1
|
Gao D, Luster J, Zürcher A, Arend M, Bai E, Gessler A, Rigling A, Schaub M, Hartmann M, Werner RA, Joseph J, Poll C, Hagedorn F. Drought resistance and resilience of rhizosphere communities in forest soils from the cellular to ecosystem scale - insights from 13C pulse labeling. THE NEW PHYTOLOGIST 2024; 242:960-974. [PMID: 38402527 DOI: 10.1111/nph.19612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/06/2024] [Indexed: 02/26/2024]
Abstract
The link between above- and belowground communities is a key uncertainty in drought and rewetting effects on forest carbon (C) cycle. In young beech model ecosystems and mature naturally dry pine forest exposed to 15-yr-long irrigation, we performed 13C pulse labeling experiments, one during drought and one 2 wk after rewetting, tracing tree assimilates into rhizosphere communities. The 13C pulses applied in tree crowns reached soil microbial communities of the young and mature forests one and 4 d later, respectively. Drought decreased the transfer of labeled assimilates relative to the irrigation treatment. The 13C label in phospholipid fatty acids (PLFAs) indicated greater drought reduction of assimilate incorporation by fungi (-85%) than by gram-positive (-43%) and gram-negative bacteria (-58%). 13C label incorporation was more strongly reduced for PLFAs (cell membrane) than for microbial cytoplasm extracted by chloroform. This suggests that fresh rhizodeposits are predominantly used for osmoregulation or storage under drought, at the expense of new cell formation. Two weeks after rewetting, 13C enrichment in PLFAs was greater in previously dry than in continuously moist soils. Drought and rewetting effects were greater in beech systems than in pine forest. Belowground C allocation and rhizosphere communities are highly resilient to drought.
Collapse
Affiliation(s)
- Decai Gao
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, 100190, Beijing, China
| | - Jörg Luster
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| | - Alois Zürcher
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| | - Matthias Arend
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Physiological Plant Ecology, University of Basel, 4056, Basel, Switzerland
| | - Edith Bai
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, Northeast Normal University, 130024, Changchun, China
| | - Arthur Gessler
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Terrestrial Ecosystems, ETH Zürich, 8092, Zürich, Switzerland
| | - Andreas Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Terrestrial Ecosystems, ETH Zürich, 8092, Zürich, Switzerland
| | - Marcus Schaub
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, 8092, Zürich, Switzerland
| | - Roland A Werner
- Agricultural Sciences, ETH Zürich, 8092, Zürich, Switzerland
| | - Jobin Joseph
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| | - Christian Poll
- Soil Biology, University of Hohenheim, 70599, Stuttgart, Germany
| | - Frank Hagedorn
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
| |
Collapse
|
2
|
Zhao S, Liu X, Banerjee S, Hartmann M, Peng B, Elvers R, Zhao ZY, Zhou N, Liu JJ, Wang B, Tian CY, Jiang J, Lian TX. Continuous planting of euhalophyte Suaeda salsa enhances microbial diversity and multifunctionality of saline soil. Appl Environ Microbiol 2024; 90:e0235523. [PMID: 38535171 PMCID: PMC11022556 DOI: 10.1128/aem.02355-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/04/2024] [Indexed: 04/18/2024] Open
Abstract
Halophyte-based remediation emerges as a novel strategy for ameliorating saline soils, offering a sustainable alternative to conventional leaching methods. While bioremediation is recognized for its ability to energize soil fertility and structure, the complex interplays among plant traits, soil functions, and soil microbial diversity remain greatly unknown. Here, we conducted a 5-year field experiment involving the continuous cultivation of the annual halophyte Suaeda salsa in saline soils to explore soil microbial diversity and their relationships with plant traits and soil functions. Our findings demonstrate that a decline in soil salinity corresponded with increases in the biomass and seed yield of S. salsa, which sustained a consistent seed oil content of approximately 22% across various salinity levels. Significantly, prolonged cultivation of halophytes substantially augmented soil microbial diversity, particularly from the third year of cultivation. Moreover, we identified positive associations between soil multifunctionality, seed yield, and taxonomic richness within a pivotal microbial network module. Soils enriched with taxa from this module showed enhanced multifunctionality and greater seed yields, correlating with the presence of functional genes implicated in nitrogen fixation and nitrification. Genomic analysis suggests that these taxa have elevated gene copy numbers of crucial functional genes related to nutrient cycling. Overall, our study emphasizes that the continuous cultivation of S. salsa enhances soil microbial diversity and recovers soil multifunctionality, expanding the understanding of plant-soil-microbe feedback in bioremediation.IMPORTANCEThe restoration of saline soils utilizing euhalophytes offers a viable alternative to conventional irrigation techniques for salt abatement and soil quality enhancement. The ongoing cultivation of the annual Suaeda salsa and its associated plant traits, soil microbial diversity, and functionalities are, however, largely underexplored. Our investigation sheds light on these dynamics, revealing that cultivation of S. salsa sustains robust plant productivity while fostering soil microbial diversity and multifunctionality. Notably, the links between enhanced soil multifunctionality, increased seed yield, and network-dependent taxa were found, emphasizing the importance of key microbial taxa linked with functional genes vital to nitrogen fixation and nitrification. These findings introduce a novel understanding of the role of soil microbes in bioremediation and advance our knowledge of the ecological processes that are vital for the rehabilitation of saline environments.
Collapse
Affiliation(s)
- Shuai Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xu Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Martin Hartmann
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Bin Peng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Rylie Elvers
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Zhen-Yong Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Na Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Jun-Jie Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Chang-Yan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Teng-Xiang Lian
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| |
Collapse
|
3
|
Sun Y, Guo J, Alejandro Jose Mur L, Xu X, Chen H, Yang Y, Yuan H. Nitrogen starvation modulates the sensitivity of rhizobacterial community to drought stress in Stevia rebaudiana. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120486. [PMID: 38417363 DOI: 10.1016/j.jenvman.2024.120486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/06/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Alterations in water regimes or nitrogen (N) availability lead to shifts in the assemblage of rhizosphere microbial community; however, how the rhizosphere microbiome response to concurrent changes in water and N availability remains largely unclear. Herein, we investigated the taxonomic and functional characteristics of rhizobacteria associated with stevia (Stevia rebaudiana Bertoni) under varying combinations of water and N levels. Community diversity and predicted functions of rhizobacteria were predominantly altered by drought stress, with N-starvation modulating these effects. Moreover, N fertilization simplified the ecological interactions within rhizobacterial communities and heightened the relative role of stochastic processes on community assembly. In terms of rhizobacterial composition, we observed both common and distinctive changes in drought-responsive bacterial taxa under different N conditions. Generally, the relative abundance of Proteobacteria and Bacteroidetes phyla were depleted by drought stress but the Actinobacteria phylum showed increases. The rhizobacterial responses to drought stress were influenced by N availability, where the positive response of δ-proteobacteria and the negative response of α- and γ-proteobacteria, along with Bacteroidetes, were further heightened under N starvation. By contrast, under N fertilization conditions, an amplified negative or positive response to drought were demonstrated in Firmicutes and Actinobacteria phyla, respectively. Further, the drought-responsive rhizobacteria were mostly phylogenetically similar, but this pattern was modulated under N-rich conditions. Overall, our findings indicate an N-dependent specific restructuring of rhizosphere bacteria under drought stress. These changes in the rhizosphere microbiome could contribute to enhancing plant stress tolerance.
Collapse
Affiliation(s)
- Yuming Sun
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Junjie Guo
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.
| | - Luis Alejandro Jose Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Xiaoyang Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Hao Chen
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Yongheng Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Haiyan Yuan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China.
| |
Collapse
|
4
|
Sharma V, Mohammed SA, Devi N, Vats G, Tuli HS, Saini AK, Dhir YW, Dhir S, Singh B. Unveiling the dynamic relationship of viruses and/or symbiotic bacteria with plant resilience in abiotic stress. STRESS BIOLOGY 2024; 4:10. [PMID: 38311681 PMCID: PMC10838894 DOI: 10.1007/s44154-023-00126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/22/2023] [Indexed: 02/06/2024]
Abstract
In the ecosphere, plants interact with environmental biotic and abiotic partners, where unbalanced interactions can induce unfavourable stress conditions. Abiotic factors (temperature, water, and salt) are primarily required for plants healthy survival, and any change in their availability is reflected as a stress signal. In certain cases, the presence of infectious pathogens such as viruses, bacteria, fungi, protozoa, nematodes, and insects can also create stress conditions in plants, leading to the emergence of disease or deficiency symptoms. While these symptoms are often typical of abiotic or biotic stress, however, there are instances where they can intensify under specific conditions. Here, we primarily summarize the viral interactions with plants during abiotic stress to understand how these associations are linked together during viral pathogenesis. Secondly, focus is given to the beneficial effects of root-associated symbiotic bacteria in fulfilling the basic needs of plants during normal as well as abiotic stress conditions. The modulations of plant functional proteins, and their occurrence/cross-talk, with pathogen (virus) and symbiont (bacteria) molecules are also discussed. Furthermore, we have highlighted the biochemical and systematic adaptations that develop in plants due to bacterial symbiosis to encounter stress hallmarks. Lastly, directions are provided towards exploring potential rhizospheric bacteria to maintain plant-microbes ecosystem and manage abiotic stress in plants to achieve better trait health in the horticulture crops.
Collapse
Affiliation(s)
- Vasudha Sharma
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Shakeel A Mohammed
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Nisha Devi
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Gourav Vats
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Hardeep S Tuli
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Adesh K Saini
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Yashika W Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Sunny Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Bharat Singh
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| |
Collapse
|
5
|
Jaeger ACH, Hartmann M, Conz RF, Six J, Solly EF. Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13211. [PMID: 37991154 PMCID: PMC10866073 DOI: 10.1111/1758-2229.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.
Collapse
Affiliation(s)
- Astrid C. H. Jaeger
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Johan Six
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Emily F. Solly
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
- Helmholtz Centre for Environmental Research—UFZLeipzigGermany
| |
Collapse
|
6
|
Huo C, Mao J, Zhang J, Yang X, Gao S, Li J, He Q, Tang G, Xie X, Chen Z. Fertilization- and Irrigation-Modified Bacterial Community Composition and Stimulated Enzyme Activity of Eucalyptus Plantations Soil. Int J Mol Sci 2024; 25:1385. [PMID: 38338664 PMCID: PMC10855151 DOI: 10.3390/ijms25031385] [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: 12/30/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Irrigation and fertilization are essential management practices for increasing forest productivity. They also impact the soil ecosystem and the microbial population. In order to examine the soil bacterial community composition and structure in response to irrigation and fertilization in a Eucalyptus plantations, a total of 20 soil samples collected from Eucalyptus plantations were analyzed using high-throughput sequencing. Experimental treatments consisting of control (CK, no irrigation or fertilization), fertilization only (F), irrigation only (W), and irrigation and fertilization (WF). The results showed a positive correlation between soil enzyme activities (urease, cellulase, and chitinase) and fertilization treatments. These enzyme activities were also significantly correlated with the diversity of soil bacterial communities in Eucalyptus plantations.. Bacteria diversity was considerably increased under irrigation and fertilization (W, F, and WF) treatments when compared with the CK treatment. Additionally, the soil bacterial richness was increased in the Eucalyptus plantations soil under irrigation (W and WF) treatments. The Acidobacteria (38.92-47.9%), Proteobacteria (20.50-28.30%), and Chloroflexi (13.88-15.55%) were the predominant phyla found in the Eucalyptus plantations soil. Specifically, compared to the CK treatment, the relative abundance of Proteobacteria was considerably higher under the W, F, and WF treatments, while the relative abundance of Acidobacteria was considerably lower. The contents of total phosphorus, accessible potassium, and organic carbon in the soil were all positively associated with fertilization and irrigation treatments. Under the WF treatment, the abundance of bacteria associated with nitrogen and carbon metabolisms, enzyme activity, and soil nutrient contents showed an increase, indicating the positive impact of irrigation and fertilization on Eucalyptus plantations production. Collectively, these findings provide the scientific and managerial bases for improving the productivity of Eucalyptus plantations.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zujing Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (C.H.); (J.M.); (J.Z.); (X.Y.); (S.G.); (J.L.); (Q.H.); (G.T.); (X.X.)
| |
Collapse
|
7
|
Li J, Deng L, Peñuelas J, Wu J, Shangguan Z, Sardans J, Peng C, Kuzyakov Y. C:N:P stoichiometry of plants, soils, and microorganisms: Response to altered precipitation. GLOBAL CHANGE BIOLOGY 2023; 29:7051-7071. [PMID: 37787740 DOI: 10.1111/gcb.16959] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 10/04/2023]
Abstract
Precipitation changes modify C, N, and P cycles, which regulate the functions and structure of terrestrial ecosystems. Although altered precipitation affects above- and belowground C:N:P stoichiometry, considerable uncertainties remain regarding plant-microbial nutrient allocation strategies under increased (IPPT) and decreased (DPPT) precipitation. We meta-analyzed 827 observations from 235 field studies to investigate the effects of IPPT and DPPT on the C:N:P stoichiometry of plants, soils, and microorganisms. DPPT reduced leaf C:N ratio, but increased the leaf and root N:P ratios reflecting stronger decrease of P compared with N mobility in soil under drought. IPPT increased microbial biomass C (+13%), N (+15%), P (26%), and the C:N ratio, whereas DPPT decreased microbial biomass N (-12%) and the N:P ratio. The C:N and N:P ratios of plant leaves were more sensitive to medium DPPT than to IPPT because drought increased plant N content, particularly in humid areas. The responses of plant and soil C:N:P stoichiometry to altered precipitation did not fit the double asymmetry model with a positive asymmetry under IPPT and a negative asymmetry under extreme DPPT. Soil microorganisms were more sensitive to IPPT than to DPPT, but they were more sensitive to extreme DPPT than extreme IPPT, consistent with the double asymmetry model. Soil microorganisms maintained stoichiometric homeostasis, whereas N:P ratios of plants follow that of the soils under altered precipitation. In conclusion, specific N allocation strategies of plants and microbial communities as well as N and P availability in soil critically mediate C:N:P stoichiometry by altered precipitation that need to be considered by prediction of ecosystem functions and C cycling under future climate change scenarios.
Collapse
Affiliation(s)
- Jiwei Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation), Northwest A&F University, Yangling, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
- College of Forestry, Northwest A&F University, Yangling, China
| | - Lei Deng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation), Northwest A&F University, Yangling, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
- College of Forestry, Northwest A&F University, Yangling, China
| | - Josep Peñuelas
- CREAF, Cerdanyola del Vallès, Barcelona, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Barcelona, Spain
| | - Jianzhao Wu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation), Northwest A&F University, Yangling, China
| | - Zhouping Shangguan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation), Northwest A&F University, Yangling, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
| | - Jordi Sardans
- CREAF, Cerdanyola del Vallès, Barcelona, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Barcelona, Spain
| | - Changhui Peng
- Center of CEF/ESCER, Department of Biological Science, University of Quebec at Montreal, Montreal, Quebec, Canada
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Goettingen, Göttingen, Germany
- Department of Agricultural Soil Science, University of Goettingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| |
Collapse
|
8
|
Hartmann M, Herzog C, Brunner I, Stierli B, Meyer F, Buchmann N, Frey B. Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition. Front Microbiol 2023; 14:1267270. [PMID: 37840720 PMCID: PMC10570739 DOI: 10.3389/fmicb.2023.1267270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.
Collapse
Affiliation(s)
- Martin Hartmann
- Department of Environmental Systems Science, Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Claude Herzog
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Folker Meyer
- Data Science, Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Argonne National Laboratory, Argonne, IL, United States
- Computation Institute, University of Chicago, Chicago, IL, United States
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Nina Buchmann
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| |
Collapse
|
9
|
Guo B, Zhang H, Liu Y, Chen J, Li J. Drought-resistant trait of different crop genotypes determines assembly patterns of soil and phyllosphere microbial communities. Microbiol Spectr 2023; 11:e0006823. [PMID: 37754752 PMCID: PMC10581042 DOI: 10.1128/spectrum.00068-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023] Open
Abstract
Crop microbiomes are widely recognized to play a role in crop stress resistance, but the ecological processes that shape crop microbiomes under water stress are unclear. Therefore, we investigated the bacterial communities of two oat (Avena sativa) and two wheat (Triticum aestivum) genotypes under different water stress conditions. Our results show that the microbial assemblage was determined by the crop compartment niche. Host selection pressure on the bacterial community increased progressively from soil to epiphyte to endophyte pathways, leading to a decrease in bacterial community diversity and network complexity. Source tracing shows that soil is the primary source of crop microbial communities and that bulk soil is the main potential source of crop microbiota. It filters gradually through the different compartment niches of the crop. We found that the phyla Actinobacteria, Proteobacteria, Gemmatimonadota, and Myxococcota were significantly enriched in bacterial communities associated with crop-resistance enzyme activity. Crop genotype influenced the composition of the rhizosphere soil microbial community, and the composition of the phylloplane microbial community was affected by water stress. IMPORTANCE In this paper, we investigated the assembly of the plant microbiome in response to water stress. We found that the determinant of microbiome assembly under water stress was the host type and that microbial communities were progressively filtered and enriched as they moved from soil to epiphyte to endophyte communities, with the main potential source being bulk soil. We also screened for bacterial communities that were significantly associated with crop enzyme activity. Our research provides insights into the manipulation of microbes in response to crop resistance to water stress.
Collapse
Affiliation(s)
- Baobei Guo
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Hong Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Yong Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Jianwen Chen
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| |
Collapse
|
10
|
Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.
Collapse
Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benjamin J Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Schaumberger
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria.
| |
Collapse
|
11
|
Williams CE, Williams CL, Logan ML. Climate change is not just global warming: Multidimensional impacts on animal gut microbiota. Microb Biotechnol 2023; 16:1736-1744. [PMID: 37247194 PMCID: PMC10443335 DOI: 10.1111/1751-7915.14276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 05/30/2023] Open
Abstract
Climate change has rapidly altered many ecosystems, with detrimental effects for biodiversity across the globe. In recent years, it has become increasingly apparent that the microorganisms that live in and on animals can substantially affect host health and physiology, and the structure and function of these microbial communities can be highly sensitive to environmental variables. To date, most studies have focused on the effects of increasing mean temperature on gut microbiota, yet other aspects of climate are also shifting, including temperature variation, seasonal dynamics, precipitation and the frequency of severe weather events. This array of environmental pressures might interact in complex and non-intuitive ways to impact gut microbiota and consequently alter animal fitness. Therefore, understanding the impacts of climate change on animals requires a consideration of multiple types of environmental stressors and their interactive effects on gut microbiota. Here, we present an overview of some of the major findings in research on climatic effects on microbial communities in the animal gut. Although ample evidence has now accumulated that shifts in mean temperature can have important effects on gut microbiota and their hosts, much less work has been conducted on the effects of other climatic variables and their interactions. We provide recommendations for additional research needed to mechanistically link climate change with shifts in animal gut microbiota and host fitness.
Collapse
|
12
|
Yang Z, Lou Y, Yan X, Pan H, Wang H, Yang Q, Sun Y, Zhuge Y. The Microbiome and Antibiotic Resistome in Soil under Biodegradable Composite Carbon Source Amendment. J Xenobiot 2023; 13:424-438. [PMID: 37606424 PMCID: PMC10443276 DOI: 10.3390/jox13030027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
The decomposition of biodegradable composite carbon sources generates a large amount of biodegradable microplastics, which may not only furnish microbial denitrification, but might also pose potential environmental risks. In the present study, the effects of different dosages of a biodegradable composite carbon source on the microbial communities, the nitrogen metabolic pathways and the antibiotic resistome were explored through Illumina MiSeq sequencing analysis and metagenomic analysis. The results of partial least-square discriminant analysis (PLS-DA) and analysis of similarity (ANOSIM) demonstrated that the response of the bacterial community to a biodegradable composite carbon source was more obvious than the fungal community. The application of biodegradable microplastics diminished the complexity of the microbial communities to some extent and obviously stimulated denitrification. Antibiotics resistance gene (ARG) dispersal was not evidently accelerated after the addition of biodegradable composite carbon source. Lysobacter, Methylobacillus, Phyllobacterium, Sinorhizobium, Sphingomonas from Proteobacteria and Actinomadura, Agromyces, Gaiella and Micromonospora from Actinobacteria were the major ARG hosts. Overall, the addition of a biodegradable composite carbon source shaped microbial communities and their antibiotic resistance profiles in this study.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Yuping Zhuge
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (Z.Y.); (Y.L.); (X.Y.); (H.P.); (H.W.); (Q.Y.); (Y.S.)
| |
Collapse
|
13
|
Zhang H, Zhang M, Hou X, Li Y, Zhang W, Wang L, Niu L. Responses of bacterial community and N-cycling functions stability to different wetting-drying alternation frequencies in a riparian zone. ENVIRONMENTAL RESEARCH 2023; 228:115778. [PMID: 36997041 DOI: 10.1016/j.envres.2023.115778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 05/16/2023]
Abstract
Wetting-drying alternation (WD) of the soil is one of the key characteristics of riparian zones shaped by dam construction, profoundly impacting the soil microenvironment that determines the bacterial community. Knowledge concerning the stability of bacterial community and N-cycling functions in response to different frequencies of WD remains unclear. In this study, samples were taken from a riparian zone in the Three Gorges Reservoir (TGR) and an incubation experiment was conducted including four treatments: constant flooding (W), varied wetting-drying alternation frequencies (WD1 and WD2), and constant drying (D) (simulating water level of 145 m, 155 m, 165 m, and 175 m in the riparian zone respectively). The results revealed that there was no significant difference in the diversity among the four treatments. Following the WD1 and WD2 treatments, the relative abundances of Proteobacteria increased, while those of Chloroflexi and Acidobacteriota decreased compared to the W treatment. However, the stability of bacterial community was not affected by WD. Relative to the W treatment, the stability of N-cycling functions estimated by resistance, which refers to the ability of functional genes to adapt to changes in the environment, decreased following the WD1 treatment, but showed no significant change following the WD2 treatment. Random forest analysis showed that the resistances of the nirS and hzo genes were core contributors to the stability of N-cycling functions. This study provides a new perspective for investigating the impacts of wetting-drying alternation on soil microbes.
Collapse
Affiliation(s)
- Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Mengzhu Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Xing Hou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| |
Collapse
|
14
|
Solly EF, Jaeger ACH, Barthel M, Werner RA, Zürcher A, Hagedorn F, Six J, Hartmann M. Water limitation intensity shifts carbon allocation dynamics in Scots pine mesocosms. PLANT AND SOIL 2023; 490:499-519. [PMID: 37780069 PMCID: PMC10533586 DOI: 10.1007/s11104-023-06093-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/23/2023] [Indexed: 10/03/2023]
Abstract
Background and aims Tree species worldwide suffer from extended periods of water limitation. These conditions not only affect the growth and vitality of trees but also feed back on the cycling of carbon (C) at the plant-soil interface. However, the impact of progressing water loss from soils on the transfer of assimilated C belowground remains unresolved. Methods Using mesocosms, we assessed how increasing levels of water deficit affect the growth of Pinus sylvestris saplings and performed a 13C-CO2 pulse labelling experiment to trace the pathway of assimilated C into needles, fine roots, soil pore CO2, and phospholipid fatty acids of soil microbial groups. Results With increasing water limitation, trees partitioned more biomass belowground at the expense of aboveground growth. Moderate levels of water limitation barely affected the uptake of 13C label and the transit time of C from needles to the soil pore CO2. Comparatively, more severe water limitation increased the fraction of 13C label that trees allocated to fine roots and soil fungi while a lower fraction of 13CO2 was readily respired from the soil. Conclusions When soil water becomes largely unavailable, C cycling within trees becomes slower, and a fraction of C allocated belowground may accumulate in fine roots or be transferred to the soil and associated microorganisms without being metabolically used. Supplementary Information The online version contains supplementary material available at 10.1007/s11104-023-06093-5.
Collapse
Affiliation(s)
- Emily F. Solly
- Department of Environmental Systems Science, Sustainable Agroecosystems Group, ETH Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Astrid C. H. Jaeger
- Department of Environmental Systems Science, Sustainable Agroecosystems Group, ETH Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Matti Barthel
- Department of Environmental Systems Science, Sustainable Agroecosystems Group, ETH Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Roland A. Werner
- Department of Environmental Systems Science, Grassland Sciences Group, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Alois Zürcher
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Biogeochemistry Group, Zürcherstrasse 111, Birmensdorf, 8903 Switzerland
| | - Frank Hagedorn
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Biogeochemistry Group, Zürcherstrasse 111, Birmensdorf, 8903 Switzerland
| | - Johan Six
- Department of Environmental Systems Science, Sustainable Agroecosystems Group, ETH Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Martin Hartmann
- Department of Environmental Systems Science, Sustainable Agroecosystems Group, ETH Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| |
Collapse
|
15
|
Zhang D, He J, Cheng P, Zhang Y, Khan A, Wang S, Li Z, Zhao S, Zhan X, Ma F, Li X, Guan Q. 4-methylumbelliferone (4-MU) enhances drought tolerance of apple by regulating rhizosphere microbial diversity and root architecture. HORTICULTURE RESEARCH 2023; 10:uhad099. [PMID: 37427035 PMCID: PMC10327542 DOI: 10.1093/hr/uhad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/04/2023] [Indexed: 07/11/2023]
Abstract
The dwarfing rootstocks-mediated high-density apple orchard is becoming the main practice management. Currently, dwarfing rootstocks are widely used worldwide, but their shallow root system and drought sensitivity necessitate high irrigation requirements. Here, the root transcriptome and metabolome of dwarfing (M9-T337, a drought-sensitive rootstock) and vigorous rootstocks (Malus sieversii, a drought-tolerant species, is commonly used as a rootstock) showed that a coumarin derivative, 4-Methylumbelliferon (4-MU), was found to accumulate significantly in the roots of vigorous rootstock under drought condition. When exogenous 4-MU was applied to the roots of dwarfing rootstock under drought treatment, the plants displayed increased root biomass, higher root-to-shoot ratio, greater photosynthesis, and elevated water use efficiency. In addition, diversity and structure analysis of the rhizosphere soil microbial community demonstrated that 4-MU treatment increased the relative abundance of putatively beneficial bacteria and fungi. Of these, Pseudomonas, Bacillus, Streptomyces, and Chryseolinea bacterial strains and Acremonium, Trichoderma, and Phoma fungal strains known for root growth, or systemic resistance against drought stress, were significantly accumulated in the roots of dwarfing rootstock after 4-MU treatment under drought stress condition. Taken together, we identified a promising compound-4-MU, as a useful tool, to strengthen the drought tolerance of apple dwarfing rootstock.
Collapse
Affiliation(s)
- Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
- College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Pengda Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Yutian Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Abid Khan
- Department of Horticulture, The University of Haripur, Haripur 22620, Pakistan
| | - Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Shuang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
16
|
Wilhelm RC, Muñoz-Ucros J, Weikl F, Pritsch K, Goebel M, Buckley DH, Bauerle TL. The effects of mixed-species root zones on the resistance of soil bacteria and fungi to long-term experimental and natural reductions in soil moisture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162266. [PMID: 36822431 DOI: 10.1016/j.scitotenv.2023.162266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
Mixed forest stands tend to be more resistant to drought than species-specific stands partially due to complementarity in root ecology and physiology. We asked whether complementary differences in the drought resistance of soil microbiomes might contribute to this phenomenon. We experimented on the effects of reduced soil moisture on bacterial and fungal community composition in species-specific (single species) and mixed-species root zones of Norway spruce and European beech forests in a 5-year-old throughfall-exclusion experiment and across seasonal (spring-summer-fall) and latitudinal moisture gradients. Bacteria were most responsive to changes in soil moisture, especially members of Rhizobiales, while fungi were largely unaffected, including ectomycorrhizal fungi (EMF). Community resistance was higher in spruce relative to beech root zones, corresponding with the proportions of drought-favored (more in spruce) and drought-sensitive bacterial taxa (more in beech). The spruce soil microbiome also exhibited greater resistance to seasonal changes between spring (wettest) and fall (driest). Mixed-species root zones contained a hybrid of beech- and spruce-associated microbiomes. Several bacterial populations exhibited either enhanced resistance or greater susceptibility to drought in mixed root zones. Overall, patterns in the relative abundances of soil bacteria closely tracked moisture in seasonal and latitudinal precipitation gradients and were more predictive of soil water content than other environmental variables. We conclude that complementary differences in the drought resistance of soil microbiomes can occur and the likeliest form of complementarity in mixed-root zones coincides with the enrichment of drought-tolerant bacteria associated with spruce and the sustenance of EMF by beech.
Collapse
Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA; Agronomy Department, Lilly Hall of Life Sciences, Purdue University, West Lafayette, IN, 47904, USA
| | - Juana Muñoz-Ucros
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Fabian Weikl
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany; Technical University of Munich, Professorship of Land Surface Atmosphere Interactions, Freising, Germany
| | - Karin Pritsch
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marc Goebel
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Taryn L Bauerle
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
17
|
Bai Z, Jia A, Li H, Wang M, Qu S. Explore the soil factors driving soil microbial community and structure in Songnen alkaline salt degraded grassland. FRONTIERS IN PLANT SCIENCE 2023; 14:1110685. [PMID: 37229114 PMCID: PMC10203596 DOI: 10.3389/fpls.2023.1110685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/03/2023] [Indexed: 05/27/2023]
Abstract
Introduction Saline-alkali degradation in grassland significantly affects plant community composition and soil physical and chemical properties. However, it remains unclear whether different degradation gradients affect soil microbial community and the main soil driving factors. Therefore, it is important to elucidate the effects of saline-alkali degradation on soil microbial community and the soil factors affecting soil microbial community in order to develop effective solutions to restore the degraded grassland ecosystem. Methods In this study, Illumina high-throughput sequencing technology was used to study the effects of different saline-alkali degradation gradients on soil microbial diversity and composition. Three different gradients were qualitatively selected, which were the light degradation gradient (LD), the moderate degradation gradient (MD) and the severe degradation gradient (SD). Results The results showed that salt and alkali degradation decreased the diversity of soil bacterial and fungal communities, and changed the composition of bacterial and fungal communities. Different degradation gradients had different adaptability and tolerance species. With the deterioration of salinity in grassland, the relative abundance of Actinobacteriota and Chytridiomycota showed a decreasing trend. EC, pH and AP were the main drivers of soil bacterial community composition, while EC, pH and SOC were the main drivers of soil fungal community composition. Different microorganisms are affected by different soil properties. The changes of plant community and soil environment are the main factors limiting the diversity and composition of soil microbial community. Discussion The results show that saline-alkali degradation of grassland has a negative effect on microbial biodiversity, so it is important to develop effective solutions to restore degraded grassland to maintain biodiversity and ecosystem function.
Collapse
Affiliation(s)
- Zhenyin Bai
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Aomei Jia
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Haixian Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Mingjun Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Shanmin Qu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| |
Collapse
|
18
|
Du Y, Wang YP, Hui D, Su F, Yan J. Significant effects of precipitation frequency on soil respiration and its components-A global synthesis. GLOBAL CHANGE BIOLOGY 2023; 29:1188-1205. [PMID: 36408676 DOI: 10.1111/gcb.16532] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Global warming intensifies the hydrological cycle, which results in changes in precipitation regime (frequency and amount), and will likely have significant impacts on soil respiration (Rs ). Although the responses of Rs to changes in precipitation amount have been extensively studied, there is little consensus on how Rs will be affected by changes in precipitation frequency (PF) across the globe. Here, we synthesized the field observations from 296 published papers to quantify the effects of PF on Rs and its components using meta-analysis. Our results indicated that the effects of PF on Rs decreased with an increase in background mean annual precipitation. When the data were grouped by climate conditions, increased PF showed positive effects on Rs under the arid condition but not under the semi-humid or humid conditions, whereas decreased PF suppressed Rs across all the climate conditions. The positive effects of increased PF mainly resulted from the positive response of heterotrophic respiration under the arid condition while the negative effects of decreased PF were mainly attributed to the reductions in root biomass and respiration. Overall, our global synthesis provided for the first time a comprehensive analysis of the divergent effects of PF on Rs and its components across climate regions. This study also provided a framework for understanding and modeling responses of ecosystem carbon cycling to global precipitation change.
Collapse
Affiliation(s)
- Yue Du
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Geography and Environmental Science, Henan University, Kaifeng, China
| | - Ying-Ping Wang
- CSIRO Oceans and Atmosphere, Aspendale, Victoria, Australia
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, USA
| | - Fanglong Su
- School of Life Sciences, Henan University, Kaifeng, China
| | - Junhua Yan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
19
|
Xu H, Fu B, Lei J, Kang H, Wang J, Huang X, Zhu F. Soil microbial communities and their co-occurrence networks in response to long-term Pb-Zn contaminated soil in southern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:26687-26702. [PMID: 36369447 DOI: 10.1007/s11356-022-23962-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Mining causes extreme heavy metal (HM) contamination to surrounding environments and poses threats to soil microbial community. The effects of HMs on soil microbial communities are not only related to their total amounts but also associated with the distribution of chemical fractions. However, the effects of chemical fractions on soil microbes and their interactions remain largely unclear. Here we investigated soil physicochemical properties and bacterial and fungal communities of soil samples from the control area and lightly (L), moderately (M), and heavily (H) contaminated areas, respectively, which were collected from long-term Pb-Zn slag contamination area in the southern China. The results showed that bacterial and fungal community composition and structure were significantly affected by HMs, while community diversity was not significantly affected by HMs. The critical environmental factor affecting bacterial and fungal communities was pH, and the impacts of chemical fractions on their changes were more significant than the total amounts of HMs. Variance partitioning analysis (VPA) revealed fungal community changes were mostly driven by HM total amounts, but bacterial community changes were mostly driven by soil chemical properties. Co-occurrence network indicated that interactions among species of fungal network were sparser than that of bacterial network, but fungal network was more stable, due to a more significant number of keystone taxa and a lower percentage of positive associations. These illustrated that the fungal community might serve as indicator taxa for HM-contaminated status, and specific HM-responsive fungal species such as Triangularia mangenotii, Saitozyma podzolica, and Cladosporium endophytica, and genus Rhizophagus can be considered relevant bioindicators due to their less relative abundance in contaminated areas. Additionally, HM-responsive bacterial OTUs representing five genera within Sulfurifustis, Thiobacillus, Sphingomonas, Qipengyuania, and Sulfurirhabdus were found to be tolerant to HM stress due to their high relative abundance in contaminated levels.
Collapse
Affiliation(s)
- Hongyang Xu
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Bingqing Fu
- College of Life Science and Technology, Central-South, University of Forestry and Technology, Changsha, 410004, People's Republic of China
| | - Jiaqi Lei
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha, Hunan, 410128, People's Republic of China
| | - Hui Kang
- Changsha Environmental Protection College, Changsha, 410004, People's Republic of China
| | - Jun Wang
- College of Life Science and Technology, Central-South, University of Forestry and Technology, Changsha, 410004, People's Republic of China
| | - Xinhao Huang
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha, Hunan, 410128, People's Republic of China
| | - Fan Zhu
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha, Hunan, 410128, People's Republic of China.
| |
Collapse
|
20
|
Hu J, Miller G, Shi W. Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit. Front Microbiol 2023; 13:1078836. [PMID: 36713160 PMCID: PMC9878326 DOI: 10.3389/fmicb.2022.1078836] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
The plant breeding program has developed many cultivars of tall fescue (Festuca arundinacea) with low maintenance and stress tolerance. While the root-associated microbial community helps confer stress tolerance in the host plant, it is still largely unknown how the microbiota varies with plant cultivars under water stress. The study aimed to characterize drought-responsive bacteria and fungi in the roots and rhizosphere of different tall fescue cultivars. Intact grass-soil cores were collected from six cultivars grown in a field trial under no-irrigation for 3 years. Tall fescue under irrigation was also sampled from an adjacent area as the contrast. Bacterial and fungal communities in roots, rhizosphere, and bulk soil were examined for abundance, diversity, and composition using quantitative-PCR and high-throughput amplicon sequencing of 16S rRNA gene and ITS regions, respectively. Differences in microbial community composition and structure between non-irrigated and irrigated samples were statistically significant in all three microhabitats. No-irrigation enriched Actinobacteria in all three microhabitats, but mainly enriched Basidiomycota in the root endosphere and only Glomeromycota in bulk soil. Tall fescue cultivars slightly yet significantly modified endophytic microbial communities. Cultivars showing better adaptability to drought encompassed more relatively abundant Actinobacteria, Basidiomycota, or Glomeromycota in roots and the rhizosphere. PICRUSt2-based predictions revealed that the relative abundance of functional genes in roots related to phytohormones, antioxidant enzymes, and nutrient acquisition was enhanced under no-irrigation. Significant associations between Streptomyces and putative drought-ameliorating genes underscore possible mechanics for microbes to confer tall fescue with water stress tolerance. This work sheds important insight into the potential use of endophytic microbes for screening drought-adaptive genotypes and cultivars.
Collapse
|
21
|
Sui X, Frey B, Yang L, Liu Y, Zhang R, Ni H, Li MH. Soil Acidobacterial community composition changes sensitively with wetland degradation in northeastern of China. Front Microbiol 2022; 13:1052161. [PMID: 36620014 PMCID: PMC9816132 DOI: 10.3389/fmicb.2022.1052161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Acidobacteria are a major component of the soil bacteria and are conducted for many soil functions, and the soil Acidobacterial structure and diversity are affected by climate changes and human activities. However, soil Acidobacterial structure and diversity in wetland ecosystems are still limited recognized. The current study aimed to study the Acidobacterial community and diversity in relation to soil environmental factors along a typical degradation series from primitive wetland to forest in a representative fresh wetland in northeastern China. In this research, we assessed the soil Acidobacterial community composition, using Illumina MiSeq sequencing along a typical degradation series from primitive wetland to forest in a representative fresh wetland in northeastern China. The soil physico chemical properties changed significantly among the eight degrade stages (p < 0.05). The α diversity index (Shannon and Chao1 index) of soil Acidobacteria changed significantly between different degradation stages (p < 0.05). Principal Coordinates Analysis (PCoA) revealed that the soil acidobacteiral communities obviously separated into wetland group and forest group. The most abundant subgroups of Acidobacteria accounted for 31% (Gp1), 5% (Gp2), 12% (Gp3), 2% (Gp4), 5% (Gp6), and 2% (Gp7) in soils within eight successional series. The compositions of soil Acidobacteria in wetland stages were significantly affected by soil moisture content, soil total nitrogen and available nitrogen contents, while those in forest stages were significantly driven by soil pH, soil organic carbon, total nitrogen, available phosphorus and soil moisture content. Our results indicated that the soil Acidobacterial community was mainly structured by soil physico chemical parameters, and wetland degradation towards forests will greatly influence the soil Acidobacterial structure and thus the wetland functions.
Collapse
Affiliation(s)
- Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Beat Frey
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
| | - Libin Yang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Yingnan Liu
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Rongtao Zhang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Hongwei Ni
- Heilongjiang Academy of Forestry, Harbin, China
| | - Mai-He Li
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- School of Life Science, Hebei University, Baoding, China
| |
Collapse
|
22
|
Wu Y, Wang B, Wu L, Liu S, Yue L, Wu J, Chen D. Fifty-year habitat subdivision enhances soil microbial biomass and diversity across subtropical land-bridge islands. Front Microbiol 2022; 13:1063340. [PMID: 36569066 PMCID: PMC9780280 DOI: 10.3389/fmicb.2022.1063340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Although habitat loss and subdivision are considered main causes of sharp declines in biodiversity, there is still great uncertainty concerning the response of soil microbial biomass, diversity, and assemblage to habitat subdivision at the regional scale. Here, we selected 61 subtropical land-bridge islands (with small, medium, and large land areas) with a 50-year history of habitat subdivision and 9 adjacent mainland sites to investigate how habitat subdivision-induced unequal-sized patches and isolation affects biomass, diversity, and assemblages of soil bacteria and fungi. We found that the soil bacterial and fungal biomass on all unequal-sized islands were higher than that on mainland, while soil bacterial and fungal richness on the medium-sized islands were higher than that on mainland and other-sized islands. The habitat subdivision-induced increases in microbial biomass or richness were mainly associated with the changes in subdivision-specified habitat heterogeneities, especial for soil pH and soil moisture. Habitat subdivision reduced soil bacterial dissimilarity on medium-sized islands but did not affect soil fungal dissimilarity on islands of any size. The habitat fragment-induced changes in soil microbial dissimilarity were mainly associated with microbial richness. In summary, our results based on the responses of soil microbial communities from subtropical land-bridge islands are not consistent with the island biogeographical hypotheses but are to some extent consistent with the tradeoff between competition and dispersal. These findings indicate that the response of soil microbial communities to habitat subdivision differed by degree of subdivision and strongly related to habitat heterogeneity, and the distribution of microbial diversity among islands is also affected by tradeoff between competition and dispersal.
Collapse
Affiliation(s)
- Ying Wu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China,Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China,Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Bing Wang
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Liji Wu
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Shengen Liu
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Lingyan Yue
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Jianping Wu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China,Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China,Jianping Wu,
| | - Dima Chen
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China,*Correspondence: Dima Chen,
| |
Collapse
|
23
|
Sui X, Li M, Frey B, Wang M, Weng X, Wang X, Chen F, Li X, Du Z, Yang L, Li M. Climax forest has a higher soil bacterial diversity but lower soil nutrient contents than degraded forests in temperate northern China. Ecol Evol 2022; 12:e9535. [DOI: 10.1002/ece3.9535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences Heilongjiang University Harbin China
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
| | - Mengsha Li
- Institute of Nature and Ecology Heilongjiang Academy of Sciences Harbin China
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
| | - Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences Heilongjiang University Harbin China
| | - Xiaohong Weng
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences Heilongjiang University Harbin China
| | - Xin Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences Heilongjiang University Harbin China
| | - Fuyuan Chen
- Heilongjiang Zhongyangzhan Black‐Billed Capercaillie Nature Reserve Administration Bureau Nenjiang China
| | - Xianda Li
- Heilongjiang Zhongyangzhan Black‐Billed Capercaillie Nature Reserve Administration Bureau Nenjiang China
| | - Zhong Du
- School of Geographical Sciences West Normal University Nanchong China
| | - Libin Yang
- Heilongjiang Zhongyangzhan Black‐Billed Capercaillie Nature Reserve Administration Bureau Nenjiang China
| | - Mai‐He Li
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences Northeast Normal University Changchun China
- School of Life Science Hebei University Baoding China
| |
Collapse
|
24
|
Peng B, Zhao S, Banerjee S, Mai W, Tian C. Contrasting effect of irrigation practices on the cotton rhizosphere microbiota and soil functionality in fields. FRONTIERS IN PLANT SCIENCE 2022; 13:973919. [PMID: 36330236 PMCID: PMC9623166 DOI: 10.3389/fpls.2022.973919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Drip irrigation under plastic film mulch is a common agricultural practice used to conserve water. However, compared to traditional flood irrigation with film mulch, this practice limit cotton root development from early flowering stage and may cause premature senescence in cotton. Changes of root will consequently shape the composition and activity of rhizosphere microbial communities, however, the effect of this farming practice on cotton rhizosphere microbiota remains poorly understood. This study investigated rhizosphere bacteria and soil functionality in response to different irrigation practices -including how changes in rhizosphere bacterial diversity alter soil nutrient cycling. Drip irrigation under plastic film mulch was shown to enhance bacterial diversity by lowering the salinity and increasing the soil moisture. However, the reduced root biomass and soluble sugar content of roots decreased potential copiotrophic taxa, such as Bacteroidetes, Firmicutes, and Gamma-proteobacteria, and increased potential oligotrophic taxa, such as Actinobacteria, Acidobacteria, and Armatimonadetes. A core network module was strongly correlated with the functional potential of soil. This module not only contained most of the keystone taxa but also comprised taxa belonging to Planctomycetaceae, Gemmatimonadaceae, Nitrosomonadaceae, and Rhodospirillaceae that were positively associated with functional genes involved in nutrient cycling. Drip irrigation significantly decreased the richness of the core module and reduced the functional potential of soil in the rhizosphere. Overall, this study provides evidence that drip irrigation under plastic film mulch alters the core bacterial network module and suppresses soil nutrient cycling.
Collapse
Affiliation(s)
- Bin Peng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Wenxuan Mai
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| |
Collapse
|
25
|
Absence of oxygen effect on microbial structure and methane production during drying and rewetting events. Sci Rep 2022; 12:16570. [PMID: 36195651 PMCID: PMC9532411 DOI: 10.1038/s41598-022-20448-5] [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: 07/11/2022] [Accepted: 09/13/2022] [Indexed: 11/15/2022] Open
Abstract
Natural environments with frequent drainage experience drying and rewetting events that impose fluctuations in water availability and oxygen exposure. These relatively dramatic cycles profoundly impact microbial activity in the environment and subsequent emissions of methane and carbon dioxide. In this study, we mimicked drying and rewetting events by submitting methanogenic communities from strictly anaerobic environments (anaerobic digestors) with different phylogenetic structures to consecutive desiccation events under aerobic (air) and anaerobic (nitrogen) conditions followed by rewetting. We showed that methane production quickly recovered after each rewetting, and surprisingly, no significant difference was observed between the effects of the aerobic or anaerobic desiccation events. There was a slight change in the microbial community structure and a decrease in methane production rates after consecutive drying and rewetting, which can be attributed to a depletion of the pool of available organic matter or the inhibition of the methanogenic communities. These observations indicate that in comparison to the drying and rewetting events or oxygen exposure, the initial phylogenetic structure and the organic matter quantity and quality exhibited a stronger influence on the methanogenic communities and overall microbial community responses. These results change the current paradigm of the sensitivity of strict anaerobic microorganisms to oxygen exposure.
Collapse
|
26
|
Ji T, Guo X, Wu F, Wei M, Li J, Ji P, Wang N, Yang F. Proper irrigation amount for eggplant cultivation in a solar greenhouse improved plant growth, fruit quality and yield by influencing the soil microbial community and rhizosphere environment. Front Microbiol 2022; 13:981288. [PMID: 36212834 PMCID: PMC9537383 DOI: 10.3389/fmicb.2022.981288] [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: 06/29/2022] [Accepted: 09/07/2022] [Indexed: 01/10/2023] Open
Abstract
Water scarcity is a worldwide problem, and in order to obtain plenty of production, agricultural irrigation water accounts for a large portion. Many studies have shown that the interaction of root microorganisms and soil can promote crop growth. Developing ways to reduce irrigation to maintain soil fertility and ensure crop yield by regulating the root microenvironment is an important research goal. Here, we developed a reasonable irrigation plan for eggplant cultivation in a solar greenhouse. The maximum theoretical amount of water demand during eggplant planting obtained from a previous study was used as the control (CK), and the irrigation in the treatments was reduced by 10, 20 and 30% relative to this amount. The 10% irrigation reduction treatment (T1) significantly improved soil nutrients and increased soil catalase, urease and alkaline phosphatase activities (p < 0.05). Further analysis of rhizosphere microorganisms revealed the highest richness and diversity of the microbial community under the T1 treatment, with Bacilli as the most abundant bacteria and Aspergillaceae as the most abundant fungi and lower relative abundances of Chloroflexi and Acidobacteria (p < 0.05). Changes in microbial community structure under the influence of different irrigation treatments resulted in improvements in rhizosphere N cycling and nutrient catabolism. The plant–microbe interactions led to significant increases in eggplant plant height, root vigour, root surface area, leaf chlorophyll a, leaf net photosynthetic rate, water use efficiency, transpiration rate, and stomatal conductance under the T1 treatment compared to the CK treatment; soluble sugar, soluble protein and free amino acid contents in eggplant fruit increased by 10.8, 12.3 and 6.7%, respectively; and yield increased by 3.9%. Our research proved that the 10% irrigation reduction treatment (T1) could improve microbial community richness and fruit yield, which would improve irrigation efficiency and cost reduction in agriculture.
Collapse
Affiliation(s)
- Tuo Ji
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xinyong Guo
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Fengling Wu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Min Wei
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- Scientific Observing and Experimental Station of Facility Agricultural Engineering (Huang-Huai-Hai Region), Ministry of Agriculture and Rural Affairs, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
| | - Jing Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crop (Huang-Huai Region), Ministry of Agriculture and Rural Affairs, Tai’an, Shandong, China
| | - Ping Ji
- School of Economics, Qingdao University, Qingdao, Shandong, China
| | - Ningxin Wang
- College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong, China
- *Correspondence: Ningxin Wang, ; Fengjuan Yang,
| | - Fengjuan Yang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai’an, Shandong, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crop (Huang-Huai Region), Ministry of Agriculture and Rural Affairs, Tai’an, Shandong, China
- *Correspondence: Ningxin Wang, ; Fengjuan Yang,
| |
Collapse
|
27
|
Doniger T, Kerfahi D, Wachtel C, Marais E, Maggs-Kölling G, Sherman C, Adams JM, Steinberger Y. Plant Gender Affects Soil Fungal Microbiota Associated with Welwitschia mirabilis, an Unusual Desert Gymnosperm. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02039-z. [PMID: 35648154 DOI: 10.1007/s00248-022-02039-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
In a recent study, we found a distinct soil bacterial community associated with male and female plants of the desert gymnosperm Welwitschia mirabilis. In this subsequent study, we also found that the soil fungal community associated with Welwitschia differs between male and female plants, and between unvegetated areas and the soil under plants. Site location, pH, and soil moisture also had an important influence on the composition of the fungal community. A number of Ascomycota and Chytrid species were found to be distinct indicators of male and female plants, respectively, but there was no overall difference at the phylum level or in terms of diversity. The unvegetated areas between plants also differed in terms of several Ascomycota OTUs. Network connectivity of the fungal communities was found to be higher under both male and female Welwitschia plants than in unvegetated control areas. As with the bacterial community, it is unclear what processes produce the gender-distinct fungal community, and also the more general plant-associated community, and also what the effects on the biology of the plants are. One possibility behind the gender-related difference in fungal community is that there are differences in the production of pollen or nectar between the two plant genders, affecting the below-ground soil community.
Collapse
Affiliation(s)
- Tirza Doniger
- The Mina & Everard Goodman Faculty of Life Sciences Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, 42601, Republic of Korea
| | | | - Eugene Marais
- Gobabeb Research and Training Centre, Gobabeb, Namibia
| | | | - Chen Sherman
- The Mina & Everard Goodman Faculty of Life Sciences Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Jonathan M Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210008, China.
| | - Yosef Steinberger
- The Mina & Everard Goodman Faculty of Life Sciences Bar-Ilan University, 5290002, Ramat-Gan, Israel.
| |
Collapse
|
28
|
Silva I, Alves M, Malheiro C, Silva ARR, Loureiro S, Henriques I, González-Alcaraz MN. Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation. Genes (Basel) 2022; 13:genes13050850. [PMID: 35627235 PMCID: PMC9142034 DOI: 10.3390/genes13050850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 01/31/2023] Open
Abstract
We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community’s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15–25 °C or 20–30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community’s physiological profile and the bacterial community’s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20–30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome–invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.
Collapse
Affiliation(s)
- Isabel Silva
- CEF (Center for Functional Ecology), Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal;
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Marta Alves
- CBQF—Center for Biotechnology and Fine Chemistry, School of Biotechnology, Portuguese Catholic University, 4169-005 Porto, Portugal;
| | - Catarina Malheiro
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Ana Rita R. Silva
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Susana Loureiro
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Isabel Henriques
- CEF (Center for Functional Ecology), Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal;
- Correspondence: (I.H.); (M.N.G.-A.)
| | - M. Nazaret González-Alcaraz
- Department of Agricultural Engineering of the E.T.S.I.A. & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, 30203 Cartagena, Spain
- Correspondence: (I.H.); (M.N.G.-A.)
| |
Collapse
|
29
|
Guidi C, Frey B, Brunner I, Meusburger K, Vogel ME, Chen X, Stucky T, Gwiazdowicz DJ, Skubała P, Bose AK, Schaub M, Rigling A, Hagedorn F. Soil fauna drives vertical redistribution of soil organic carbon in a long-term irrigated dry pine forest. GLOBAL CHANGE BIOLOGY 2022; 28:3145-3160. [PMID: 35124879 PMCID: PMC9306871 DOI: 10.1111/gcb.16122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Summer droughts strongly affect soil organic carbon (SOC) cycling, but net effects on SOC storage are unclear as drought affects both C inputs and outputs from soils. Here, we explored the overlooked role of soil fauna on SOC storage in forests, hypothesizing that soil faunal activity is particularly drought-sensitive, thereby reducing litter incorporation into the mineral soil and, eventually, long-term SOC storage. In a drought-prone pine forest (Switzerland), we performed a large-scale irrigation experiment for 17 years and assessed its impact on vertical SOC distribution and composition. We also examined litter mass loss of dominant tree species using different mesh-size litterbags and determined soil fauna abundance and community composition. The 17-year-long irrigation resulted in a C loss in the organic layers (-1.0 kg C m-2 ) and a comparable C gain in the mineral soil (+0.8 kg C m-2 ) and thus did not affect total SOC stocks. Irrigation increased the mass loss of Quercus pubescens and Viburnum lantana leaf litter, with greater effect sizes when meso- and macrofauna were included (+215%) than when excluded (+44%). The enhanced faunal-mediated litter mass loss was paralleled by a many-fold increase in the abundance of meso- and macrofauna during irrigation. Moreover, Acari and Collembola community composition shifted, with a higher presence of drought-sensitive species in irrigated soils. In comparison, microbial SOC mineralization was less sensitive to soil moisture. Our results suggest that the vertical redistribution of SOC with irrigation was mainly driven by faunal-mediated litter incorporation, together with increased root C inputs. Our study shows that soil fauna is highly sensitive to natural drought, which leads to a reduced C transfer from organic layers to the mineral soil. In the longer term, this potentially affects SOC storage and, therefore, soil fauna plays a key but so far largely overlooked role in shaping SOC responses to drought.
Collapse
Affiliation(s)
- Claudia Guidi
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Ivano Brunner
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Katrin Meusburger
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Michael E. Vogel
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Xiaomei Chen
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
- Present address:
School of Geography and Remote SensingGuangzhou UniversityGuangzhouChina
| | - Tobias Stucky
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | | | - Piotr Skubała
- Faculty of Natural SciencesUniversity of Silesia in KatowiceKatowicePoland
| | - Arun K. Bose
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
- Forestry and Wood Technology DisciplineKhulna UniversityKhulnaBangladesh
| | - Marcus Schaub
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Andreas Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
- Institute of Terrestrial EcosystemsETH ZurichZürichSwitzerland
| | - Frank Hagedorn
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| |
Collapse
|
30
|
Wang D, Zhou H, Zuo J, Chen P, She Y, Yao B, Dong S, Wu J, Li F, Njoroge DM, Shi G, Mao X, Ma L, Zhang Z, Mao Z. Responses of Soil Microbial Metabolic Activity and Community Structure to Different Degraded and Restored Grassland Gradients of the Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:770315. [PMID: 35463442 PMCID: PMC9024238 DOI: 10.3389/fpls.2022.770315] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/22/2022] [Indexed: 05/31/2023]
Abstract
Climate change and land-use disturbances are supposed to have severely affected the degraded alpine grasslands on the Tibetan Plateau. Artificial grassland establishment has been implemented as a restoration tool against grassland degradation. However, the impact of such degradation and restoration processes on soil microbial communities and soil quality is not clearly understood. Here, we aim to investigate how the dynamics of microbial community and soil quality of alpine grasslands respond to a gradient of degradation and that of restoration, respectively. We conducted a randomised experiment with four degradation stages (light, moderate, heavy, and extreme degradation) and three restoration stages (artificial restoration for 1, 5, and 10 years). We analysed the abundance and diversity of soil bacteria and fungi, and measured soil nutrients, enzymatic activity and microbial biomass. The concentration of soil nitrogen (TN), soil organic matter (OM) in heavy degraded grassland decreased significantly by 37.4 and 45.08% compared with that in light degraded grassland. TN and OM in 10-years restored grassland also increased significantly by 33.10 and 30.42% compared to that in 1-year restored grassland. Four soil enzymatic activity indicators related to microbial biomass decreased with degradation gradient and increased with recovery time (i.e., restoration gradient). Both bacterial and fungal community structure was significantly different among grassland degradation or restoration successional stages. The LEfSe analysis revealed that 29 fungal clades and 9 bacterial clades were susceptible to degraded succession, while16 fungal clades and 5 bacterial clades were susceptible to restoration succession. We conclude that soil quality (TN, OM, and enzymatic activity) deteriorated significantly in heavy degraded alpine grassland. Soil microbial community structure of alpine is profoundly impacted by both degradation and restoration processes, fungal communities are more sensitive to grassland succession than bacterial communities. Artificial grasslands can be used as an effective method of restoring degraded grassland, but the soil functions of artificial grassland, even after 10 years of recovery, cannot be restored to the original state of alpine grassland.
Collapse
Affiliation(s)
- Dangjun Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huakun Zhou
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Juan Zuo
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Peng Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yandi She
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Buqing Yao
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Shikui Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Jianshuang Wu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Denis Mburu Njoroge
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoxi Shi
- Key Laboratory of Utilization of Agriculture Solid Waste Resources, College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, China
| | - Xufeng Mao
- School of Geographical Sciences, Qinghai Normal University, Xining, China
| | - Li Ma
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhonghua Zhang
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhun Mao
- AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| |
Collapse
|
31
|
Plant-Microbe Interaction in Sustainable Agriculture: The Factors That May Influence the Efficacy of PGPM Application. SUSTAINABILITY 2022. [DOI: 10.3390/su14042253] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The indiscriminate use of chemical fertilizers and pesticides has caused considerable environmental damage over the years. However, the growing demand for food in the coming years and decades requires the use of increasingly productive and efficient agriculture. Several studies carried out in recent years have shown how the application of plant growth-promoting microbes (PGPMs) can be a valid substitute for chemical industry products and represent a valid eco-friendly alternative. However, because of the complexity of interactions created with the numerous biotic and abiotic factors (i.e., environment, soil, interactions between microorganisms, etc.), the different formulates often show variable effects. In this review, we analyze the main factors that influence the effectiveness of PGPM applications and some of the applications that make them a useful tool for agroecological transition.
Collapse
|
32
|
Huber KJ, Vieira S, Sikorski J, Wüst PK, Fösel BU, Gröngröft A, Overmann J. Differential Response of Acidobacteria to Water Content, Soil Type, and Land Use During an Extended Drought in African Savannah Soils. Front Microbiol 2022; 13:750456. [PMID: 35222321 PMCID: PMC8874233 DOI: 10.3389/fmicb.2022.750456] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Although climate change is expected to increase the extent of drylands worldwide, the effect of drought on the soil microbiome is still insufficiently understood as for dominant but little characterized phyla like the Acidobacteria. In the present study the active acidobacterial communities of Namibian soils differing in type, physicochemical parameters, and land use were characterized by high-throughput sequencing. Water content, pH, major ions and nutrients were distinct for sandy soils, woodlands or dry agriculture on loamy sands. Soils were repeatedly sampled over a 2-year time period and covered consecutively a strong rainy, a dry, a normal rainy and a weak rainy season. The increasing drought had differential effects on different soils. Linear modeling of the soil water content across all sampling locations and sampling dates revealed that the accumulated precipitation of the preceding season had only a weak, but statistically significant effect, whereas woodland and irrigation exerted a strong positive effect on water content. The decrease in soil water content was accompanied by a pronounced decrease in the fraction of active Acidobacteria (7.9-0.7%) while overall bacterial community size/cell counts remained constant. Notably, the strongest decline in the relative fraction of Acidobacteria was observed after the first cycle of rainy and dry season, rather than after the weakest rainy season at the end of the observation period. Over the 2-year period, also the β-diversity of soil Acidobacteria changed. During the first year this change in composition was related to soil type (loamy sand) and land use (woodland) as explanatory variables. A total of 188 different acidobacterial sequence variants affiliated with the "Acidobacteriia," Blastocatellia, and Vicinamibacteria changed significantly in abundance, suggesting either drought sensitivity or formation of dormant cell forms. Comparative physiological testing of 15 Namibian isolates revealed species-specific and differential responses in viability during long-term continuous desiccation or drying-rewetting cycles. These different responses were not determined by phylogenetic affiliation and provide a first explanation for the effect of drought on soil Acidobacteria. In conclusion, the response of acidobacterial communities to water availability is non-linear, most likely caused by the different physiological adaptations of the different taxa present.
Collapse
Affiliation(s)
- Katharina J. Huber
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Selma Vieira
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K. Wüst
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Bärbel U. Fösel
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alexander Gröngröft
- Department of Geosciences, Institute of Soil Science, University of Hamburg, Hamburg, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| |
Collapse
|
33
|
Wang DD, Zhao W, Reyila M, Huang KC, Liu S, Cui BK. Diversity of Microbial Communities of Pinus sylvestris var. mongolica at Spatial Scale. Microorganisms 2022; 10:microorganisms10020371. [PMID: 35208826 PMCID: PMC8877128 DOI: 10.3390/microorganisms10020371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/30/2022] [Accepted: 02/03/2022] [Indexed: 02/06/2023] Open
Abstract
Soil microorganisms play an indispensable role in the forest ecosystem. It is necessary to study the soil microorganisms in Pinus sylvestris var. mongolica, which is one of the afforestation species widely planted in the northern sandy region of China. We collected soil samples of P. sylvestris at large spatial scales and analyzed bacterial and fungal community composition differences using high-throughput sequencing techniques. The results showed that: (1) the richness index of different sandy lands was significantly different. The α-diversity of bacteria was the highest in Mu Us Sandy Land, and the α-diversity of fungi was the highest in Horqin Sandy Land. (2) The dominant phyla of bacteria were Actinobacteria, Proteobacteria, Chloroflexi and Acidobacteria, while the dominant phyla of fungi were Ascomycota and Basidiomycota. The relative abundance of dominant phyla was different. (3) Temperature and precipitation were the main driving factors of bacterial and fungal community change at large spatial scale. In addition, bacteria were also affected by total nitrogen, soil organic carbon and pH content; fungal community was affected by pH. The microorganisms showed obvious differences in geographical distribution, which could provide ideas for promoting sustainable management of P. sylvestris stand.
Collapse
Affiliation(s)
| | | | | | | | | | - Bao-Kai Cui
- Correspondence: ; Tel./Fax: +86-10-6233-6309
| |
Collapse
|
34
|
Tan C, Luo Y, Fu T. Soil microbial community responses to the application of a combined amendment in a historical zinc smelting area. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:13056-13070. [PMID: 34564816 DOI: 10.1007/s11356-021-16631-2] [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: 06/01/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Farmland soils that surround a historical zinc smelting area in northwestern Guizhou, China, are characterized by high levels of heavy metal accumulation. Previous studies have mainly focused on the potential risk evaluations of heavy metals in soil and crops. However, at present, the effects of amendment applications on the bioavailability of heavy metals and on microbial community in the heavily contaminated soils of the mining region are still unclear. A pot experiment was conducted to determine the effect of applying a combined amendment (e.g. lime, sepiolite, and vermicompost) on the diversity and composition of microbial community in the contaminated soil. The results showed that the contents of DTPA- and TCLP-extractable heavy metals (e.g. Cd, Pb, and Zn) decreased and that the pH, SWC, EC, and soil available nutrient (e.g. AN, AP, and AK) contents increased after the application of the combined amendment. Furthermore, application of the combined amendment decreased the diversity of soil bacterial and fungal communities and increased the relative abundances of the dominant bacterial and fungal communities such as Proteobacteria, Bacteroidetes, and Ascomycota; however, the relative abundances of Acidobacteria and Actinobacteria decreased. Redundancy analysis (RDA) and structural equation model (SEM) analysis showed that the bioavailability of heavy metals decreased and that soil physicochemical characteristics improved and had positive or negative effects on the diversity and composition of soil microbial community.
Collapse
Affiliation(s)
- Chuanjiang Tan
- College of Resource and Environmental Engineering, Guizhou University, Guiyang, 550025, China
| | - Youfa Luo
- Key Laboratory of Kast Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Key Laboratory of Karst Environment and Geohazard Prevention, Guizhou University, Guiyang, 550025, China.
- Guizhou Kast Environmental Ecosystem Observation and Research Station, Ministry of Education, Guiyang, 550025, China.
| | - Tianling Fu
- Guizhou Kast Environmental Ecosystem Observation and Research Station, Ministry of Education, Guiyang, 550025, China
- The New Rural Development Research Institute, Guizhou University, Guiyang, 550025, China
| |
Collapse
|
35
|
Benaffari W, Boutasknit A, Anli M, Ait-El-Mokhtar M, Ait-Rahou Y, Ben-Laouane R, Ben Ahmed H, Mitsui T, Baslam M, Meddich A. The Native Arbuscular Mycorrhizal Fungi and Vermicompost-Based Organic Amendments Enhance Soil Fertility, Growth Performance, and the Drought Stress Tolerance of Quinoa. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030393. [PMID: 35161374 PMCID: PMC8838481 DOI: 10.3390/plants11030393] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 05/17/2023]
Abstract
The present study aimed to determine the effects of biostimulants on the physicochemical parameters of the agricultural soil of quinoa under two water regimes and to understand the mode of action of the biostimulants on quinoa for drought adaptation. We investigated the impact of two doses of vermicompost (5 and 10 t/ha) and arbuscular mycorrhizal fungi applied individually, or in joint application, on attenuating the negative impacts of water shortage and improving the agro-physiological and biochemical traits of quinoa, as well as soil fertility, under two water regimes (well-watered and drought stress) in open field conditions. Exposure to drought decreased biomass, leaf water potential, and stomatal conductance, and increased malondialdehyde and hydrogen peroxide content. Mycorrhiza and/or vermicompost promoted plant growth by activating photosynthesis machinery and nutrient assimilation, leading to increased total soluble sugars, proteins, and antioxidant enzyme activities in the leaf and root. After the experiment, the soil's total organic matter, phosphorus, nitrogen, calcium, and soil glomalin content improved by the single or combined application of mycorrhiza and vermicompost. This knowledge suggests that the combination of mycorrhiza and vermicompost regulates the physiological and biochemical processes employed by quinoa in coping with drought and improves the understanding of soil-plant interaction.
Collapse
Affiliation(s)
- Wissal Benaffari
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
| | - Abderrahim Boutasknit
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
| | - Mohamed Anli
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
| | - Mohamed Ait-El-Mokhtar
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
| | - Youssef Ait-Rahou
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
| | - Raja Ben-Laouane
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
| | - Hela Ben Ahmed
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan;
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan;
- Correspondence: (M.B.); (A.M.); Tel.: +81-252627637 (M.B.); +212-661873158 (A.M.)
| | - Abdelilah Meddich
- Center of Agrobiotechnology and Bioengineering, Research Unit labelled CNRST (Centre AgroBiotech-URL-CNRST-05), “Physiology of Abiotic Stresses” Team, Cadi Ayyad University, Marrakesh 40000, Morocco; (W.B.); (A.B.); (M.A.); (Y.A.-R.); (R.B.-L.)
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco;
- Laboratoire Mixte Tuniso-Marocain (LMTM) de Physiologie et Biotechnologie Végétales et Changements Climatiques LPBV2C, Tunis 1000, Tunisia;
- Correspondence: (M.B.); (A.M.); Tel.: +81-252627637 (M.B.); +212-661873158 (A.M.)
| |
Collapse
|
36
|
Bose AK, Rigling A, Gessler A, Hagedorn F, Brunner I, Feichtinger L, Bigler C, Egli S, Etzold S, Gossner MM, Guidi C, Lévesque M, Meusburger K, Peter M, Saurer M, Scherrer D, Schleppi P, Schönbeck L, Vogel ME, Arx G, Wermelinger B, Wohlgemuth T, Zweifel R, Schaub M. Lessons learned from a long‐term irrigation experiment in a dry Scots pine forest: Impacts on traits and functioning. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Arun K. Bose
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
- Forestry and Wood Technology Discipline Khulna University Khulna Bangladesh
| | - Andreas Rigling
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
- Institute of Terrestrial Ecosystems ETH Zurich, Universitätstrasse 16 Zurich Switzerland
| | - Arthur Gessler
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
- Institute of Terrestrial Ecosystems ETH Zurich, Universitätstrasse 16 Zurich Switzerland
| | - Frank Hagedorn
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Ivano Brunner
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Linda Feichtinger
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Christof Bigler
- Department of Environmental Systems Science, Forest Ecology, Universitätstrasse 22 ETH Zurich Zurich Switzerland
| | - Simon Egli
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Sophia Etzold
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Martin M. Gossner
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
- Institute of Terrestrial Ecosystems ETH Zurich, Universitätstrasse 16 Zurich Switzerland
| | - Claudia Guidi
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Mathieu Lévesque
- Department of Environmental Systems Science, Forest Ecology, Universitätstrasse 22 ETH Zurich Zurich Switzerland
| | - Katrin Meusburger
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Martina Peter
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Matthias Saurer
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Daniel Scherrer
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Patrick Schleppi
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Leonie Schönbeck
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
- Plant Ecology Research Laboratory, School of Architecture, Civil and Environmental Engineering ENAC École Polytechnique Fédérale de Lausanne EPFL, Station 2 Lausanne Switzerland
| | - Michael E. Vogel
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Georg Arx
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Beat Wermelinger
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Thomas Wohlgemuth
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Roman Zweifel
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| | - Marcus Schaub
- Swiss Federal Research Institute WSL, Zürcherstrasse 111 Birmensdorf Switzerland
| |
Collapse
|
37
|
Gschwend F, Hartmann M, Mayerhofer J, Hug AS, Enkerli J, Gubler A, Meuli RG, Frey B, Widmer F. Site and land-use associations of soil bacteria and fungi define core and indicative taxa. FEMS Microbiol Ecol 2022; 97:fiab165. [PMID: 34940884 PMCID: PMC8752248 DOI: 10.1093/femsec/fiab165] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.
Collapse
Affiliation(s)
- Florian Gschwend
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, CH-8092 Zürich, Switzerland
| | - Johanna Mayerhofer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Anna-Sofia Hug
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Andreas Gubler
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Reto G Meuli
- Swiss Soil Monitoring Network NABO, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Franco Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| |
Collapse
|
38
|
Tatsumi C, Azuma WA, Ogawa Y, Komada N. Nitrogen Availability and Microbial Communities of Canopy Soils in a Large Cercidiphyllum japonicum Tree of a Cool-Temperate Old Growth Forest. MICROBIAL ECOLOGY 2021; 82:919-931. [PMID: 33606088 DOI: 10.1007/s00248-021-01707-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Canopy soils on large trees are important for supporting the lives of many canopy plants, and thereby increasing regional biodiversity. However, because of the less accessibility to canopy soils, there is insufficient knowledge on how canopy soils produce available nitrogen (N) for canopy plants through the activity of canopy soil microbes. Canopy soils usually have different soil properties from ground soils, so we hypothesized that canopy soils would have unique microbial communities compared to ground soils, but still provide available N for canopy plants. Here, we compared soil N availability, including net N mineralization and nitrification rate, and microbial communities between canopy soils (organic soils) collected at various heights of a large Cercidiphyllum japonicum tree and ground soils (organic and mineral soils) in a cool-temperate old-growth forest of Japan. The canopy soils had significantly different N availability (mass-based higher but volume-based lower) and microbial communities from the ground mineral soils. Among organic soils, the height of the soil had an impact on the microbial communities but not on the N availability, which agreed with our hypothesis. Despite the decrease in fungal abundance in the higher soils, the increase in certain components of the cellulose-decomposing fungi and oligotrophic bacteria may contribute to the available N production. Also, the abundance of ammonia-oxidizers did not change with the height, which would be important for the nitrification rate. Our study implied canopy soils could provide N to canopy plants partly through the functional redundancy within different microbial communities and constant population of ammonia-oxidizers.
Collapse
Affiliation(s)
- Chikae Tatsumi
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Wakana A Azuma
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, 657-8501, Japan.
| | - Yuya Ogawa
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Natsuki Komada
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| |
Collapse
|
39
|
Adamo I, Castaño C, Bonet JA, Colinas C, Martínez de Aragón J, Alday JG. Lack of Phylogenetic Differences in Ectomycorrhizal Fungi among Distinct Mediterranean Pine Forest Habitats. J Fungi (Basel) 2021; 7:jof7100793. [PMID: 34682215 PMCID: PMC8538088 DOI: 10.3390/jof7100793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 01/22/2023] Open
Abstract
Understanding whether the occurrences of ectomycorrhizal species in a given tree host are phylogenetically determined can help in assessing different conservational needs for each fungal species. In this study, we characterized ectomycorrhizal phylogenetic composition and phylogenetic structure in 42 plots with five different Mediterranean pine forests: i.e., pure forests dominated by P. nigra, P. halepensis, and P. sylvestris, and mixed forests of P. nigra-P. halepensis and P. nigra-P. sylvestris, and tested whether the phylogenetic structure of ectomycorrhizal communities differs among these. We found that ectomycorrhizal communities were not different among pine tree hosts neither in phylogenetic composition nor in structure and phylogenetic diversity. Moreover, we detected a weak abiotic filtering effect (4%), with pH being the only significant variable influencing the phylogenetic ectomycorrhizal community, while the phylogenetic structure was slightly influenced by the shared effect of stand structure, soil, and geographic distance. However, the phylogenetic community similarity increased at lower pH values, supporting that fewer, closely related species were found at lower pH values. Also, no phylogenetic signal was detected among exploration types, although short and contact were the most abundant types in these forest ecosystems. Our results demonstrate that pH but not tree host, acts as a strong abiotic filter on ectomycorrhizal phylogenetic communities in Mediterranean pine forests at a local scale. Finally, our study shed light on dominant ectomycorrhizal foraging strategies in drought-prone ecosystems such as Mediterranean forests.
Collapse
Affiliation(s)
- Irene Adamo
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
- Correspondence:
| | - Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden;
| | - José Antonio Bonet
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
| | - Carlos Colinas
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
- Forest Science and Technology Centre of Catalonia, Ctra. Sant Llorenç de Morunys km 2, E25280 Solsona, Spain
| | - Juan Martínez de Aragón
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Forest Science and Technology Centre of Catalonia, Ctra. Sant Llorenç de Morunys km 2, E25280 Solsona, Spain
| | - Josu G. Alday
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
| |
Collapse
|
40
|
Gao D, Joseph J, Werner RA, Brunner I, Zürcher A, Hug C, Wang A, Zhao C, Bai E, Meusburger K, Gessler A, Hagedorn F. Drought alters the carbon footprint of trees in soils-tracking the spatio-temporal fate of 13 C-labelled assimilates in the soil of an old-growth pine forest. GLOBAL CHANGE BIOLOGY 2021; 27:2491-2506. [PMID: 33739617 PMCID: PMC8251913 DOI: 10.1111/gcb.15557] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/22/2021] [Accepted: 02/03/2021] [Indexed: 05/04/2023]
Abstract
Above and belowground compartments in ecosystems are closely coupled on daily to annual timescales. In mature forests, this interlinkage and how it is impacted by drought is still poorly understood. Here, we pulse-labelled 100-year-old trees with 13 CO2 within a 15-year-long irrigation experiment in a naturally dry pine forest to quantify how drought regime affects the transfer and use of assimilates from trees to the rhizosphere and associated microbial communities. It took 4 days until new 13 C-labelled assimilates were allocated to the rhizosphere. One year later, the 13 C signal of the 3-h long pulse labelling was still detectable in stem and soil respiration, which provides evidence that parts of the assimilates are stored in trees before they are used for metabolic processes in the rhizosphere. Irrigation removing the natural water stress reduced the mean C residence time from canopy uptake until soil respiration from 89 to 40 days. Moreover, irrigation increased the amount of assimilates transferred to and respired in the soil within the first 10 days by 370%. A small precipitation event rewetting surface soils altered this pattern rapidly and reduced the effect size to +35%. Microbial biomass incorporated 46 ± 5% and 31 ± 7% of the C used in the rhizosphere in the dry control and irrigation treatment respectively. Mapping the spatial distribution of soil-respired 13 CO2 around the 10 pulse-labelled trees showed that tree rhizospheres extended laterally 2.8 times beyond tree canopies, implying that there is a strong overlap of the rhizosphere among adjacent trees. Irrigation increased the rhizosphere area by 60%, which gives evidence of a long-term acclimation of trees and their rhizosphere to the drought regime. The moisture-sensitive transfer and use of C in the rhizosphere has consequences for C allocation within trees, soil microbial communities and soil carbon storage.
Collapse
Affiliation(s)
- Decai Gao
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
- Key Laboratory of Geographical Processes and Ecological Security of Changbai MountainsMinistry of EducationNortheast Normal UniversityChangchunChina
| | - Jobin Joseph
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Roland A Werner
- Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Ivano Brunner
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Alois Zürcher
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Christian Hug
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Ao Wang
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
- Terrestrial EcosystemsETH ZurichZurichSwitzerland
| | - Chunhong Zhao
- Key Laboratory of Geographical Processes and Ecological Security of Changbai MountainsMinistry of EducationNortheast Normal UniversityChangchunChina
| | - Edith Bai
- Key Laboratory of Geographical Processes and Ecological Security of Changbai MountainsMinistry of EducationNortheast Normal UniversityChangchunChina
| | | | - Arthur Gessler
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
- Terrestrial EcosystemsETH ZurichZurichSwitzerland
| | - Frank Hagedorn
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
| |
Collapse
|
41
|
Microbial Community Resilience across Ecosystems and Multiple Disturbances. Microbiol Mol Biol Rev 2021; 85:85/2/e00026-20. [PMID: 33789927 DOI: 10.1128/mmbr.00026-20] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.
Collapse
|
42
|
Frey B, Walthert L, Perez-Mon C, Stierli B, Köchli R, Dharmarajah A, Brunner I. Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities. Front Microbiol 2021; 12:674160. [PMID: 34025630 PMCID: PMC8137989 DOI: 10.3389/fmicb.2021.674160] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
Soil microorganisms such as bacteria and fungi play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of the soil microbiome to a depth of 2 m in Swiss drought-exposed forests of European beech and oaks on calcareous bedrock. We aimed to disentangle the effects of soil depth, tree (beech, oak), and substrate (soil, roots) on microbial abundance, diversity, and community structure. With increasing soil depth, organic carbon, nitrogen, and clay content decreased significantly. Similarly, fine root biomass, microbial biomass (DNA content, fungal abundance), and microbial alpha-diversity decreased and were consequently significantly related to these physicochemical parameters. In contrast, bacterial abundance tended to increase with soil depth, and the bacteria to fungi ratio increased significantly with greater depth. Tree species was only significantly related to the fungal Shannon index but not to the bacterial Shannon index. Microbial community analyses revealed that bacterial and fungal communities varied significantly across the soil layers, more strongly for bacteria than for fungi. Both communities were also significantly affected by tree species and substrate. In deep soil layers, poorly known bacterial taxa from Nitrospirae, Chloroflexi, Rokubacteria, Gemmatimonadetes, Firmicutes and GAL 15 were overrepresented. Furthermore, archaeal phyla such as Thaumarchaeota and Euryarchaeota were more abundant in subsoils than topsoils. Fungal taxa that were predominantly found in deep soil layers belong to the ectomycorrhizal Boletus luridus and Hydnum vesterholtii. Both taxa are reported for the first time in such deep soil layers. Saprotrophic fungal taxa predominantly recorded in deep soil layers were unknown species of Xylaria. Finally, our results show that the microbial community structure found in fine roots was well represented in the bulk soil. Overall, we recorded poorly known bacterial and archaeal phyla, as well as ectomycorrhizal fungi that were not previously known to colonize deep soil layers. Our study contributes to an integrated perspective on the vertical distribution of the soil microbiome at a fine spatial scale in drought-exposed forests.
Collapse
Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Lorenz Walthert
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Roger Köchli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Alexander Dharmarajah
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| |
Collapse
|
43
|
Doniger T, Adams JM, Marais E, Maggs-Kölling G, Sherman C, Kerfahi D, Yang Y, Steinberger Y. The 'fertile island effect' of Welwitschia plants on soil microbiota is influenced by plant gender. FEMS Microbiol Ecol 2021; 96:5910483. [PMID: 32966571 DOI: 10.1093/femsec/fiaa186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/17/2020] [Indexed: 01/19/2023] Open
Abstract
Desert and semi-desert plants are often associated with a distinct soil biota under the plants and close to the root system. We aimed to understand if similar effects could be found in the taxonomically isolated desert gymnosperm Welwitschia mirabilis in the Namib Desert, and whether this island effect varied with climate and with gender of plants. We took soil cores adjacent to the plants in environments ranging from extreme desert to arid shrubland, and in nearby control sites between the plants. Soil chemistry was analysed, and deoxyribonucleic acid was extracted and sequenced for the bacterial 16s region. Soil under the plants was richer in organic C, N and moisture. Despite the range of climates, the soil around Welwitschia plants was consistently associated with a particular bacterial community composition that was distinct from samples further away. Compared to unvegetated control patches, bacterial diversity close to the plants was reduced. In the plant-associated soil community, there was a clear gender effect across all sites with a distinct community composition and greater diversity under male plants. It is unclear what differences in the soil environment might be producing these gender-associated differences, which provide an additional dimension to the fertile island effect.
Collapse
Affiliation(s)
- Tirza Doniger
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Jonathan M Adams
- School of Geography and Oceanography, Nanjing University, Xianlin, Nanjing, 210023, P.R. China
| | - Eugene Marais
- Gobabeb Namib Research and Training Center PO Box 953, Walvis Bay 13103, Namibia
| | | | - Chen Sherman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, 42601, Republic of Korea
| | - Ying Yang
- School of Geography and Oceanography, Nanjing University, Xianlin, Nanjing, 210023, P.R. China
| | - Yosef Steinberger
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| |
Collapse
|
44
|
Bhattacharyya A, Pablo CHD, Mavrodi OV, Weller DM, Thomashow LS, Mavrodi DV. Rhizosphere plant-microbe interactions under water stress. ADVANCES IN APPLIED MICROBIOLOGY 2021; 115:65-113. [PMID: 34140134 DOI: 10.1016/bs.aambs.2021.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Climate change, with its extreme temperature, weather and precipitation patterns, is a major global concern of dryland farmers, who currently meet the challenges of climate change agronomically and with growth of drought-tolerant crops. Plants themselves compensate for water stress by modifying aerial surfaces to control transpiration and altering root hydraulic conductance to increase water uptake. These responses are complemented by metabolic changes involving phytohormone network-mediated activation of stress response pathways, resulting in decreased photosynthetic activity and the accumulation of metabolites to maintain osmotic and redox homeostasis. Phylogenetically diverse microbial communities sustained by plants contribute to host drought tolerance by modulating phytohormone levels in the rhizosphere and producing water-sequestering biofilms. Drylands of the Inland Pacific Northwest, USA, illustrate the interdependence of dryland crops and their associated microbiota. Indigenous Pseudomonas spp. selected there by long-term wheat monoculture suppress root diseases via the production of antibiotics, with soil moisture a critical determinant of the bacterial distribution, dynamics and activity. Those pseudomonads producing phenazine antibiotics on wheat had more abundant rhizosphere biofilms and provided improved tolerance to drought, suggesting a role of the antibiotic in alleviation of drought stress. The transcriptome and metabolome studies suggest the importance of wheat root exudate-derived osmoprotectants for the adaptation of these pseudomonads to the rhizosphere lifestyle and support the idea that the exchange of metabolites between plant roots and microorganisms profoundly affects and shapes the belowground plant microbiome under water stress.
Collapse
Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Clint H D Pablo
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States.
| |
Collapse
|
45
|
French E, Kaplan I, Iyer-Pascuzzi A, Nakatsu CH, Enders L. Emerging strategies for precision microbiome management in diverse agroecosystems. NATURE PLANTS 2021; 7:256-267. [PMID: 33686226 DOI: 10.1038/s41477-020-00830-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/08/2020] [Indexed: 05/18/2023]
Abstract
Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems.
Collapse
Affiliation(s)
- Elizabeth French
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Ian Kaplan
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Anjali Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Cindy H Nakatsu
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Laramy Enders
- Department of Entomology, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
46
|
Hereira-Pacheco SE, Navarro-Noya YE, Dendooven L. The root endophytic bacterial community of Ricinus communis L. resembles the seeds community more than the rhizosphere bacteria independent of soil water content. Sci Rep 2021; 11:2173. [PMID: 33500437 PMCID: PMC7838207 DOI: 10.1038/s41598-021-81551-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/20/2020] [Indexed: 01/25/2023] Open
Abstract
Rhizosphere and root endophytic bacteria are crucial for plant development, but the question remains if their composition is similar and how environmental conditions, such as water content, affect their resemblance. Ricinus communis L., a highly drought resistant plant, was used to study how varying soil water content affected the bacterial community in uncultivated, non-rhizosphere and rhizosphere soil, and in its roots. Additionally, the bacterial community structure was determined in the seeds of R. communis at the onset of the experiment. Plants were cultivated in soil at three different watering regimes, i.e. 50% water holding capacity (WHC) or adjusted to 50% WHC every two weeks or every month. Reducing the soil water content strongly reduced plant and root dry biomass and plant development, but had little effect on the bacterial community structure. The bacterial community structure was affected significantly by cultivation of R. communis and showed large variations over time. After 6 months, the root endophytic bacterial community resembled that in the seeds more than in the rhizosphere. It was found that water content had only a limited effect on the bacterial community structure and the different bacterial groups, but R. communis affected the bacterial community profoundly.
Collapse
Affiliation(s)
| | - Yendi E Navarro-Noya
- Cátedras CONACYT, Centro Tlaxcala de Biología de La Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City, Mexico.
| |
Collapse
|
47
|
Adamczyk M, Rüthi J, Frey B. Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils. Environ Microbiol 2021; 23:2152-2168. [PMID: 33393203 DOI: 10.1111/1462-2920.15383] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.
Collapse
Affiliation(s)
- Magdalene Adamczyk
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Joel Rüthi
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| |
Collapse
|
48
|
Tan B, Li Y, Liu T, Tan X, He Y, You X, Leong KH, Liu C, Li L. Response of Plant Rhizosphere Microenvironment to Water Management in Soil- and Substrate-Based Controlled Environment Agriculture (CEA) Systems: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:691651. [PMID: 34456936 PMCID: PMC8385539 DOI: 10.3389/fpls.2021.691651] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
As natural agroecology deteriorates, controlled environment agriculture (CEA) systems become the backup support for coping with future resource consumption and potential food crises. Compared with natural agroecology, most of the environmental parameters of the CEA system rely on manual management. Such a system is dependent and fragile and prone to degradation, which includes harmful bacteria proliferation and productivity decline. Proper water management is significant for constructing a stabilized rhizosphere microenvironment. It has been proved that water is an efficient tool for changing the availability of nutrients, plant physiological processes, and microbial communities within. However, for CEA issues, relevant research is lacking at present. The article reviews the interactive mechanism between water management and rhizosphere microenvironments from the perspectives of physicochemical properties, physiological processes, and microbiology in CEA systems. We presented a synthesis of relevant research on water-root-microbes interplay, which aimed to provide detailed references to the conceptualization, research, diagnosis, and troubleshooting for CEA systems, and attempted to give suggestions for the construction of a high-tech artificial agricultural ecology.
Collapse
Affiliation(s)
- Bo Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yihan Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Tiegang Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yuxin He
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xueji You
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Kah Hon Leong
- Department of Environmental Engineering, Faculty of Engineering and Green Technology, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| | - Chao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- *Correspondence: Chao Liu,
| | - Longguo Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- Longguo Li,
| |
Collapse
|
49
|
Azarbad H, Tremblay J, Giard-Laliberté C, Bainard LD, Yergeau E. Four decades of soil water stress history together with host genotype constrain the response of the wheat microbiome to soil moisture. FEMS Microbiol Ecol 2020; 96:5841940. [PMID: 32440671 DOI: 10.1093/femsec/fiaa098] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/20/2020] [Indexed: 11/14/2022] Open
Abstract
There is little understanding about how soil water stress history and host genotype influence the response of wheat-associated microbiome under short-term decreases in soil moisture. To address this, we investigated how plant breeding history (four wheat genotypes; two with recognized drought resistance and two without) and soil water stress history (same wheat field soil from Saskatchewan with contrasting long-term irrigation) independently or interactively influenced the response of the rhizosphere, root and leaf bacterial and fungal microbiota to short-term decreases in soil water content (SWC). We used amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) to characterize the wheat microbiome. Fungal and bacterial communities responses to short-term decreases in SWC were mainly constrained by soil water stress history, with some smaller, but significant influence of plant genotype. One exception was the leaf-associated fungal communities, for which the largest constraint was genotype, resulting in a clear differentiation of the communities based on the genotype's sensitivity to water stress. Our results clearly indicate that soil legacy does not only affect the response to water stress of the microbes inhabiting the soil, but also of the microorganisms more closely associated with the plant tissues, and even of the plant itself.
Collapse
Affiliation(s)
- Hamed Azarbad
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Québec, H7V 1B7, Canada
| | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - Charlotte Giard-Laliberté
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Québec, H7V 1B7, Canada
| | - Luke D Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, Swift Current, SK, S9H 3X2, Canada
| | - Etienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Québec, H7V 1B7, Canada
| |
Collapse
|
50
|
Marí T, Castaño C, Rodríguez A, Ibáñez M, Lobo A, Sebastià MT. Fairy rings harbor distinct soil fungal communities and high fungal diversity in a montane grassland. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|