanding on the hyperaccumulator-biochar-functional microbe interactions, and provided a feasible strategy for promoting the phytoextraction efficiency of heavy metal contaminated soils.
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Affiliation(s)
- An Shi
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying Hu
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiao Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Zhou
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Junlong Xu
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liming Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shihe Xing
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wuzhong Ni
- College of Environment and Resources, Zhejiang University, Hangzhou, 310058, China
| | - Wenhao Yang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Ozen M, Lopez CF. Data-driven structural analysis of Small Cell Lung Cancer transcription factor network suggests potential subtype regulators and transition pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535226. [PMID: 37066351 PMCID: PMC10104011 DOI: 10.1101/2023.04.01.535226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Small Cell Lung Cancer (SCLC) is an aggressive disease and challenging to treat due to its mixture of transcriptional subtypes and subtype transitions. Transcription factor (TF) networks have been the focus of studies to identify SCLC subtype regulators via systems approaches. Yet, their structures, which can provide clues on subtype drivers and transitions, are barely investigated. Here, we analyze the structure of an SCLC TF network by using graph theory concepts and identify its structurally important components responsible for complex signal processing, called hubs. We show that the hubs of the network are regulators of different SCLC subtypes by analyzing first the unbiased network structure and then integrating RNA-seq data as weights assigned to each interaction. Data-driven analysis emphasizes MYC as a hub, consistent with recent reports. Furthermore, we hypothesize that the pathways connecting functionally distinct hubs may control subtype transitions and test this hypothesis via network simulations on a candidate pathway and observe subtype transition. Overall, structural analyses of complex networks can identify their functionally important components and pathways driving the network dynamics. Such analyses can be an initial step for generating hypotheses and can guide the discovery of target pathways whose perturbation may change the network dynamics phenotypically.
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Affiliation(s)
- Mustafa Ozen
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
- Currently at: Computational Innovation Hub, Multiscale Modeling Group, Altos Labs, Redwood City, CA 94065, USA
| | - Carlos F. Lopez
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
- Currently at: Computational Innovation Hub, Multiscale Modeling Group, Altos Labs, Redwood City, CA 94065, USA
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Zhang M, Shi C, Li X, Wang K, Qiu Z, Shi F. Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion. Front Microbiol 2023; 14:1114388. [PMID: 37056750 PMCID: PMC10089265 DOI: 10.3389/fmicb.2023.1114388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
IntroductionPlant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood.MethodsHere, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies.ResultsAs a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils.DiscussionOur study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.
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Affiliation(s)
- Mei Zhang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Cong Shi
- School of Environmental Science and Engineering, Tiangong University, Tianjin, China
| | - Xueying Li
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Kefan Wang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhenlu Qiu
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Fuchen Shi
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
- *Correspondence: Fuchen Shi,
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Liu L, Wang N, Liu M, Guo Z, Shi S. Assembly processes underlying bacterial community differentiation among geographically close mangrove forests. MLIFE 2023; 2:73-88. [PMID: 38818341 PMCID: PMC10989747 DOI: 10.1002/mlf2.12060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/01/2023] [Accepted: 02/14/2023] [Indexed: 06/01/2024]
Abstract
Bacterial communities play pivotal roles in nutrient cycling in mangrove forests. The assembly of mangrove microbial communities has been found to be influenced by complex factors, such as geographic distance, physicochemical conditions, and plant identity, but the relative importance of these factors and how these factors shape the assembling process remain elusive. We analyzed the bacterial communities sampled from three mangrove species (Aegiceras corniculatum, Bruguiera sexangula, and Kandelia obovata) at three locations along the estuarine Dongzhai Harbor in Hainan, China. We revealed larger differences in rhizosphere bacterial communities among geographical locations than among plant species, indicated by differences in diversity, composition, and interaction networks. We found that dispersal limitation and homogeneous selection have substantial contributions to the assembly of mangrove rhizosphere bacterial communities in all three locations. Following the phylogenetic-bin-based null model analysis (iCAMP) framework, we also found dispersal limitation and homogeneous selection showing dominance in some bins. The greater differences among geographic locations may be mainly attributed to the larger proportions of dispersal limitation even at such a short geographic distance. We also found that beta diversity was positively correlated with environmental distances, implying that the more similar environmental conditions (such as rich carbon and nitrogen contents) among plant species may have shaped similar bacterial communities. We concluded that the geographic distances, which are associated with dispersal limitation, played a key role in assembling mangrove rhizosphere bacterial communities, while physicochemical conditions and plant identity contributed less.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Nan Wang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Min Liu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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Tang F, Li Q, Yue J, Ge F, Li F, Liu Y, Zhang D, Tian J. Penicillium oxalicum augments soil lead immobilization by affecting indigenous microbial community structure and inorganic phosphate solubilization potential during microbial-induced phosphate precipitation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 319:120953. [PMID: 36584858 DOI: 10.1016/j.envpol.2022.120953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Phosphate-solubilizing microorganisms (PSMs) are critically important for increasing soil phosphate (P) and decreasing lead (Pb) bioavailability during microbial-induced phosphate precipitation (MIPP). However, their relative contributions to the indigenous soil microbial communities and P-cycling genes during the MIPP process remain unclear. In this study, inoculation of the PSM P. oxalicum in hydroxyapatite-cultured and Pb-contaminated soil increased soil phosphatase activities, available P (AP) concentrations and reduced available Pb levels. Metagenomics revealed a 3.9-44.0% increase in the abundance of P-cycling genes by P. oxalicum inoculation. No P-cycling genes were assigned to Penicillium. While P. oxalicum increased the complexity of microbial community co-occurrence networks, and improved the directly interrelationships between Penicillium and genera containing P-cycling gene. These results suggesting that P. oxalicum obviously positively affected the regulation of indigenous P-cycling functional communities during the MIPP process. Inorganic P solubilization genes (gcd, ppa, and ppx) have been shown to affect soil AP, suggesting that inorganic P solubilization is the major driver of Pb immobilization improvement following P. oxalicum inoculation. These results enhance our understanding of the significant ecological role of PSMs in governing soil P-cycling and alleviating Pb2+ biotoxicity during the MIPP process.
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Affiliation(s)
- Fei Tang
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Qiqiang Li
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Jiaru Yue
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Fei Ge
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Feng Li
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Yun Liu
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Jiang Tian
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, PR China.
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Scott-Fordsmand JJ, Amorim MJB. Using Machine Learning to make nanomaterials sustainable. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160303. [PMID: 36410486 DOI: 10.1016/j.scitotenv.2022.160303] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/06/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Sustainable development is a key challenge for contemporary human societies; failure to achieve sustainability could threaten human survival. In this review article, we illustrate how Machine Learning (ML) could support more sustainable development, covering the basics of data gathering through each step of the Environmental Risk Assessment (ERA). The literature provides several examples showing how ML can be employed in most steps of a typical ERA.A key observation is that there are currently no clear guidance for using such autonomous technologies in ERAs or which standards/checks are required. Steering thus seems to be the most important task for supporting the use of ML in the ERA of nano- and smart-materials. Resources should be devoted to developing a strategy for implementing ML in ERA with a strong emphasis on data foundations, methodologies, and the related sensitivities/uncertainties. We should recognise historical errors and biases (e.g., in data) to avoid embedding them during ML programming.
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Affiliation(s)
| | - Mónica J B Amorim
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal.
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Luo J, Li Y, Cao H, Zhu Y, Liu X, Li H, Liao X. Variations of microbiota in three types of typical military contaminated sites: Diversities, structures, influence factors, and co-occurrence patterns. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130290. [PMID: 36335906 DOI: 10.1016/j.jhazmat.2022.130290] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/15/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Contamination with energetic compounds (ECs) is common in military sites and poses a great risk to the environment and human health. However, its effects on the soil bacterial communities remain unclear. This study assessed the variations of bacterial communities, co-occurrence patterns, and their influence factors in three types of typical military-contaminated sites (artillery range, military-industrial site, and ammunition destruction site). The results showed that the most polluted sites were ammunition destruction sites, followed by military-industrial sites, whereas pollution in the artillery ranges was minimal. The average concentrations of ECs including 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in the study sites ranged 120-1.67 × 105, 20-7.20 × 104, and 180-2.38 × 105 μg/kg, respectively. Bacterial diversity and community structure in military-industrial and ammunition destruction sites were significantly changed, but not in artillery ranges. TNT, pH, and soil moisture are the critical factors affecting bacterial communities in contaminated military sites. Co-occurrence network analysis indicated that the pressure of ECs affected bacterial interactions and microbiota function. Our findings provide new insights into the variations in bacterial communities in EC-contaminated military sites and references for the bioremediation of ECs.
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Affiliation(s)
- Junpeng Luo
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; Beijing Key Laboratory of Environmental Damage Assessment and Remediation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - You Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; Beijing Key Laboratory of Environmental Damage Assessment and Remediation, Beijing 100101, China.
| | - Hongying Cao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; Beijing Key Laboratory of Environmental Damage Assessment and Remediation, Beijing 100101, China
| | - Yongbing Zhu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Xiaodong Liu
- Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Haonan Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; Beijing Key Laboratory of Environmental Damage Assessment and Remediation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyong Liao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; Beijing Key Laboratory of Environmental Damage Assessment and Remediation, Beijing 100101, China.
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