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Jiang Y, Zhang Z, Jiang J, Zhu F, Guo X, Jia P, Li H, Liu Z, Huang S, Zhang Y, Xue S. Enhancement of nitrogen on core taxa recruitment by Penicillium oxalicum stimulated microbially-driven soil formation in bauxite residue. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134647. [PMID: 38762986 DOI: 10.1016/j.jhazmat.2024.134647] [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: 02/26/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Microbially-driven soil formation process is an emerging technology for the ecological rehabilitation of alkaline tailings. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. Herein, a 1-year field-scale experiment was applied to demonstrate the effect of nitrogen input on the structure and function of the microbiome in alkaline bauxite residue. Results showed that the contents of nutrient components were increased with Penicillium oxalicum (P. oxalicum) incorporation, as indicated by the increasing of carbon and nitrogen mineralization and enzyme metabolic efficiency. Specifically, the increasing enzyme metabolic efficiency was associated with nitrogen input, which shaped the microbial nutrient acquisition strategy. Subsequently, we evidenced that P. oxalicum played a significant role in shaping the assemblages of core bacterial taxa and influencing ecological functioning through intra- and cross-kingdom network analysis. Furthermore, a recruitment experiment indicated that nitrogen enhanced the enrichment of core microbiota (Nitrosomonas, Bacillus, Pseudomonas, and Saccharomyces) and may provide benefits to fungal community bio-diversity and microbial network stability. Collectively, these results demonstrated nitrogen-based coexistence patterns among P. oxalicum and microbiome and revealed P. oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. It will aid in promoting soil formation and ecological rehabilitation of bauxite residue. ENVIRONMENT IMPLICATION: Bauxite residue is a highly alkaline solid waste generated during the Bayer process for producing alumina. Attempting to transform bauxite residue into a stable soil-like substrate using low-cost microbial resources is a highly promising engineering. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. In this study, we evidenced the nitrogen-based coexistence patterns among Penicillium oxalicum and microbiome and revealed Penicillium oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. This study can improve the understanding of core microbes' assemblies that affect the microbiome physiological traits in soil formation processes.
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Affiliation(s)
- Yifan Jiang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Ziying Zhang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Jun Jiang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Feng Zhu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Xuyao Guo
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Pu Jia
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hongzhe Li
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhongkai Liu
- Zhengzhou Non-ferrous Metals Research Institute Co., Ltd of Chalco, Zhengzhou 450000, China
| | - Shiwei Huang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Yufei Zhang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Shengguo Xue
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
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Li DD, Wang J, Jiang Y, Zhang P, Liu Y, Li YZ, Zhang Z. Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities. MICROBIOME 2024; 12:120. [PMID: 38956705 PMCID: PMC11218364 DOI: 10.1186/s40168-024-01838-5] [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: 04/19/2022] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.
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Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Jia X, Lin S, Wang Y, Zhang Q, Jia M, Li M, Chen Y, Cheng P, Hong L, Zhang Y, Ye J, Wang H. Recruitment and Aggregation Capacity of Tea Trees to Rhizosphere Soil Characteristic Bacteria Affects the Quality of Tea Leaves. PLANTS (BASEL, SWITZERLAND) 2024; 13:1686. [PMID: 38931118 PMCID: PMC11207862 DOI: 10.3390/plants13121686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
There are obvious differences in quality between different varieties of the same plant, and it is not clear whether they can be effectively distinguished from each other from a bacterial point of view. In this study, 44 tea tree varieties (Camellia sinensis) were used to analyze the rhizosphere soil bacterial community using high-throughput sequencing technology, and five types of machine deep learning were used for modeling to obtain characteristic microorganisms that can effectively differentiate different varieties, and validation was performed. The relationship between characteristic microorganisms, soil nutrient transformation, and tea quality formation was further analyzed. It was found that 44 tea tree varieties were classified into two groups (group A and group B) and the characteristic bacteria that distinguished them came from 23 genera. Secondly, the content of rhizosphere soil available nutrients (available nitrogen, available phosphorus, and available potassium) and tea quality indexes (tea polyphenols, theanine, and caffeine) was significantly higher in group A than in group B. The classification result based on both was consistent with the above bacteria. This study provides a new insight and research methodology into the main reasons for the formation of quality differences among different varieties of the same plant.
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Affiliation(s)
- Xiaoli Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan 364012, China
| | - Yuhua Wang
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qi Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Miao Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Mingzhe Li
- College of Life Science, Longyan University, Longyan 364012, China
| | - Yiling Chen
- College of Life Science, Longyan University, Longyan 364012, China
| | - Pengyuan Cheng
- College of Life Science, Longyan University, Longyan 364012, China
| | - Lei Hong
- College of Life Science, Longyan University, Longyan 364012, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Jianghua Ye
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Haibin Wang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
- College of Life Science, Longyan University, Longyan 364012, China
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Wang Y, Liao R, Pan H, Wang X, Wan X, Han B, Song C. Comparative metabolic profiling of the mycelium and fermentation broth of Penicillium restrictum from Peucedanum praeruptorum rhizosphere. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13286. [PMID: 38844388 PMCID: PMC11156492 DOI: 10.1111/1758-2229.13286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/30/2024] [Indexed: 06/10/2024]
Abstract
Microorganisms in the rhizosphere, particularly arbuscular mycorrhiza, have a broad symbiotic relationship with their host plants. One of the major fungi isolated from the rhizosphere of Peucedanum praeruptorum is Penicillium restrictum. The relationship between the metabolites of P. restrictum and the root exudates of P. praeruptorum is being investigated. The accumulation of metabolites in the mycelium and fermentation broth of P. restrictum was analysed over different fermentation periods. Non-targeted metabolomics was used to compare the differences in intracellular and extracellular metabolites over six periods. There were significant differences in the content and types of mycelial metabolites during the incubation. Marmesin, an important intermediate in the biosynthesis of coumarins, was found in the highest amount on the fourth day of incubation. The differential metabolites were screened to obtain 799 intracellular and 468 extracellular differential metabolites. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the highly enriched extracellular metabolic pathways were alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, and terpenoid backbone biosynthesis. In addition, the enrichment analysis associated with intracellular and extracellular ATP-binding cassette transporter proteins revealed that some ATP-binding cassette transporters may be involved in the transportation of certain amino acids and carbohydrates. Our results provide some theoretical basis for the regulatory mechanisms between the rhizosphere and the host plant and pave the way for the heterologous production of furanocoumarin.
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Affiliation(s)
- Yuanyuan Wang
- School of PharmacyAnhui University of Chinese MedicineHefeiChina
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco‐agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
| | - Ranran Liao
- School of PharmacyAnhui University of Chinese MedicineHefeiChina
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco‐agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
| | - Haoyu Pan
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco‐agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
- School of Life ScienceAnhui Agricultural UniversityHefeiChina
| | - Xuejun Wang
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco‐agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
| | - Xiaoting Wan
- School of PharmacyAnhui University of Chinese MedicineHefeiChina
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco‐agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
| | - Bangxing Han
- School of PharmacyAnhui University of Chinese MedicineHefeiChina
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco‐agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
| | - Cheng Song
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco‐agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical EngineeringWest Anhui UniversityLuanChina
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Gholizadeh S, Nemati I, Vestergård M, Barnes CJ, Kudjordjie EN, Nicolaisen M. Harnessing root-soil-microbiota interactions for drought-resilient cereals. Microbiol Res 2024; 283:127698. [PMID: 38537330 DOI: 10.1016/j.micres.2024.127698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.
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Affiliation(s)
- Somayeh Gholizadeh
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mette Vestergård
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Christopher James Barnes
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Enoch Narh Kudjordjie
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Mogens Nicolaisen
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark.
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Gao D, Luster J, Zürcher A, Arend M, Bai E, Gessler A, Rigling A, Schaub M, Hartmann M, Werner RA, Joseph J, Poll C, Hagedorn F. Drought resistance and resilience of rhizosphere communities in forest soils from the cellular to ecosystem scale - insights from 13C pulse labeling. THE NEW PHYTOLOGIST 2024; 242:960-974. [PMID: 38402527 DOI: 10.1111/nph.19612] [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: 12/01/2023] [Accepted: 02/06/2024] [Indexed: 02/26/2024]
Abstract
The link between above- and belowground communities is a key uncertainty in drought and rewetting effects on forest carbon (C) cycle. In young beech model ecosystems and mature naturally dry pine forest exposed to 15-yr-long irrigation, we performed 13C pulse labeling experiments, one during drought and one 2 wk after rewetting, tracing tree assimilates into rhizosphere communities. The 13C pulses applied in tree crowns reached soil microbial communities of the young and mature forests one and 4 d later, respectively. Drought decreased the transfer of labeled assimilates relative to the irrigation treatment. The 13C label in phospholipid fatty acids (PLFAs) indicated greater drought reduction of assimilate incorporation by fungi (-85%) than by gram-positive (-43%) and gram-negative bacteria (-58%). 13C label incorporation was more strongly reduced for PLFAs (cell membrane) than for microbial cytoplasm extracted by chloroform. This suggests that fresh rhizodeposits are predominantly used for osmoregulation or storage under drought, at the expense of new cell formation. Two weeks after rewetting, 13C enrichment in PLFAs was greater in previously dry than in continuously moist soils. Drought and rewetting effects were greater in beech systems than in pine forest. Belowground C allocation and rhizosphere communities are highly resilient to drought.
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Affiliation(s)
- Decai Gao
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, 100190, Beijing, China
| | - Jörg Luster
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| | - Alois Zürcher
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| | - Matthias Arend
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Physiological Plant Ecology, University of Basel, 4056, Basel, Switzerland
| | - Edith Bai
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, Northeast Normal University, 130024, Changchun, China
| | - Arthur Gessler
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Terrestrial Ecosystems, ETH Zürich, 8092, Zürich, Switzerland
| | - Andreas Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Terrestrial Ecosystems, ETH Zürich, 8092, Zürich, Switzerland
| | - Marcus Schaub
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, 8092, Zürich, Switzerland
| | - Roland A Werner
- Agricultural Sciences, ETH Zürich, 8092, Zürich, Switzerland
| | - Jobin Joseph
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| | - Christian Poll
- Soil Biology, University of Hohenheim, 70599, Stuttgart, Germany
| | - Frank Hagedorn
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
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Vimal SR, Singh JS, Kumar A, Prasad SM. The plant endomicrobiome: Structure and strategies to produce stress resilient future crop. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100236. [PMID: 38756233 PMCID: PMC11097330 DOI: 10.1016/j.crmicr.2024.100236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Plants have a microbiome, a diverse community of microorganisms, including bacteria, fungi, and viruses, living inside and on their tissues. Versatile endophytic microorganisms inhabited in every plant part without causing disease and develop endophytic microbiome or endo-microbiome. Plant endo-microbiome are drawn by the nutrient rich micro-environment, and in turn some microbes mutualistically endorse and protect plant from adverse environmental stresses. Plant endo-microbiome interact within well-designed host equilibrium containing xylem, phloem, nutrients, phytohormones, metabolites and shift according to environmental and nutritional change. Plant endo-microbiome regulate and respond to environmental variations, pathogens, herbivores by producing stress regulators, organic acids, secondary metabolites, stress hormones as well as unknown substances and signalling molecules. Endomicrobiome efficiently synthesizes multiple bioactive compounds, stress phytohormones with high competence. The technological innovation as next generation genomics biology and high-throughput multiomics techniques stepping stones on the illumination of critical endo-microbiome communities and functional characterization that aid in improving plant physiology, biochemistry and immunity interplay for best crop productivity. This review article contains deeper insight in endomicrobiome related research work in last years, recruitment, niche development, nutrient dynamics, stress removal mechanisms, bioactive services in plant health development, community architecture and communication, and immunity interplay in producing stress resilient future crop.
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Affiliation(s)
- Shobhit Raj Vimal
- Ranjan Plant Physiology & Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, Uttar Pradesh, India
| | - Jay Shankar Singh
- Department of Environmental Microbiology, School for Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, Uttar Pradesh, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, University of Allahabad (A Central University), Prayagraj 211002, Uttar Pradesh, India
| | - Sheo Mohan Prasad
- Ranjan Plant Physiology & Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, Uttar Pradesh, India
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Yue H, Sun X, Wang T, Zhang A, Han D, Wei G, Song W, Shu D. Host genotype-specific rhizosphere fungus enhances drought resistance in wheat. MICROBIOME 2024; 12:44. [PMID: 38433268 PMCID: PMC10910722 DOI: 10.1186/s40168-024-01770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses. RESULTS Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum). CONCLUSIONS Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.
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Affiliation(s)
- Hong Yue
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuming Sun
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Wang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ali Zhang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dejun Han
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
| | - Weining Song
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Duntao Shu
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
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9
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Liu M, Wang C, Zhu B. Independent and combined effects of microplastics pollution and drought on soil bacterial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169749. [PMID: 38160843 DOI: 10.1016/j.scitotenv.2023.169749] [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: 09/22/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Global terrestrial ecosystems are simultaneously threatened by multiple environmental pressures, with microplastics (MPs) pollution and drought possibly being the most pressing, both of which may have unanticipated effects on soil organisms. Here, we investigated the responses of diversity, composition and functions of soil bacterial community to MPs pollution (including two MPs types: polyethylene (PE) and polylactic acid (PLA); two MPs sizes: < 20 μm and <300 μm) and drought in microcosms. We found that only 20 μm PLA MPs significantly decreased soil bacterial diversity by 17.4 % and altered soil bacterial community composition, while PE MPs and 300 μm PLA MPs had no significant effects. The copiotrophic bacteria (i.e., Proteobacteria and Firmicutes) were enriched in the 20 μm PLA MPs pollution soils due to the enhanced dissolved organic carbon contents. Moreover, our results showed that the 20 μm PLA MPs also affected the potential phenotypes and functions of soil bacterial community, increasing the potentially pathogenic, stress-tolerant, containing mobile elements and forming biofilms phenotypes, and promoting membrane transport and signal transduction pathways. These results suggested that the effects of MPs on soil bacterial community varied depending on MPs types and sizes. However, drought significantly increased soil bacterial diversity by 10.3 % and affected soil bacterial community composition in the 20 μm PLA MPs pollution soils. We also found that drought inhibited the levels of potentially pathogenic, containing mobile elements and forming biofilms phenotypes in the 20 μm PLA MPs pollution soils. Taken together, these findings reveal that drought may alleviate the adverse effects of MPs pollution on soil bacterial community, which enhances our understanding of the interactive effects of multiple global change factors on agroecosystem functions.
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Affiliation(s)
- Mengli Liu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Chong Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.
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10
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Fu Q, Qiu Y, Zhao J, Li J, Xie S, Liao Q, Fu X, Huang Y, Yao Z, Dai Z, Qiu Y, Yang Y, Li F, Chen H. Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169351. [PMID: 38123079 DOI: 10.1016/j.scitotenv.2023.169351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3- increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.
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Affiliation(s)
- Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Siqi Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qiuchang Liao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yu Huang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Furong Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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11
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Ranheim Sveen T, Hannula SE, Bahram M. Microbial regulation of feedbacks to ecosystem change. Trends Microbiol 2024; 32:68-78. [PMID: 37500365 DOI: 10.1016/j.tim.2023.06.006] [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: 11/01/2022] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023]
Abstract
Microbes are key biodiversity components of all ecosystems and control vital ecosystem functions. Although we have just begun to unravel the scales and factors that regulate microbial communities, their role in mediating ecosystem stability in response to disturbances remains underexplored. Here, we review evidence of how, when, and where microbes regulate or drive disturbance feedbacks. Negative feedbacks dampen the impacts of disturbance, which maintain ecosystem stability, whereas positive feedbacks instead erode stability by amplifying the disturbance. Here we describe the processes underlying the responses to disturbance using a hierarchy of functional traits, and we exemplify how these may drive biogeochemical feedbacks. We suggest that the feedback potential of functional traits at different hierarchical levels is contingent on the complexity and heterogeneity of the environment.
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Affiliation(s)
- T Ranheim Sveen
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51 Uppsala, Sweden.
| | - S E Hannula
- Institute of Environmental Sciences, Leiden University, Leiden 2333, The Netherlands
| | - M Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51 Uppsala, Sweden; Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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12
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Hao Z, Wang Q, Wang J, Deng Y, Yan Z, Tian L, Jiang H. Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains. MICROBIAL ECOLOGY 2023; 87:24. [PMID: 38159125 DOI: 10.1007/s00248-023-02331-6] [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: 07/30/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.
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Affiliation(s)
- Zheng Hao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qianhong Wang
- Changjiang Nanjing Waterway Engineering Bureau, Nanjing, 210011, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Linqi Tian
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.
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13
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Cordero I, Leizeaga A, Hicks LC, Rousk J, Bardgett RD. High intensity perturbations induce an abrupt shift in soil microbial state. THE ISME JOURNAL 2023; 17:2190-2199. [PMID: 37814127 PMCID: PMC10690886 DOI: 10.1038/s41396-023-01512-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 10/11/2023]
Abstract
Soil microbial communities play a pivotal role in regulating ecosystem functioning. But they are increasingly being shaped by human-induced environmental change, including intense "pulse" perturbations, such as droughts, which are predicted to increase in frequency and intensity with climate change. While it is known that soil microbial communities are sensitive to such perturbations and that effects can be long-lasting, it remains untested whether there is a threshold in the intensity and frequency of perturbations that can trigger abrupt and persistent transitions in the taxonomic and functional characteristics of soil microbial communities. Here we demonstrate experimentally that intense pulses of drought equivalent to a 30-year drought event (<15% WHC) induce a major shift in the soil microbial community characterised by significantly altered bacterial and fungal community structures of reduced complexity and functionality. Moreover, the characteristics of this transformed microbial community persisted after returning soil to its previous moisture status. As a result, we found that drought had a strong legacy effect on bacterial community function, inducing an enhanced growth rate following subsequent drought. Abrupt transitions are widely documented in aquatic and terrestrial plant communities in response to human-induced perturbations. Our findings demonstrate that such transitions also occur in soil microbial communities in response to high intensity pulse perturbations, with potentially deleterious consequences for soil health.
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Affiliation(s)
- Irene Cordero
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
- Department of Community Ecology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland.
| | - Ainara Leizeaga
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Department of Biology, Lund University, Lund, Sweden
| | | | | | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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14
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Liu L, Guan J, Zheng J, Wang Y, Han W, Liu Y. Cumulative effects of drought have an impact on net primary productivity stability in Central Asian grasslands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118734. [PMID: 37572401 DOI: 10.1016/j.jenvman.2023.118734] [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: 04/26/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/14/2023]
Abstract
Global warming has exacerbated the threat of drought in Central Asia, amplifying its ecological implications within the region's grassland ecosystems. This has become an increasingly prominent issue that requires attention and action. The temporal link between grassland development and drought is asymmetric. However, a quantitative assessment of the temporal effects of multiscale drought on Central Asian grasslands has yet to be explored. Based on correlation analysis and the coefficient of variation method, this study analysed the cumulative and lag effects of multitimescale drought on grassland NPP (net primary productivity) under different climatic zones, altitudes and water availabilities in Central Asia from 1982 to 2018, and discussed the impact of temporal effects on grassland NPP stability. Our results on the cumulative effects of drought on grasslands indicate the 6.72 months preceding NPP measurement was the duration for which, on average, drought was most strongly correlated with NPP. Additionally, we found a mean lagged effect of 5.36 months, meaning that the monthly drought 5.36 months prior to NPP measurement was, on average, most strongly correlated with NPP. The degree to which grassland NPP was affected by cumulative drought at a given level of water availability was inversely proportional to the number of cumulative drought months. Under different water availabilities, the lagged effect of grassland NPP was stronger in dry areas than in wet areas, and the number of lag months tended to decrease and then increase as the water availability increased. The percentage of areas where grassland NPP was dominated by the cumulative and lagging effects of drought was 30.02% and 69.98%, respectively. The stability of grassland NPP was adversely affected by the drought accumulation effect. The findings of this study contribute to a deeper understanding of the long-term effects of drought on grassland ecosystems. Additionally, it will aid in the development of strategies for mitigating and adapting to drought events, thereby minimizing their negative impacts on agriculture, livestock, and ecosystems.
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Affiliation(s)
- Liang Liu
- College of Geography and Remote Sensing Sciences, Xinjiang University, Urumqi, 830046, China
| | - Jingyun Guan
- College of Geography and Remote Sensing Sciences, Xinjiang University, Urumqi, 830046, China; College of Tourism, Xinjiang University of Finance & Economics, Urumqi, 830012, China
| | - Jianghua Zheng
- College of Geography and Remote Sensing Sciences, Xinjiang University, Urumqi, 830046, China; Xinjiang Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China.
| | - Yongdong Wang
- College of Geography and Remote Sensing Sciences, Xinjiang University, Urumqi, 830046, China
| | - Wanqiang Han
- College of Geography and Remote Sensing Sciences, Xinjiang University, Urumqi, 830046, China
| | - Yujia Liu
- College of Geography and Remote Sensing Sciences, Xinjiang University, Urumqi, 830046, China
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15
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Bei Q, Reitz T, Schnabel B, Eisenhauer N, Schädler M, Buscot F, Heintz-Buschart A. Extreme summers impact cropland and grassland soil microbiomes. THE ISME JOURNAL 2023; 17:1589-1600. [PMID: 37419993 PMCID: PMC10504347 DOI: 10.1038/s41396-023-01470-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.
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Affiliation(s)
- Qicheng Bei
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany.
| | - Thomas Reitz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Beatrix Schnabel
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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16
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Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benjamin J Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Schaumberger
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria.
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17
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Qu Q, Wang Z, Gan Q, Liu R, Xu H. Impact of drought on soil microbial biomass and extracellular enzyme activity. FRONTIERS IN PLANT SCIENCE 2023; 14:1221288. [PMID: 37692424 PMCID: PMC10491016 DOI: 10.3389/fpls.2023.1221288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023]
Abstract
Introduction With the continuous changes in climate patterns due to global warming, drought has become an important limiting factor in the development of terrestrial ecosystems. However, a comprehensive understanding of the impact of drought on soil microbial activity at a global scale is lacking. Methods In this study, we aimed to examine the effects of drought on soil microbial biomass (carbon [MBC], nitrogen [MBN], and phosphorus [MBP]) and enzyme activity (β-1, 4-glucosidase [BG]; β-D-cellobiosidase [CBH]; β-1, 4-N-acetylglucosaminidase [NAG]; L-leucine aminopeptidase [LAP]; and acid phosphatase [AP]). Additionally, we conducted a meta-analysis to determine the degree to which these effects are regulated by vegetation type, drought intensity, drought duration, and mean annual temperature (MAT). Result and discussion Our results showed that drought significantly decreased the MBC, MBN, and MBP and the activity levels of BG and AP by 22.7%, 21.2%, 21.6%, 26.8%, and 16.1%, respectively. In terms of vegetation type, drought mainly affected the MBC and MBN in croplands and grasslands. Furthermore, the response ratio of BG, CBH, NAG, and LAP were negatively correlated with drought intensity, whereas MBN and MBP and the activity levels of BG and CBH were negatively correlated with drought duration. Additionally, the response ratio of BG and NAG were negatively correlated with MAT. In conclusion, drought significantly reduced soil microbial biomass and enzyme activity on a global scale. Our results highlight the strong impact of drought on soil microbial biomass and carbon- and phosphorus-acquiring enzyme activity.
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Affiliation(s)
- Qing Qu
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwestern China, Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
| | - Zhen Wang
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwestern China, Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan, China
| | - Quan Gan
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Rentao Liu
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwestern China, Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Ningxia University, Yinchuan, China
| | - Hongwei Xu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
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18
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Wang J, Wang C, Wu X, Zhang J, Zhao G, Hou Y, Sun H. Effects of moderate drought extension on bacterial network structure in the rhizosphere soil of Leymus chinensis in semi-arid grasslands. Front Microbiol 2023; 14:1217557. [PMID: 37637130 PMCID: PMC10448527 DOI: 10.3389/fmicb.2023.1217557] [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: 05/05/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Grasslands are home to complex bacterial communities whose dynamic interactions play a crucial role in organic matter and nutrient cycling. However, there is limited understanding regarding the impact of changes in rainfall amount and the duration of dry intervals on bacterial interactions. Methods To assess the impact of changes in precipitation volume and dry intervals on bacterial co-occurrence networks, we carried out precipitation manipulation experiments in the Eastern Eurasian Steppe of China. Results and Discussion We found that alterations in precipitation and dry intervals did not significantly affect bacterial alpha and beta diversity. However, we observed significant changes in the co-occurrence network structure of bacteria in the rhizosphere ecosystem, with the 12-day dry interval showing the most notable reduction in the number of degrees, edges, and clustering coefficient. Additionally, the study identified putative keystone taxa and observed that the moderately prolonged dry intervals between precipitation events had a major effect on the robustness of bacterial networks. The complexity and stability of the network were found to be positively correlated, and were primarily influenced by soil water content, phosphorous, and aboveground biomass, followed by available phosphorus (AP) and total biomass. These findings have the potential to enhance our comprehension of how bacterial co-occurrence pattern react to variations in dry intervals, by regulating their interactions in water-limited ecosystems. This, in turn, could aid in predicting the impact of precipitation regime alterations on ecosystem nutrient cycling, as well as the feedback between ecosystem processes and global climate change.
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Affiliation(s)
- Jinlong Wang
- College of Science, Traditional Chinese Medicine Biotechnology Innovation Center in Jilin Province, Beihua University, Jilin, China
| | - Chunjuan Wang
- College of Science, Traditional Chinese Medicine Biotechnology Innovation Center in Jilin Province, Beihua University, Jilin, China
| | - Xuefeng Wu
- Chongqing Institute of Quality and Standardization, Chongqing, China
| | - Jinwei Zhang
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Guiyun Zhao
- College of Science, Traditional Chinese Medicine Biotechnology Innovation Center in Jilin Province, Beihua University, Jilin, China
| | - Yu Hou
- College of Science, Traditional Chinese Medicine Biotechnology Innovation Center in Jilin Province, Beihua University, Jilin, China
| | - Haiming Sun
- College of Science, Traditional Chinese Medicine Biotechnology Innovation Center in Jilin Province, Beihua University, Jilin, China
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19
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Yang R, Yang Z, Yang S, Chen LL, Xin J, Xu L, Zhang X, Zhai B, Wang Z, Zheng W, Li Z. Nitrogen inhibitors improve soil ecosystem multifunctionality by enhancing soil quality and alleviating microbial nitrogen limitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163238. [PMID: 37011677 DOI: 10.1016/j.scitotenv.2023.163238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/27/2023]
Abstract
Soil quality (SQI) is a comprehensive indicator reflecting the agricultural productivity of soil, and soil ecosystem multifunctionality (performing multiple functions simultaneously; EMF) can reflect complex biogeochemical processes. However, the effects of enhanced efficiency nitrogen fertilizers (EENFs; urease inhibitors (NBPT), nitrification inhibitors (DCD), and coated controlled-release urea (RCN)) application on the SQI and soil EMF and their relationships are still unclear. Therefore, we conducted a field experiment to study the effects of different EENFs on the SQI, enzyme stoichiometry and soil EMF in semiarid areas of Northwest China (Gansu, Ningxia, Shaanxi, Shanxi). Across the four study sites, DCD and NBPT increased SQI by 7.61-16.80 % and 2.61 %-23.20 % compared to mineral fertilizer, respectively. N fertilizer application (N200 and EENFs) alleviated microbial N limitation, and EENFs alleviated microbial N and C limitations to a greater extent in Gansu and Shanxi. Moreover, nitrogen inhibitors (Nis; DCD and NBPT) improved the soil EMF to a greater extent than N200 and RCN, DCD increased by 205.82-340.00 % and 145.00-215.47 % in Gansu and Shanxi, respectively; NBPT increased by 332.75-778.59 % and 364.44-929.62 % in Ningxia and Shanxi, respectively. A random forest model showed that the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and soil water content (SWC) of the SQI factors were the main driving forces of soil EMF. Moreover, SQI improvement could alleviate microbial C and N limitations and promote the improvement of soil EMF. It is worth noting that soil EMF was mainly affected by microbial N limitation rather than C limitation. Overall, NIs application is an effective way to improve the SQI and soil EMF in the semiarid region of Northwest China.
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Affiliation(s)
- Ruizhe Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Ze Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Shilong Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lan-Lan Chen
- College of Resources and Environmental Sciences, Gansu Agricultural University/Gansu Provincial Key Laboratory of Arid-land Crop Science, Lanzhou 730070, PR China
| | - Jia Xin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Changshu National Agro-Ecosystem Observation and Research Station, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Lingying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Changshu National Agro-Ecosystem Observation and Research Station, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xuechen Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Bingnian Zhai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Zhaohui Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Wei Zheng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Ziyan Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China.
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20
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Xie P, Huang K, Deng A, Mo P, Xiao F, Wu F, Xiao D, Wang Y. The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties. Front Microbiol 2023; 14:1111087. [PMID: 37378294 PMCID: PMC10292655 DOI: 10.3389/fmicb.2023.1111087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.
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Affiliation(s)
- Peng Xie
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
- College of Agriculture, Forestry and Technology, Hunan Applied Technology University, Changde, Hunan, China
| | - Kerui Huang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Aihua Deng
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Ping Mo
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Fen Xiao
- Central South University of Forestry and Technology Changsha, Hunan, China
| | - Fei Wu
- Qingjie Mountain State Forest Farm, Chengbu, Hunan, China
| | - Dewei Xiao
- Chukou State-Owned Forest Farm, Zixing, Hunan, China
| | - Yun Wang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
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21
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Zhou L, Wang S. The bright side of ecological stressors. Trends Ecol Evol 2023; 38:568-578. [PMID: 36906435 DOI: 10.1016/j.tree.2023.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 03/12/2023]
Abstract
Ecological stressors are considered to negatively affect biological systems; however, corresponding responses to stressors can be complex, depending on the ecological functions and the number and duration of the stressors. Mounting evidence indicates potential benefits of stressors. Here, we develop an integrative framework to understand stressor-induced benefits by clarifying three categories of mechanisms: seesaw effects, cross-tolerance, and memory effects. These mechanisms operate across various organizational levels (e.g., individual, population, community) and can be extended to an evolutionary context. One remaining challenge is to develop scaling approaches for linking stressor-induced benefits across organizational levels. Our framework provides a novel platform for predicting the consequences of global environmental changes and informing management strategies in conservation and restoration practices.
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Affiliation(s)
- Libin Zhou
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, 100871 Beijing, China
| | - Shaopeng Wang
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, 100871 Beijing, China.
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22
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Hereira-Pacheco SE, Estrada-Torres A, Dendooven L, Navarro-Noya YE. Shifts in root-associated fungal communities under drought conditions in Ricinus communis. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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23
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Allsup CM, George I, Lankau RA. Shifting microbial communities can enhance tree tolerance to changing climates. Science 2023; 380:835-840. [PMID: 37228219 DOI: 10.1126/science.adf2027] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/04/2023] [Indexed: 05/27/2023]
Abstract
Climate change is pushing species outside of their evolved tolerances. Plant populations must acclimate, adapt, or migrate to avoid extinction. However, because plants associate with diverse microbial communities that shape their phenotypes, shifts in microbial associations may provide an alternative source of climate tolerance. Here, we show that tree seedlings inoculated with microbial communities sourced from drier, warmer, or colder sites displayed higher survival when faced with drought, heat, or cold stress, respectively. Microbially mediated drought tolerance was associated with increased diversity of arbuscular mycorrhizal fungi, whereas cold tolerance was associated with lower fungal richness, likely reflecting a reduced burden of nonadapted fungal taxa. Understanding microbially mediated climate tolerance may enhance our ability to predict and manage the adaptability of forest ecosystems to changing climates.
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Affiliation(s)
- Cassandra M Allsup
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Isabelle George
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Richard A Lankau
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
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24
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Zeng J, Li Y, Dai Y, Zhu Q, Wu Y, Lin X. Soil drying legacy does not affect phenanthrene fate in soil but modifies bacterial community response. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023:121909. [PMID: 37245790 DOI: 10.1016/j.envpol.2023.121909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 05/30/2023]
Abstract
Alteration of the structure of soil microbial communities following the elimination of hydrophobic organic pollutants (e.g., polycyclic aromatic hydrocarbons, PAHs) is generally assessed using DNA-based techniques, and soil is often required to dry prior to pollutant addition, to facilitate a better mix when establishing microcosms. However, the drying practice may have a legacy effect on soil microbial community structure, which would in turn influence the biodegradation process. Here, we used 14C-labeled phenanthrene to examine the potential side effects of precedent short-term drought events. The results indicate that the drying practice had legacy effects on soil microbial community structure, illustrated by irreversible shifts in the communities. The legacy effects had no significant impact on phenanthrene mineralization and non-extractable residue formation. However, they altered the response of bacterial communities to PAH degradation, leading to a decrease in the abundance of potential PAH degradation genes plausibly attributed to moderately abundant taxa. Based on a comparison of the varied effects of different drying intensity levels, an accurate description of microbial responses to phenanthrene degradation strongly relies on the establishment of stable microbial communities before PAH amendment. Concurrent alterations in the communities resulting from environmental perturbation could greatly mask minor alterations from the degradation of recalcitrant hydrophobic PAH. In practice, to minimize the legacy effects, a soil equilibration step with a reduced drying intensity is indispensable.
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Affiliation(s)
- Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Yanjie Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Yeliang Dai
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Qinghe Zhu
- State Environmental Protection Engineering Center for Urban Soil Contamination Control and Remediation, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, China.
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25
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Xiong X, Li Y, Zhang C, Zhou X. Water quality improvement and consequent N 2O emission reduction in hypoxic freshwater utilizing green oxygen-carrying biochar. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162251. [PMID: 36796685 DOI: 10.1016/j.scitotenv.2023.162251] [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: 12/06/2022] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Declines in dissolved oxygen (DO) levels in aquatic systems worldwide negatively influence biodiversity, nutrient biogeochemistry, drinking water quality, and greenhouse gas emission. As a response, oxygen-carrying dual-modified sediment-based biochar (O-DM-SBC) as a green and sustainable emerging material was utilized for simultaneous hypoxia restoration, water quality improvement, and greenhouse gas reduction. Column incubation experiments were carried out using the water and sediment samples from a tributary of the Yangtze River. The application of O-DM-SBC effectively increased the DO concentration from ~1.99 mg/L to ~6.44 mg/L and decreased the concentrations of TN and NH4+-N by 61.1 % and 78.3 %, respectively, during the 30-day incubation period. Moreover, the N2O emission was apparently inhibited by O-DM-SBC with a 50.2 % decrease in daily flux under the functional coupling of biochar (SBC) and oxygen nanobubbles (ONBs). Path analysis supported that the treatments (SBC, modification, and ONBs) had joint effects on N2O emission by changing the concentration and composition of dissolved inorganic nitrogen (e.g., NH4+-N, NO2--N and NO3--N). The nitrogen-transforming bacteria were found to be significantly promoted by O-DM-SBC at the end of the incubation, while the archaeal community seemed to be more active in the SBC groups without ONB, confirming their different mechanisms. The PICRUSt2 prediction results revealed that most nitrogen metabolism genes including nitrification (i.e., amoABC), denitrification (i.e., nirK and nosZ), and assimilatory nitrate reduction (i.e., nirB and gdhA) were largely enriched in O-DM-SBC, indicating the active nitrogen-cycling network was established, thus achieving simultaneous nitrogen pollution control and N2O emission reduction. Our findings not only confirm the beneficial effect of O-DM-SBC amendment on nitrogen pollution control and N2O emission mitigation in hypoxic freshwater, but also contribute to a more comprehensive understanding of the effect of oxygen-carrying biochar on nitrogen cycling microbial communities.
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Affiliation(s)
- Xinyan Xiong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Chi Zhang
- College of Mechanics and Materials, Hohai University, Xikang Road #1, Nanjing 210098, PR China.
| | - Xinyi Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
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26
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Singavarapu B, Du J, Beugnon R, Cesarz S, Eisenhauer N, Xue K, Wang Y, Bruelheide H, Wubet T. Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity. Microbiol Spectr 2023; 11:e0457822. [PMID: 36951585 PMCID: PMC10111882 DOI: 10.1128/spectrum.04578-22] [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: 11/09/2022] [Accepted: 02/11/2023] [Indexed: 03/24/2023] Open
Abstract
Soil microbial communities play crucial roles in the earth's biogeochemical cycles. Yet, their genomic potential for nutrient cycling in association with tree mycorrhizal type and tree-tree interactions remained unclear, especially in diverse tree communities. Here, we studied the genomic potential of soil fungi and bacteria with arbuscular (AM) and ectomycorrhizal (EcM) conspecific tree species pairs (TSPs) at three tree diversity levels in a subtropical tree diversity experiment (BEF-China). The soil fungi and bacteria of the TSPs' interaction zone were characterized by amplicon sequencing, and their subcommunities were determined using a microbial interkingdom co-occurrence network approach. Their potential genomic functions were predicted with regard to the three major nutrients carbon (C), nitrogen (N), and phosphorus (P) and their combinations. We found the microbial subcommunities that were significantly responding to different soil characteristics. The tree mycorrhizal type significantly influenced the functional composition of these co-occurring subcommunities in monospecific stands and two-tree-species mixtures but not in mixtures with more than three tree species (here multi-tree-species mixtures). Differentiation of subcommunities was driven by differentially abundant taxa producing different sets of nutrient cycling enzymes across the tree diversity levels, predominantly enzymes of the P (n = 11 and 16) cycles, followed by the N (n = 9) and C (n = 9) cycles, in monospecific stands and two-tree-species mixtures, respectively. Fungi of the Agaricomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes and bacteria of the Verrucomicrobia, Acidobacteria, Alphaproteobacteria, and Actinobacteria were the major differential contributors (48% to 62%) to the nutrient cycling functional abundances of soil microbial communities across tree diversity levels. Our study demonstrated the versatility and significance of microbial subcommunities in different soil nutrient cycling processes of forest ecosystems. IMPORTANCE Loss of multifunctional microbial communities can negatively affect ecosystem services, especially forest soil nutrient cycling. Therefore, exploration of the genomic potential of soil microbial communities, particularly their constituting subcommunities and taxa for nutrient cycling, is vital to get an in-depth mechanistic understanding for better management of forest soil ecosystems. This study revealed soil microbes with rich nutrient cycling potential, organized in subcommunities that are functionally resilient and abundant. Such microbial communities mainly found in multi-tree-species mixtures associated with different mycorrhizal partners can foster soil microbiome stability. A stable and functionally rich soil microbiome is involved in the cycling of nutrients, such as carbon, nitrogen, and phosphorus, and their combinations could have positive effects on ecosystem functioning, including increased forest productivity. The new findings could be highly relevant for afforestation and reforestation regimes, notably in the face of growing deforestation and global warming scenarios.
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Affiliation(s)
- Bala Singavarapu
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Jianqing Du
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Leipzig, Germany
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources, Chinese Academy of Sciences, Beijing, China
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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27
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de Vries F, Lau J, Hawkes C, Semchenko M. Plant-soil feedback under drought: does history shape the future? Trends Ecol Evol 2023:S0169-5347(23)00054-X. [PMID: 36973124 DOI: 10.1016/j.tree.2023.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
Plant-soil feedback (PSF) is widely recognised as a driver of plant community composition, but understanding of its response to drought remains in its infancy. Here, we provide a conceptual framework for the role of drought in PSF, considering plant traits, drought severity, and historical precipitation over ecological and evolutionary timescales. Comparing experimental studies where plants and microbes do or do not share a drought history (through co-sourcing or conditioning), we hypothesise that plants and microbes with a shared drought history experience more positive PSF under subsequent drought. To reflect real-world responses to drought, future studies need to explicitly include plant-microbial co-occurrence and potential co-adaptation and consider the precipitation history experienced by both plants and microbes.
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Affiliation(s)
- Franciska de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
| | - Jennifer Lau
- Department of Biology and Environmental Resilience Institute, Indiana University, IN, USA
| | - Christine Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
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28
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Allison SD. Microbial drought resistance may destabilize soil carbon. Trends Microbiol 2023:S0966-842X(23)00078-1. [PMID: 37059647 DOI: 10.1016/j.tim.2023.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/09/2023] [Accepted: 03/02/2023] [Indexed: 04/16/2023]
Abstract
Droughts are becoming more frequent and intense with climate change. As plants and microbes respond to drought, there may be consequences for the vast stocks of organic carbon stored in soils. If microbes sustain their activity under drought, soils could lose carbon, especially if inputs from plants decline. Empirical and theoretical studies reveal multiple mechanisms of microbial drought resistance, including tolerance and avoidance. Physiological responses allow microbes to acclimate to drought within minutes to days. Along with dispersal, shifts in community composition could allow microbiomes to maintain functioning despite drought. Microbes might also adapt to drier conditions through evolutionary processes. Together, these mechanisms could result in soil carbon losses larger than currently anticipated under climate change.
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Affiliation(s)
- Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA; Department of Earth System Science, University of California, Irvine, CA, USA.
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29
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Ma X, Li Y, Niu L, Shang J, Yang N. Microbial community structure and denitrification responses to cascade low-head dams and their contribution to eutrophication in urban rivers. ENVIRONMENTAL RESEARCH 2023; 221:115242. [PMID: 36634891 DOI: 10.1016/j.envres.2023.115242] [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: 12/08/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Low-head dams are one of the most common hydraulic facilities, yet they often fragment rivers, leading to profound changes in aquatic biodiversity and river eutrophication levels. Systematic assessments of river ecosystem structure and functions, and their contribution to eutrophication, are however lacking, especially for urban rivers where low-head dams prevail. In this study, we address this gap with a field survey on microbial community structure and ecosystem function, in combination with hydrological, environmental and ecological factors. Our findings revealed that microbial communities showed significant differences among the cascade impoundments, which may be due to the environment heterogeneity resulting from the cascade low-head dams. The alternating lentic-lotic flow environment created by the low-head dams caused nutrient accumulation in the cascade impoundments, enhancing environmental sorting and interspecific competition relationships, and thus possibly contributing to the reduction in sediment denitrification function. Decreased denitrification led to excessive accumulation of nutrients, which may have aggravated river eutrophication. In addition, structural equation model analysis showed that flow velocity may be the key controlling factor for river eutrophication. Therefore, in the construction of river flood control and water storage systems, the location, type and water storage capacity of low-head dams should be fully considered to optimize the hydrodynamic conditions of rivers. To summarize, our findings revealed the cumulative effects of cascade low-head dams in an urban river, and provided new insights into the trade-off between construction and decommissioning of low-head dams in urban river systems.
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Affiliation(s)
- Xin Ma
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, PR China; Research Institute of Mulan Ecological River, Putian, 351100, PR China
| | - Yi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, PR China; Research Institute of Mulan Ecological River, Putian, 351100, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China; Research Institute of Mulan Ecological River, Putian, 351100, PR China.
| | - Jiahui Shang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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30
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Wan Q, Li L, Liu B, Zhang Z, Liu Y, Xie M. Different and unified responses of soil bacterial and fungal community composition and predicted functional potential to 3 years’ drought stress in a semiarid alpine grassland. Front Microbiol 2023; 14:1104944. [PMID: 37082184 PMCID: PMC10112540 DOI: 10.3389/fmicb.2023.1104944] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
IntroductionSoil microbial communities are key to functional processes in terrestrial ecosystems, and they serve as an important indicator of grasslands status. However, the responses of soil microbial communities and functional potential to drought stress in semiarid alpine grasslands remain unclear.MethodsHere, a field experiment was conducted under ambient precipitation as a control, −20% and −40% of precipitation to explore the responses of soil microbial diversity, community composition, and predicted functional potential to drought stress in a semiarid alpine grassland located in the northwest of China. Moreover, 16S rRNA gene and ITS sequencing were used to detect bacterial and fungal communities, and the PICRUST and FUNGuild databases were used to predict bacterial and fungal functional groups.ResultsResults showed drought stress substantially changes the community diversity of bacteria and fungi, among which the bacteria community is more sensitive to drought stress than fungi, indicating that the diversity or structure of soil bacteria community could serve as an indicator of alpine grasslands status. However, the fungal community still has difficulty maintaining resistance under excessive drought stress. Our paper also highlighted that soil moisture content, plant diversity (Shannon Wiener, Pieiou, and Simpson), and soil organic matter are the main drivers affecting soil bacterial and fungal community composition and predicted functional potential. Notably, the soil microbial functional potential could be predictable through taxonomic community profiles.ConclusionOur research provides insight for exploring the mechanisms of microbial community composition and functional response to climate change (longer drought) in a semiarid alpine grassland.
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Affiliation(s)
- Qian Wan
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Lei Li,
| | - Bo Liu
- Shandong Provincial Key Laboratory of Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, China
| | - Zhihao Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yalan Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingyu Xie
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
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Hu J, Miller G, Shi W. Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit. Front Microbiol 2023; 13:1078836. [PMID: 36713160 PMCID: PMC9878326 DOI: 10.3389/fmicb.2022.1078836] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
The plant breeding program has developed many cultivars of tall fescue (Festuca arundinacea) with low maintenance and stress tolerance. While the root-associated microbial community helps confer stress tolerance in the host plant, it is still largely unknown how the microbiota varies with plant cultivars under water stress. The study aimed to characterize drought-responsive bacteria and fungi in the roots and rhizosphere of different tall fescue cultivars. Intact grass-soil cores were collected from six cultivars grown in a field trial under no-irrigation for 3 years. Tall fescue under irrigation was also sampled from an adjacent area as the contrast. Bacterial and fungal communities in roots, rhizosphere, and bulk soil were examined for abundance, diversity, and composition using quantitative-PCR and high-throughput amplicon sequencing of 16S rRNA gene and ITS regions, respectively. Differences in microbial community composition and structure between non-irrigated and irrigated samples were statistically significant in all three microhabitats. No-irrigation enriched Actinobacteria in all three microhabitats, but mainly enriched Basidiomycota in the root endosphere and only Glomeromycota in bulk soil. Tall fescue cultivars slightly yet significantly modified endophytic microbial communities. Cultivars showing better adaptability to drought encompassed more relatively abundant Actinobacteria, Basidiomycota, or Glomeromycota in roots and the rhizosphere. PICRUSt2-based predictions revealed that the relative abundance of functional genes in roots related to phytohormones, antioxidant enzymes, and nutrient acquisition was enhanced under no-irrigation. Significant associations between Streptomyces and putative drought-ameliorating genes underscore possible mechanics for microbes to confer tall fescue with water stress tolerance. This work sheds important insight into the potential use of endophytic microbes for screening drought-adaptive genotypes and cultivars.
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Huang H, He Z, Li M, Zhou Y, Zhang J, Jin X, Chen J. Influence of exposure history on the particle retention capacity and physiological responses of Euonymus japonicus Thunb. var. aurea-marginatus Hort. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120593. [PMID: 36336181 DOI: 10.1016/j.envpol.2022.120593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/18/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Green plants in urban environments experience cyclical particulate matter stress. And this history of exhaust exposure may generate stress memory in plants, which may alter their subsequent response. Studies combining urban pollution characteristics and stress memory are limited. Therefore, we selected E. japonicus var. aurea-marginatus, a common urban greening tree species in the Yangtze River Delta, and conducted an experiment in three periods: the initial pollution period (S1: 28 days), the recovery period (R: 14 days) and the secondary pollution period (S2: 28 days). The experimental design consisted of an elevated pollution treatment (173 μg•cm-3) and an ambient control (34 μg•cm-3) with three replicates. In S2, the net total particle retention and saturated particle retention decreased by 11.5% and 19.3%, respectively, while PM10 and PM2.5 did not change significantly. E. japonicus var. aurea-marginatus exhibited recovery of chlorophyll levels, slower degradation of carotenoid, faster accumulation of ASA, lower accumulation of MDA, reduced activity of SOD under the second pollution period, and the period had a significant effect on the physiological indicators. Collectively, the effect of autoexhaust exposure history on the particle retention capacity of selected plant varied across particle sizes, and stress memory may confer plant resistance to recurrent exhaust pollution via combined regulations of physiological responses. Fine particles which pose a great risk to human health arise predominantly from vehicular traffic and energy production. So, E. japonicus tends to play a stabilising role in particle retention in industrial, traffic and residential areas.
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Affiliation(s)
- Hanhan Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, China
| | - Zhengxuan He
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, China
| | - Ming Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, China
| | - Yuanhong Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, China
| | - Jing Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, China
| | - Xinjie Jin
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Jian Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, China.
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Zi X, Wang W, Zhou S, Zhou F, Rao D, Shen P, Fang S, Wu B. Prolonged drought regulates the silage quality of maize ( Zea mays L.): Alterations in fermentation microecology. FRONTIERS IN PLANT SCIENCE 2022; 13:1075407. [PMID: 36570957 PMCID: PMC9780442 DOI: 10.3389/fpls.2022.1075407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Prolonged drought stress caused by global warming poses a tremendous challenge to silage production of maize. Drought during maize growth and development resulted in altered micro-environment for silage fermentation. How fermentation of silage maize responds to moisture scales remains uncharted territory. In this research, Maize water control trials were conducted and the silage quality and microbial community of drought-affected maize were determined. The results showed that drought stress significantly reduced the dry matter but increased root-to-shoot ratio, soluble sugar and malonaldehyde content in maize. Before fermentation, the crude protein, crude ash and acid detergent fiber contents were significantly increased but the ether extract content was decreased under drought. The crude protein and acid detergent fiber were significantly decreased in the drought affected group after fermentation. Furthermore, water stress at maize maturity stage greatly reduced the number of total bacteria in silage fermentation but increased the proportion of the lactobacillus and lactic acid content of silage. Drought stress alters the microbial ecosystem of the fermentation process and reconstitutes the diversity of the bacterial community and its metabolites. This study provides a theoretical basis for the study of changes in silage fermentation as affected by abiotic stresses.
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Affiliation(s)
- Xuejing Zi
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wan Wang
- Kunming Seed Management Station, Kunming, Yunnan, China
| | - Shiyong Zhou
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Feng Zhou
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dongyun Rao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Peng Shen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Siyang Fang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Bozhi Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
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Yang X, Huang X, Cheng J, Cheng Z, Yang Q, Hu L, Xu J, He Y. Diversity-triggered bottom-up trophic interactions impair key soil functions under lindane pollution stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120293. [PMID: 36183873 DOI: 10.1016/j.envpol.2022.120293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/29/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
A growing amount of evidence suggests that microbial diversity loss may have negative effects on soil ecosystem function. However, less attention has been paid to the determinants of the relationship between community diversity and soil functioning under pollution stress. Here we manipulated microbial diversity to observe how biotic and abiotic factors influenced soil multi-functions (e.g. lindane degradation, soil respiration and nutrient cycling). Results showed that protist community was more sensitive to dilution, pollution stress, and sodium acetate addition than bacterial and fungal community. Acetate addition accelerated the lindane removal. Any declines in microbial diversity reduced the specialized soil processes (NO3-N production, and N2O flux), but increased soil respiration rate. Dilution led to a significant increase in consumers-bacterial and fungi-bacterial interaction as evidenced by co-occurrence network, which possibly played roles in maintaining microbiome stability and resilience. Interestingly, pollution stress and resource availability weaken the relationship between microbial diversity and soil functions through the bottom-up trophic interaction and environmental preference of soil microbiome. Overall, this work provides experimental evidence that loss in microbial diversity, accompanied with changes in trophic interactions mediated biotic and abiotic factors, could have important consequences for specialized soil functioning in farmland ecosystems.
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Affiliation(s)
- Xueling Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xiaowei Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Jie Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Zhongyi Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Qi Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
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Liu L, Wang X, Chen S, Liu D, Song C, Yi S, Zhu F, Wang W, Wang F, Wang G, Song X, Jia B, Chen C, Peng H, Guo L, Han B. Fungal isolates influence the quality of Peucedanum praeruptorum Dunn. FRONTIERS IN PLANT SCIENCE 2022; 13:1011001. [PMID: 36352875 PMCID: PMC9638934 DOI: 10.3389/fpls.2022.1011001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The symbiotic relationship between beneficial microorganisms and plants plays a vital role in natural and agricultural ecosystems. Although Peucedanum praeruptorum Dunn is widely distributed, its development is greatly limited by early bolting. The reason for early bolting in P. praeruptorum remains poorly characterized. We focus on the plant related microorganisms, including endophytes and rhizosphere microorganisms, by combining the traditional isolation and culture method with metagenomic sequencing technology. We found that the OTUs of endophytes and rhizosphere microorganisms showed a positive correlation in the whole growth stage of P. praeruptorum. Meanwhile, the community diversity of endophytic and rhizosphere fungi showed an opposite change trend, and bacteria showed a similar change trend. Besides, the microbial communities differed during the pre- and post-bolting stages of P. praeruptorum. Beneficial bacterial taxa, such as Pseudomonas and Burkholderia, and fungal taxa, such as Didymella and Fusarium, were abundant in the roots in the pre-bolting stage. Further, a strain belonging to Didymella was obtained by traditional culture and was found to contain praeruptorin A, praeruptorin B, praeruptorin E. In addition, we showed that the fungus could affect its effective components when it was inoculated into P. praeruptorum. This work provided a research reference for the similar biological characteristics of perennial one-time flowering plants, such as Saposhnikovia divaricate, Angelica sinensis and Angelica dahurica.
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Affiliation(s)
- Li Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Xuejun Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Shaotong Chen
- College of Life Science, South China Agricultural University, Guangzhou, China
| | - Dong Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Shanyong Yi
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Fucheng Zhu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Wei Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Fang Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Guanglin Wang
- Analytical and Testing Center, West Anhui University, Lu’an, China
| | - Xiangwen Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Bin Jia
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Cunwu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Huasheng Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
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Phour M, Sindhu SS. Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability. PLANTA 2022; 256:85. [PMID: 36125564 DOI: 10.1007/s00425-022-03997-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
The responses of plants to different abiotic stresses and mechanisms involved in their mitigation are discussed. Production of osmoprotectants, antioxidants, enzymes and other metabolites by beneficial microorganisms and their bioengineering ameliorates environmental stresses to improve food production. Progressive intensification of global agriculture, injudicious use of agrochemicals and change in climate conditions have deteriorated soil health, diminished the microbial biodiversity and resulted in environment pollution along with increase in biotic and abiotic stresses. Extreme weather conditions and erratic rains have further imposed additional stress for the growth and development of plants. Dominant abiotic stresses comprise drought, temperature, increased salinity, acidity, metal toxicity and nutrient starvation in soil, which severely limit crop production. For promoting sustainable crop production in environmentally challenging environments, use of beneficial microbes has emerged as a safer and sustainable means for mitigation of abiotic stresses resulting in improved crop productivity. These stress-tolerant microorganisms play an effective role against abiotic stresses by enhancing the antioxidant potential, improving nutrient acquisition, regulating the production of plant hormones, ACC deaminase, siderophore and exopolysaccharides and accumulating osmoprotectants and, thus, stimulating plant biomass and crop yield. In addition, bioengineering of beneficial microorganisms provides an innovative approach to enhance stress tolerance in plants. The use of genetically engineered stress-tolerant microbes as inoculants of crop plants may facilitate their use for enhanced nutrient cycling along with amelioration of abiotic stresses to improve food production for the ever-increasing population. In this chapter, an overview is provided about the current understanding of plant-bacterial interactions that help in alleviating abiotic stress in different crop systems in the face of climate change. This review largely focuses on the importance and need of sustainable and environmentally friendly approaches using beneficial microbes for ameliorating the environmental stresses in our agricultural systems.
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Affiliation(s)
- Manisha Phour
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, 125004, India
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Satyavir S Sindhu
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, 125004, India.
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Lin Q, Li L, Fang X, Li X. Substrate complexity affects the prevalence and interconnections of antibiotic, metal and biocide resistance genes, integron-integrase genes, human pathogens and virulence factors in anaerobic digestion. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129441. [PMID: 35777143 DOI: 10.1016/j.jhazmat.2022.129441] [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: 03/11/2022] [Revised: 05/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic digestion (AD) is widely used to treat livestock manure that harbors diverse pollutants (resistance genes (ARGs), metal/biocide resistance genes (MBRGs), integron-integrase genes, human pathogens and pathogen virulence factors (VFs)). However, the interplays of these pollutants and the effects of substrate complexity on pollutants in AD are elusive. This study investigated the dynamics of these pollutants and bacterial communities during AD of swine manure, by metatranscriptomic sequencing and amplicon sequencing of 16 S rRNA and 16 S rRNA gene. The pollutant profiles and bacterial communities differed across AD processes, nevertheless with consistent dominance of ARGs of multi-drugs, tetracycline, aminoglycoside and rifamycin, MBRGs of multi-biocides, multi-metals, copper and arsenic, the integron-integrase gene intI1, potential pathogens of Escherichia coli, Streptococcus gallolyticus and Clostridium perfringens, VFs involved in pathogen adherence, and bacterial phyla of Firmicutes, Bacteroidetes and Proteobacteria. Reduced substrate complexity (replacing a part of swine manure, a complex substrate, with a simple substrate, apple waste or fructose) decreased the prevalence and stochastic turnover of ARGs and MBRGs. Network analyses revealed decreased interplays among pollutants under reduced substrate complexity. Our findings provide a mechanical understanding of diverse pollutants dynamics during AD, and reveal the importance of substrate complexity in controlling prevalence and interplays of pollutants.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Lingjuan Li
- Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Xiaoyu Fang
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Chen Z, Jin P, Wang H, Hu T, Lin X, Xie Z. Ecoenzymatic stoichiometry reveals stronger microbial carbon and nitrogen limitation in biochar amendment soils: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156532. [PMID: 35679926 DOI: 10.1016/j.scitotenv.2022.156532] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/26/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Soil extracellular enzyme activities of microbes to acquire carbon (C), nitrogen (N) and phosphorus (P) exert great roles on soil C sequestration and N, P availability. However, a lack of biochar-induced changes of C, N and P acquisition enzyme activities hinders us from understanding if biochar application will lead to microbial C, N and P limitation based on ecoenzymatic stoichiometry. In this study, through ecoenzymatic stoichiometry, a meta-analysis was conducted to evaluate responses of microbial metabolic limitation to biochar amendment by collecting data of ecoenzymatic activities (EEAs) of the C, N and P acquisition from peer-reviewed papers. The results showed that biochar application increased activities of C, N acquisition enzymes significantly by 9.3 % and 15.1 % on average, respectively. But the influence on P acquisition enzymes activities (Acid, neutral or alkaline phosphatase, abbreviated wholly as PHOS) was not significant. Biochar increased ratio of C acquisition enzymes activities (EC) over P enzymes activities (EP) and ratio of N enzymes activities (EN) over EP, but decreased EC:EN, indicating an increased N limitation or a shift from P limitation to N limitation in microbial metabolism. Enzyme vector analysis showed that soil microbial metabolism was limited by C relative to nutrients (N and P) under biochar amendment according to the overall increased vector length (~1.5 %). Wood biochar caused the strongest microbial C limitation, followed by crop residue biochar as indicated by increased enzyme vector length of 3.6 % and 1.2 % on average, respectively. The stronger microbial C limitation was also found when initial soil total organic carbon (SOC) was <20 g·kg-1. Our results illustrated that available nitrogen and organic carbon should be provided to meet microbial stoichiometric requirements to improve plant productivity, especially in low fertile soils under biochar amendment.
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Affiliation(s)
- Zhe Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Penghui Jin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Hui Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Tianlong Hu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Xingwu Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China
| | - Zubin Xie
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China.
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Müller LM, Bahn M. Drought legacies and ecosystem responses to subsequent drought. GLOBAL CHANGE BIOLOGY 2022; 28:5086-5103. [PMID: 35607942 PMCID: PMC9542112 DOI: 10.1111/gcb.16270] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 05/19/2023]
Abstract
Climate change is expected to increase the frequency and severity of droughts. These events, which can cause significant perturbations of terrestrial ecosystems and potentially long-term impacts on ecosystem structure and functioning after the drought has subsided are often called 'drought legacies'. While the immediate effects of drought on ecosystems have been comparatively well characterized, our broader understanding of drought legacies is just emerging. Drought legacies can relate to all aspects of ecosystem structure and functioning, involving changes at the species and the community scale as well as alterations of soil properties. This has consequences for ecosystem responses to subsequent drought. Here, we synthesize current knowledge on drought legacies and the underlying mechanisms. We highlight the relevance of legacy duration to different ecosystem processes using examples of carbon cycling and community composition. We present hypotheses characterizing how intrinsic (i.e. biotic and abiotic properties and processes) and extrinsic (i.e. drought timing, severity, and frequency) factors could alter resilience trajectories under scenarios of recurrent drought events. We propose ways for improving our understanding of drought legacies and their implications for subsequent drought events, needed to assess the longer-term consequences of droughts on ecosystem structure and functioning.
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Affiliation(s)
- Lena M. Müller
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Michael Bahn
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
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Exogenous Melatonin Reprograms the Rhizosphere Microbial Community to Modulate the Responses of Barley to Drought Stress. Int J Mol Sci 2022; 23:ijms23179665. [PMID: 36077064 PMCID: PMC9456345 DOI: 10.3390/ijms23179665] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 02/08/2023] Open
Abstract
The rhizospheric melatonin application-induced drought tolerance has been illuminated in various plant species, while the roles of the rhizosphere microbial community in this process are still unclear. Here, the diversity and functions of the rhizosphere microbial community and related physiological parameters were tested in barley under the rhizospheric melatonin application and drought. Exogenous melatonin improved plant performance under drought via increasing the activities of non-structural carbohydrate metabolism enzymes and activating the antioxidant enzyme systems in barley roots under drought. The 16S/ITS rRNA gene sequencing revealed that drought and melatonin altered the compositions of the microbiome. Exogenous melatonin increased the relative abundance of the bacterial community in carbohydrate and carboxylate degradation, while decreasing the relative abundance in the pathways of fatty acid and lipid degradation and inorganic nutrient metabolism under drought. These results suggest that the effects of melatonin on rhizosphere microbes and nutrient condition need to be considered in its application for crop drought-resistant cultivation.
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Whitehead J, Roy J, Hempel S, Rillig MC. Soil microbial communities shift along an urban gradient in Berlin, Germany. Front Microbiol 2022; 13:972052. [PMID: 36033838 PMCID: PMC9412169 DOI: 10.3389/fmicb.2022.972052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
The microbial communities inhabiting urban soils determine the functioning of these soils, in regards to their ability to cycle nutrients and support plant communities. In an increasingly urbanized world these properties are of the utmost importance, and the microbial communities responsible are worthy of exploration. We used 53 grassland sites spread across Berlin to describe and explain the impacts of urbanity and other environmental parameters upon the diversity and community composition of four microbial groups. These groups were (i) the Fungi, with a separate dataset for (ii) the Glomeromycota, (iii) the Bacteria, and (iv) the protist phylum Cercozoa. We found that urbanity had distinct impacts on fungal richness, which tended to increase. Geographic distance between sites and soil chemistry, in addition to urbanity, drove microbial community composition, with site connectivity being important for Glomeromycotan communities, potentially due to plant host communities. Our findings suggest that many microbial species are well adapted to urban soils, as supported by an increase in diversity being a far more common result of urbanity than the reverse. However, we also found distinctly separate distributions of operational taxonomic unit (OTU)s from the same species, shedding doubt of the reliability of indicator species, and the use of taxonomy to draw conclusion on functionality. Our observational study employed an extensive set of sites across an urbanity gradient, in the region of the German capital, to produce a rich microbial dataset; as such it can serve as a blueprint for other such investigations.
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Affiliation(s)
- James Whitehead
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Julien Roy
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefan Hempel
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C. Rillig
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Jing J, Cong WF, Bezemer TM. Legacies at work: plant-soil-microbiome interactions underpinning agricultural sustainability. TRENDS IN PLANT SCIENCE 2022; 27:781-792. [PMID: 35701291 DOI: 10.1016/j.tplants.2022.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/29/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Agricultural intensification has had long-lasting negative legacies largely because of excessive inputs of agrochemicals (e.g., fertilizers) and simplification of cropping systems (e.g., continuous monocropping). Conventional agricultural management focuses on suppressing these negative legacies. However, there is now increasing attention for creating positive above- and belowground legacies through selecting crop species/genotypes, optimizing temporal and spatial crop combinations, improving nutrient inputs, developing intelligent fertilizers, and applying soil or microbiome inoculations. This can lead to enhanced yields and reduced pest and disease pressure in cropping systems, and can also mitigate greenhouse gas emissions and enhance carbon sequestration in soils. Strengthening positive legacies requires a deeper understanding of plant-soil-microbiome interactions and innovative crop, input, and soil management which can help to achieve agricultural sustainability.
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Affiliation(s)
- Jingying Jing
- College of Grass Science and Technology, China Agricultural University, 100193 Beijing, China.
| | - Wen-Feng Cong
- College of Resources and Environmental Sciences, Laboratory of Plant-Soil Interactions, Ministry of Education, National Observation and Research Station of Agriculture Green Development at Quzhou, China Agricultural University, 100193 Beijing, China.
| | - T Martijn Bezemer
- Institute of Biology, Above-Belowground Interactions Group, Leiden University, 2333 BE Leiden, The Netherlands; Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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43
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Cui S, Han X, Xiao Y, Wu P, Zhang S, Abid A, Zheng G. Increase in rainfall intensity promotes soil nematode diversity but offset by nitrogen addition in a temperate grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:154039. [PMID: 35202692 DOI: 10.1016/j.scitotenv.2022.154039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Precipitation regime in arid and semi-arid regions is exhibiting a trend of increase in rainfall intensity but reduction in frequency under global climate change. In addition, nitrogen (N) deposition occurs simultaneously in the same regions. Nematodes are the dominant soil biota in terrestrial ecosystems and are involved in various underground processes. How the diversity of nematode communities responds to changing precipitation regime and how N deposition regulates the responses remain unclear. Here, we performed a field experiment initiated in 2012 to examine the effect of changes in the precipitation regime (2 mm precipitation intensity, 5 mm precipitation intensity, 10 mm precipitation intensity, 20 mm precipitation intensity, and 40 mm precipitation intensity) and N addition (10 g N m-2 yr-1) on soil nematode community in a semi-arid grassland in Inner Mongolia of China. We found that the abundance and diversity of nematodes increased under the treatments with fewer but stronger precipitation events (the largest abundance of total nematodes was 1458.37 individuals/100 g dry soil occurred under 40 mm intensity treatment). However, N addition reduced nematode diversity under these treatments, which largely offset the positive effects of increased rainfall intensity alone. Soil pH and plant belowground biomass were the main factors affecting nematode diversity. Our results imply that, as a consequence of global climate change, an increase in the intensity of rainfall events in the coming decades may favor the nematode communities within arid and semi-arid ecosystems. However, this positive effect may be largely offset by soil acidification in the regions experiencing heavy N deposition.
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Affiliation(s)
- Shuyan Cui
- College of Life Science, Shenyang Normal University, Shenyang 110016, China
| | - Xu Han
- Forestry College, Beihua University, Jilin 132013, China; Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Yushan Xiao
- College of Life Science, Shenyang Normal University, Shenyang 110016, China
| | - Pengfeng Wu
- College of Life Science, Shenyang Normal University, Shenyang 110016, China
| | - Shixiu Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130012, China
| | - Ali Abid
- College of Life Science, Shenyang Normal University, Shenyang 110016, China; Department of Entomology, University of Agriculture, Faisalabad 38040, Punjab, Pakistan
| | - Guo Zheng
- College of Life Science, Shenyang Normal University, Shenyang 110016, China.
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Gebauer L, Breitkreuz C, Heintz-Buschart A, Reitz T, Buscot F, Tarkka M, Bouffaud ML. Water Deficit History Selects Plant Beneficial Soil Bacteria Differently Under Conventional and Organic Farming. Front Microbiol 2022; 13:824437. [PMID: 35770171 PMCID: PMC9234553 DOI: 10.3389/fmicb.2022.824437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023] Open
Abstract
Water deficit tolerance is critical for plant fitness and survival, especially when successive drought events happen. Specific soil microorganisms are however able to improve plant tolerance to stresses, such as those displaying a 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Microorganisms adapted to dry conditions can be selected by plants over time because of properties such as sporulation, substrate preference, or cell-wall thickness. However, the complexity and interconnection between abiotic factors, like drought or soil management, and biotic factors, like plant species identity, make it difficult to elucidate the general selection processes of such microorganisms. Using a pot experiment in which wheat and barley were grown on conventional and organic farming soils, we determined the effect of water deficit history on soil microorganisms by comparing single and successive events of water limitation. The analysis showed that water deficit strongly impacts the composition of both the total microbial community (16S rRNA genes) and one of ACC deaminase-positive (acdS+) microorganisms in the rhizosphere. In contrast, successive dry conditions moderately influence the abundance and diversity of both communities compared to a single dry event. We revealed interactive effects of the farming soil type and the water deficit conditioning treatment. Indeed, possibly due to better nutrient status, plants grown on soils from conventional farming showed higher growth and were able to select more adapted microbial taxa. Some of them are already known for their plant-beneficial properties like the Actinobacteria Streptomyces, but interestingly, some Proteobacteria were also enriched after a water deficit history under conventional farming. Our approach allowed us to identify key microbial taxa promoting drought adaptation of cereals, thus improving our understanding of drought effects on plant-microbe interactions.
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Affiliation(s)
- Lucie Gebauer
- Helmholtz Centre for Environmental Research, Halle, Germany
| | | | - Anna Heintz-Buschart
- Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Thomas Reitz
- Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Mika Tarkka
- Helmholtz Centre for Environmental Research, Halle, Germany
| | - Marie-Lara Bouffaud
- Helmholtz Centre for Environmental Research, Halle, Germany
- *Correspondence: Marie-Lara Bouffaud
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45
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Sadhukhan A, Prasad SS, Mitra J, Siddiqui N, Sahoo L, Kobayashi Y, Koyama H. How do plants remember drought? PLANTA 2022; 256:7. [PMID: 35687165 DOI: 10.1007/s00425-022-03924-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Plants develop both short-term and transgenerational memory of drought stress through epigenetic regulation of transcription for a better response to subsequent exposure. Recurrent spells of droughts are more common than a single drought, with intermittent moist recovery intervals. While the detrimental effects of the first drought on plant structure and physiology are unavoidable, if survived, plants can memorize the first drought to present a more robust response to the following droughts. This includes a partial stomatal opening in the watered recovery interval, higher levels of osmoprotectants and ABA, and attenuation of photosynthesis in the subsequent exposure. Short-term drought memory is regulated by ABA and other phytohormone signaling with transcriptional memory behavior in various genes. High levels of methylated histones are deposited at the drought-tolerance genes. During the recovery interval, the RNA polymerase is stalled to be activated by a pause-breaking factor in the subsequent drought. Drought leads to DNA demethylation near drought-response genes, with genetic control of the process. Progenies of the drought-exposed plants can better adapt to drought owing to the inheritance of particular methylation patterns. However, a prolonged watered recovery interval leads to loss of drought memory, mediated by certain demethylases and chromatin accessibility factors. Small RNAs act as critical regulators of drought memory by altering transcript levels of drought-responsive target genes. Further studies in the future will throw more light on the genetic control of drought memory and the interplay of genetic and epigenetic factors in its inheritance. Plants from extreme environments can give queues to understanding robust memory responses at the ecosystem level.
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Affiliation(s)
- Ayan Sadhukhan
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, Jodhpur, 342037, India.
| | - Shiva Sai Prasad
- Department of Agriculture, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh, 522502, India
| | - Jayeeta Mitra
- Department of Botany, Arunachal University of Studies, Arunachal Pradesh, Namsai, 792103, India
| | - Nadeem Siddiqui
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh, 522502, India
| | - Lingaraj Sahoo
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Yuriko Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Hiroyuki Koyama
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
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46
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Wu JY, Hua ZL, Gu L. Per-, poly-fluoroalkyl substances (PFASs) and planktonic microbiomes: Identification of biotic and abiotic regulations in community coalescence and food webs. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 302:119078. [PMID: 35245616 DOI: 10.1016/j.envpol.2022.119078] [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: 11/08/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The importance of per-, poly-fluoroalkyl substances (PFASs) effects on riverine microbiomes is receiving increased recognition in the environmental sciences. However, few studies have explored how PFASs affect microbiomes across trophic levels, specifically through predator-prey interactions. This study examined the community profiles of planktonic archaea, bacteria, fungi, algae, protozoa, and metazoa in a semi-industrial and agricultural river alongside their interactions with 15 detected PFASs. As abiotic factors, PFASs affected community coalescence more than biogenic substances (p < 0.05). For biotic regulations, sub-communities in rare biospheres (including always rare taxa-ART and critically rare taxa-CRT) contributed to spatial community coalescence more than sub-communities in abundant biospheres (always abundant taxa-AAT and critically abundant taxa-CAT) (p < 0.05). Metazoa-bacteria (Modularity = 1.971) and protozoa-fungi (1.723) were determined to be the most stable predator-prey networks. Based on pathway models, short-chain PFBA (C4) was shown to weaken the trophic transfer efficiencies from heterotrophic bacteria (HB) to heterotrophic flagellates (HF) (p < 0.05). Long-chain PFTeDA (C14) promoted HB to amoeba (p < 0.05), which we postulate is the pathway for PFTeDA to enter the microbial food chain. Our preliminary results elucidated the influence of PFASs on planktonic microbial food webs and highlighted the need to consider protecting and remediating riverine ecosystems containing PFASs.
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Affiliation(s)
- Jian-Yi Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Zu-Lin Hua
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Li Gu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China.
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47
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Bazany KE, Wang JT, Delgado-Baquerizo M, Singh BK, Trivedi P. Water deficit affects inter-kingdom microbial connections in plant rhizosphere. Environ Microbiol 2022; 24:3722-3734. [PMID: 35582745 PMCID: PMC9545320 DOI: 10.1111/1462-2920.16031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/03/2022]
Abstract
The frequency and severity of drought are increasing due to anthropogenic climate change and are already limiting cropping system productivity in many regions around the world. Few microbial groups within plant microbiomes can potentially contribute towards the fitness and productivity of their hosts under abiotic stress events including water deficits. However, microbial communities are complex and integrative work considering the multiple co-existing groups of organisms is needed to better understand how the entire microbiome responds to environmental stresses. We hypothesize that water deficit stress will differentially shape bacterial, fungal, and protistan microbiome composition and influence inter-kingdom microbial interactions in the rhizospheres of corn and sugar beet. We used amplicon sequencing to profile bacterial, fungal, and protistan communities in corn and sugar beet rhizospheres grown under irrigated and water deficit conditions. The water deficit treatment had a stronger influence than host species on bacterial composition, whereas the opposite was true for protists. These results indicate that different microbial kingdoms have variable responses to environmental stress and host factors. Water deficit also influenced intra- and inter-kingdom microbial associations, wherein the protist taxa formed a separate cluster under water deficit conditions. Our findings help elucidate the influence of environmental and host drivers of bacterial, fungal, and protistan community assembly and co-occurrence in agricultural rhizosphere environments.
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Affiliation(s)
- Kathryn E Bazany
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC Av. Reina Mercedes 10, E-41012, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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48
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Xi N, Chen D, Bahn M, Wu H, Chu C, Cadotte MW, Bloor JMG. Drought soil legacy alters drivers of plant diversity-productivity relationships in oldfield systems. SCIENCE ADVANCES 2022; 8:eabn3368. [PMID: 35507655 PMCID: PMC9067920 DOI: 10.1126/sciadv.abn3368] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/16/2022] [Indexed: 05/26/2023]
Abstract
Ecosystem functions are threatened by both recurrent droughts and declines in biodiversity at a global scale, but the drought dependency of diversity-productivity relationships remains poorly understood. Here, we use a two-phase mesocosm experiment with simulated drought and model oldfield communities (360 experimental mesocosms/plant communities) to examine drought-induced changes in soil microbial communities along a plant species richness gradient and to assess interactions between past drought (soil legacies) and subsequent drought on plant diversity-productivity relationships. We show that (i) drought decreases bacterial and fungal richness and modifies relationships between plant species richness and microbial groups; (ii) drought soil legacy increases net biodiversity effects, but responses of net biodiversity effects to plant species richness are unaffected; and (iii) linkages between plant species richness and complementarity/selection effects vary depending on past and subsequent drought. These results provide mechanistic insight into biodiversity-productivity relationships in a changing environment, with implications for the stability of ecosystem function under climate change.
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Affiliation(s)
- Nianxun Xi
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Dongxia Chen
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Hangyu Wu
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Life Sciences/School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Marc W. Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Juliette M. G. Bloor
- Université Clermont Auvergne, INRAE, VetAgro-Sup, UREP, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
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49
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Li C, Liao H, Xu L, Wang C, He N, Wang J, Li X. The adjustment of life history strategies drives the ecological adaptations of soil microbiota to aridity. Mol Ecol 2022; 31:2920-2934. [PMID: 35344623 DOI: 10.1111/mec.16445] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
Soil microbiota increase their fitness to local habitats by adjusting their life history strategies. Yet, how such adjustments drive their ecological adaptations in xeric grasslands remains elusive. In this study, shifts in the traits that potentially represent microbial life history strategies were studied along two aridity gradients with different climates using metagenomic and trait-based approaches. The results indicated that resource acquisition (e.g., higher activities of β-D-glucosidase and N-acetyl-beta-D-glucosidase, higher degradation rates of cellulose and chitin as well as genes involved in cell motilities, biodegradations, transportations and competitions) and growth yield (e.g., higher biomass and respiration) strategies were depleted with a higher aridity. However, cellular and high growth potential maintenance (e.g., higher metabolic quotients and genes related to DNA replication, transcription, translation, central carbon metabolisms and biosynthesis) and stress tolerance (e.g., genes involved in DNA damage repair, cation transporter, sporulation and osmolyte biosynthesis) strategies were enriched with a higher aridity. This implied that microbiota have lower growth yields but are probably well primed for rapid responses to pulse rainfalls in more arid soils, whereas those in less arid soils may have stronger resource acquisition and growth yield abilities. By integrating a large amount of evidence involved in taxonomic, metagenomic, genomic and biochemical properties, this study demonstrated that the ecological adaptations of soil microbiota to aridity made by adjusting and optimizing their life history strategies are universal in xeric grasslands and provided an underlying mechanistic understanding of soil microbial responses to climate changes.
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Affiliation(s)
- Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Haijun Liao
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Lin Xu
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Changting Wang
- Institute of Qinghai-Tibet Plateau, Southwest Minzu University, Chengdu, 610041, China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junming Wang
- Section of Climate Science, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
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50
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Lin Q, Dini-Andreote F, Meador TB, Angel R, Meszárošová L, Heděnec P, Li L, Baldrian P, Frouz J. Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities. Environ Microbiol 2022; 24:3985-4000. [PMID: 35238127 DOI: 10.1111/1462-2920.15936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023]
Abstract
The mechanisms underlying microbial community dynamics and co-occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Bacterial community structures became increasingly phylogenetically clustered with soil age at early successional stages and varied less at later successional stages. The dynamics of bacterial community phylogenetic structures were determined by the changes in the soil vegetation cover along succession. The dynamics of fungal community phylogenetic structures did not significantly correlate with soil age, soil properties or vegetation cover, and were mainly attributed to stochastic processes. Along succession, the common decrease in the bacterial co-occurrence complexity and in the average pairwise phylogenetic distances between co-occurring bacteria implied a decrease in potential bacterial cooperation. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic relatedness between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.
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Affiliation(s)
- Qiang Lin
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Francisco Dini-Andreote
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Travis B Meador
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Roey Angel
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Lenka Meszárošová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Praha 4, 14220, Czech Republic
| | - Petr Heděnec
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu, 21030, Malaysia
| | - Lingjuan Li
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Praha 4, 14220, Czech Republic
| | - Jan Frouz
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic.,Institute for environmental studies, Faculty of Science, Charles University, Benátská 2, Praha 2, 12800, Czech Republic
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