1
|
Wang F, Gao Y, Li X, Luan M, Wang X, Zhao Y, Zhou X, Du G, Wang P, Ye C, Guo H. Changes in microbial composition explain the contrasting responses of glucose and lignin decomposition to soil acidification in an alpine grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172671. [PMID: 38653407 DOI: 10.1016/j.scitotenv.2024.172671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Soil acidification often suppresses microbial growth and activities, resulting in a negative impact on soil organic carbon (C) decomposition. While the detrimental effects of acidification on soil and plant properties have been extensively studied, less attention has been paid on the shifts in soil microbial communities and their influences of the decomposition of organic C with different chemical complexities. Taking advantage of an acid addition experiment in a Tibetan alpine meadow, here we examined the response of soil microbial communities to soil acidification and microbial effect on the decomposition of organic C with different chemical complexities (i.e., glucose and lignin, representing labile and recalcitrant C respectively). We found that soil acidification had no impact on microbial respiration and microbial abundance even though it decreased bacterial diversity significantly. Soil acidification increased the relative abundance of some microbial taxa, like Alphaproteobacteria and Acidobacteriia in bacteria increased by 36 %, 284 %, and Eurotiomycetes, Sordariomycetes and Leotiomycetes in fungi increased by 145 %, 279 % and 12.7-fold, but decreased the relative abundance of Acidimicrobiia by 33 % in highest acid addition treatment. Changes in microbial communities (bacterial and fungal community composition, the diversity of bacterial community and the ratio of fungi to bacteria) are significantly related to the decomposition of glucose and lignin. More specifically, soil acidification decreased the decomposition of glucose but increased the decomposition of lignin, indicating a trade-off between the decomposition of labile and recalcitrant soil organic C under soil acidification. Overall, shifts in microbial communities under soil acidification might be accompanied by an increased ability to break down more recalcitrant C. This trade-off between the decomposition of labile and recalcitrant C may change soil C quality under future acid deposition scenarios.
Collapse
Affiliation(s)
- Fuwei Wang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; College of Resource and Environment, Anhui Science and Technology University, Fengyang 233100, China
| | - Yue Gao
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Li
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengdi Luan
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyi Wang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanwen Zhao
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xianhui Zhou
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Guozhen Du
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Peng Wang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chenglong Ye
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hui Guo
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
2
|
Bashian-Victoroff C, Brown A, Loyd AL, Carrino-Kyker SR, Burke DJ. Beech Leaf Disease Severity Affects Ectomycorrhizal Colonization and Fungal Taxa Composition. J Fungi (Basel) 2023; 9:jof9040497. [PMID: 37108950 PMCID: PMC10146144 DOI: 10.3390/jof9040497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Beech leaf disease (BLD) is an emerging forest infestation affecting beech trees (Fagus spp.) in the midwestern and northeastern United States and southeastern Canada. BLD is attributed to the newly recognized nematode Litylenchus crenatae subsp. mccannii. First described in Lake County, Ohio, BLD leads to the disfigurement of leaves, canopy loss, and eventual tree mortality. Canopy loss limits photosynthetic capacity, likely impacting tree allocation to belowground carbon storage. Ectomycorrhizal fungi are root symbionts, which rely on the photosynthesis of autotrophs for nutrition and growth. Because BLD limits tree photosynthetic capacity, ECM fungi may receive less carbohydrates when associating with severely affected trees compared with trees without BLD symptoms. We sampled root fragments from cultivated F. grandifolia sourced from two provenances (Michigan and Maine) at two timepoints (fall 2020 and spring 2021) to test whether BLD symptom severity alters colonization by ectomycorrhizal fungi and fungal community composition. The studied trees are part of a long-term beech bark disease resistance plantation at the Holden Arboretum. We sampled from replicates across three levels of BLD symptom severity and compared fungal colonization via visual scoring of ectomycorrhizal root tip abundance. Effects of BLD on fungal communities were determined through high-throughput sequencing. We found that ectomycorrhizal root tip abundance was significantly reduced on the roots of individuals of the poor canopy condition resulting from BLD, but only in the fall 2020 collection. We found significantly more ectomycorrhizal root tips from root fragments collected in fall 2020 than in spring 2021, suggesting a seasonal effect. Community composition of ectomycorrhizal fungi was not impacted by tree condition but did vary between provenances. We found significant species level responses of ectomycorrhizal fungi between levels of both provenance and tree condition. Of the taxa analyzed, two zOTUs had significantly lower abundance in high-symptomatology trees compared with low-symptomatology trees. These results provide the first indication of a belowground effect of BLD on ectomycorrhizal fungi and contribute further evidence to the role of these root symbionts in studies of tree disease and forest pathology.
Collapse
Affiliation(s)
| | - Alexis Brown
- The Holden Arboretum, 9500 Sperry Road, Kirtland, OH 44094, USA
| | - Andrew L Loyd
- Bartlett Tree Research Laboratories, 13768 Hamilton Rd., Charlotte, NC 28278, USA
| | | | - David J Burke
- The Holden Arboretum, 9500 Sperry Road, Kirtland, OH 44094, USA
| |
Collapse
|
3
|
Kaushal M, Tumuhairwe JB, Kaingo J, Richard M, Nakamanya F, Taulya G, Coyne D. Compositional Shifts in Microbial Diversity under Traditional Banana Cropping Systems of Sub-Saharan Africa. BIOLOGY 2022; 11:biology11050756. [PMID: 35625484 PMCID: PMC9138362 DOI: 10.3390/biology11050756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/29/2022] [Accepted: 04/15/2022] [Indexed: 12/04/2022]
Abstract
Simple Summary In soil, the connection between microbial diversity and plant health is vital in terms of achieving the food security. Here, we suggested the study on soil microbial diversity in diverse cropping systems of banana adopted and followed by small holder farmers over the years. We tracked down the bacterial and fungal diversity in mono cropping and intercropping systems using advanced molecular techniques. Our outcomes likewise uncovered that the impact of cropping systems on bacterial and fungal increments in plant roots and rhizosphere soil. Hence, safeguarding of soil microbial diversity is profoundly significant taking into consideration of the contributions for plant buildups and rhizodeposits into the soil. Abstract Improvements in the crop productivity, soil health, and sustainable intensification should be premised on the better understanding of interactions between the cropping systems and soil microbial diversity. In this study, we assessed variations in the microbial communities across the traditional banana-based cropping systems of contrasting monocrop vigor (vigorous or V vs. non-vigorous or NV) and the cropping system (monocrop or MC vs. intercropped or IC) using 16S rDNA (V3–V4) and ITS2 amplicon deep sequencing via Illumina platform. Sequencing results of the bacterial and fungal communities showed high variability among MC and V cropping systems. The abundances of Proteobacteria, Firmicutes, and Actinobacteria were significantly higher in NV (non-vigorous) and V (vigorous) cropping systems; and the abundances of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes in the MC (monocropping) than IC (intercropping). There were high relative abundances of Pseudomonas (6.1–37.43%), Bacillus (4.5–20.4%), Rhizobium (1.4–6.5%), and Devosia (1.5–6.7%) in the cropping systems. The dominant family of fungal class Incertae_sedis was Mortierellales, which accounted for 8.79–41.12% of total taxa. This result indicated that the cropping systems are vital for supporting the dynamic microbial diversity specifically beneficial for bacterial communities that helps in promoting synergistic plant-soil interactions and total productivity under resource poor conditions of smallholder farmers in sub-Saharan Africa (SSA).
Collapse
Affiliation(s)
- Manoj Kaushal
- International Institute of Tropical Agriculture (IITA), Mikocheni B, Dar es Salaam P.O. Box 34441, Tanzania;
- Correspondence:
| | - John Baptist Tumuhairwe
- College of Agriculture and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (J.B.T.); (G.T.)
| | - Jacob Kaingo
- International Institute of Tropical Agriculture (IITA), Mikocheni B, Dar es Salaam P.O. Box 34441, Tanzania;
| | - Malingumu Richard
- Faculty of Agriculture and Environmental Sciences, Muni University, Arua P.O. Box 725, Uganda;
| | - Florence Nakamanya
- International Institute of Tropical Agriculture (IITA), Kampala P.O. Box 7878, Uganda;
| | - Godfrey Taulya
- College of Agriculture and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (J.B.T.); (G.T.)
- International Institute of Tropical Agriculture (IITA), Kampala P.O. Box 7878, Uganda;
| | - Danny Coyne
- International Institute of Tropical Agriculture (IITA), Nairobi P.O. Box 30772-00100, Kenya;
| |
Collapse
|
4
|
Lin Q, Dini-Andreote F, Meador TB, Angel R, Meszárošová L, Heděnec P, Li L, Baldrian P, Frouz J. Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities. Environ Microbiol 2022; 24:3985-4000. [PMID: 35238127 DOI: 10.1111/1462-2920.15936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023]
Abstract
The mechanisms underlying microbial community dynamics and co-occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Bacterial community structures became increasingly phylogenetically clustered with soil age at early successional stages and varied less at later successional stages. The dynamics of bacterial community phylogenetic structures were determined by the changes in the soil vegetation cover along succession. The dynamics of fungal community phylogenetic structures did not significantly correlate with soil age, soil properties or vegetation cover, and were mainly attributed to stochastic processes. Along succession, the common decrease in the bacterial co-occurrence complexity and in the average pairwise phylogenetic distances between co-occurring bacteria implied a decrease in potential bacterial cooperation. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic relatedness between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.
Collapse
Affiliation(s)
- Qiang Lin
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Francisco Dini-Andreote
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Travis B Meador
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Roey Angel
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Lenka Meszárošová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Praha 4, 14220, Czech Republic
| | - Petr Heděnec
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu, 21030, Malaysia
| | - Lingjuan Li
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Praha 4, 14220, Czech Republic
| | - Jan Frouz
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic.,Institute for environmental studies, Faculty of Science, Charles University, Benátská 2, Praha 2, 12800, Czech Republic
| |
Collapse
|
5
|
Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield. mSphere 2021; 6:e0013021. [PMID: 34378980 PMCID: PMC8386434 DOI: 10.1128/msphere.00130-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Understanding the effectiveness and potential mechanism of action of agricultural biological products under different soil profiles and crops will allow more precise product recommendations based on local conditions and will ultimately result in increased crop yield. This study aimed to use bulk soil and rhizosphere microbial composition and structure to evaluate the potential effect of a Bacillus amyloliquefaciens inoculant (strain QST713) on potatoes and to explore its relationship with crop yield. We implemented next-generation sequencing (NGS) and bioinformatics approaches to assess the bacterial and fungal biodiversity in 185 soil samples, distributed over four different time points—from planting to harvest—from three different geographical locations in the United States. In addition to location and sampling time (which includes the difference between bulk soil and rhizosphere) as the main variables defining the microbiome composition, the microbial inoculant applied as a treatment also had a small but significant effect in fungal communities and a marginally significant effect in bacterial communities. However, treatment preserved the native communities without causing a detectable long-lasting effect on the alpha- and beta-diversity patterns after harvest. Using information about the application of the microbial inoculant and considering microbiome composition and structure data, we were able to train a Random Forest model to estimate if a bulk soil or rhizosphere sample came from a low- or high-yield block with relatively high accuracy (84.6%), concluding that the structure of fungal communities gives us more information as an estimator of potato yield than the structure of bacterial communities. IMPORTANCE Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield. The data obtained, from in-field assays, allowed training a predictive model to estimate the yield of a certain block, identifying microbiome variables—especially those related to microbial community structure—even with a higher predictive power than the geographical location of the block (that is, the principal determinant of microbial beta-diversity). The methods described here can be replicated to fit new models in any other crop and to evaluate the effect of any agricultural input in the composition and structure of the soil microbiome.
Collapse
|
6
|
Bian X, Xiao S, Zhao Y, Xu Y, Yang H, Zhang L. Comparative analysis of rhizosphere soil physiochemical characteristics and microbial communities between rusty and healthy ginseng root. Sci Rep 2020; 10:15756. [PMID: 32978430 PMCID: PMC7519692 DOI: 10.1038/s41598-020-71024-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/06/2020] [Indexed: 01/09/2023] Open
Abstract
Ginseng rusty root (GRR) symptom is one of the primary diseases of ginseng. There has been a problem of ginseng rusty root, leading to a severe decline in the quality of ginseng. To clarify the relationship between root symptoms of ginseng rust and soil, the physical and chemical properties, enzyme activity, community structure and microbial diversity of GRR and healthy ginseng (HG) rhizosphere soil were analyzed and compared. The pH and redox potential (Eh) of GRR soil decreased, and the contents of total phosphorus (TP), available phosphorus (AP), and available potassium (AK) decreased. The activity of catalase and phosphatase and invertase was lower than that of HG groups. Besides, the microbial community of GRR rhizosphere soil changes much, and its abundance and diversity are significantly reduced. The community structure of GRR rhizosphere soil also shows apparent differences, and the samples of the HG group gathered together, and the samples of the GRR group were dispersed. In general, GRR was closely associated with decreases in soil pH and Eh; decreases in TP, AP, and AK; decreases in the activity of several enzymes. Additionally, it is strongly associated with an increase in pathogenic microorganisms such as Ilyonectria and a reduction of beneficial microorganisms such as Tremellomycetes Acidobacteria subgroup 6 and Gemmatimonadetes.
Collapse
Affiliation(s)
- Xingbo Bian
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Shengyuan Xiao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.,National and Local Joint Engineering Research Center for Ginseng Breeding and Development, Changchun, 130118, China
| | - Yan Zhao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Yonghua Xu
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - He Yang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Lianxue Zhang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
| |
Collapse
|