1
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Yang X, Li Q, Lu Y, Zhang L, Bian X. Insight into the short-term effects of TiO 2 nanoparticles on the cultivation of medicinal plants: Comprehensive analysis of Panax ginseng physiological indicators, soil physicochemical properties and microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175581. [PMID: 39153613 DOI: 10.1016/j.scitotenv.2024.175581] [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: 04/26/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
To meet societal needs, a large number of medicinal plants are cultivated artificially. However, issues such as diseases and continuous cropping obstacles (CCO) have severely impacted their quality and yield. Exploring and innovating the cultivation technology for medicinal plants is essential to meet their high demand and ensure sustainable development. The role of titanium dioxide nanoparticles (nano-TiO2) in medicinal plant cultivation remains unclear. To advance the application of nanotechnology in this field, a comprehensive exploration of its potential benefits is necessary. In this study, nano-TiO2 was applied to ginseng (Panax ginseng C.A. Meyer) to acquire a holistic comprehension of its impact on ginseng growth, rhizosphere, and ginseng-used soil. Our findings reveal that nano-TiO2 significantly enhances ginseng root activity and has notable effects on antioxidant enzyme systems. The two concentrations of nano-TiO2 markedly influenced the structure and composition of microbial communities in the rhizosphere and ginseng-used soil, including key microorganisms such as Chloroflexi and Acidobacteriota, which are closely involved in soil function. Furthermore, nano-TiO2 altered the competitive and cooperative relationships within microbial networks. Nano-TiO2 application significantly increased soil organic matter (SOM) content in rhizosphere and ginseng-used soils and affected the activities of several important soil enzymes. Environmental factors, such as EC, pH, and soil nutrients, were found to be the main factors influencing the microbial community. In conclusion, our findings illuminate the complex effects of nano-TiO2 on the "plant-microbial-soil" system in the context of ginseng cultivation. This work offers novel strategies for optimizing medicinal plant growth and development, as well as improving cultivated soil by using nanomaterials.
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Affiliation(s)
- Xiaohang Yang
- College of Pharmacy, Jilin Medical University, Jilin 132013, Jilin, China
| | - Qiong Li
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, Jilin, China
| | - Yi Lu
- Wuhan University of Technology, The State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan 430070, Hubei, China
| | - Lianxue Zhang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Xingbo Bian
- College of Pharmacy, Jilin Medical University, Jilin 132013, Jilin, China.
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2
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Chen H, Lei L, Li Z, Zhou H, Cheng H, Chen Z, Wang Y, Wang Y. Redundancy and resilience of microbial community under aniline stress during wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175822. [PMID: 39197768 DOI: 10.1016/j.scitotenv.2024.175822] [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: 04/21/2024] [Revised: 08/15/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Aniline is one of the most toxic and widespread organic pollutants. Although biological treatment is cost-effective and generates minimal secondary pollution, microbial communities are significantly affected by high aniline concentrations, which result in low degradation efficiency. However, a comprehensive understanding of the microbial community response to aniline stress is lacking. Here, we performed a cyclic experiment with aniline concentrations (200, 600, 1200, 600, and 200 mg/L) to investigate the ability of microbial communities to recover their performance after exposure to high aniline concentrations. At aniline concentrations up to 600 mg/L, the bioreactor exhibited high aniline removal efficiency (almost 100 %). Comamonas, Zoogloea, and Delftia played crucial roles in removing aniline and microbial beta diversity changed. Additionally, alpha diversity and network complexity decreased with increasing aniline concentration, but these metrics recovered to their original levels when the aniline concentration was returned to 200 mg/L. Homogeneous and heterogeneous selection dominated microbial community assembly. Therefore, according to the observed variations in community structure and the recovery of keystones after aniline stress, microbial community redundancy and resilience are pivotal for ensuring system stability. Overall, this study provides valuable insights into the redundancy and resilience of microbial communities under aniline stress and establishes a scientific basis for managing and evaluating wastewater treatment plants.
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Affiliation(s)
- Hui Chen
- Institute of Zhejiang University - Quzhou, Quzhou 32400, China; Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lecheng Lei
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Yangyang Wang
- National Demonstration Center for Environmental and Planning, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China.
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3
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Cui S, Zhou L, Fang Q, Xiao H, Jin D, Liu Y. Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175334. [PMID: 39117232 DOI: 10.1016/j.scitotenv.2024.175334] [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: 06/01/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
Phyllosphere microbes play a crucial role in plant health and productivity. However, the influence of abiotic and biotic factors on these communities is poorly understood. Here, we used amplicon sequencing to investigate the microbiome variations across eight grape cultivars and three distinct leaf ages. The diversity and richness of phyllosphere microbiomes were significantly affected by cultivars and leaf age. Young leaves of most grape cultivars had a higher diversity. Beta-diversity analyses revealed notable differences in microbial communities across leaf ages, with bacterial communities varying substantially between cultivars. The main bacterial genera included Staphylococcus, Exiguobacterium, Acinetobacter, Enterococcus, and Erwinia; the principal fungal genera were Cladosporium, Moesziomyces, Alternaria, Didymella, and Coprinellus across all samples. LEfSe analysis revealed significant differences in bacterial and fungal biomarkers at different leaf ages, with no biomarkers identified among different cultivars. Fungal biomarkers were more abundant than bacterial at three leaf ages, and older leaves had more fungal biomarkers. Notably, beneficial microbial taxa with biocontrol potential were present on the phyllosphere at 45 d, whereas certain fungal groups associated with increased disease risk were first detected at 100 d. The bacterial network was more complex than the fungal network, and young leaves had a more complex network in most cultivars. Our study elucidated the dynamics of early grape phyllosphere microbes, providing valuable insights for early detection and prediction of grape diseases and a foundation for leveraging the grape leaf microbiome for agricultural purposes.
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Affiliation(s)
- Shaowei Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Lianzhu Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiandong Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haijun Xiao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Yongqiang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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4
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Xin Y, Gao Q, Chen X, Sun S, Liu J, Gao H, Zhou J, Xia X. High biological N fixation potential dominated by heterotrophic diazotrophs in alpine permafrost rivers on the Qinghai‒Tibet Plateau. WATER RESEARCH 2024; 264:122239. [PMID: 39137482 DOI: 10.1016/j.watres.2024.122239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 07/02/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
Biological nitrogen (N) fixation is a pivotal N source in N-deficient ecosystems. The Qinghai‒Tibet Plateau (QTP) region, which is assumed to be N limited and suboxic, is an ideal habitat for diazotrophs. However, the diazotrophic communities and associated N fixation rates in these high-altitude alpine permafrost QTP rivers remain largely unknown. Herein, we examined diazotrophic communities in the sediment and biofilm of QTP rivers via the nitrogenase (nifH) gene sequencing and assessed their N fixing activities via a 15N isotope incubation assay. Strikingly, anaerobic heterotrophic diazotrophs, such as sulfate- and iron-reducing bacteria, had emerged as dominant N fixers. Remarkably, the nifH gene abundance and N fixation rates increased with altitude, and the average nifH gene abundance (2.57 ± 2.60 × 108 copies g-1) and N fixation rate (2.29 ± 3.36 nmol N g-1d-1) surpassed that documented in most aquatic environments (nifH gene abundance: 1.31 × 105 ∼ 2.57 × 108 copies g-1, nitrogen fixation rates: 2.34 × 10-4 ∼ 4.11 nmol N g-1d-1). Such distinctive heterotrophic diazotrophic communities and high N fixation potential in QTP rivers were associated with low-nitrogen, abundant organic carbon and unique C:N:P stoichiometries. Additionally, the significant presence of psychrophilic bacteria within the diazotrophic communities, along with the enhanced stability and complexity of the diazotrophic networks at higher altitudes, clearly demonstrate the adaptability of diazotrophic communities to extreme cold and high-altitude conditions in QTP rivers. We further determined that altitude, coupled with organic carbon and phosphorus, was the predominant driver shaping diazotrophic communities and their N-fixing activities. Overall, our study reveals high N fixation potential in N-deficient QTP rivers, which provides novel insights into nitrogen dynamics in alpine permafrost rivers.
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Affiliation(s)
- Yuan Xin
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qun Gao
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Xin Chen
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Siyue Sun
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jiao Liu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Hui Gao
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA; School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA; School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA; School of Computer Science, University of Oklahoma, Norman, OK, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xinghui Xia
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
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5
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Malla MA, Ansari FA, Bux F, Kumari S. Re-vitalizing wastewater: Nutrient recovery and carbon capture through microbe-algae synergy using omics-biology. ENVIRONMENTAL RESEARCH 2024; 259:119439. [PMID: 38901811 DOI: 10.1016/j.envres.2024.119439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/23/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Increasing amounts of wastewater is the most pervasive and challenging environmental problem globally. Conventional treatment methods are costly and entail huge energy, carbon consumption and greenhouse gas emissions. Owing to their unique ability of carbon capturing and resource recovery, microalgae-microbiome based treatment is a potential approach and is widely used for carbon-neutral wastewater treatment. Microalgae-bacteria synergy (i.e., the functionally beneficial microbial synthetic communities) performs better and enhances carbon-sequestration and nutrient recovery from wastewater treatment plants. This review presents a comprehensive information regarding the potential of microalgae-microbiome as a sustainable agent for wastewater and discusses synergistic approaches for effective nutrient removal. Moreover, this review discusses, the role of omics-biology and Insilco approaches in unravelling and understanding the algae-microbe synergism and their response toward wastewater treatment. Finally, it discusses various microbiome engineering approaches for developing the effective microalgae-bacteria partners for carbon sequestration and nutrient recovery from wastewater, and summarizes future research perspectives on microalgae-microbiome based bioremediation.
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Affiliation(s)
- Muneer Ahmad Malla
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Faiz Ahmad Ansari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa.
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6
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Lv H, Yang M, Cheng Y, Li K, Ji G, Huang T, Wen G. Disentangling the assembly patterns and drivers of microbial communities during thermal stratification and mixed periods in a deep-water reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174398. [PMID: 38960188 DOI: 10.1016/j.scitotenv.2024.174398] [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: 04/26/2024] [Revised: 06/18/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024]
Abstract
Effect of periodic thermal stratification in deep-water reservoirs on aquatic ecosystems has been a research hotspot. Nevertheless, there is limited information on the response patterns of microbial communities to environmental changes under such specialized conditions. To fill this gap, samples were collected from a typical deep-water reservoir during the thermal stratification period (SP) and mixed period (MP). Three crucial questions were answered: 1) How microbial communities develop with stratified to mixed succession, 2) how the relative importance of stochastic and deterministic processes to microbial community assembly, shifted in two periods, and 3) how environmental variables drive microbial co-occurrence networks and functional group alteration. We used Illumina Miseq high-throughput sequencing to investigate the dynamics of the microbial community over two periods, constructed molecular ecological networks (MENs), and unraveled assembly processes based on null and neutral models. The results indicated that a total of 33.9 % and 27.7 % of bacterial taxa, and 23.1 % and 19.4 % of fungal taxa were enriched in the stratified and mixed periods, respectively. Nitrate, water temperature, and total phosphorus drove the variation of microbial community structure. During the thermal stratification period, stochastic processes (dispersal limitation) and deterministic processes (variable selection) dominated the assembly of bacterial and fungal communities, followed by a shift to stochastic processes dominated by dispersal limitation in two communities. The MENs results revealed that thermal stratification-induced environmental stresses increased the complexity of microbial networks but decreased its robustness, resulting in more vulnerable ecological networks. Therefore, this work provides critical ecological insights for the longevity and sustainability of water quality management in an artificially regulated engineered system.
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Affiliation(s)
- He Lv
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Meng Yang
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ya Cheng
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kai Li
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Gang Ji
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Gang Wen
- Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
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7
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Caravaca F, Torres P, Díaz G, Roldán A. Selective shifts in the rhizosphere microbiome during the drought season could explain the success of the invader Nicotiana glauca in semiarid ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174444. [PMID: 38964394 DOI: 10.1016/j.scitotenv.2024.174444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The rhizosphere microbiome plays a crucial role in the ability of plants to colonize and thrive in stressful conditions such as drought, which could be decisive for the success of exotic plant invasion in the context of global climate change. The aim of this investigation was to examine differences in the composition, structure, and functional traits of the microbial community of the invader Nicotiana glauca R.C. Graham and native species growing at seven different Mediterranean semiarid locations under two distinct levels of water availability, corresponding to the wet and dry seasons. The results show that the phylum Actinobacteriota was an indicator phylum of the dry season as well as for the community of N. glauca. The dominant indicator bacterial families of the dry season were 67-14 (unclassified family), Pseudonocardiaceae, and Sphingomonadaceae, being relatively more abundant in the invasive rhizosphere. The relative abundances of the indicator fungal families Aspergillaceae (particularly the indicator genus Aspergillus), Glomeraceae, and Claroideoglomeraceae were higher in the invasive rhizosphere. The relative abundance of mycorrhizal fungi was higher in the invasive rhizosphere in the dry season (by about 40 % in comparison to that of native plants), without significant differences between invasive and native plants in the wet season. Bacterial potential functional traits related to energy and precursor metabolites production and also biosynthesis of cell wall, cofactors, vitamins, and amino acids as well as catabolic enzymes involved in the P cycle prevailed in the invasive rhizosphere under drought conditions. This study shows that the pronounced and beneficial shifts in the microbiome assembly and functions in the rhizosphere of N. glauca under conditions of low soil water availability can represent a clear advantage for its establishment.
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Affiliation(s)
- F Caravaca
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo 30100, Murcia, Spain.
| | - P Torres
- Universidad Miguel Hernández de Elche, Department of Applied Biology, Avda. Ferrocarril, s/n. Edf. Laboratorios-03202-Elche, Alicante, Spain
| | - G Díaz
- Universidad Miguel Hernández de Elche, Department of Applied Biology, Avda. Ferrocarril, s/n. Edf. Laboratorios-03202-Elche, Alicante, Spain
| | - A Roldán
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo 30100, Murcia, Spain
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8
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Jin J, Zhao D, Wang J, Wang Y, Zhu H, Wu Y, Fang L, Bing H. Fungal community determines soil multifunctionality during vegetation restoration in metallic tailing reservoir. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135438. [PMID: 39116750 DOI: 10.1016/j.jhazmat.2024.135438] [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: 05/28/2024] [Revised: 07/15/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Microorganisms are pivotal in sustaining soil functions, yet the specific contributions of bacterial and fungal succession on the functions during vegetation restoration in metallic tailing reservoirs remains elusive. Here, we explored bacterial and fungal succession and their impacts on soil multifunctionality along a ∼50-year vegetation restoration chronosequence in China's largest vanadium titano-magnetite tailing reservoir. We found a significant increase in soil multifunctionality, an index comprising factors pertinent to soil fertility and microbially mediated nutrient cycling, along the chronosequence. Despite increasing heavy metal levels, both bacterial and fungal communities exhibited significant increase in richness and network complexity over time. However, fungi demonstrated a slower succession rate and more consistent composition than bacteria, indicating their relatively higher resilience to environmental changes. Soil multifunctionality was intimately linked to bacterial and fungal richness or complexity. Nevertheless, when scrutinizing both richness and complexity concurrently, the correlations disappeared for bacteria but remained robust for fungi. This persistence reveals the critical role of the fungal community resilience in sustaining soil multifunctionality, particularly through their stable interactions with powerful core taxa. Our findings highlight the importance of fungal succession in enhancing soil multifunctionality during vegetation restoration in metallic tailing reservoirs, and manipulating fungal community may expedite ecological recovery of areas polluted with heavy metals.
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Affiliation(s)
- Jiyuan Jin
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China; School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210093, China
| | - Dongyan Zhao
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China; College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Jipeng Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yuhan Wang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China; Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Wuhan 430070, China
| | - He Zhu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China
| | - Yanhong Wu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China
| | - Linchuan Fang
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Wuhan 430070, China
| | - Haijian Bing
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China.
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9
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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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10
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Wang JL, Liu XY, Jiang PK, Yu QR, Xu QF. Half substitution of mineral N with fish protein hydrolysate enhancing microbial residue C and N storage and climate benefits under high straw residue return. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122488. [PMID: 39270338 DOI: 10.1016/j.jenvman.2024.122488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 09/10/2024] [Accepted: 09/10/2024] [Indexed: 09/15/2024]
Abstract
The widespread utilization of straw return was a popular practice straw disposal for highly intensive agriculture in China, which has brought about some negative impacts such as less time for straw complete biodegradation, aggravation of greenhouse gas evolution, and lower efficient of carbon accumulation. It was urgent to find an eco-friendly N-rich organic fertilizer instead of mineral N as activator to solve the above problems and lead a carbon accumulation in long tern management. Besides, microbial necromass was considered as a crucial contributor to persistent soil carbon (C) and nitrogen (N) pool. How organic fertilizer activators influence microbial residue under different amount of crop residues input remained unclear. Thus, soils incorporating moderate and high rate of rice straw residue with additions of half and full of organic activators (fish protein hydrolysates vs. manure) were incubated for measuring carbon dioxide (CO2) and nitrous oxide (N2O) emission, microbial community and necromass. It was found that soil CO2 emission was rapidest during the first 13 days of straw decomposition but remained lowest in the treatments of 50% mineral N substituted by fish protein hydrolysate. There were that 81%-89% of total CO2 release and 59%-65% of total N2O emission occurred within 60 days of incubation period, and bacterial community and nitrate positively affected soil CO2 and N2O release respectively. Straw incorporation amount and organic activator application interactively influenced soil CO2 emission but not affected soil N2O emission. After 360 days of incubation, the difference of bacterial necromass was noticeable but fungal necromass remained almost unaltered across all treatments. All treatments showed generally comparable contribution of microbial necromass N to the total N pool. The treatment of 50% mineral N substituted by fish protein hydrolysate under high rate of straw input (HSF50) promoted the highest proportion of microbial necromass C in soil organic C because of alleviating N limitation for microorganisms. Finally, HSF50 was recommended as an eco-friendly strategy for enhancing microbial necromass C and N storage and climate benefits in agroecosystems.
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Affiliation(s)
- Jia Lin Wang
- College of Environment and Resources, College of Carbon Neutrality, Zhejiang A&F University, Hangzhou, 311300, China; The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xin Yu Liu
- College of Environment and Resources, College of Carbon Neutrality, Zhejiang A&F University, Hangzhou, 311300, China; The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Pei Kun Jiang
- College of Environment and Resources, College of Carbon Neutrality, Zhejiang A&F University, Hangzhou, 311300, China; The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Qiu Ran Yu
- College of Environment and Resources, College of Carbon Neutrality, Zhejiang A&F University, Hangzhou, 311300, China; The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Qiu Fang Xu
- College of Environment and Resources, College of Carbon Neutrality, Zhejiang A&F University, Hangzhou, 311300, China; The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China.
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11
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Huang C, He Y, Zhou L, Liu R, Chen H, Du Z, Fu Y, Zhu Y, Zhou Y, Wu C, Zhou G, Zhou X. Opposite effects of soil pH on bacteria and fungi β diversity in forests at a continental scale. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122428. [PMID: 39260281 DOI: 10.1016/j.jenvman.2024.122428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/28/2024] [Accepted: 09/04/2024] [Indexed: 09/13/2024]
Abstract
Soil microbial diversity is crucial for regulating biogeochemical cycles, including soil carbon (C) dynamics and nutrient cycling. However, how climate, plants, and soil properties influence the microbiome in forests remains unclear, especially at the continental scale, hindering us to better understand forest C-climate change feedback. Here, we investigated the spatial patterns of microbial diversity across China's forests and explored the controlling factors of microbial β diversity and network complexity. Our results showed that soil pH strongly influenced bacterial and fungal β diversity compared to climate, soil nutrient and plant properties. To further investigate the environmental preference of the microbial networks, we classified the amplicon sequence variants (ASVs) into five groups ranging from acidic to alkaline soils. Co-occurrence network analysis revealed that the topological structure of the bacterial network (e.g., edge and degree) increased with pH and was negatively correlated with β diversity but not for fungal diversity. Soil fungi exhibited higher β diversity and network complexity (i.e., degree and betweenness) than bacteria in acidic soils (pH < 5.1), and vice versa in neutral and alkaline soils (pH > 5.5). Within the pH range of 5.1-5.5, the bacterial-fungal network displayed the highest network complexity with the lowest fungal β diversity, and significant positive correlations were found between fungal β diversity and soil properties. In addition, bacterial growth in acidic soil (pH < 5.5) showed positive correlations with acid phosphatase (AP), but negative ones with β-1,4-glucosidase (BG), and vice versa in neutral and alkaline soils (pH > 5.5). Furthermore, 46 bacterial core species were identified, and their abundance had significant correlation with soil pH. These findings highlight the critical role of soil pH in driving soil microbial β diversity across China's forests and reveal the effects of pH thresholds on changes in the soil microbial network and core species.
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Affiliation(s)
- Changjiang Huang
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Yanghui He
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Lingyan Zhou
- Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai Botanical Garden, Shanghai, 200030, China
| | - Ruiqiang Liu
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Hongyang Chen
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Zhenggang Du
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Yuling Fu
- Center for Global Change and Ecological Forecasting, Tiantong National Field Observation Station for Forest Ecosystem, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Yimin Zhu
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Yuxuan Zhou
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Chuansheng Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China
| | - Guiyao Zhou
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xuhui Zhou
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China; Center for Global Change and Ecological Forecasting, Tiantong National Field Observation Station for Forest Ecosystem, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China.
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12
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Xing K, Lu W, Huang Q, Wu J, Shang H, Wang Q, Guo F, Du Q, Yin Z, Zhang Y, Li F. Soil eDNA biomonitoring reveals changes in multitrophic biodiversity and ecological health of agroecosystems. ENVIRONMENTAL RESEARCH 2024; 262:119931. [PMID: 39260717 DOI: 10.1016/j.envres.2024.119931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/13/2024]
Abstract
Soil health is integral to sustainable agroecosystem management. Current monitoring and assessment practices primarily focus on soil physicochemical properties, yet the perspective of multitrophic biodiversity remains underexplored. Here we used environmental DNA (eDNA) technology to monitor multitrophic biodiversity in four typical agroecosystems, and analyzed the species composition and diversity changes in fungi, bacteria and metazoan, and combined with the traditional physicochemical variables to establish a soil health assessment framework centered on biodiversity data. First, eDNA technology detected rich multitrophic biodiversity in four agroecosystems, including 100 phyla, 273 classes, 611 orders, 1026 families, 1668 genera and 1146 species with annotated classification, and the relative sequence abundance of dominant taxa fluctuates tens of times across agroecosystems. Second, significant differences in soil physicochemical variables such as organic matter (OM), total nitrogen (TN) and available phosphorus (AP) were observed among different agroecosystems, nutrients were higher in cropland and rice paddies, while heavy metals were higher in fish ponds and lotus ponds. Third, biodiversity metrics, including α and β diversity, also showed significant changes across agroecosystems, the soil biota was generally more sensitive to nutrients (e.g., OM, TN or AP), while the fungal communities were mainly affected by heavy metals in October (e.g., Cu and Cr). Finally, we screened 48 sensitive organismal indicators and found significant positive consistency between the developed eDNA indices and the traditional soil quality index (SQI, reaching up to R2 = 0.58). In general, this study demonstrated the potential of eDNA technology in soil health assessment and underscored the importance of a multitrophic perspective for efficient monitoring and managing agroecosystems.
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Affiliation(s)
- Kaihang Xing
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Weijun Lu
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Qiqi Huang
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jingze Wu
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Heping Shang
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Qian Wang
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing, 100012, China
| | - Fen Guo
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Qingping Du
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Zhonglong Yin
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Yuan Zhang
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Feilong Li
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
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13
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Zhou Z, Hua J, Xue J, Yu C. Differential impacts of polyethylene microplastic and additives on soil nitrogen cycling: A deeper dive into microbial interactions and transformation mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173771. [PMID: 38851351 DOI: 10.1016/j.scitotenv.2024.173771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/20/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
The impact of microplastics and their additives on soil nutrient cycling, particularly through microbial mechanisms, remains underexplored. This study investigated the effects of polyethylene microplastics, polyethylene resin, and plastic additives on soil nitrogen content, physicochemical properties, nitrogen cycling functional genes, microbial composition, and nitrogen transformation rates. Results showed that all amendments increased total nitrogen but decreased dissolved total nitrogen. Polyethylene microplastics and additives increased dissolved organic nitrogen, while polyethylene resin reduced it and exhibited higher microbial biomass. Amendments reduced or did not change inorganic nitrogen levels, with additives showing the lowest values. Polyethylene resin favored microbial nitrogen immobilization, while additives were more inhibitory. Amendment type and content significantly interacted with nitrogen cycling genes and microbial composition. Distinct functional microbial biomarkers and network structures were identified for different amendments. Polyethylene microplastics had higher gross ammonification, nitrification, and immobilization rates, followed by polyethylene resin and additives. Nitrogen transformation was driven by multiple functional genes, with Proteobacteria playing a significant role. Soil physicochemical properties affected nitrogen content through transformation rates, with C/N ratio having an indirect effect and water holding capacity directly impacting it. In summary, plastic additives, compared to polyethylene microplastics and resin, are less conducive to nitrogen degradation and microbial immobilization, exert significant effects on microbial community structure, inhibit transformation rates, and ultimately impact nitrogen cycling.
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Affiliation(s)
- Zhidong Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianfeng Hua
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China.
| | - Jianhui Xue
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China; College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Chaoguang Yu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
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14
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Crosta A, Valle B, Caccianiga M, Gobbi M, Ficetola FG, Pittino F, Franzetti A, Azzoni RS, Lencioni V, Senese A, Corlatti L, Buda J, Poniecka E, Novotná Jaroměřská T, Zawierucha K, Ambrosini R. Ecological interactions in glacier environments: a review of studies on a model Alpine glacier. Biol Rev Camb Philos Soc 2024. [PMID: 39247954 DOI: 10.1111/brv.13138] [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: 01/18/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/10/2024]
Abstract
Glaciers host a variety of cold-adapted taxa, many of which have not yet been described. Interactions among glacier organisms are even less clear. Understanding ecological interactions is crucial to unravelling the functioning of glacier ecosystems, particularly in light of current glacier retreat. Through a review of the existing literature, we aim to provide a first overview of the biodiversity, primary production, trophic networks, and matter flow of a glacier ecosystem. We use the Forni Glacier (Central Italian Alps) - one of the best studied alpine glaciers in the world - as a model system for our literature review and integrate additional original data. We reveal the importance of allochthonous organic matter inputs, of Cyanobacteria and eukaryotic green algae in primary production, and the key role of springtails (Vertagopus glacialis) on the glacier surface in sustaining populations of two apex terrestrial predators: Nebria castanea (Coleoptera: Carabidae) and Pardosa saturatior (Araneae: Lycosidae). The cryophilic tardigrade Cryobiotus klebelsbergi is the apex consumer in cryoconite holes. This short food web highlights the fragility of nodes represented by invertebrates, contrasting with structured microbial communities in all glacier habitats. Although further research is necessary to quantify the ecological interactions of glacier organisms, this review summarises and integrates existing knowledge about the ecological processes on alpine glaciers and supports the importance of glacier-adapted organisms in providing ecosystem services.
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Affiliation(s)
- Arianna Crosta
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, Milan, 20133, Italy
| | - Barbara Valle
- Department of Life Sciences, Università degli Studi di Siena, Via A. Moro 2, Siena, 53100, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina, 61, Palermo, 90133, Italy
| | - Marco Caccianiga
- Department of Bioscience, University of Milan, via Celoria 26, Milan, 20133, Italy
| | - Mauro Gobbi
- Climate and Ecology Unit, Research and Museum Collections Office, MUSE-Science Museum, Corso del Lavoro e della Scienza 3, Trento, 38122, Italy
| | - Francesco Gentile Ficetola
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, Milan, 20133, Italy
| | - Francesca Pittino
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milan, 20126, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milan, 20126, Italy
| | - Roberto Sergio Azzoni
- Department of Earth Sciences 'A. Desio', University of Milan, via Mangiagalli 34, Milan, 20133, Italy
| | - Valeria Lencioni
- Climate and Ecology Unit, Research and Museum Collections Office, MUSE-Science Museum, Corso del Lavoro e della Scienza 3, Trento, 38122, Italy
| | - Antonella Senese
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, Milan, 20133, Italy
| | - Luca Corlatti
- ERSAF - Direzione Parco Stelvio, via De Simoni 42, Bormio, (SO) 23032, Italy
- Chair of Wildlife Ecology and Management, University of Freiburg, Tennenbacher Str. 4, Freiburg, 79106, Germany
| | - Jakub Buda
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Ewa Poniecka
- Laboratory of RNA Biology - ERA Chairs Group, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, Warsaw, 02-109, Poland
| | - Tereza Novotná Jaroměřská
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, 37005, Czech Republic
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, Milan, 20133, Italy
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15
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Xian S, Zhao F, Huang X, Liu X, Zhang Z, Zhou M, Shen G, Li M, Chen A. Effects of Pre-Dehydration Treatments on Physicochemical Properties, Non-Volatile Flavor Characteristics, and Microbial Communities during Paocai Fermentation. Foods 2024; 13:2852. [PMID: 39272618 DOI: 10.3390/foods13172852] [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: 08/20/2024] [Revised: 08/30/2024] [Accepted: 09/06/2024] [Indexed: 09/15/2024] Open
Abstract
The paocai industry faces challenges related to the production of large volumes of high-salinity and acidic brine by-products. Maintaining paocai quality while reducing brine production is crucial. This study utilized high-throughput sequencing technology to analyze microbial changes throughout the fermentation process, along with the non-volatile flavor compounds and physicochemical properties, to assess the impact of hot-air and salt-pressing pre-dehydration treatments on paocai quality. The findings indicate that pre-dehydration of raw material slowed the fermentation process but enhanced the concentration of non-volatile flavor substances, including free amino acids and organic acids. Hot-air pre-dehydration effectively reduced initial salinity to levels comparable to those in high-salinity fermentation of fresh vegetables. Furthermore, pre-dehydration altered microbial community structures and simplified inter-microbial relationships during fermentation. However, the key microorganisms such as Lactobacillus, Weissella, Enterobacter, Wallemia, Aspergillus, and Kazachstania remained consistent across all groups. Additionally, this study found that biomarkers influenced non-volatile flavor formation differently depending on the treatment, but these substances had minimal impact on the biomarkers and showed no clear correlation with high-abundance microorganisms. Overall, fermenting pre-dehydrated raw materials presents an environmentally friendly alternative to traditional paocai production.
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Affiliation(s)
- Shuang Xian
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Feng Zhao
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Xinyan Huang
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Xingyan Liu
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Zhiqing Zhang
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Man Zhou
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Guanghui Shen
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Meiliang Li
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Anjun Chen
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
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16
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Xie ST, Zhu D, Song YQ, Zhu YG, Ding LJ. Unveiling potential roles of earthworms in mitigating the presence of virulence factor genes in terrestrial ecosystems. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135133. [PMID: 38986408 DOI: 10.1016/j.jhazmat.2024.135133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Earthworms can redistribute soil microbiota, and thus might affect the profile of virulence factor genes (VFGs) which are carried by pathogens in soils. Nevertheless, the knowledge of VFG profile in the earthworm guts and its interaction with earthworm gut microbiome is still lacking. Herein, we characterized earthworm gut and soil microbiome and VFG profiles in natural and agricultural ecosystems at a national scale using metagenomics. VFG profiles in the earthworm guts significantly differed from those in the surrounding soils, which was mainly driven by variations of bacterial communities. Furthermore, the total abundance of different types of VFGs in the earthworm guts was about 20-fold lower than that in the soils due to the dramatic decline (also by approximately 20-fold) of VFG-carrying bacterial pathogens in the earthworm guts. Additionally, five VFGs related to nutritional/metabolic factors and stress survival were identified as keystones merely in the microbe-VFG network in the earthworm guts, implying their pivotal roles in facilitating pathogen colonization in earthworm gut microhabitats. These findings suggest the potential roles of earthworms in reducing risks related to the presence of VFGs in soils, providing novel insights into earthworm-based bioremediation of VFG contamination in terrestrial ecosystems.
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Affiliation(s)
- Shu-Ting Xie
- 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, 19A Yuquan Road, Beijing 100049, China
| | - Dong Zhu
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; 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; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Ya-Qiong Song
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101400, China; Sino-Danish Centre for Education and Research, Beijing 100049, China; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Yong-Guan Zhu
- 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, 19A Yuquan Road, Beijing 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Jimei District, Xiamen 361021, China
| | - Long-Jun Ding
- 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, 19A Yuquan Road, Beijing 100049, China.
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17
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Camuy-Vélez LA, Banerjee S, Sedivec K. Grazing intensity alters network complexity and predator-prey relationships in the soil microbiome. Appl Environ Microbiol 2024:e0042524. [PMID: 39235241 DOI: 10.1128/aem.00425-24] [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: 03/05/2024] [Accepted: 08/13/2024] [Indexed: 09/06/2024] Open
Abstract
Grasslands are recognized as important reservoirs of soil biodiversity. Livestock grazing is implemented as a grassland management strategy to improve soil quality and enhance plant diversity. Soil microbial communities play a pivotal role in grassland ecosystems, so it is important to examine whether grazing practices affect the soil microbiome. Previous studies on grazing have primarily focused on bacteria and fungi, overlooking an important group-protists. Protists are vital in soil microbiomes as they drive nutrient availability and trophic interactions. Determining the impact of grazing on protists and their relationships with bacterial and fungal communities is important for understanding soil microbiome dynamics in grazed ecosystems. In this study, we investigated soil bacterial, fungal, and protist communities under four grazing levels: no grazing, moderate-use grazing, full-use grazing, and heavy-use grazing. Our results showed that heavy grazing led to a greater diversity of protists with specific groups, such as Discoba and Conosa, increasing in abundance. We also found strong associations between protist and bacterial/fungal members, indicating their intricate relationships within the soil microbiome. For example, the abundance of predatory protists increased under grazing while arbuscular mycorrhizal fungi decreased. Notably, arbuscular mycorrhizae were negatively associated with predatory groups. Furthermore, we observed that microbial network complexity increased with grazing intensity, with fungal members playing an important role in the network. Overall, our study reports the impact of temporal grazing intensity on soil microbial dynamics and highlights the importance of considering protist ecology when evaluating the effects of grazing on belowground communities in grassland ecosystems. IMPORTANCE The significance of this study lies in its exploration of the effects of temporal grazing intensity on the dynamics of the soil microbiome, specifically focusing on the often-neglected role of protists. Our findings provide insights into the complex relationships between protists, bacteria, and fungi, emphasizing their impact on trophic interactions in the soil. Gaining a better understanding of these dynamics is essential for developing effective strategies for grassland management and conservation, underscoring the importance of incorporating protist ecology into microbiome studies in grasslands.
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Affiliation(s)
- Lennel A Camuy-Vélez
- Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Samiran Banerjee
- Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Kevin Sedivec
- School of Natural Resource Science, North Dakota State University, Fargo, North Dakota, USA
- Central Grasslands Research Extension Center, North Dakota State University, Streeter, North Dakota, USA
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Huang X, Hong Y, Li Q, Liu Z, Liu K. Characteristics and driving forces of the soil microbial community during 35 years of natural restoration in abandoned areas of the Daxin manganese mine, China. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:413. [PMID: 39230730 DOI: 10.1007/s10653-024-02204-y] [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: 01/26/2024] [Accepted: 08/28/2024] [Indexed: 09/05/2024]
Abstract
The restoration of mining wastelands, particularly in karst regions contaminated by heavy metals, is an environmental challenge in need of urgent attention. Soil microbes play a vital role in nutrient cycling and ecosystem recovery, yet the long-term evolution of soil microbial communities in such settings remains poorly understood. This study explored the dynamics and influencing factors of soil microbial communities during 35 years of natural restoration in abandoned manganese (Mn) mine areas in Guangxi Province, China. The results revealed that the concentrations of Mn, Cd, Zn, and Cu were significantly (p < 0.05) reduced by 80.4-85.3%, 55.3-70.0%, 21.0-38.1%, and 29.4-49.4%, respectively, in the mid-late restoration periods (R19 and R35) compared with R1. The α diversities of the bacterial and fungal communities significantly increased in the middle-late restoration periods (R19 and R35), indicating increased microbial diversity as restoration progressed. The bacterial community structure exhibited more pronounced changes than did the fungal community structure, with significant shifts observed in dominant phyla such as Proteobacteria, Actinobacteria, Acidobacteriota, and Ascomycota. Notably, the relative abundances of Rhizobiales, Burkholderiales, and Hypocreales increased gradually with succession. Co-occurrence network analysis revealed that bacterial interactions became stronger over time, whereas interactions between bacteria and fungi weakened. Mantel tests and partial least squares path modeling (PLS‒PM) identified soil pH, heavy metals (Mn, Cd, Zn, and Cu), and nutrients (SOM and TN) as key drivers shaping the microbial community composition. These factors were more strongly correlated with bacterial communities than with fungal communities, underscoring the different responses of microbial groups to environmental changes during natural restoration. These findings enhance our understanding of the ecological processes governing microbial community succession in heavy metal-contaminated soils undergoing natural restoration.
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Affiliation(s)
- Xiaofang Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, 541004, China
| | - Yanyan Hong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, 541004, China
| | - Quanzeng Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, 541004, China
| | - Zongbao Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, 541004, China.
| | - Kehui Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, 541004, China.
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Ma X, Zhai T, Wang X, Cai C, Qiu D, Yin R, Li J, Liu G. Salinity-induced variations in bacterial composition and co-occurrence patterns within Salicornia-based constructed wetlands in mariculture. CHEMOSPHERE 2024; 363:142795. [PMID: 38986781 DOI: 10.1016/j.chemosphere.2024.142795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Constructed wetlands use vegetation and microorganisms to remove contaminants like nitrogen and phosphorus from water. For mariculture, the impact of salinity on the efficiency of wastewater treatment of wetlands is unneglectable. However, little is known about their impact on the microbiome in constructed wetlands. Here, we set four salinity levels (15, 22, 29, and 36) in Salicornia constructed wetlands, and the experiment was conducted for a period of 72 days. The 15 group exhibited the highest removal rates of nitrogen compounds and phosphate, compared to the other salinity groups, the nosZ gene exhibited significantly higher expression in the 22 group (p < 0.05), indicated that microorganisms in 22 salinity have higher denitrification abilities. The three dominant phyla identified within the microbiomes were Proteobacteria, known for their diverse metabolic capabilities; Cyanobacteria, important for photosynthesis and nitrogen fixation; and Firmicutes, which include many fermenters. The ecological network analysis revealed a 'small world' model, characterized by high interconnectivity and short path lengths between microbial species, and had higher co-occurrence (45.13%) observed in this study comparing to the Erdös-Réyni random one (32.35%). The genus Microbulbifer emerged as the sole connector taxon, pivotal for integrating different microbial communities involved in nitrogen removal. A negative correlation was observed between salinity levels and network complexity, as assessed by the number of connections and diversity of interactions within the microbial community. Collectively, these findings underscore the critical role of microbial community interactions in optimizing nitrogen removal in constructed wetlands, with potential applications in the design and management of such systems for improved wastewater treatment in mariculture.
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Affiliation(s)
- Xiaona Ma
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China; College of Bio-systems Engineering and Food Science, Zhejiang University, Hangzhou, China; Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
| | - Tangfang Zhai
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Xinyuan Wang
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Chen Cai
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Denggao Qiu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Rui Yin
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Jiayu Li
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
| | - Gang Liu
- College of Bio-systems Engineering and Food Science, Zhejiang University, Hangzhou, China; Ocean Academy, Zhejiang University, Zhoushan, China.
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20
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Lu J, Yu P, Zhang J, Guo Z, Li Y, Wang S, Hu Z. Biotic/abiotic transformation mechanisms of phenanthrene in iron-rich constructed wetland under redox fluctuation. WATER RESEARCH 2024; 261:122033. [PMID: 38996732 DOI: 10.1016/j.watres.2024.122033] [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: 04/28/2024] [Revised: 06/16/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
Iron-rich constructed wetlands (CWs) could promote phenanthrene bioremediation efficiently through biotic and abiotic pathways, which have gained increasing attention. However, the biotic/abiotic transformation mechanisms of trace organic contaminants in iron-rich CW are still ambiguous. Herein, three CWs (i.e., CW-A: Control; CW-B: Iron-rich CW, CW-C: Iron-rich CW + tidal flow) were constructed to investigate the transformation mechanisms of phenanthrene through Mössbauer spectroscopy and metagenomics. Results demonstrated CW-C achieved the highest phenanthrene removal (94.0 %) and bacterial toxicity reduction (92.1 %) due to the optimized degradation pathway, and subsequently achieved the safe transformation of phenanthrene. Surface-bound/low-crystalline iron regulated hydroxyl radical (·OH) production predominantly, and its utilization was promoted in CW-C, which also improved electron transfer capacity. The enhanced electron transfer capacity led to the enrichment of PAH-degrading microorganisms (e.g., Thauera) and keystone species (Sphingobacteriales bacterium 46-32) in CW-C. Additionally, the abundances of phenanthrene transformation (e.g., EC:1.14.12.-) and tricarboxylic-acid-cycle (e.g., EC:2.3.3.1) enzyme were up-regulated in CW-C. Further analysis indicated that the safe transformation of phenanthrene was mainly attributed to the combined effect of abiotic (·OH and surface-bound/low-crystalline iron) and biotic (microbial community and diversity) mechanisms in CW-C, which contributed similarly. Our study revealed the essential role of active iron in the safe transformation of phenanthrene, and was beneficial for enhanced performance of iron-rich CW.
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Affiliation(s)
- Jiaxing Lu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Peihan Yu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Jian Zhang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China; College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Zizhang Guo
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Shuo Wang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Zhen Hu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China.
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21
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Xu Q, Wu Z, Xu Z, Li G. Soil moisture-dependent tire wear particles aging processes shift soil microbial communities and elevated nitrous oxide emission on drylands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175948. [PMID: 39222808 DOI: 10.1016/j.scitotenv.2024.175948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
Tire wear particles (TWPs) have been an emerging threat to the soil ecosystem, while impact of the TWPs aging on soil microbial communities remains poorly understood. This study investigated the dynamic responses of soil microbial communities to the TWPs aging under both wet and flooded conditions. We found that different soil moisture conditions resulted in distinct microbial community structures. Soil bacteria were more sensitive to wet conditions, while soil fungi were more sensitive to flooded conditions. The family Symbiobacteraceae was predominant in the TWP-sphere under both wet and flooded conditions after 60 days, followed by Brevibacillaceae. Notably, we observed that TWPs input significantly increased nitrous oxide (N2O) emission from dryland soil. Several taxa including Cyanobacteriales, Blastocatellaceae and Pyrinomonadaceae were identified as TWP-biomarkers in soils and potentially played significant roles in N2O emissions from drylands. Their responses to the TWPs input correlated closely with changes in the relative abundance of genes involved in ammonia oxidation (amoA/B), nitrite reduction (nirS/K) and N2O reduction (nosZ) in drylands. Our results demonstrate that soil moisture-dependent TWP aging influences N2O emission by altering both the associated microbial communities and the relevant genes.
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Affiliation(s)
- Qiao Xu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Zhiyong Wu
- College of Chemical Engineering, Zhejiang University of Technology, Zhejiang 310014, People's Republic of China
| | - Zhihong Xu
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, Brisbane, QLD 4111, Australia
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China.
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22
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Li B, Yang P, Feng Y, Du C, Qi G, Zhao X. Rhizospheric microbiota of suppressive soil protect plants against Fusarium solani infection. PEST MANAGEMENT SCIENCE 2024; 80:4186-4198. [PMID: 38578633 DOI: 10.1002/ps.8122] [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: 08/31/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Fusarium infection has caused huge economic losses in many crops. The study aimed to compare the microbial community of suppressive and conducive soils and relate to the reduction of Fusarium wilt. RESULTS High-throughput sequencing and microbial network analysis were used to investigate the differences in the rhizosphere microbiota of the suppressive and conducive soils and to identify the beneficial keystone taxa. Plant pathogens were enriched in the conducive soil. Potential plant-beneficial microorganisms and antagonistic microorganisms were enriched in the suppressive soil. More positive interactions and keystone taxa existed in the suppressive soil network. Thirty-nine and 16 keystone taxa were identified in the suppressive and conducive soil networks, respectively. Sixteen fungal strains and 168 bacterial strains were isolated from suppressive soil, some of which exhibited plant growth-promotion traits. Thirty-nine bacterial strains and 10 fungal strains showed antagonistic activity against F. solani. Keystone taxa Bacillus and Trichoderma exhibited high antifungal activity. Lipopeptides produced by Bacillus sp. RB150 and chitinase from Trichoderma spp. inhibited the growth of F. solani. Microbial consortium I (Bacillus sp. RB150, Pseudomonas sp. RB70 and Trichoderma asperellum RF10) and II (Bacillus sp. RB196, Bacillus sp. RB150 and T. asperellum RF10) effectively controlled root rot disease, the spore number of F. solani was reduced by 94.2% and 83.3%. CONCLUSION Rhizospheric microbiota of suppressive soil protects plants against F. solani infection. Antagonistic microorganisms in suppressive soil inhibit pathogen growth and infection. Microbial consortia consisted of keystone taxa well control root rot disease. These findings help control Fusarium wilt. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Baolong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ping Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yali Feng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chenyang Du
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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23
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Wu R, Xia H, Wu Y, Zhang S, Fang J, Wang Y, Wang H, Zhu Y, Liu L, Du S. Graphene oxide inhibits the transfer of ARGs in rice by reducing the root endophytic bacterial complexity. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122241. [PMID: 39186855 DOI: 10.1016/j.jenvman.2024.122241] [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: 06/04/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 08/28/2024]
Abstract
Antibiotic resistance genes (ARGs) as an emerging contaminant have attracted much attention for their transfer in agricultural ecosystems. Meanwhile, graphene oxide (GO), due to its high adsorption capacity and antibacterial properties, poses potential environmental ecological risks to the occurrence of ARGs, bacteria, and plant physiological ecology. However, the impact and mechanism of GO on the transfer of ARGs in host plants remain unclear. Therefore, this study selected rice as the research object and inoculated Bacillus subtilis carrying ARGs to investigate the influence of GO on the migration of ARGs into rice and its microbiological mechanism. The study found that GO had a certain inhibitory effect on the transfer of ARGs in rice. Although GO reduced the rhizosphere pH in rice, leading to a transition in endophytic bacteria from dominance by Burkholderia to dominance by Gordonia, this process did not directly affect the transfer of ARGs in rice. Further analysis of bacterial interactions revealed that GO could inhibit the transfer of ARGs in rice by reducing the network complexity of endophytic bacteria. Additionally, GO inhibited the formation of endophytic bacterial biofilms and mobile elements, which might affect ARGs' migration in rice. This study elucidated the key microbiological ecological processes of GO on the transfer of ARGs in rice, providing fundamental information for the ecological risk assessment of GO.
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Affiliation(s)
- Ran Wu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Hanche Xia
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Yue Wu
- Zhejiang Zhongyi Testing Research Institute Co., Ltd, Ningbo, 315040, China
| | - Siyu Zhang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Jin Fang
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yuying Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Hua Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yaxin Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Lijuan Liu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Shaoting Du
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China.
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24
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Zhang Q, Liu X, Peng S, Dong W, Chen Z. One-year monitoring of grass-type architectural waterscapes with long-term operation: Water quality and microorganism. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124849. [PMID: 39214442 DOI: 10.1016/j.envpol.2024.124849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Grass-type architectural waterscapes (GAWs) utilize submerged plants to enhance self-purification ability and maintain a clear-water state. However, knowledge about their long-term water quality and microbial community dynamics remains limited. This study monitored the water quality, microbial community composition, and networks in two GAWs. GAW1 consisted solely Hydrilla verticillata with a water depth of 0.70 m, while GAW2 primarily contained Vallisneria natans, Microsorum pteropus, and Aquarius grisebachii with a water depth of 0.30 m. Results show that both water depth and submerged plant species play crucial roles in GAW establishment. The water depth of 0.7 m enabled Hydrilla verticillata to thrive underwater despite temperature variations, which demonstrated excellent nutrient uptake capacity. Thus, GAW1 exhibited superior self-purification ability, consistently meeting Class III standard for surface water in China. In contrast, GAW2 had a shallow water depth and contained ornamental plants, only meeting Class V standard. Furthermore, microbial communities were shaped by water quality, with distinct enriched genera serving as potential "microbial indicators". Enrichment of the hgcI clade and Sporichthyaceae_unclassified indicated superior water quality in GAW1, while prevalence of Comamonadaceae_unclassified, Flavobacterium, Rhodoluna, and Pseudarcicella suggested poor water quality in GAW2. Additionally, highly complex and connected microbial networks suggested elevated pollutant levels in GAWs. This study emphasized the significance of submerged plant species and water depth in GAWs construction and highlighted microbial communities and networks as potential indicators of water quality.
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Affiliation(s)
- Quan Zhang
- Shenzhen Institute of Building Research Co., Ltd., 518049 Shenzhen, Guangdong, China; School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, Guangdong, China.
| | - Xiang Liu
- Shenzhen Jianyan Testing Co., Ltd., 518031 Shenzhen, Guangdong, China
| | - Shijin Peng
- Shenzhen Institute of Building Research Co., Ltd., 518049 Shenzhen, Guangdong, China
| | - Wenyi Dong
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, Guangdong, China
| | - Zeguang Chen
- Shenzhen Institute of Building Research Co., Ltd., 518049 Shenzhen, Guangdong, China
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Zhu A, Liang Z, Gao L, Xie Z. Dispersal limitation determines the ecological processes that regulate the seasonal assembly of bacterial communities in a subtropical river. Front Microbiol 2024; 15:1430073. [PMID: 39252829 PMCID: PMC11381306 DOI: 10.3389/fmicb.2024.1430073] [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: 05/09/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024] Open
Abstract
Bacteria play a crucial role in pollutant degradation, biogeochemical cycling, and energy flow within river ecosystems. However, the underlying mechanisms governing bacterial community assembly and their response to environmental factors at seasonal scales in subtropical rivers remain poorly understood. In this study, we conducted 16S rRNA gene amplicon sequencing on water samples from the Liuxi River to investigate the composition, assembly processes, and co-occurrence relationships of bacterial communities during the wet season and dry season. The results demonstrated that seasonal differences in hydrochemistry significantly influenced the composition of bacterial communities. A more heterogeneous community structure and increased alpha diversity were observed during the dry season. Water temperature emerged as the primary driver for seasonal changes in bacterial communities. Dispersal limitation predominantly governed community assembly, however, during the dry season, its contribution increased due to decreased immigration rates. Co-occurrence network analysis reveals that mutualism played a prevailing role in shaping bacterial community structure. Compared to the wet season, the network of bacterial communities exhibited higher modularity, competition, and keystone species during the dry season, resulting in a more stable community structure. Although keystone species displayed distinct seasonal variations, Proteobacteria and Actinobacteria were consistently abundant keystone species maintaining network structure in both seasons. Our findings provide insights into how bacterial communities respond to seasonal environmental changes, uncovering underlying mechanisms governing community assembly in subtropical rivers, which are crucial for the effective management and conservation of riverine ecosystems.
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Affiliation(s)
- Aiping Zhu
- School of Geography and Tourism, Anhui Normal University, Wuhu, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Chinese Academy of Sciences, Guangzhou, China
| | - Zuobing Liang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Gao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Chinese Academy of Sciences, Guangzhou, China
| | - Zhenglan Xie
- School of Geomatics and Municipal Engineering, Zhejiang University of Water Resources and Electric Power, Hangzhou, China
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Thomson T, Ellis JI, Fusi M, Prinz N, Lundquist CJ, Bury SJ, Shankar U, Cary SC, Pilditch CA. Effects of catchment land use on temperate mangrove forests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 940:173579. [PMID: 38823713 DOI: 10.1016/j.scitotenv.2024.173579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 05/25/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Human land use changes are threatening the integrity and health of coastal ecosystems worldwide. Intensified land use for anthropogenic purposes increases sedimentation rates, pollutants, and nutrient concentrations into adjacent coastal areas, often with detrimental effects on marine life and ecosystem functioning. However, how these factors interact to influence ecosystem health in mangrove forests is poorly understood. This study investigates the effects of catchment human land use on mangrove forest architecture and sedimentary attributes at a landscape-scale. Thirty sites were selected along a gradient of human land use within a narrow latitudinal range, to minimise the effects of varying climatic conditions. Land use was quantified using spatial analysis tools with existing land use databases (LCDB5). Twenty-six forest architectural and sedimentary variables were collected from each site. The results revealed a significant effect of human land use on ten out of 26 environmental variables. Eutrophication, characterised by changes in redox potential, pH, and sediment nutrient concentrations, was strongly associated with increasing human land use. The δ15N values of sediments and leaves also indicated increased anthropogenic nitrogen input. Furthermore, the study identified a positive correlation between human land use and tree density, indicating that increased nutrient delivery from catchments contributes to enhanced mangrove growth. Propagule and seedling densities were also positively correlated with human land use, suggesting potential recruitment success mechanisms. This research underpins the complex interactions between human land use and mangrove ecosystems, revealing changes in carbon dynamics, potential alterations in ecosystem services, and a need for holistic management approaches that consider the interconnectedness of species and their environment. These findings provide essential insights for regional ecosystem models, coastal management, and restoration strategies to address the impacts of human pressures on temperate mangrove forests, even in estuaries that may be relatively healthy.
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Affiliation(s)
- Timothy Thomson
- University of Waikato, School of Science, Tauranga, New Zealand.
| | - Joanne I Ellis
- University of Waikato, School of Science, Tauranga, New Zealand
| | - Marco Fusi
- Dove Marine Laboratory, School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne 1NE 7RU, United Kingdom
| | - Natalie Prinz
- University of Waikato, School of Science, Tauranga, New Zealand
| | - Carolyn J Lundquist
- National Institute of Water and Atmospheric Research, Hamilton, New Zealand; School of Environment, University of Auckland, Auckland, New Zealand
| | - Sarah J Bury
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Ude Shankar
- National Institute of Water and Atmospheric Research, Christchurch, New Zealand
| | - S Craig Cary
- School of Science, University of Waikato, Hamilton, New Zealand
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27
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Zhang B, Zhu S, Li J, Fu F, Guo L, Li J, Zhang Y, Liu Y, Chen G, Zhang G. Elevational distribution patterns and drivers factors of fungal community diversity at different soil depths in the Abies georgei var. smithii forests on Sygera Mountains, southeastern Tibet, China. Front Microbiol 2024; 15:1444260. [PMID: 39184024 PMCID: PMC11342059 DOI: 10.3389/fmicb.2024.1444260] [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: 06/05/2024] [Accepted: 07/22/2024] [Indexed: 08/27/2024] Open
Abstract
Introduction Soil fungal communities play a crucial role in maintaining the ecological functions of alpine forest soil ecosystems. However, it is currently unclear how the distribution patterns of fungal communities in different soil layers of alpine forests will change along the elevational gradients. Material and methods Therefore, Illumina MiSeq sequencing technology was employed to investigate fungal communities in three soil layers (0-10, 10-20, and 20-30 cm) along an elevational gradient (3500 m to 4300 m) at Sygera Mountains, located in Bayi District, Nyingchi City, Tibet. Results and discussion The results indicated that: 1) Soil depth had a greater impact on fungal diversity than elevation, demonstrating a significant reduction in fungal diversity with increased soil depth but showing no significant difference with elevation changes in all soil layers. Within the 0-10 cm soil layer, both Basidiomycota and Ascomycota co-dominate the microbial community. However, as the soil depth increases to 10-20 and 20-30 cm soil layers, the Basidiomycota predominantly dominates. 2) Deterministic processes were dominant in the assembly mechanism of the 0-10 cm fungal community and remained unchanged with increasing elevation. By contrast, the assembly mechanisms of the 10-20 and 20-30 cm fungal communities shifted from deterministic to stochastic processes as elevation increased. 3) The network complexity of the 0-10 cm fungal community gradually increased with elevation, while that of the 10-20 and 20-30 cm fungal communities exhibited a decreasing trend. Compared to the 0-10 cm soil layer, more changes in the relative abundance of fungal biomarkers occurred in the 10-20 and 20-30 cm soil layers, indicating that the fungal communities at these depths are more sensitive to climate changes. Among the key factors driving these alterations, soil temperature and moisture soil water content stood out as pivotal in shaping the assembly mechanisms and network complexity of fungal communities. This study contributes to the understanding of soil fungal community patterns and drivers along elevational gradients in alpine ecosystems and provides important scientific evidence for predicting the functional responses of soil microbial ecosystems in alpine forests.
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Affiliation(s)
- Bo Zhang
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
| | - Sijie Zhu
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
| | - Jiangrong Li
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Fangwei Fu
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
| | - Liangna Guo
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
| | - Jieting Li
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
| | - Yibo Zhang
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
| | - Yuzhuo Liu
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
| | - Ganggang Chen
- Research Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, China
- National Key Station of Field Scientific Observation and Experiment, Nyingchi, China
- Key Laboratory of Alpine Vegetation Ecological Security in Tibet, Nyingchi, China
| | - Gengxin Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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Kelliher JM, Johnson LYD, Robinson AJ, Longley R, Hanson BT, Cailleau G, Bindschedler S, Junier P, Chain PSG. Fabricated devices for performing bacterial-fungal interaction experiments across scales. Front Microbiol 2024; 15:1380199. [PMID: 39171270 PMCID: PMC11335632 DOI: 10.3389/fmicb.2024.1380199] [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: 02/02/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Diverse and complex microbiomes are found in virtually every environment on Earth. Bacteria and fungi often co-dominate environmental microbiomes, and there is growing recognition that bacterial-fungal interactions (BFI) have significant impacts on the functioning of their associated microbiomes, environments, and hosts. Investigating BFI in vitro remains a challenge, particularly when attempting to examine interactions at multiple scales of system complexity. Fabricated devices can provide control over both biotic composition and abiotic factors within an experiment to enable the characterization of diverse BFI phenotypes such as modulation of growth rate, production of biomolecules, and alterations to physical movements. Engineered devices ranging from microfluidic chips to simulated rhizosphere systems have been and will continue to be invaluable to BFI research, and it is anticipated that such devices will continue to be developed for diverse applications in the field. This will allow researchers to address specific questions regarding the nature of BFI and how they impact larger microbiome and environmental processes such as biogeochemical cycles, plant productivity, and overall ecosystem resilience. Devices that are currently used for experimental investigations of bacteria, fungi, and BFI are discussed herein along with some of the associated challenges and several recommendations for future device design and applications.
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Affiliation(s)
- Julia M. Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Leah Y. D. Johnson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Aaron J. Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Reid Longley
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Buck T. Hanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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29
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Zhang N, Chen K, Chen J, Ji W, Yang Z, Chen Z. Response Characteristics and Community Assembly Mechanisms of nirS-Type Denitrifiers in the Alpine Wetland under Simulated Precipitation Conditions. BIOLOGY 2024; 13:596. [PMID: 39194534 DOI: 10.3390/biology13080596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/18/2024] [Accepted: 08/06/2024] [Indexed: 08/29/2024]
Abstract
The nitrogen cycling process in alpine wetlands is profoundly affected by precipitation changes, yet the dynamic response mechanism of denitrifiers to long-term precipitation shifts in the alpine wetland of the Qinghai-Tibet Plateau remains enigmatic. Utilizing high-throughput sequencing analysis of nirS-type functional genes, this study delved into the dynamic response mechanism of nirS-type denitrifiers to precipitation changes in the alpine wetland of Qinghai Lake. The findings revealed that nirS-type denitrifiers in the alpine wetland of Qinghai Lake were primarily Proteobacteria, and Alpha diversity exhibited a negative correlation with the precipitation gradient, with deterministic processes predominating in the community assembly of denitrifying microbes. A 50% increase in rainfall shifted the community assembly process of denitrifiers from deterministic to stochastic. Dominant microflora at the genus level responded significantly to precipitation changes, with aerobic bacteria comprising the majority of differentially abundant taxa (55.56%). As precipitation increased, the complexity of the microbial interaction network decreased, and a 25% reduction in precipitation notably elevated the relative abundance of three key functional groups: chemoheterotrophic, aerobic chemoheterotrophic, and nitrogen fixation. Precipitation notably emerged as the primary regulator of nirS-type denitrifiers in the alpine wetland of Qinghai Lake, accounting for 51% of the variation in community composition. In summary, this study offers a fresh perspective for investigating the ecological processes of nitrogen cycling in alpine ecosystems by examining the diversity and community composition of nirS-type denitrifiers in response to precipitation changes.
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Affiliation(s)
- Ni Zhang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Kelong Chen
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Department of Earth and Environmental Science, Institute of Global Environmental Change, School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an 710061, China
- Guanzhong Plain Ecological Environment Change and Comprehensive Treatment National Observation and Research Station, Xi'an 710061, China
| | - Wei Ji
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Ziwei Yang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Zhirong Chen
- College of Resources, Environment and Life Sciences, Ningxia Normal University, Guyuan 756099, China
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30
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La S, Li J, Ma S, Liu X, Gao L, Tian Y. Protective role of native root-associated bacterial consortium against root-knot nematode infection in susceptible plants. Nat Commun 2024; 15:6723. [PMID: 39112511 PMCID: PMC11306399 DOI: 10.1038/s41467-024-51073-7] [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: 11/02/2023] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Root-knot nematodes (RKNs) are a global menace to agricultural crop production. The role of root-associated microbes (RAMs) in plant protection against RKN infection remains unclear. Here we observe that cucumber (highly susceptible to Meloidogyne incognita) exhibits a consistently lower susceptibility to M. incognita in the presence of native RAMs in three distinct soils. Nematode infection alters the assembly of bacterial RAMs along the life cycle of M. incognita. Particularly, the loss of bacterial diversity of RAMs exacerbates plant susceptibility to M. incognita. A diverse range of native bacterial strains isolated from M. incognita-infected roots has nematode-antagonistic activity. Increasing the number of native bacterial strains causes decreasing nematode infection, which is lowest when six or more bacterial strains are present. Multiple simplified synthetic communities consisting of six bacterial strains show pronounced inhibitory effects on M. incognita infection in plants. These inhibitory effects are underpinned via multiple mechanisms including direct inhibition of infection, secretion of anti-nematode substances, and regulation of plant defense responses. This study highlights the role of native bacterial RAMs in plant resistance against RKNs and provides a useful insight into the development of a sustainable way to protect susceptible plants.
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Affiliation(s)
- Shikai La
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
- Institute of Economic Crops, Hebei Academy of Agricultural and Forestry Sciences, Heping West Road No. 598, Shijiazhuang, 050051, China
| | - Jiafan Li
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Si Ma
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Xingqun Liu
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China
| | - Lihong Gao
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China.
| | - Yongqiang Tian
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, China.
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31
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Anthony WE, Allison SD, Broderick CM, Chavez Rodriguez L, Clum A, Cross H, Eloe-Fadrosh E, Evans S, Fairbanks D, Gallery R, Gontijo JB, Jones J, McDermott J, Pett-Ridge J, Record S, Rodrigues JLM, Rodriguez-Reillo W, Shek KL, Takacs-Vesbach T, Blanchard JL. From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology. ENVIRONMENTAL MICROBIOME 2024; 19:56. [PMID: 39095861 PMCID: PMC11295382 DOI: 10.1186/s40793-024-00599-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.
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Affiliation(s)
| | - Steven D Allison
- University of California Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Caitlin M Broderick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | | | - Alicia Clum
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hugh Cross
- National Ecological Observatory Network - Battelle, Boulder, CO, USA
| | | | - Sarah Evans
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Dawson Fairbanks
- University of California Riverside, Riverside, CA, USA
- The University of Arizona, Tucson, AZ, USA
| | | | | | - Jennifer Jones
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Jason McDermott
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, 95343, USA
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Niu Y, Kang E, Li Y, Zhang X, Yan Z, Li M, Yan L, Zhang K, Wang X, Yang A, Yu X, Kang X, Cui X. Non-flooding conditions caused by water table drawdown alter microbial network complexity and decrease multifunctionality in alpine wetland soils. ENVIRONMENTAL RESEARCH 2024; 254:119152. [PMID: 38754612 DOI: 10.1016/j.envres.2024.119152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Several soil functions of alpine wetland depend on microbial communities, including carbon storage and nutrient cycling, and soil microbes are highly sensitive to hydrological conditions. Wetland degradation is often accompanied by a decline in water table. With the water table drawdown, the effects of microbial network complexity on various soil functions remain insufficiently understood. In this research, we quantified soil multifunctionality of flooded and non-flooded sites in the Lalu Wetland on the Tibetan Plateau. We employed high-throughput sequencing to investigate the microbial community responses to water table depth changes, as well as the relationships between microbial network properties and soil multifunctionality. Our findings revealed a substantial reduction in soil multifunctionality at both surface and subsurface soil layers (0-20 cm and 20-40 cm) in non-flooded sites compared to flooded sites. The α-diversity of bacteria in the surface soil of non-flooded sites was significantly lower than that in flooded sites. Microbial network properties (including the number of nodes, number of edges, average degree, density, and modularity of co-occurrence networks) exhibited significant correlations with soil multifunctionality. This study underscores the adverse impact of non-flooded conditions resulting from water table drawdown on soil multifunctionality in alpine wetland soils, driven by alterations in microbial community structure. Additionally, we identified soil pH and moisture content as pivotal abiotic factors influencing soil multifunctionality, with microbial network complexity emerging as a valuable predictor of multifunctionality.
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Affiliation(s)
- Yuechuan Niu
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Enze Kang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaodong Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Zhongqing Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Meng Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Liang Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Kerou Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaodong Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ao Yang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaoshun Yu
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaoming Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China.
| | - Xiaoyong Cui
- University of Chinese Academy of Sciences, Beijing 100049, China.
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Jiang P, Wang Y, Zhang Y, Fei J, Rong X, Peng J, Yin L, Luo G. Intercropping enhances maize growth and nutrient uptake by driving the link between rhizosphere metabolites and microbiomes. THE NEW PHYTOLOGIST 2024; 243:1506-1521. [PMID: 38874414 DOI: 10.1111/nph.19906] [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: 10/24/2023] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields and resource utilization. However, the precise mechanisms through which the interactions between rhizosphere metabolites and the microbiome contribute to plant production remain ambiguous, thus impeding the understanding of the yield-enhancing advantages of intercropping. This study conducted field experiments (initiated in 2013) and pot experiments, coupled with multi-omics analysis, to investigate plant-metabolite-microbiome interactions in the rhizosphere of maize. Field-based data revealed significant differences in metabolite and microbiome profiles between the rhizosphere soils of maize monoculture and intercropping. In particular, intercropping soils exhibited higher microbial diversity and metabolite chemodiversity. The chemodiversity and composition of rhizosphere metabolites were significantly related to the diversity, community composition, and network complexity of soil microbiomes, and this relationship further impacted plant nutrient uptake. Pot-based findings demonstrated that the exogenous application of a metabolic mixture comprising key components enriched by intercropping (soyasapogenol B, 6-hydroxynicotinic acid, lycorine, shikimic acid, and phosphocreatine) significantly enhanced root activity, nutrient content, and biomass of maize in natural soil, but not in sterilized soil. Overall, this study emphasized the significance of rhizosphere metabolite-microbe interactions in enhancing yields in intercropping systems. It can provide new insights into rhizosphere controls within intensive agroecosystems, aiming to enhance crop production and ecosystem services.
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Affiliation(s)
- Pan Jiang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
| | - Yizhe Wang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
| | - Yuping Zhang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jiangchi Fei
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Xiangmin Rong
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jianwei Peng
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Lichu Yin
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Gongwen Luo
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
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Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 PMCID: PMC11323152 DOI: 10.1016/j.mib.2024.102496] [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: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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35
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Zhang T, Song B, Wang L, Li Y, Wang Y, Yuan M. Spartina alterniflora invasion reduces soil microbial diversity and weakens soil microbial inter-species relationships in coastal wetlands. Front Microbiol 2024; 15:1422534. [PMID: 39149207 PMCID: PMC11325588 DOI: 10.3389/fmicb.2024.1422534] [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: 04/24/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024] Open
Abstract
Soil microorganisms play a crucial role in the plant invasion process, acting as both drivers of and responders to plant invasion. However, the effects of plant invasion on the complexity and stability of co-occurrence networks of soil microbial communities remain unclear. Here, we investigated how the invasion of Spartina alterniflora affected the diversity, composition, and co-occurrence networks of soil bacterial and fungal communities in the Yellow River Delta, China. Compared to the native plant (Suaeda salsa), S. alterniflora invasion decreased the α-diversity of soil bacterial communities but did not affect that of fungal communities. The β-diversity of soil bacterial and fungal communities under S. salsa and S. alterniflora habitats also differed dramatically. S. alterniflora invasion increased the relative abundance of the copiotrophic phylum Bacteroidota, whereas decreased the relative abundances of the oligotrophic phyla Acidobacteriota and Gemmatimonadota. Additionally, the relative abundance of Chytridiomycota, known for its role in degrading recalcitrant organic matter, increased substantially within the soil fungal community. Functional predictions revealed that S. alterniflora invasion increased the relative abundance of certain soil bacteria involved in carbon and nitrogen cycling, including aerobic chemoheterotrophy, nitrate reduction, and nitrate respiration. More importantly, S. alterniflora invasion reduced the complexity and stability of both soil bacterial and fungal community networks. The shifts in soil microbial community structure and diversity were mainly induced by soil available nutrients and soil salinity. Overall, our study highlights the profound impacts of S. alterniflora invasion on soil microbial communities, which could further indicate the modification of ecosystem functioning by invasive species.
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Affiliation(s)
- Tao Zhang
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute for Peat and Mire Research, Northeast Normal University, Changchun, China
| | - Bing Song
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Luwen Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yong Li
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Yi Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Min Yuan
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
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36
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Qin S, Zhang D, Wei B, Yang Y. Dual roles of microbes in mediating soil carbon dynamics in response to warming. Nat Commun 2024; 15:6439. [PMID: 39085268 PMCID: PMC11291496 DOI: 10.1038/s41467-024-50800-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Understanding the alterations in soil microbial communities in response to climate warming and their controls over soil carbon (C) processes is crucial for projecting permafrost C-climate feedback. However, previous studies have mainly focused on microorganism-mediated soil C release, and little is known about whether and how climate warming affects microbial anabolism and the subsequent C input in permafrost regions. Here, based on a more than half-decade of in situ warming experiment, we show that compared with ambient control, warming significantly reduces microbial C use efficiency and enhances microbial network complexity, which promotes soil heterotrophic respiration. Meanwhile, microbial necromass markedly accumulates under warming likely due to preferential microbial decomposition of plant-derived C, further leading to the increase in mineral-associated organic C. Altogether, these results demonstrate dual roles of microbes in affecting soil C release and stabilization, implying that permafrost C-climate feedback would weaken over time with dampened response of microbial respiration and increased proportion of stable C pool.
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Affiliation(s)
- Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- China National Botanical Garden, 100093, Beijing, China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- China National Botanical Garden, 100093, Beijing, China
| | - Bin Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- China National Botanical Garden, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- China National Botanical Garden, 100093, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Lei L, Zhao LY, Cheng R, Zhang H, Xia M, Chen XL, Kudriashov V, Liu K, Zhang WH, Jiang H, Chen Y, Zhu L, Zhou H, Yang K, Hu T, Hu JK. Distinct oral-associated gastric microbiota and Helicobacter pylori communities for spatial microbial heterogeneity in gastric cancer. mSystems 2024; 9:e0008924. [PMID: 38940519 PMCID: PMC11265414 DOI: 10.1128/msystems.00089-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
The gastric microbial community plays a fundamental role in gastric cancer (GC), and the two main anatomical subtypes of GC, non-cardia and cardia GC, are associated with different risk factors (Helicobacter pylori for non-cardia GC). To decipher the different microbial spatial communities of GC, we performed a multicenter retrospective analysis to characterize the gastric microbiota in 223 GC patients, including H. pylori-positive or -negative patients, with tumors and paired adjacent normal tissues, using third-generation sequencing. In the independent validation cohort, both dental plaque and GC tumoral tissue samples were collected and sequenced. The prevalence of H. pylori and oral-associated bacteria was verified using fluorescence in situ hybridization (FISH) assays in GC tumoral tissues and matched nontumoral tissues. We found that the vertical distribution of the gastric microbiota, at the upper, middle, and lower third sites of GC, was likely an important factor causing microbial diversity in GC tumor tissues. The oral-associated microbiota cluster, which included Veillonella parvula, Streptococcus oralis, and Prevotella intermedia, was more abundant in the upper third of the GC. However, H. pylori was more abundant in the lower third of the GC and exhibited a significantly high degree of microbial correlation. The oral-associated microbiota module was co-exclusive with H. pylori in the lower third site of the GC tumoral tissue. Importantly, H. pylori-negative GC patients with oral-associated gastric microbiota showed worse overall survival, while the increase in microbial abundance in H. pylori-positive GC patients showed no difference in overall survival. The prevalence of V. parvula in both the dental plaque and GC tissue samples was concordant in the independent validation phase. We showed that the oral-associated species V. parvula and S. oralis were correlated with overall survival. Our study highlights the roles of the oral-associated microbiota in the upper third of the GC. In addition, oral-associated species may serve as noninvasive screening tools for the management of GC and an independent prognostic factor for H. pylori-negative GCs. IMPORTANCE Our study highlights the roles of the oral-associated microbiota in the upper third of gastric cancer (GC).We showed that the oral-associated species Veillonella parvula and Streptococcus oralis were correlated with overall survival. In addition, oral-associated species may serve as noninvasive screening tools for the management of GC and an independent prognostic factor for Helicobacter pylori-negative GCs.
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Affiliation(s)
- Lei Lei
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Lin-Yong Zhao
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Ran Cheng
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hongyu Zhang
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mengying Xia
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiao-Long Chen
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Valentin Kudriashov
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Kai Liu
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Wei-Han Zhang
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Han Jiang
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Chen
- Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
| | - Liang Zhu
- Nuffield Department of Medicine, University of Oxford, Target Discovery Institute, Center for Medicines Discovery, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Oxford, United Kingdom
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Kun Yang
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Tao Hu
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jian-Kun Hu
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
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Gangwar RK, Táncsics A, Makádi M, Farkas M, Cserháti M, Michéli E, Fuchs M, Szegi T. Bacterial community composition of Hungarian salt-affected soils under different land uses. Biol Futur 2024:10.1007/s42977-024-00235-1. [PMID: 39030426 DOI: 10.1007/s42977-024-00235-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
Salinization and sodification are serious and worldwide growing threats to healthy soil functions. Although plants developed a plethora of traits to cope with high salinity, soil bacteria are also essential players of the adaptation process. However, there is still lack of knowledge on how other biotic and abiotic factors, such as land use or different soil properties, affect the bacterial community structure of these soils. Therefore, besides soil chemical and physical investigations, bacterial communities of differently managed salt-affected soils were analysed through 16S rRNA gene Illumina amplicon sequencing and compared. Results have shown that land use and soil texture were the main drivers in shaping the bacterial community structure of the Hungarian salt-affected soils. It was observed that at undisturbed pasture and meadow sites, soil texture and the ratio of vegetation cover were the determinative factors shaping the bacterial community structures, mainly at the level of phylum Acidobacteriota. Sandy soil texture promoted the high abundance of members of the class Blastocatellia, while at the slightly disturbed meadow soil showing high clay content was dominated by members of the class Acidobacteriia. The OTUs belonging to the class Ktedonobacteria, which were reported mostly in geothermal sediments, reached a relatively high abundance in the meadow soil.
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Affiliation(s)
- Ravi Kumar Gangwar
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary.
| | - Marianna Makádi
- Research Institute of Nyíregyháza, IAREF, University of Debrecen, Westsik Vilmos utca 4-6, Nyíregyháza, 4400, Hungary
| | - Milán Farkas
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - Mátyás Cserháti
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - Erika Michéli
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - Márta Fuchs
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - Tamás Szegi
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
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Guo Y, Wang H, Du L, Shi P, Du S, Xu Z, Jiao S, Chen W, Chen S, Wei G. Microbial communities mediate the effect of cover cropping on soil ecosystem functions under precipitation reduction in an agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174572. [PMID: 38986707 DOI: 10.1016/j.scitotenv.2024.174572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Cover cropping is a sustainable agricultural practice that profoundly influences soil microbial communities and ecosystem functions. However, the responses of soil ecosystem functions and microbial communities to cover cropping under the projected changes in precipitation, remain largely unexplored. To address this gap, a field experiment with cover cropping (control, hairy vetch, ryegrass, and hairy vetch plus ryegrass) and precipitation reduction (ambient precipitation and 50 % reduction in ambient precipitation) treatments was conducted from 2018 to 2020 in an agroecosystem located in the Guanzhong Plain of China. Soil ecosystem functions related to nutrient storage, nutrient cycling, and organic matter decomposition were measured to assess the soil multifunctionality index and bacterial and fungal communities were determined by Illumina NovaSeq sequencing. The results indicated that cover cropping enhanced soil multifunctionality index, and reduced precipitation strengthened this effect. Microbial community composition, rather than microbial diversity, was significantly altered by cover cropping regardless of precipitation reduction. Cover cropping increased the microbial network complexity and stability, but this effect was dampened by reduced precipitation. The microbial community composition and network complexity significantly and positively correlated with soil multifunctionality index under ambient and reduced precipitation conditions. Linear regression analyses and structural equation models collectively demonstrated that the increase in soil multifunctionality index was attributed to cover cropping-induced changes in microbial community composition and network complexity, irrespective of precipitation reduction. This study highlights the crucial role of microbial communities in driving the response of soil multifunctionality to cover cropping in the context of reduced precipitation, which has important implications for agricultural management and sustainability under future climate change scenarios.
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Affiliation(s)
- Yanqing Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; College of Life Sciences, Linyi University, Linyi 276000, China
| | - Huan Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lanlan Du
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi 276000, China
| | - Peng Shi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Sen Du
- National Agro-Tech Extension and Service Center, Beijing 100125, China
| | - Zhiwen Xu
- Lingxian Biological Agriculture Co., Ltd., Qinhuangdao 066000, China
| | - Shuo Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Sanfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Kumar D, Ali M, Sharma N, Sharma R, Manhas RK, Ohri P. Unboxing PGPR-mediated management of abiotic stress and environmental cleanup: what lies inside? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:47423-47460. [PMID: 38992305 DOI: 10.1007/s11356-024-34157-1] [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: 02/16/2024] [Accepted: 06/24/2024] [Indexed: 07/13/2024]
Abstract
Abiotic stresses including heavy metal toxicity, drought, salt and temperature extremes disrupt the plant growth and development and lowers crop output. Presence of environmental pollutants further causes plants suffering and restrict their ability to thrive. Overuse of chemical fertilizers to reduce the negative impact of these stresses is deteriorating the environment and induces various secondary stresses to plants. Therefore, an environmentally friendly strategy like utilizing plant growth-promoting rhizobacteria (PGPR) is a promising way to lessen the negative effects of stressors and to boost plant growth in stressful conditions. These are naturally occurring inhabitants of various environments, an essential component of the natural ecosystem and have remarkable abilities to promote plant growth. Furthermore, multifarious role of PGPR has recently been widely exploited to restore natural soil against a range of contaminants and to mitigate abiotic stress. For instance, PGPR may mitigate metal phytotoxicity by boosting metal translocation inside the plant and changing the metal bioavailability in the soil. PGPR have been also reported to mitigate other abiotic stress and to degrade environmental contaminants remarkably. Nevertheless, despite the substantial quantity of information that has been produced in the meantime, there has not been much advancement in either the knowledge of the processes behind the alleged positive benefits or in effective yield improvements by PGPR inoculation. This review focuses on addressing the progress accomplished in understanding various mechanisms behind the protective benefits of PGPR against a variety of abiotic stressors and in environmental cleanups and identifying the cause of the restricted applicability in real-world.
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Affiliation(s)
- Deepak Kumar
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Mohd Ali
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Nandni Sharma
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Roohi Sharma
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Rajesh Kumari Manhas
- Department of Microbiology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
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41
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Kang Y, Shen L, Li C, Huang Y, Chen L. Effects of vegetation degradation on soil microbial communities and ecosystem multifunctionality in a karst region, southwest China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 363:121395. [PMID: 38852407 DOI: 10.1016/j.jenvman.2024.121395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/20/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Vegetation degradation caused by intense human disturbances poses a significant challenge to the preservation and improvement of ecosystem functions and services in the karst region of southwest China. Soil microorganisms are major regulators of ecosystem multifunctionality (EMF). Currently, there is a dearth of knowledge regarding the effects of vegetation degradation on soil microbial communities and their corresponding multiple ecosystem functions in karst regions. In this study, we selected the vegetation degradation sequences of second natural forest (NF), agroforestry (AS) and cropland (CL) to investigate the diversity of bacterial, fungal and protistan communities, and their hierarchical co-occurrence network, and EMF to explore the relationships between them. Compared to the NF, the carbon cycling index, nitrogen cycling index, soil water regulation power, and the EMF were significantly decreased by 8.2%-50.6%, 48.7%-86.8%, 19.8%-24.5%, and 31.4%-69.5% in the AS and CL, respectively. The development of EMF can be explained by the fungal, protistan and microbial hierarchical β-diversity, as well as the complexity (e.g. degree) of microbial hierarchical interactions during the process of vegetation degradation. Notably, correlations between the abundances of sensitive amplicon sequence variants (sASVs) for different karst vegetation types and EMF varied in distinct network modules, being positive in module 1 and negative in module 2. Moreover, the relative abundance of keystone taxa in fungal and protistan communities provided greater contributions to EMF than the bacterial communities. Additionally, random forest modeling showed that carbon and nitrogen sources, and soil water content, and trace elements (e.g. exchangeable magnesium, iron, manganese, and zinc) were identified as key driving factors of the EMF. Collectively, our findings demonstrate that vegetation degradation obviously alters soil microbial diversities and hierarchical interactions, emphasizing their key role in maintaining ecosystem functions and health in karst regions.
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Affiliation(s)
- Yalong Kang
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China; Ministry of Education Key Laboratory for Transboundary Eco-Security of Southwest, Kuming, China
| | - Linjun Shen
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China; Ministry of Education Key Laboratory for Transboundary Eco-Security of Southwest, Kuming, China
| | - Canfeng Li
- Kunming Natural Resources Comprehensive Survey Center of China Geological Survey/Technology Innovation Center for Natural Ecosystem Carbon Sink, Ministry of Natural Resources, 650100: Kunming, China
| | - Yong Huang
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China.
| | - Liding Chen
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China; Ministry of Education Key Laboratory for Transboundary Eco-Security of Southwest, Kuming, China
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Li K, Chen A, Sheng R, Hou H, Zhu B, Wei W, Zhang W. Long-term chemical and organic fertilization induces distinct variations of microbial associations but unanimous elevation of soil multifunctionality. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172862. [PMID: 38705286 DOI: 10.1016/j.scitotenv.2024.172862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024]
Abstract
Intricate microbial associations contribute greatly to the multiple functions (multifunctionality) of natural ecosystems. However, the relationship between microbial associations and soil multifunctionality (SMF) in artificial ecosystems, particularly in agricultural ecosystem with frequent fertilization, remains unclear. In this study, based on a 28-year paddy field experiment, high-throughput sequencing and networks analysis was performed to investigate changes in soil microbial (archaea, bacteria, fungi, and protists) associations and how these changes correlate with SMF under long-term fertilization. Compared to no fertilization (CK), both chemical fertilization with N, P, and K (CF) and chemical fertilization plus rice straw retention (CFR) treatments showed significantly higher soil nutrient content, grain yield, microbial abundance, and SMF. With the exception of archaeal diversity, the CF treatment exhibited the lowest bacterial, fungal, and protist diversity, and the simplest microbial co-occurrence network. In contrast, the CFR treatment had the lowest archaeal diversity, but the highest bacterial, fungal, and protist diversity. Moreover, the CFR treatment exhibited the most complex microbial co-occurrence network with the highest number of nodes, edges, and interkingdom edges. These results highlight that both chemical fertilization with and without straw retention caused high ecosystem multifunctionality while changing microbial association oppositely. Furthermore, these results indicate that rice straw retention contributes to the development of the soil microbiome and ensures the sustainability of high-level ecosystem multifunctionality.
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Affiliation(s)
- Ke Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; College of Resource and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anlei Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Rong Sheng
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Haijun Hou
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Baoli Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wenxue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wenzhao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
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43
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Gao C, Bezemer TM, de Vries FT, van Bodegom PM. Trade-offs in soil microbial functions and soil health in agroecosystems. Trends Ecol Evol 2024:S0169-5347(24)00138-1. [PMID: 38910081 DOI: 10.1016/j.tree.2024.05.013] [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: 01/31/2024] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/25/2024]
Abstract
Soil microbial communities play pivotal roles in maintaining soil health in agroecosystems. However, how the delivery of multiple microbial functions in agroecosystems is maintained remains poorly understood. This may put us at risk of incurring unexpected trade-offs between soil functions. We elucidate how interactions between soil microbes can lead to trade-offs in the functioning of agricultural soils. Interactions within soil microbial communities can result in not only positive but also neutral and negative relationships among soil functions. Altering soil conditions through soil health-improving agricultural management can alleviate these functional trade-offs by promoting the diversity and interrelationships of soil microbes, which can help to achieve more productive and sustainable agroecosystems.
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Affiliation(s)
- Chenguang Gao
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands.
| | - Thiemo Martijn Bezemer
- Institute of Biology, Above-Belowground Interactions Group, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1090 GE Amsterdam, The Netherlands
| | - Peter M van Bodegom
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
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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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Li D, Wu C, Wu J. Soil fungal community has higher network stability than bacterial community in response to warming and nitrogen addition in a subtropical primary forest. Appl Environ Microbiol 2024; 90:e0000124. [PMID: 38771056 PMCID: PMC11218647 DOI: 10.1128/aem.00001-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Global change factors are known to strongly affect soil microbial community function and composition. However, as of yet, the effects of warming and increased anthropogenic nitrogen deposition on soil microbial network complexity and stability are still unclear. Here, we examined the effects of experimental warming (3°C above ambient soil temperature) and nitrogen addition (5 g N m-2 year-1) on the complexity and stability of the soil microbial network in a subtropical primary forest. Compared to the control, warming increased |negative cohesion|:positive cohesion by 7% and decreased network vulnerability by 5%; nitrogen addition decreased |negative cohesion|:positive cohesion by 10% and increased network vulnerability by 11%. Warming and decreased soil moisture acted as strong filtering factors that led to higher bacterial network stability. Nitrogen addition reduced bacterial network stability by inhibiting soil respiration and increasing resource availability. Neither warming nor nitrogen addition changed fungal network complexity and stability. These findings suggest that the fungal community is more tolerant than the bacterial community to climate warming and nitrogen addition. The link between bacterial network stability and microbial community functional potential was significantly impacted by nitrogen addition and warming, while the response of soil microbial network stability to climate warming and nitrogen deposition may be independent of its complexity. Our findings demonstrate that changes in microbial network structure are crucial to ecosystem management and to predict the ecological consequences of global change in the future. IMPORTANCE Soil microbes play a very important role in maintaining the function and health of forest ecosystems. Unfortunately, global change factors are profoundly affecting soil microbial structure and function. In this study, we found that climate warming promoted bacterial network stability and nitrogen deposition decreased bacterial network stability. Changes in bacterial network stability had strong effects on bacterial community functional potentials linked to metabolism, nitrogen cycling, and carbon cycling, which would change the biogeochemical cycle in primary forests.
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Affiliation(s)
- Debao Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Laboratory of Soil Ecology and Health in Universities of Yunnan Province, Yunnan University, Kunming, China
| | - Chuansheng Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, China
| | - Jianping Wu
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Laboratory of Soil Ecology and Health in Universities of Yunnan Province, Yunnan University, Kunming, China
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Wu WF, Li XY, Chen SC, Jin BJ, Wu CY, Li G, Sun CL, Zhu YG, Lin XY. Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172622. [PMID: 38642761 DOI: 10.1016/j.scitotenv.2024.172622] [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: 01/25/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.
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Affiliation(s)
- Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Bing-Jie Jin
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Cheng-Liang Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
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Hu Y, Zhang H, Sun X, Zhang B, Wang Y, Rafiq A, Jia H, Liang C, An S. Impact of grassland degradation on soil multifunctionality: Linking to protozoan network complexity and stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172724. [PMID: 38663601 DOI: 10.1016/j.scitotenv.2024.172724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.
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Affiliation(s)
- Yang Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haolin Zhang
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Xinya Sun
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Bicheng Zhang
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, Shannxi 712100, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Yubin Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Anum Rafiq
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Hongtao Jia
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, 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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49
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Yu Y, Guo Q, Zhang S, Guan Y, Jiang N, Zhang Y, Mao R, Bai K, Buriyev S, Samatov N, Zhang X, Yang W. Maize residue retention shapes soil microbial communities and co-occurrence networks upon freeze-thawing cycles. PeerJ 2024; 12:e17543. [PMID: 38887621 PMCID: PMC11182024 DOI: 10.7717/peerj.17543] [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: 01/30/2024] [Accepted: 05/19/2024] [Indexed: 06/20/2024] Open
Abstract
Maize residue retention is an effective agricultural practice for improving soil fertility in black soil region, where suffered from long freezing-thawing periods and intense freeze-thawing (FT) cycles. However, very few studies have examined the influence of maize residue retention on soil microbial communities under FT cycles. We investigated the response of soil microbial communities and co-occurrence networks to maize residue retention at different FT intensities over 12 cycles using a microcosm experiment conditioned in a temperature incubator. Our results indicated that maize residue retention induced dramatic shifts in soil archaeal, bacterial and fungal communities towards copiotroph-dominated communities. Maize residue retention consistently reduced soil fungal richness across all cycles, but this effect was weaker for archaea and bacteria. Normalized stochastic ratio analysis revealed that maize residue retention significantly enhanced the deterministic process of archaeal, bacterial and fungal communities. Although FT intensity significantly impacted soil respiration, it did not induce profound changes in soil microbial diversity and community composition. Co-occurrence network analysis revealed that maize residue retention simplified prokaryotic network, while did not impact fungal network complexity. The network robustness index suggested that maize residue retention enhanced the fungal network stability, but reduced prokaryotic network stability. Moreover, the fungal network in severe FT treatment harbored the most abundant keystone taxa, mainly being cold-adapted fungi. By identifying modules in networks, we observed that prokaryotic Module #1 and fungal Module #3 were enhanced by maize residue retention and contributed greatly to soil quality. Together, our results showed that maize residue retention exerted stronger influence on soil microbial communities and co-occurrence network patterns than FT intensity and highlighted the potential of microbial interactions in improving soil functionality.
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Affiliation(s)
- Yang Yu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Quankuan Guo
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Shuhan Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yupeng Guan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nana Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Yang Zhang
- College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Rong Mao
- College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Keyu Bai
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Salimjan Buriyev
- Institute of Environment and Nature Conservation Technologies of the Ministry of Ecology, Environmental Protection, and Climate Change of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Nuriddin Samatov
- Institute of Environment and Nature Conservation Technologies of the Ministry of Ecology, Environmental Protection, and Climate Change of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ximei Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Yang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
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50
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Li L, Huang J, Liu Y, Zhang Q, Han Q, Liu Y, Zhang G, Wang X, Zhao W, Liu L. Analysis of microbial community composition and diversity in the rhizosphere of Salvia miltiorrhiza at different growth stages. Int Microbiol 2024:10.1007/s10123-024-00542-6. [PMID: 38833100 DOI: 10.1007/s10123-024-00542-6] [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: 01/30/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024]
Abstract
Salvia miltiorrhiza is a kind of medicinal plant with various pharmacological activities. Few studies on the composition and diversity of rhizosphere microbial communities at different growth stages have been conducted on Salvia miltiorrhiz; in particular, salviorrhiza grows in soil that has been continuously planted for 3 years. The purpose of this study was to understand the changes of soil physicochemical properties of Salvia miltiorrhiza at different growth stages, and to study the composition and diversity of rhizosphere microbial community at different growth stages. Illumina NovaSeq sequencing technology was used to analyze the bacterial 16S rRNA gene and the fungal ITS region in the rhizosphere soil of Salvia miltiorrhiza at different growth stages. The results showed that the dominant bacterial phyla in the Salvia miltiorrhiza rhizosphere were Proteobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The dominant fungal phyla were Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota. During the growth of Salvia miltiorrhiza, the physical and chemical properties of soil changed. As the Salvia miltiorrhiza grew, the content of available phosphorus, available potassium, pH, nitrate nitrogen, and ammonium nitrogen significantly decreased. Ammonium nitrogen and nitrate nitrogen had a greater impact on the bacterial community structure in the rhizosphere than on the fungal community structure. The work was to reveal differences in the rhizosphere bacterial and fungal community structure during different growth stages of Salvia miltiorrhiza, further understand the changes of rhizosphere microbial ecological characteristics and soil physicochemical properties during the cultivation of Salvia miltiorrhiza.
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Affiliation(s)
- Lina Li
- College of Agriculture and Forestry, Linyi University, Linyi, 276000, China
| | - Juying Huang
- College of Agriculture and Forestry, Linyi University, Linyi, 276000, China
| | - Yushan Liu
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China
| | - Qian Zhang
- Linyi Academy of Agricultural Sciences, Linyi, 276012, China
| | - Qingdian Han
- College of Agriculture and Forestry, Linyi University, Linyi, 276000, China.
| | - Yunguo Liu
- College of Agriculture and Forestry, Linyi University, Linyi, 276000, China
| | - Guangna Zhang
- College of Agriculture and Forestry, Linyi University, Linyi, 276000, China
| | - Xiao Wang
- Specialized Cooperative for Planting Traditional Chinese Medicine, Yuantong, Pingyi County, 273300, China
| | - Wenfei Zhao
- Linyi Academy of Agricultural Sciences, Linyi, 276012, China
| | - Lingxiao Liu
- Linyi Academy of Agricultural Sciences, Linyi, 276012, China
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