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Maciag T, Kozieł E, Otulak-Kozieł K, Jafra S, Czajkowski R. Looking for Resistance to Soft Rot Disease of Potatoes Facing Environmental Hypoxia. Int J Mol Sci 2024; 25:3757. [PMID: 38612570 PMCID: PMC11011919 DOI: 10.3390/ijms25073757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Plants are exposed to various stressors, including pathogens, requiring specific environmental conditions to provoke/induce plant disease. This phenomenon is called the "disease triangle" and is directly connected with a particular plant-pathogen interaction. Only a virulent pathogen interacting with a susceptible plant cultivar will lead to disease under specific environmental conditions. This may seem difficult to accomplish, but soft rot Pectobacteriaceae (SRPs) is a group virulent of pathogenic bacteria with a broad host range. Additionally, waterlogging (and, resulting from it, hypoxia), which is becoming a frequent problem in farming, is a favoring condition for this group of pathogens. Waterlogging by itself is an important source of abiotic stress for plants due to lowered gas exchange. Therefore, plants have evolved an ethylene-based system for hypoxia sensing. Plant response is coordinated by hormonal changes which induce metabolic and physiological adjustment to the environmental conditions. Wetland species such as rice (Oryza sativa L.), and bittersweet nightshade (Solanum dulcamara L.) have developed adaptations enabling them to withstand prolonged periods of decreased oxygen availability. On the other hand, potato (Solanum tuberosum L.), although able to sense and response to hypoxia, is sensitive to this environmental stress. This situation is exploited by SRPs which in response to hypoxia induce the production of virulence factors with the use of cyclic diguanylate (c-di-GMP). Potato tubers in turn reduce their defenses to preserve energy to prevent the negative effects of reactive oxygen species and acidification, making them prone to soft rot disease. To reduce the losses caused by the soft rot disease we need sensitive and reliable methods for the detection of the pathogens, to isolate infected plant material. However, due to the high prevalence of SRPs in the environment, we also need to create new potato varieties more resistant to the disease. To reach that goal, we can look to wild potatoes and other Solanum species for mechanisms of resistance to waterlogging. Potato resistance can also be aided by beneficial microorganisms which can induce the plant's natural defenses to bacterial infections but also waterlogging. However, most of the known plant-beneficial microorganisms suffer from hypoxia and can be outcompeted by plant pathogens. Therefore, it is important to look for microorganisms that can withstand hypoxia or alleviate its effects on the plant, e.g., by improving soil structure. Therefore, this review aims to present crucial elements of potato response to hypoxia and SRP infection and future outlooks for the prevention of soft rot disease considering the influence of environmental conditions.
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Affiliation(s)
- Tomasz Maciag
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Edmund Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Katarzyna Otulak-Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland;
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Zhang A, Wang Y, Li Y, Tan Y, Liu P, Lv X, Lei K. Multiple isotopes reveal the driving forces of nitrogen cycling from freshwater to brackish water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165396. [PMID: 37437639 DOI: 10.1016/j.scitotenv.2023.165396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023]
Abstract
Rivers play a crucial role in global nitrogen (N) cycling, but revealing the driving mechanism of N cycling remains challenging because of the complex natural background gradients. The Qiantang River Basin provides an opportunity to elucidate the driving mechanism due to the complex climatic and hydrological conditions. In this study, the multiple stable isotopes suggested that the conservative mixing of two end members was insufficient to explain the complex behavior of N in both seasons. In-soil processes were the primary N cycling processes that controlled riverine N loading during the wet season, whereas in-stream N biological transformation processes (nitrification and assimilation) were more prevalent during the dry season. The results of MixSIAR revealed that soil sources (soil N and N fertilizer) contributed the most to NO3- during the wet season, accounting for 64.3 %, followed by manure and sewage (31.6 %) and atmospheric precipitation (4.1 %). During the dry season, manure and sewage were the predominant contributors to NO3- (52.1 %), followed by soil N (26.6 %), N fertilizer (18.8 %), and atmospheric precipitation (2.5 %). The relationships between d-excess and δ15N-NH4+ or δ15N-NO3- suggested that both climatic and hydrological conditions would be the driving forces regulating the N transportation and transformation in this basin, leading to the high spatiotemporal heterogeneity in N loading and isotopic compositions. In the wet season, precipitation patterns served as the primary driving forces regulating in-soil biological processes and soil leaching. While the hydrological conditions, especially water residence time, were the crucial factors controlling in-stream biological processes during the dry season. This study elucidates N sources, biotransformation processes, and their driving forces from freshwater to brackish water, which has applications for understanding the N fate from terrene to ocean.
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Affiliation(s)
- Anqi Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; Key Lab of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling 712100, PR China
| | - Yan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Yi Li
- Key Lab of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling 712100, PR China
| | - Yingyu Tan
- Key Laboratory of Environmental Pollution Control Technology of Zhejiang Province, Eco-Environmental Science Research & Design Institute of Zhejiang Province, Hangzhou, Zhejiang 310007, PR China
| | - Pengxia Liu
- Ecology and Environment Monitoring and Scientific Research Center of Taihu Basin & East China Sea Ecology and Environment Supervision Authority, Ministry of Ecology and Environment, Shanghai 200120, China
| | - Xubo Lv
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Kun Lei
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
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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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Simanjuntak C, Gaiser T, Ahrends HE, Ceglar A, Singh M, Ewert F, Srivastava AK. Impact of climate extreme events and their causality on maize yield in South Africa. Sci Rep 2023; 13:12462. [PMID: 37528122 PMCID: PMC10393995 DOI: 10.1038/s41598-023-38921-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023] Open
Abstract
Extreme climate events can have a significant negative impact on maize productivity, resulting in food scarcity and socioeconomic losses. Thus, quantifying their effect is needed for developing future adaptation and mitigation strategies, especially for countries relying on maize as a staple crop, such as South Africa. While several studies have analyzed the impact of climate extremes on maize yields in South Africa, little is known on the quantitative contribution of combined extreme events to maize yield variability and the causality link of extreme events. This study uses existing stress indices to investigate temporal and spatial patterns of heatwaves, drought, and extreme precipitation during maize growing season between 1986/87 and 2015/16 for South Africa provinces and at national level and quantifies their contribution to yield variability. A causal discovery algorithm was applied to investigate the causal relationship among extreme events. At the province and national levels, heatwaves and extreme precipitation showed no significant trend. However, drought severity increased in several provinces. The modified Combined Stress Index (CSIm) model showed that the maize yield nationwide was associated with drought events (explaining 25% of maize yield variability). Heatwaves has significant influence on maize yield variability (35%) in Free State. In North West province, the maize yield variability (46%) was sensitive to the combination of drought and extreme precipitation. The causal analysis suggests that the occurrence of heatwaves intensified drought, while a causal link between heatwaves and extreme precipitation was not detected. The presented findings provide a deeper insight into the sensitivity of yield data to climate extremes and serve as a basis for future studies on maize yield anomalies.
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Affiliation(s)
- Christian Simanjuntak
- Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
| | - Thomas Gaiser
- Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Hella Ellen Ahrends
- Department of Agricultural Sciences, University of Helsinki, Koetilantie 5, 00014, Helsinki, Finland
| | - Andrej Ceglar
- Climate Change Centre of the European Central Bank, Sonnemannstrasse 20, 60314, Frankfurt Am Main, Germany
| | - Manmeet Singh
- Indian Institute of Tropical Meteorology, Ministry of Earth Sciences, Pune, India
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Straße 84, 15374, Müncheberg, Germany
| | - Amit Kumar Srivastava
- Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
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Yuan T, Ren W, Wang Z, Fry EL, Tang S, Yin J, Zhang J, Jia Z. How does the pattern of root metabolites regulating beneficial microorganisms change with different grazing pressures? FRONTIERS IN PLANT SCIENCE 2023; 14:1180576. [PMID: 37484473 PMCID: PMC10361787 DOI: 10.3389/fpls.2023.1180576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023]
Abstract
Grazing disturbance can change the structure of plant rhizosphere microbial communities and thereby alter the feedback to promote plant growth or induce plant defenses. However, little is known about how such changes occur and vary under different grazing pressures or the roles of root metabolites in altering the composition of rhizosphere microbial communities. In this study, the effects of different grazing pressures on the composition of microbial communities were investigated, and the mechanisms by which different grazing pressures changed rhizosphere microbiomes were explored with metabolomics. Grazing changed composition, functions, and co-expression networks of microbial communities. Under light grazing (LG), some saprophytic fungi, such as Lentinus sp., Ramichloridium sp., Ascobolus sp. and Hyphoderma sp., were significantly enriched, whereas under heavy grazing (HG), potentially beneficial rhizobacteria, such as Stenotrophomonas sp., Microbacterium sp., and Lysobacter sp., were significantly enriched. The beneficial mycorrhizal fungus Schizothecium sp. was significantly enriched in both LG and HG. Moreover, all enriched beneficial microorganisms were positively correlated with root metabolites, including amino acids (AAs), short-chain organic acids (SCOAs), and alkaloids. This suggests that these significantly enriched rhizosphere microbial changes may be caused by these differential root metabolites. Under LG, it is inferred that root metabolites, especially AAs such as L-Histidine, may regulate specific saprophytic fungi to participate in material transformations and the energy cycle and promote plant growth. Furthermore, to help alleviate the stress of HG and improve plant defenses, it is inferred that the root system actively regulates the synthesis of these root metabolites such as AAs, SCOAs, and alkaloids under grazing interference, and then secretes them to promote the growth of some specific plant growth-promoting rhizobacteria and fungi. To summarize, grasses can regulate beneficial microorganisms by changing root metabolites composition, and the response strategies vary under different grazing pressure in typical grassland ecosystems.
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Affiliation(s)
- Ting Yuan
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Weibo Ren
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zhaoming Wang
- Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd., Hohhot, China
| | - Ellen L. Fry
- Department of Biology, Edge Hill University, Ormskirk, United Kingdom
| | - Shiming Tang
- Key Laboratory of Model Innovation in Forage Production Efficiency, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jingjing Yin
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiatao Zhang
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zhenyu Jia
- Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd., Hohhot, China
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Artificial Cultivation Changes Foliar Endophytic Fungal Community of the Ornamental Plant Lirianthe delavayi. Microorganisms 2023; 11:microorganisms11030775. [PMID: 36985348 PMCID: PMC10059682 DOI: 10.3390/microorganisms11030775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Many wild ornamental plant species have been introduced to improve the landscape of cities; however, until now, no study has been performed to explore the composition and function of foliar endophytes associated with cultivated rare plants in cities after their introduction. In this study, we collected the leaves of the healthy ornamental plant Lirianthe delavayi from wild and artificially cultivated habitats in Yunnan and compared their diversity, species composition, and functional predictions of their foliar endophytic fungal community based on high-throughput sequencing technology. In total, 3125 ASVs of fungi were obtained. The alpha diversity indices of wild L. delavayi populations are similar to those of cultivated samples; however, the species compositions of endophytic fungal ASVs were significantly varied in the two habitats. The dominant phylum is Ascomycota, accounting for more than 90% of foliar endophytes in both populations; relatively, artificial cultivation trends to increase the frequency of common phytopathogens of L. delavayi, such as Alternaria, Erysiphe. The relative abundance of 55 functional predictions is different between wild and cultivated L. delavayi leaves (p < 0.05); in particular, chromosome, purine metabolism, and peptidases are significantly increased in wild samples, while flagellar assembly, bacterial chemotaxis, and fatty acid metabolism are significantly enhanced in cultivated samples. Our results indicated that artificial cultivation can greatly change the foliar endophytic fungal community of L. delavayi, which is valuable for understanding the influence of the domestication process on the foliar fungal community associated with rare ornamental plants in urban environments.
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Zhu W, Ding C, Zhu K, Zhang W, Liang D, Wang X, Li A, Su X. Characterization of ectomycorrhizal fungal communities associated with tree species on an iron tailings deposit undergoing restoration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:84396-84409. [PMID: 35780265 PMCID: PMC9646614 DOI: 10.1007/s11356-022-21690-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Vegetation restoration is an effective method to improve the ecological environment of mine tailings, which has a profound impact on the potential ecological functions of soil fungal communities; yet, little is known about its beneficial effect on soil ectomycorrhizal fungal community. In this study, the responses of soil characteristics and soil ectomycorrhizal fungal community diversity and structure to different revegetation, as well as the contribution of soil factors to soil ectomycorrhizal community were investigated in Liaoning Province, China. As we anticipated, the presence of vegetation significantly improved most soil properties we studied. What's more, compared to Korean pine (Pinus koraiensis Sieb. et Zucc.), Chinese poplar (Populus simonii Carr), and black locust (Robinia pseudoacacia L) could better improve soil total carbon, total nitrogen, total phosphorus, and available phosphorus. In addition, soil ectomycorrhizal fungal community diversity in black locust was greater than Korean pine and Populus simonii. Nonmetric multidimensional scaling analyses indicated that soil ectomycorrhizal community significantly differed depending on different revegetation types. Thus, these results indicated that black locust could be a suitable species for the revegetation of iron mine tailings. The study provided theoretical basis for ecological restoration of iron mine tailings using local plant species.
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Affiliation(s)
- Wenxu Zhu
- College of Foresty, The University of Shenyang Agriculture, Dongling Road, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
| | - Keye Zhu
- College of Foresty, The University of Shenyang Agriculture, Dongling Road, Shenyang, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Dejun Liang
- Liaoning Provincial Poplar Institute, Gaizhou, Liaoning, China
| | - XiaoJiang Wang
- Inner Mongolia Academy of Forestry Sciences, Hohhot, Inner Mongolia, China
| | - Aiping Li
- Inner Mongolia Academy of Forestry Sciences, Hohhot, Inner Mongolia, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Response of the wheat mycobiota to flooding revealed substantial shifts towards plant pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:1028153. [PMID: 36518495 PMCID: PMC9742542 DOI: 10.3389/fpls.2022.1028153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Rainfall extremes are intensifying as a result of climate change, leading to increased flood risk. Flooding affects above- and belowground ecosystem processes, representing a substantial threat to crop productivity under climate change. Plant-associated fungi play important roles in plant performance, but their response to abnormal rain events is unresolved. Here, we established a glasshouse experiment to determine the effects of flooding stress on the spring wheat-mycobiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages, such as tillering, booting and flowering. We assessed the wheat mycobiota response to flooding in three soil-plant compartments (phyllosphere, roots and rhizosphere) using metabarcoding. Key soil and plant traits were measured to correlate physiological plant and edaphic changes with shifts in mycobiota structure and functional guilds. Flooding reduced plant fitness, and caused dramatic shifts in mycobiota assembly across the entire plant. Notably, we observed a functional transition consisting of a decline in mutualist abundance and richness with a concomitant increase in plant pathogens. Indeed, fungal pathogens associated with important cereal diseases, such as Gibberella intricans, Mycosphaerella graminicola, Typhula incarnata and Olpidium brassicae significantly increased their abundance under flooding. Overall, our study demonstrate the detrimental effect of flooding on the wheat mycobiota complex, highlighting the urgent need to understand how climate change-associated abiotic stressors alter plant-microbe interactions in cereal crops.
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Affiliation(s)
- Davide Francioli
- Institute of Crop Science, Faculty of Agricultural Sciences, University of Hohenheim, Stuttgart, Germany
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Marčiulynienė D, Marčiulynas A, Mishcherikova V, Lynikienė J, Gedminas A, Franic I, Menkis A. Principal Drivers of Fungal Communities Associated with Needles, Shoots, Roots and Adjacent Soil of Pinus sylvestris. J Fungi (Basel) 2022; 8:jof8101112. [PMID: 36294677 PMCID: PMC9604598 DOI: 10.3390/jof8101112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023] Open
Abstract
The plant- and soil-associated microbial communities are critical to plant health and their resilience to stressors, such as drought, pathogens, and pest outbreaks. A better understanding of the structure of microbial communities and how they are affected by different environmental factors is needed to predict and manage ecosystem responses to climate change. In this study, we carried out a country-wide analysis of fungal communities associated with Pinus sylvestris growing under different environmental conditions. Needle, shoot, root, mineral, and organic soil samples were collected at 30 sites. By interconnecting the high-throughput sequencing data, environmental variables, and soil chemical properties, we were able to identify key factors that drive the diversity and composition of fungal communities associated with P. sylvestris. The fungal species richness and community composition were also found to be highly dependent on the site and the substrate they colonize. The results demonstrated that different functional tissues and the rhizosphere soil of P. sylvestris are associated with diverse fungal communities, which are driven by a combination of climatic (temperature and precipitation) and edaphic factors (soil pH), and stand characteristics.
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Affiliation(s)
- Diana Marčiulynienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
- Correspondence:
| | - Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Valeriia Mishcherikova
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Jūratė Lynikienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Artūras Gedminas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Iva Franic
- Department of Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden;
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007 Uppsala, Sweden;
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Wang Y, Xu Y, Maitra P, Babalola BJ, Zhao Y. Temporal variations in root-associated fungal communities of Potaninia mongolica, an endangered relict shrub species in the semi-arid desert of Northwest China. FRONTIERS IN PLANT SCIENCE 2022; 13:975369. [PMID: 36311128 PMCID: PMC9597089 DOI: 10.3389/fpls.2022.975369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The semi-arid region of the Western Ordos plateau in Inner Mongolia, China, is home to a critically endangered shrub species, Potaninia mongolica, which originates from ancient Mediterranean regions. Root-associated microbiomes play important roles in plant nutrition, productivity, and resistance to environmental stress particularly in the harsh desert environment; however, the succession of root-associated fungi during the growth stages of P. mongolica is still unclear. This study aimed to examine root-associated fungal communities of this relict plant species across three seasons (spring, summer and autumn) using root sampling and Illumina Miseq sequencing of internal transcribed spacer 2 (ITS 2) region to target fungi. The analysis detected 698 fungal OTUs in association with P. mongolica roots, and the fungal richness increased significantly from spring to summer and autumn. Eurotiales, Hypocreales, Chaetothyriales, Pleosporales, Helotiales, Agaricales and Xylariales were the dominant fungal orders. Fungal community composition was significantly different between the three seasons, and the fungal taxa at various levels showed biased distribution and preferences. Stochastic processes predominantly drove community assembly of fungi in spring while deterministic processes acted more in the later seasons. The findings revealed the temporal dynamics of root-associated fungal communities of P. mongolica, which may enhance our understanding of biodiversity and changes along with seasonal alteration in the desert, and predict the response of fungal community to future global changes.
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Affiliation(s)
- Yonglong Wang
- Faculty of Biological Science and Technology, Baotou Teacher’s College, Baotou, China
| | - Ying Xu
- Faculty of Biological Science and Technology, Baotou Teacher’s College, Baotou, China
| | - Pulak Maitra
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - Busayo Joshua Babalola
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanling Zhao
- Faculty of Biological Science and Technology, Baotou Teacher’s College, Baotou, China
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Martínez‐Arias C, Witzell J, Solla A, Martin JA, Rodríguez‐Calcerrada J. Beneficial and pathogenic plant-microbe interactions during flooding stress. PLANT, CELL & ENVIRONMENT 2022; 45:2875-2897. [PMID: 35864739 PMCID: PMC9543564 DOI: 10.1111/pce.14403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 05/29/2023]
Abstract
The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.
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Affiliation(s)
- Clara Martínez‐Arias
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
| | - Johanna Witzell
- Department of Forestry and Wood TechnologyLinnaeus UniversityVäxjöSweden
| | - Alejandro Solla
- Faculty of Forestry, Institute for Dehesa Research (INDEHESA)Universidad de ExtremaduraPlasenciaSpain
| | - Juan Antonio Martin
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
| | - Jesús Rodríguez‐Calcerrada
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
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12
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Dong L, Yao X, Deng Y, Zhang H, Zeng W, Li X, Tang J, Wang W. Nitrogen deficiency in soil mediates multifunctionality responses to global climatic drivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156533. [PMID: 35679931 DOI: 10.1016/j.scitotenv.2022.156533] [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: 03/12/2022] [Revised: 05/23/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Natural and anthropogenic processes that decrease the availability of nitrogen (N) frequently occur in soil. Losses of N may limit the multiple functions linked to carbon, N and phosphorous cycling of soil (soil multifunctionality, SMF). Microbial communities and SMF are intimately linked. However, the relationship between soil microbial communities and SMF in response to global changes under N deficiency has never been examined in natural ecosystems. Here, soil samples from nine temperate arid grassland sites were used to assess the importance of microbial communities as driver of SMF to climate change and N deficiency. SMF was significantly decreased by drought and drought-wetting cycles, independent of the availability of soil N. Interestingly, temperature changes (variable temperature and warming) significantly increased SMF in N-poor conditions. However, this was at the expense of decreased SMF resistance. Deterministic assembly-driven microbial α-diversity and particularly fungal α-diversity, but not β-diversity, were generally found to play key roles in maintaining SMF in N-poor soil, irrespective of the climate. The results have two important implications. First, the absence of the stability offered by β-diversity means N-poor ecosystems will be particularly sensitive to global climate changes. Second, fungi are more important than bacteria for maintaining SMF in N-poor soil under climate changes.
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Affiliation(s)
- Lizheng Dong
- Department 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
| | - Xiaodong Yao
- Department 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; School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen 518055, China; State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Yanyu Deng
- Department 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; School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Hongjin Zhang
- Department 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
| | - Wenjing Zeng
- Department 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; Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinyu Li
- Center for Statistical Science, School of Mathematical Sciences, Peking University, Beijing 100871, China
| | - Junjie Tang
- Center for Statistical Science, School of Mathematical Sciences, Peking University, Beijing 100871, China
| | - Wei Wang
- Department 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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Zuo YL, Hu QN, Qin L, Liu JQ, He XL. Species identity and combinations differ in their overall benefits to Astragalus adsurgens plants inoculated with single or multiple endophytic fungi under drought conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:933738. [PMID: 36160950 PMCID: PMC9490189 DOI: 10.3389/fpls.2022.933738] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Although desert plants often establish multiple simultaneous symbiotic associations with various endophytic fungi in their roots, most studies focus on single fungus inoculation. Therefore, combined inoculation of multiple fungi should be applied to simulate natural habitats with the presence of a local microbiome. Here, a pot experiment was conducted to test the synergistic effects between three extremely arid habitat-adapted root endophytes (Alternaria chlamydospora, Sarocladium kiliense, and Monosporascus sp.). For that, we compared the effects of single fungus vs. combined fungi inoculation, on plant morphology and rhizospheric soil microhabitat of desert plant Astragalus adsurgens grown under drought and non-sterile soil conditions. The results indicated that fungal inoculation mainly influenced root biomass of A. adsurgens, but did not affect the shoot biomass. Both single fungus and combined inoculation decreased plant height (7-17%), but increased stem branching numbers (13-34%). However, fungal inoculation influenced the root length and surface area depending on their species and combinations, with the greatest benefits occurring on S. kiliense inoculation alone and its co-inoculation with Monosporascus sp. (109% and 61%; 54% and 42%). Although A. chlamydospora and co-inoculations with S. kiliense and Monosporascus sp. also appeared to promote root growth, these inoculations resulted in obvious soil acidification. Despite no observed root growth promotion, Monosporascus sp. associated with its combined inoculations maximally facilitated soil organic carbon accumulation. However, noticeably, combined inoculation of the three species had no significant effects on root length, surface area, and biomass, but promoted rhizospheric fungal diversity and abundance most, with Sordariomycetes being the dominant fungal group. This indicates the response of plant growth to fungal inoculation may be different from that of the rhizospheric fungal community. Structural equation modeling also demonstrated that fungal inoculation significantly influenced the interactions among the growth of A. adsurgens, soil factors, and rhizospheric fungal groups. Our findings suggest that, based on species-specific and combinatorial effects, endophytic fungi enhanced the plant root growth, altered soil nutrients, and facilitated rhizospheric fungal community, possibly contributing to desert plant performance and ecological adaptability. These results will provide the basis for evaluating the potential application of fungal inoculants for developing sustainable management for desert ecosystems.
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Affiliation(s)
- Yi-Ling Zuo
- School of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Qian-Nan Hu
- School of Life Sciences, Hebei University, Baoding, China
| | - Le Qin
- School of Life Sciences, Hebei University, Baoding, China
| | - Jia-Qiang Liu
- School of Life Sciences, Hebei University, Baoding, China
| | - Xue-Li He
- School of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
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15
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Kirkman ER, Hilton S, Sethuraman G, Elias DMO, Taylor A, Clarkson J, Soh AC, Bass D, Ooi GT, McNamara NP, Bending GD. Diversity and Ecological Guild Analysis of the Oil Palm Fungal Microbiome Across Root, Rhizosphere, and Soil Compartments. Front Microbiol 2022; 13:792928. [PMID: 35222328 PMCID: PMC8874247 DOI: 10.3389/fmicb.2022.792928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 11/14/2022] Open
Abstract
The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world’s most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.
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Affiliation(s)
- Eleanor R. Kirkman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gomathy Sethuraman
- Crops for the Future Research Centre, Semenyih, Malaysia
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Dafydd M. O. Elias
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, United Kingdom
| | - Andrew Taylor
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - John Clarkson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Aik Chin Soh
- Crops for the Future Research Centre, Semenyih, Malaysia
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - Gin Teng Ooi
- Crops for the Future Research Centre, Semenyih, Malaysia
| | - Niall P. McNamara
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Gary D. Bending,
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Custódio V, Gonin M, Stabl G, Bakhoum N, Oliveira MM, Gutjahr C, Castrillo G. Sculpting the soil microbiota. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:508-522. [PMID: 34743401 DOI: 10.1111/tpj.15568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Soil is a living ecosystem, the health of which depends on fine interactions among its abiotic and biotic components. These form a delicate equilibrium maintained through a multilayer network that absorbs certain perturbations and guarantees soil functioning. Deciphering the principles governing the interactions within soils is of critical importance for their management and conservation. Here, we focus on soil microbiota and discuss the complexity of interactions that impact the composition and function of soil microbiota and their interaction with plants. We discuss how physical aspects of soils influence microbiota composition and how microbiota-plant interactions support plant growth and responses to nutrient deficiencies. We predict that understanding the principles determining the configuration and functioning of soil microbiota will contribute to the design of microbiota-based strategies to preserve natural resources and develop more environmentally friendly agricultural practices.
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Affiliation(s)
- Valéria Custódio
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Mathieu Gonin
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Georg Stabl
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
| | - Niokhor Bakhoum
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
| | - Gabriel Castrillo
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
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17
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Jaramillo A, Mendoza-Ponce A. Climate Change Overview. Fungal Biol 2022. [DOI: 10.1007/978-3-030-89664-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Liu YR, Eldridge DJ, Zeng XM, Wang J, Singh BK, Delgado-Baquerizo M. Global diversity and ecological drivers of lichenised soil fungi. THE NEW PHYTOLOGIST 2021; 231:1210-1219. [PMID: 33914920 DOI: 10.1111/nph.17433] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/16/2021] [Indexed: 05/26/2023]
Abstract
Lichens play crucial roles in sustaining the functioning of terrestrial ecosystems; however, the diversity and ecological factors associated with lichenised soil fungi remain poorly understood. To address this knowledge gap, we used a global field survey including information on fungal sequences of topsoils from 235 terrestrial ecosystems. We identified 880 lichenised fungal phylotypes across nine biomes ranging from deserts to tropical forests. The diversity and proportion of lichenised soil fungi peaked in shrublands and dry grasslands. Aridity index, plant cover and soil pH were the most important factors associated with the distribution of lichenised soil fungi. Furthermore, we identified Endocarpon, Verrucaria and Rinodina as some of the most dominant lichenised genera across the globe, and they had similar environmental preferences to the lichenised fungal community. In addition, precipitation seasonality and mean diurnal temperature range were also important in predicting the proportion of these dominant genera. Using this information, we were able to create the first global maps of the richness and the proportion of dominant genera of lichenised fungi. This work provides new insight into the global distribution and ecological preferences of lichenised soil fungi, and supports their dominance in drylands across the globe.
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Affiliation(s)
- Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Xiao-Min Zeng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, NSW, 2751, Australia
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, 41013, Spain
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Koczorski P, Furtado BU, Gołębiewski M, Hulisz P, Baum C, Weih M, Hrynkiewicz K. The Effects of Host Plant Genotype and Environmental Conditions on Fungal Community Composition and Phosphorus Solubilization in Willow Short Rotation Coppice. FRONTIERS IN PLANT SCIENCE 2021; 12:647709. [PMID: 34290719 PMCID: PMC8287252 DOI: 10.3389/fpls.2021.647709] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
Phosphorus (P) is an essential plant nutrient. Low availability of P in soil is mainly caused by high content of Fe2O3 in the clay fraction that binds to P making it unavailable. Beneficial microbes, such as P solubilizing microorganisms can increase the available P in soil and improve plant growth and productivity. In this study, we evaluated the effects of environmental conditions (climate, soil parameters), plant genotype, and level of plant association (rhizosphere or endophytic root organism) on the abundance and diversity of phosphorus solubilizing microorganisms in a Salix production system. We hypothesized that a lower number of endophytic fungi may possess the ability to solubilize P compared to the number of rhizosphere fungi with the same ability. We also expect that the plant genotype and the experimental site with its environmental conditions will influence fungal diversity. Two Salix genotypes grown in pure and mixed cultures were investigated for their fungal microbiome community and diversity in the rhizosphere and endosphere during two growing seasons. We found that the rhizosphere fungal community was more diverse. A general dominance of Ascomycota (Dothideomycetes) and Basidiomycota (Tremellomycetes) was observed. The classes Agaricomycetes and Pezizomycetes were more frequent in the endosphere, while Tremellomycetes and Mortierellomycetes were more abundant in the rhizosphere. Plot-specific soil properties (pH, total organic carbon, and nitrogen) significantly influenced the fungal community structure. Among the culturable fungal diversities, 10 strains of phosphate solubilizing fungi (PSFs) from roots and 12 strains from rhizosphere soil were identified using selective media supplemented with di-calcium and tri-calcium phosphates. The fungal density and the number of PSF were much higher in the rhizosphere than in the endosphere. Penicillium was the dominant genus of PSF isolated from both sites; other less frequent genera of PSFs were Alternaria, Cladosporium, and Clonostachys. Overall the main factors controlling the fungal communities (endophytic vs. rhizosphere fungi) were the soil properties and level of plant association, while no significant influence of growing season was observed. Differences between Salix genotypes were observed for culturable fungal diversity, while in metagenomic data analysis, only the class Dothideomycetes showed a significant effect from the plant genotype.
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Affiliation(s)
- Piotr Koczorski
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland
| | - Bliss Ursula Furtado
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland
| | - Marcin Gołębiewski
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Piotr Hulisz
- Department of Soil Science and Landscape Management, Faculty of Earth Sciences and Spatial Management, Nicolaus Copernicus University, Torun, Poland
| | - Christel Baum
- Soil Science, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Martin Weih
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland
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Thomas PW. Ectomycorrhiza resilience and recovery to extreme flood events in Tuber aestivum and Quercus robur. MYCORRHIZA 2021; 31:511-517. [PMID: 33982140 PMCID: PMC8266694 DOI: 10.1007/s00572-021-01035-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/06/2021] [Indexed: 06/01/2023]
Abstract
Very little is known about the impact of flooding and ground saturation on ectomycorrhizal fungi (EcM) and increasing flood events are expected with predicted climate change. To explore this, seedlings inoculated with the EcM species Tuber aestivum were exposed to a range of flood durations. Oak seedlings inoculated with T. aestivum were submerged for between 7 and 65 days. After a minimum of 114-day recovery, seedling growth measurements were recorded, and root systems were destructively sampled to measure the number of existing mycorrhizae in different zones. Number of mycorrhizae did not display correlation with seedling growth measurements. Seven days of submersion resulted in a significant reduction in mycorrhizae numbers and numbers reduced most drastically in the upper zones. Increases in duration of submersion further impacted mycorrhizae numbers in the lowest soil zone only. T. aestivum mycorrhizae can survive flood durations of at least 65 days. After flooding, mycorrhizae occur in higher numbers in the lowest soil zone, suggesting a mix of resilience and recovery. The results will aid in furthering our understanding of EcM but also may aid in conservation initiatives as well as providing insight for those whose livelihoods revolve around the collection of EcM fruiting bodies or cropping of the plant partners.
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Affiliation(s)
- P W Thomas
- Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
- Mycorrhizal Systems Ltd, Lancashire, PR25 2SD, UK.
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21
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Gschwend F, Hartmann M, Hug AS, Enkerli J, Gubler A, Frey B, Meuli RG, Widmer F. Long-term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions. Mol Ecol 2021; 30:4305-4320. [PMID: 34160856 PMCID: PMC8456938 DOI: 10.1111/mec.16036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
Despite the importance of soil microorganisms for ecosystem services, long‐term surveys of their communities are largely missing. Using metabarcoding, we assessed temporal dynamics of soil bacterial and fungal communities in three land‐use types, i.e., arable land, permanent grassland, and forest, over five years. Soil microbial communities remained relatively stable and differences over time were smaller than those among sites. Temporal variability was highest in arable soils. Indications for consistent shifts in community structure over five years were only detected at one site for bacteria and at two sites for fungi, which provided further support for long‐term stability of soil microbial communities. A sliding window analysis was applied to assess the effect of OTU abundance on community structures. Partial communities with decreasing OTU abundances revealed a gradually decreasing structural similarity with entire communities. This contrasted with the steep decline of OTU abundances, as subsets of rare OTUs (<0.01%) revealed correlations of up to 0.97 and 0.81 with the entire bacterial and fungal communities. Finally, 23.4% of bacterial and 19.8% of fungal OTUs were identified as scarce, i.e., neither belonging to site‐cores nor correlating to environmental factors, while 67.3% of bacterial and 64.9% of fungal OTUs were identified as rare but not scarce. Our results demonstrate high stability of soil microbial communities in their abundant and rare fractions over five years. This provides a step towards defining site‐specific normal operating ranges of soil microbial communities, which is a prerequisite for detecting community shifts that may occur due to changing environmental conditions or anthropogenic activities.
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Affiliation(s)
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Anna-Sofia Hug
- Swiss Soil Monitoring Network NABO, Agroscope, Zürich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Andreas Gubler
- Swiss Soil Monitoring Network NABO, Agroscope, Zürich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Reto G Meuli
- Swiss Soil Monitoring Network NABO, Agroscope, Zürich, Switzerland
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Parker TC, Clemmensen KE, Friggens NL, Hartley IP, Johnson D, Lindahl BD, Olofsson J, Siewert MB, Street LE, Subke JA, Wookey PA. Rhizosphere allocation by canopy-forming species dominates soil CO 2 efflux in a subarctic landscape. THE NEW PHYTOLOGIST 2020; 227:1818-1830. [PMID: 32248524 DOI: 10.1111/nph.16573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
In arctic ecosystems, climate change has increased plant productivity. As arctic carbon (C) stocks predominantly are located belowground, the effects of greater plant productivity on soil C storage will significantly determine the net sink/source potential of these ecosystems, but vegetation controls on soil CO2 efflux remain poorly resolved. In order to identify the role of canopy-forming species in belowground C dynamics, we conducted a girdling experiment with plots distributed across 1 km2 of treeline birch (Betula pubescens) forest and willow (Salix lapponum) patches in northern Sweden and quantified the contribution of canopy vegetation to soil CO2 fluxes and belowground productivity. Girdling birches reduced total soil CO2 efflux in the peak growing season by 53%, which is double the expected amount, given that trees contribute only half of the total leaf area in the forest. Root and mycorrhizal mycelial production also decreased substantially. At peak season, willow shrubs contributed 38% to soil CO2 efflux in their patches. Our findings indicate that C, recently fixed by trees and tall shrubs, makes a substantial contribution to soil respiration. It is critically important that these processes are taken into consideration in the context of a greening arctic because productivity and ecosystem C sequestration are not synonymous.
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Affiliation(s)
- Thomas C Parker
- Biological and Environmental Sciences, University of Stirling, Stirling,, FK9 4LA, UK
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Nina L Friggens
- Biological and Environmental Sciences, University of Stirling, Stirling,, FK9 4LA, UK
| | - Iain P Hartley
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter,, EX4 4RJ, UK
| | - David Johnson
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Johan Olofsson
- Department of Ecology and Environmental Sciences, Umeå University, Umeå, SE-901 87, Sweden
| | - Matthias B Siewert
- Department of Ecology and Environmental Sciences, Umeå University, Umeå, SE-901 87, Sweden
| | - Lorna E Street
- School of Geosciences, University of Edinburgh, Edinburgh,, EH9 3FF, UK
| | - Jens-Arne Subke
- Biological and Environmental Sciences, University of Stirling, Stirling,, FK9 4LA, UK
| | - Philip A Wookey
- Biological and Environmental Sciences, University of Stirling, Stirling,, FK9 4LA, UK
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23
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Collins CD, Bever JD, Hersh MH. Community context for mechanisms of disease dilution: insights from linking epidemiology and plant-soil feedback theory. Ann N Y Acad Sci 2020; 1469:65-85. [PMID: 32170775 PMCID: PMC7317922 DOI: 10.1111/nyas.14325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/31/2020] [Accepted: 02/13/2020] [Indexed: 12/21/2022]
Abstract
In many natural systems, diverse host communities can reduce disease risk, though less is known about the mechanisms driving this "dilution effect." We relate feedback theory, which focuses on pathogen-mediated coexistence, to mechanisms of dilution derived from epidemiological models, with the central goal of gaining insights into host-pathogen interactions in a community context. We first compare the origin, structure, and application of epidemiological and feedback models. We then explore the mechanisms of dilution, which are grounded in single-pathogen, single-host epidemiological models, from the perspective of feedback theory. We also draw on feedback theory to examine how coinfecting pathogens, and pathogens that vary along a host specialist-generalist continuum, apply to dilution theory. By identifying synergies among the feedback and epidemiological approaches, we reveal ways in which organisms occupying different trophic levels contribute to diversity-disease relationships. Additionally, using feedbacks to distinguish dilution in disease incidence from dilution in the net effect of disease on host fitness allows us to articulate conditions under which definitions of dilution may not align. After ascribing dilution mechanisms to macro- or microorganisms, we propose ways in which each contributes to diversity-disease and productivity-diversity relationships. Our analyses lead to predictions that can guide future research efforts.
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Affiliation(s)
| | - James D. Bever
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas
- Kansas Biological SurveyUniversity of KansasLawrenceKansas
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24
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Martinez-Swatson K, Kjøller R, Cozzi F, Simonsen HT, Rønsted N, Barnes C. Exploring evolutionary theories of plant defence investment using field populations of the deadly carrot. ANNALS OF BOTANY 2020; 125:737-750. [PMID: 31563960 PMCID: PMC7182587 DOI: 10.1093/aob/mcz151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND AIMS There are a number of disparate models predicting variation in plant chemical defences between species, and within a single species over space and time. These can give conflicting predictions. Here we review a number of these theories, before assessing their power to predict the spatial-temporal variation of thapsigargins between and within populations of the deadly carrot (Thapsia garganica). By utilizing multiple models simultaneously (optimum defence theory, growth rate hypothesis, growth-differentiation balance hypothesis, intra-specific framework and resource exchange model of plant defence), we will highlight gaps in their predictions and evaluate the performance of each. METHODS Thapsigargins are potent anti-herbivore compounds that occur in limited richness across the different plant tissues of T. garganica, and therefore represent an ideal system for exploring these models. Thapsia garganica plants were collected from six locations on the island of Ibiza, Spain, and the thapsigargins quantified within reproductive, vegetative and below-ground tissues. The effects of sampling time, location, mammalian herbivory, soil nutrition and changing root-associated fungal communities on the concentrations of thapsigargins within these in situ observations were analysed, and the results were compared with our model predictions. KEY RESULTS The models performed well in predicting the general defence strategy of T. garganica and the above-ground distribution of thapsigargins, but failed to predict the considerable proportion of defences found below ground. Models predicting variation over environmental gradients gave conflicting and less specific predictions, with intraspecific variation remaining less understood. CONCLUSION Here we found that multiple models predicting the general defence strategy of plant species could likely be integrated into a single model, while also finding a clear need to better incorporate below-ground defences into models of plant chemical defences. We found that constitutive and induced thapsigargins differed in their regulation, and suggest that models predicting intraspecific defences should consider them separately. Finally, we suggest that in situ studies be supplemented with experiments in controlled environments to identify specific environmental parameters that regulate variation in defences within species.
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Affiliation(s)
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Toft Simonsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Nina Rønsted
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- National Tropical Botanical Garden, Kalaheo, Hawaii, USA
| | - Christopher Barnes
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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25
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Zhao PS, Guo MS, Gao GL, Zhang Y, Ding GD, Ren Y, Akhtar M. Community structure and functional group of root-associated Fungi of Pinus sylvestris var. mongolica across stand ages in the Mu Us Desert. Ecol Evol 2020; 10:3032-3042. [PMID: 32211174 PMCID: PMC7083681 DOI: 10.1002/ece3.6119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 12/30/2022] Open
Abstract
Root-associated fungi (RAF) are an important factor affecting the host's growth, and their contribution to Pinus sylvestris var. mongolica plantation decline is substantial. Therefore, we selected three age groups of P. sylvestris plantations (26, 33, and 43 years), in the Mu Us Desert, to characterize the community structure and functional groups of RAF, identified by Illumina high-throughput sequencing and FUNGuild platform, respectively. The effects of soil properties and enzyme activities on fungal diversity and functional groups were also examined. The results indicated that (a) 805 operational taxonomic units of RAF associated with P. sylvestris belonged to six phyla and 163 genera. Diversity and richness were not significantly different in the three age groups, but community composition showed significant differences. Ascomycota and Basidiomycota dominated the fungal community, while Rhizopogon dominated in each plot. (b) The proportion of pathotrophs decreased with increasing age, while that of symbiotrophs increased sharply, which were mainly represented by ectomycorrhizal fungi. (c) Stand age and soil enzyme activity had a greater influence on fungal community composition than did soil properties, whereas environmental variables were not significantly correlated with fungal diversity and richness. Dynamics of fungal community composition and functional groups with the aging plantations reflected the growth state of P. sylvestris and were related to plantation degradation.
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Affiliation(s)
- Pei-Shan Zhao
- Yanchi Research Station School of Soil and Water Conservation Beijing Forestry University Beijing China
- Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation Beijing China
- Engineering Research Center of Forestry Ecological Engineering Ministry of Education Beijing Forestry University Beijing China
| | - Mi-Shan Guo
- Yanchi Research Station School of Soil and Water Conservation Beijing Forestry University Beijing China
- Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation Beijing China
- Engineering Research Center of Forestry Ecological Engineering Ministry of Education Beijing Forestry University Beijing China
| | - Guang-Lei Gao
- Yanchi Research Station School of Soil and Water Conservation Beijing Forestry University Beijing China
- Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation Beijing China
- Engineering Research Center of Forestry Ecological Engineering Ministry of Education Beijing Forestry University Beijing China
| | - Ying Zhang
- Yanchi Research Station School of Soil and Water Conservation Beijing Forestry University Beijing China
- Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation Beijing China
- Engineering Research Center of Forestry Ecological Engineering Ministry of Education Beijing Forestry University Beijing China
| | - Guo-Dong Ding
- Yanchi Research Station School of Soil and Water Conservation Beijing Forestry University Beijing China
- Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation Beijing China
- Engineering Research Center of Forestry Ecological Engineering Ministry of Education Beijing Forestry University Beijing China
| | - Yue Ren
- Yanchi Research Station School of Soil and Water Conservation Beijing Forestry University Beijing China
- Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation Beijing China
- Engineering Research Center of Forestry Ecological Engineering Ministry of Education Beijing Forestry University Beijing China
| | - Mobeen Akhtar
- Yanchi Research Station School of Soil and Water Conservation Beijing Forestry University Beijing China
- Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation Beijing China
- Engineering Research Center of Forestry Ecological Engineering Ministry of Education Beijing Forestry University Beijing China
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26
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Kim Y, Chung YS, Lee E, Tripathi P, Heo S, Kim KH. Root Response to Drought Stress in Rice ( Oryza sativa L .). Int J Mol Sci 2020; 21:E1513. [PMID: 32098434 PMCID: PMC7073213 DOI: 10.3390/ijms21041513] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 01/24/2023] Open
Abstract
The current unpredictable climate changes are causing frequent and severe droughts. Such circumstances emphasize the need to understand the response of plants to drought stress, especially in rice, one of the most important grain crops. Knowledge of the drought stress response components is especially important in plant roots, the major organ for the absorption of water and nutrients from the soil. Thus, this article reviews the root response to drought stress in rice. It is presented to provide readers with information of use for their own research and breeding program for tolerance to drought stress in rice.
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Affiliation(s)
- Yoonha Kim
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.K.); (P.T.)
| | - Yong Suk Chung
- Faculty of Bioscience and Industry, College of Applied Life Science, SARI, Jeju National University, Jeju 63243, Korea;
| | - Eungyeong Lee
- National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea;
| | - Pooja Tripathi
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.K.); (P.T.)
| | - Seong Heo
- Ganghwa Agricultural Technology Service Center, Incheon 23038, Korea;
| | - Kyung-Hwan Kim
- National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea;
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27
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Bardgett RD, Caruso T. Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190112. [PMID: 31983338 DOI: 10.1098/rstb.2019.0112] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A major challenge for advancing our understanding of the functional role of soil microbial communities is to link changes in their structure and function under climate change. To address this challenge requires new understanding of the mechanisms that underlie the capacity of soil microbial communities to resist and recover from climate extremes. Here, we synthesize emerging understanding of the intrinsic and extrinsic factors that influence the resistance and resilience of soil microbial communities to climate extremes, with a focus on drought, and identify drivers that might trigger abrupt changes to alternative states. We highlight research challenges and propose a path for advancing our understanding of the resistance and resilience of soil microbial communities to climate extremes, and of their vulnerability to transitions to alternative states, including the use of trait-based approaches. We identify a need for new approaches to quantify resistance and resilience of soil microbial communities, and to identify thresholds for transitions to alternative states. We show how high-resolution time series coupled with gradient designs will enable detecting response patterns to interacting drivers. Finally, to account for extrinsic factors, we suggest that future studies should use environmental gradients to track soil microbial community responses to climate extremes in space and time. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.
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Affiliation(s)
- Richard D Bardgett
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tancredi Caruso
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, Belfast BT9 5DL, UK.,School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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28
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Wang YL, Gao C, Chen L, Ji NN, Wu BW, Lü PP, Li XC, Qian X, Maitra P, Babalola BJ, Zheng Y, Guo LD. Community Assembly of Endophytic Fungi in Ectomycorrhizae of Betulaceae Plants at a Regional Scale. Front Microbiol 2020; 10:3105. [PMID: 32038548 PMCID: PMC6986194 DOI: 10.3389/fmicb.2019.03105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 12/23/2019] [Indexed: 11/13/2022] Open
Abstract
The interaction between aboveground and belowground biotic communities drives community assembly of plants and soil microbiota. As an important component of belowground microorganisms, root-associated fungi play pivotal roles in biodiversity maintenance and community assembly of host plants. The Betulaceae plants form ectomycorrhizae with soil fungi and widely distribute in various ecosystems. However, the community assembly of endophytic fungi in ectomycorrhizae is less investigated at a large spatial scale. Here, we examined the endophytic fungal communities in ectomycorrhizae of 22 species in four genera belonging to Betulaceae in Chinese forest ecosystems, using Illumina Miseq sequencing of internal transcribed spacer 2 amplicons. The relative contribution of host phylogeny, climate and soil (environmental filtering) and geographic distance (dispersal limitation) on endophytic fungal community was disentangled. In total, 2,106 endophytic fungal operational taxonomic units (OTUs) were obtained at a 97% sequence similarity level, dominated by Leotiomycetes, Agaricomycetes, Eurotiomycetes, and Sordariomycetes. The endophytic fungal OTU richness was significantly related with host phylogeny, geographic distance, soil and climate. The endophytic fungal community composition was significantly affected by host phylogeny (19.5% of variation explained in fungal community), geographic distance (11.2%), soil (6.1%), and climate (1.4%). This finding suggests that environmental filtering by plant and abiotic variables coupled with dispersal limitation linked to geographic distance determines endophytic fungal community assembly in ectomycorrhizae of Betulaceae plants, with host phylogeny being a stronger determinant than other predictor variables at the regional scale.
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Affiliation(s)
- Yong-Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Niu-Niu Ji
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bin-Wei Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng-Peng Lü
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Qian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Pulak Maitra
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Busayo Joshua Babalola
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Zheng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Geographical Science, Fujian Normal University, Fuzhou, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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29
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Chen KH, Liao HL, Bellenger JP, Lutzoni F. Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium. Environ Microbiol 2019; 21:2273-2289. [PMID: 30900793 DOI: 10.1111/1462-2920.14605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 02/05/2023]
Abstract
Bryophytes harbour microbiomes, including diverse communities of fungi. The molecular mechanisms by which perennial mosses interact with these fungal partners along their senescence gradients are unknown, yet this is an ideal system to study variation in gene expression associated with trophic state transitions. We investigated differentially expressed genes of fungal communities and their host Dicranum scoparium across its naturally occurring senescence gradient using a metatranscriptomic approach. Higher activity of fungal nutrient-related (carbon, nitrogen, phosphorus and sulfur) transporters and Carbohydrate-Active enZyme (CAZy) genes was detected toward the bottom, partially decomposed, layer of the moss. The most prominent variation in the expression levels of fungal nutrient transporters was from inorganic nitrogen-related transporters, whereas the breakdown of organonitrogens was detected as the most enriched gene ontology term for the host D. scoparium, for those transcripts having higher expression in the partially decomposed layer. The abundance of bacterial rRNA transcripts suggested that more living members of Cyanobacteria are associated with the photosynthetic layer of D. scoparium, while members of Rhizobiales are detected throughout the gametophytes. Plant genes for specific fungal-plant communication, including defense responses, were differentially expressed, suggesting that different genetic pathways are involved in plant-microbe crosstalk in photosynthetic tissues compared to partially decomposed tissues.
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Affiliation(s)
- Ko-Hsuan Chen
- Department of Biology, Duke University, Durham, NC, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
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30
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Martin FM, Harrison MJ, Lennon S, Lindahl B, Öpik M, Polle A, Requena N, Selosse MA. Cross-scale integration of mycorrhizal function. THE NEW PHYTOLOGIST 2018; 220:941-946. [PMID: 30408219 DOI: 10.1111/nph.15493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Francis M Martin
- INRA, Université de Lorraine, UMR Interactions Arbres/Micro-Organismes, INRA-Centre Grand Est, Champenoux, 54280, France
| | | | - Sarah Lennon
- New Phytologist Central Office, Bailrigg House, Lancaster University, Lancaster, LA1 4YE, UK
| | - Björn Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, Uppsala, SE-750 07, Sweden
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, 40 Lai St., Tartu, 51005, Estonia
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Goettingen, 37077, Germany
| | - Natalia Requena
- Molecular Phytopathology Department, Karlsruhe Institute of Technology, Fritz Haber-Weg 4, Geb. 30.43, 2. OG, Karlsruhe, D-76131, Germany
| | - Marc-André Selosse
- Département Systématique et Evolution, Muséum national d'Histoire naturelle, UMR 7205 ISYEB, CP 50, 45 rue Buffon, Paris, 75005, France
- Faculty of Biology, University of Gdańsk, ul. Wita Stwosza 59, 80-308, Gdańsk, Poland
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31
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Johnson D. Water, water everywhere … but how does it affect the functional diversity of ectomycorrhizal fungi? THE NEW PHYTOLOGIST 2018; 220:950-951. [PMID: 30408221 DOI: 10.1111/nph.15086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- David Johnson
- School of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
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32
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Meisner A, Jacquiod S, Snoek BL, Ten Hooven FC, van der Putten WH. Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities. Front Microbiol 2018; 9:294. [PMID: 29563897 PMCID: PMC5845876 DOI: 10.3389/fmicb.2018.00294] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/08/2018] [Indexed: 12/14/2022] Open
Abstract
It is increasingly acknowledged that climate change is influencing terrestrial ecosystems by increased drought and rainfall intensities. Soil microbes are key drivers of many processes in terrestrial systems and rely on water in soil pores to fulfill their life cycles and functions. However, little is known on how drought and rainfall fluctuations, which affect the composition and structure of microbial communities, persist once original moisture conditions have been restored. Here, we study how simulated short-term drying and re-wetting events shape the community composition of soil fungi and prokaryotes. In a mesocosm experiment, soil was exposed to an extreme drought, then re-wetted to optimal moisture (50% WHC, water holding capacity) or to saturation level (100% WHC). Composition, community structure and diversity of microbes were measured by sequencing ITS and 16S rRNA gene amplicons 3 weeks after original moisture content had been restored. Drying and extreme re-wetting decreased richness of microbial communities, but not evenness. Abundance changes were observed in only 8% of prokaryote OTUs, and 25% of fungal OTUs, whereas all other OTUs did not differ between drying and re-wetting treatments. Two specific legacy response groups (LRGs) were observed for both prokaryotes and fungi. OTUs belonging to the first LRG decreased in relative abundance in soil with a history of drought, whereas OTUs that increased in soil with a history of drought formed a second LRG. These microbial responses were spread among different phyla. Drought appeared to be more important for the microbial community composition than the following extreme re-wetting. 16S profiles were correlated with both inorganic N concentration and basal respiration and ITS profiles correlated with fungal biomass. We conclude that a drying and/or an extreme re-wetting history can persist in soil microbial communities via specific response groups composed of members with broad phylogenetic origins, with possible functional consequences on soil processes and plant species. As a large fraction of OTUs responding to drying and re-wetting belonged to the rare biosphere, our results suggest that low abundant microbial species are potentially important for ecosystem responses to extreme weather events.
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Affiliation(s)
- Annelein Meisner
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden.,Sections of Microbiology and Terrestrial Ecology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | | | - Basten L Snoek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
| | - Freddy C Ten Hooven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
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