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Daraz U, Erhunmwunse AS, Dubeux JCB, Mackowiak C, Liao HL, Wang XB. Soil fungal community structure and function response to rhizoma perennial peanut cultivars. BMC PLANT BIOLOGY 2024; 24:582. [PMID: 38898415 PMCID: PMC11186081 DOI: 10.1186/s12870-024-05209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars. RESULTS This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars. CONCLUSIONS Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.
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Affiliation(s)
- Umar Daraz
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | | | - José C B Dubeux
- North Florida Research and Education Center, University of Florida, Marianna, FL, USA
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Xiao-Bo Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China.
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Zhou X, Hu Y, Li H, Sheng J, Cheng J, Zhao T, Zhang Y. Phosphorus addition increases stability and complexity of co-occurrence network of soil microbes in an artificial Leymus chinensis grassland. Front Microbiol 2024; 15:1289022. [PMID: 38601937 PMCID: PMC11004269 DOI: 10.3389/fmicb.2024.1289022] [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: 09/05/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction Understanding the response of cross-domain co-occurrence networks of soil microorganisms to phosphorus stability and the resulting impacts is critical in ecosystems, but the underlying mechanism is unclear in artificial grassland ecosystems. Methods In this study, the effects of four phosphorus concentrations, P0 (0 kg P ha-1), P1 (15.3 kg P ha-1), P2 (30.6 kg P ha-1), and P3 (45.9 kg P ha-1), on the cross-domain co-occurrence network of bacteria and fungi were investigated in an artificial Leymus chinensis grassland in an arid region. Results and discussion The results of the present study showed that phosphorus addition significantly altered the stem number, biomass and plant height of the Leymus chinensis but had no significant effect on the soil bacterial or fungal alpha (ACE) diversity or beta diversity. The phosphorus treatments all increased the cross-domain co-occurrence network edge, node, proportion of positively correlated edges, edge density, average degree, proximity to centrality, and robustness and increased the complexity and stability of the bacterial-fungal cross-domain co-occurrence network after 3 years of continuous phosphorus addition. Among them, fungi (Ascomycota, Basidiomycota, Mortierellomycota and Glomeromycota) play important roles as keystone species in the co-occurrence network, and they are significantly associated with soil AN, AK and EC. Finally, the growth of Leymus chinensis was mainly due to the influence of the soil phosphorus content and AN. This study revealed the factors affecting the growth of Leymus chinense in artificial grasslands in arid areas and provided a theoretical basis for the construction of artificial grasslands.
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Affiliation(s)
- Xiaoguo Zhou
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Yutong Hu
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Huijun Li
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiandong Sheng
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Junhui Cheng
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Tingting Zhao
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Yuanmei Zhang
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
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Deshoux M, Sadet-Bourgeteau S, Gentil S, Prévost-Bouré NC. Effects of biochar on soil microbial communities: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166079. [PMID: 37553053 DOI: 10.1016/j.scitotenv.2023.166079] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use.
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Affiliation(s)
- Maëlle Deshoux
- INRAE UMR Agroécologie, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France; Groupe Bordet, Froidvent, F-21290 Leuglay, France.
| | - Sophie Sadet-Bourgeteau
- INRAE UMR Agroécologie, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France
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Rassbach J, Hilsberg N, Haensch VG, Dörner S, Gressler J, Sonnabend R, Semm C, Voigt K, Hertweck C, Gressler M. Non-canonical two-step biosynthesis of anti-oomycete indole alkaloids in Kickxellales. Fungal Biol Biotechnol 2023; 10:19. [PMID: 37670394 PMCID: PMC10478498 DOI: 10.1186/s40694-023-00166-x] [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: 05/30/2023] [Accepted: 08/06/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Fungi are prolific producers of bioactive small molecules of pharmaceutical or agricultural interest. The secondary metabolism of higher fungi (Dikarya) has been well-investigated which led to > 39,000 described compounds. However, natural product researchers scarcely drew attention to early-diverging fungi (Mucoro- and Zoopagomycota) as they are considered to rarely produce secondary metabolites. Indeed, only 15 compounds have as yet been isolated from the entire phylum of the Zoopagomycota. RESULTS Here, we showcase eight species of the order Kickxellales (phylum Zoopagomycota) as potent producers of the indole-3-acetic acid (IAA)-derived compounds lindolins A and B. The compounds are produced both under laboratory conditions and in the natural soil habitat suggesting a specialized ecological function. Indeed, lindolin A is a selective agent against plant-pathogenic oomycetes such as Phytophthora sp. Lindolin biosynthesis was reconstituted in vitro and relies on the activity of two enzymes of dissimilar evolutionary origin: Whilst the IAA-CoA ligase LinA has evolved from fungal 4-coumaryl-CoA synthetases, the subsequently acting IAA-CoA:anthranilate N-indole-3-acetyltransferase LinB is a unique enzyme across all kingdoms of life. CONCLUSIONS This is the first report on bioactive secondary metabolites in the subphylum Kickxellomycotina and the first evidence for a non-clustered, two-step biosynthetic route of secondary metabolites in early-diverging fungi. Thus, the generally accepted "gene cluster hypothesis" for natural products needs to be reconsidered for early diverging fungi.
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Affiliation(s)
- Johannes Rassbach
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Nathalie Hilsberg
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Veit G Haensch
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Sebastian Dörner
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Julia Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Robin Sonnabend
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Caroline Semm
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Kerstin Voigt
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Markus Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany.
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Shi A, Hu Y, Zhang X, Zhou D, Xu J, Rensing C, Zhang L, Xing S, Ni W, Yang W. Biochar loaded with bacteria enhanced Cd/Zn phytoextraction by facilitating plant growth and shaping rhizospheric microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121559. [PMID: 37023890 DOI: 10.1016/j.envpol.2023.121559] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/22/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Biochar and metal-tolerant bacteria have been widely used in the remediation of heavy metal contaminated soil. However, the synergistic effect of biochar-functional microbes on phytoextraction by hyperaccumulators remains unclear. In this study, the heavy metal-tolerant strain Burkholderia contaminans ZCC was selected and loaded on biochar to produce biochar-resistant bacterial material (BM), and the effects of BM on Cd/Zn phytoextraction by Sedum alfredii Hance and rhizospheric microbial community were explored. The results showed that, BM application significantly enhanced the Cd and Zn accumulation of S. alfredii by 230.13% and 381.27%, respectively. Meanwhile, BM alleviated metal toxicity of S. alfredii by reducing oxidative damage and increasing chlorophyll and antioxidant enzyme activity. High-throughput sequencing revealed that BM significantly improved soil bacterial and fungal diversity, and increased the abundance of genera with plant growth promoting and metal solubilizing functions such as Gemmatimonas, Dyella and Pseudarthrobacter. Co-occurrence network analysis showed that BM significantly increased the complexity of the rhizospheric bacterial and fungal network. Structural equation model analysis revealed that soil chemistry property, enzyme activity and microbial diversity contributed directly or indirectly to Cd and Zn extraction by S. alfredii. Overall, our results suggested that biochar- B. contaminans ZCC was able to enhance the growth and Cd/Zn accumulation by S. alfredii. This study enhanced our understanding on the hyperaccumulator-biochar-functional microbe interactions, and provided a feasible strategy for promoting the phytoextraction efficiency of heavy metal contaminated soils.
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Affiliation(s)
- An Shi
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying Hu
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiao Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Zhou
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Junlong Xu
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liming Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shihe Xing
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wuzhong Ni
- College of Environment and Resources, Zhejiang University, Hangzhou, 310058, China
| | - Wenhao Yang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Brozel VS. Special Issue "Microbial Interactions in Soil": Editorial. Microorganisms 2023; 11:1260. [PMID: 37317234 DOI: 10.3390/microorganisms11051260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Soils are home to a wide variety of microorganisms [...].
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Affiliation(s)
- Volker S Brozel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa
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Zhang K, Zentella R, Burkey KO, Liao HL, Tisdale RH. Microbial community dynamics responding to nutrient allocation associated with soybean cultivar 'Jake' ozone adaptation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161008. [PMID: 36549524 DOI: 10.1016/j.scitotenv.2022.161008] [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: 09/27/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Tropospheric ozone (O3), a major air pollutant, leads to significant global yield loss in soybean [Glycine max (L.) Merr.]. Soybean cultivar 'Jake' shows O3 resilient traits in above-ground organs, but the root system remains sensitive to elevated O3 (eO3). Changing carbon (C) and nitrogen (N) resource composition during eO3 stress suggests that eO3 presumably alters belowground soil microbial communities and their driven nutrient transformation. Yet, the responses of belowground microbes to eO3 and their feedback on nutrient cycling in 'Jake' are unknown. In this study, we holistically investigated soil microbial communities associated with C and N dynamics and bacterial-fungal inter-kingdom networks in the rhizosphere and bulk soil at different developmental stages of 'Jake' grown under sub-ambient O3 [charcoal-filtered (CF) air, 12 h mean: 20 ppb] or eO3 (12 h mean: 87 ppb). The results demonstrated eO3 significantly decreased fungal diversity and complexity of microbial networks at different 'Jake' developmental stages, whereas bacterial diversity was more tolerant to eO3 in both bulk soil and rhizosphere. In the bulk soil, no O3-responsive microbial biomarkers were found to be associated with C and N content, implying eO3 may stimulate niche-based processes during 'Jake' growth. In contrast, this study identified O3-responsive microbial biomarkers that may contribute to the N acquisition (Chloroflexales) and C dynamics (Caldilineales, Thermomicrobiales, and Hypocreales) in the rhizosphere, which may support the O3 resilience of the 'Jake' cultivar. However, further investigation is required to confirm their specific contributions by determining changes in microbial gene expression. Overall, these findings conduce to an expanding knowledge base that O3 induces temporal and spatial changes in the effects of microbial and nutrient networks in the O3-tolerant agriculture ecosystems.
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Affiliation(s)
- Kaile Zhang
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Rodolfo Zentella
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA
| | - Kent O Burkey
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Ripley H Tisdale
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA.
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Jinger D, Kaushal R, Kumar R, Paramesh V, Verma A, Shukla M, Chavan SB, Kakade V, Dobhal S, Uthappa AR, Roy T, Singhal V, Madegowda M, Kumar D, Khatri P, Dinesh D, Singh G, Singh AK, Nath AJ, Joshi N, Joshi E, Kumawat S. Degraded land rehabilitation through agroforestry in India: Achievements, current understanding, and future prospectives. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1088796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Land degradation is one of the most important factors responsible for the alarming situation of food security, human health, and socioeconomic development in the country. Currently, 120.7 M ha of land in the country is affected by land degradation, out of which 85.7 M ha of land is affected by soil erosion caused by water and wind. Moreover, physical, chemical, and biological degradation are the major forms of land degradation in the country. Deforestation or tree cover loss (2.07 M ha) from 2001 to 2021, intensive rainfall (>7.5 mm ha−1), uncontrolled grazing (5.65 M ha), indiscriminate use of fertilizers (32 MT year−1), and shifting cultivation (7.6 M ha) are other major factors that further aggravate the process of land degradation. In order to alleviate the problem of land degradation, numerous agroforestry technologies have been developed after years of research in different agroclimatic zones of the country. The major agroforestry systems observed in the country are agri-horticulture, silvipasture, and agri-silviculture. This review indicates the potential of agroforestry in enhancing carbon sequestration (1.80 Mg C ha−1 year−1 in the Western Himalayan region to 3.50 Mg C ha−1 year−1 in the island regions) and reduced soil loss and runoff by 94% and 78%, respectively, in Northeast India. This can be concluded that the adoption of the agroforestry system is imperative for the rehabilitation of degraded lands and also found to have enough potential to address the issues of food, environmental, and livelihood security. This review’s findings will benefit researchers, land managers, and decision-makers in understanding the role of agroforestry in combating land degradation to enhance ecosystem service in India and planning suitable policies for eradicating the problem effectively.
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Shang Z, Wang Y, An M, Chen X, Kulyar MFEA, Tan Z, Liu S, Li K. The successional trajectory of bacterial and fungal communities in soil are fabricated by yaks’ excrement contamination in plateau, China. Front Microbiol 2022; 13:1016852. [DOI: 10.3389/fmicb.2022.1016852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
The soil microbiome is crucial in determining contemporary realistic conditions for future terrestrial ecological and evolutionary development. However, the precise mechanism between the fecal deposition in livestock grazing and changes in the soil microbiome remains unknown. This is the first in-depth study of bacterial and fungal taxonomic changes of excrement contaminated soils in the plateau (>3,500 m). This suggests the functional shifts towards a harmful-dominated soil microbiome. According to our findings, excrement contamination significantly reduced the soil bacterial and fungal diversity and richness. Furthermore, a continuous decrease in the relative abundance of microorganisms was associated with nutrient cycling, soil pollution purification, and root-soil stability with the increasing degree of excrement contamination. In comparison, soil pathogens were found to have the opposite trend in the scenario, further deteriorating normal soil function and system resilience. Such colonization and succession of the microbiome might provide an important potential theoretical instruction for microbiome-based soil health protection measures in the plateau of China.
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Tan S, Narayanan M, Thu Huong DT, Ito N, Unpaprom Y, Pugazhendhi A, Lan Chi NT, Liu J. A perspective on the interaction between biochar and soil microbes: A way to regain soil eminence. ENVIRONMENTAL RESEARCH 2022; 214:113832. [PMID: 35810814 DOI: 10.1016/j.envres.2022.113832] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 06/15/2023]
Abstract
Soil ecosystem imparts a fundamental role in the growth and survival of the living creatures. The interaction between living and non-living constituents of the environment is important for the regulation of life in the ecosystem. Biochar is a carbon rich product present in the soil that is responsible for various applications in diversified fields. In this review, we focused on the collaboration between the soil, biochar and microbial community present in the soil and consequences of it in the ecosystem. Herein, it primarily discusses on the different approaches of the production and characterization of biochar. Furthermore, this review also discusses about the optimistic interaction of biochar with soil microbes and their role in plant growth. Eventually, it reveals the various physio-chemical properties of biochar, including its specific surface area, porous nature, ion exchange capacity, and pH, which aid in the modification of the soil environment. Furthermore, it elaborately discloses the impact of the biochar addition in the soil focusing mainly on its interaction with microbial communities such as bacteria and fungi. The physicochemical properties of biochar significantly interact with microbes and improve the beneficial microbes growth and increase soil nutrients, which resulting reasonable plant growth. The main focus remains on the role of biochar-soil microbiota in remediation of pollutants, soil amendment and inhibition of pathogenicity among plants by promoting resistance potential. It highlights the fact that adding biochar to soil modulates the soil microbial community by increasing soil fertility, paving the way for its use in farming, and pollutant removal.
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Affiliation(s)
- Shimeng Tan
- College of Biological Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China; College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Mathiyazhagan Narayanan
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science, Chennai, 602 105, Tamil Nadu, India
| | - Dinh Thi Thu Huong
- School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Viet Nam
| | - Nobutaka Ito
- School of Renewable Energy, Maejo University, Chiang Mai, Thailand
| | - Yuwalee Unpaprom
- Program in Biotechnology, Faculty of Science, Maejo University, Chiangmai, Thailand
| | - Arivalagan Pugazhendhi
- Emerging Materials for Energy and Environmental Applications Research Group, School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Viet Nam.
| | - Nguyen Thuy Lan Chi
- School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Viet Nam.
| | - Junang Liu
- College of Biological Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China; College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China.
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Zhang M, Liu Y, Wei Q, Gu X, Liu L, Gou J. Biochar application ameliorated the nutrient content and fungal community structure in different yellow soil depths in the karst area of Southwest China. FRONTIERS IN PLANT SCIENCE 2022; 13:1020832. [PMID: 36352867 PMCID: PMC9638009 DOI: 10.3389/fpls.2022.1020832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
The influence of biochar on the change of nutrient content and fungal community structure is still not clear, especially in different yellow soil depths in karst areas. A soil column leaching simulation experiment was conducted to investigate the influence of biochar on soil content, enzymatic activity, and fungal community diversity and structural composition. Three biochar amounts were studied, namely, 0%(NB, no biochar), 1.0%(LB, low-application-rate biochar), and 4.0% (HB, high-application-rate biochar). The results showed that biochar increased the pH value and the contents of soil organic matter (SOM), total nitrogen (TN), available phosphorus (AP), and available potassium (AK) but reduced the microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). Furthermore, this effect was enhanced with increasing biochar amount. Biochar was conducive to improving the nutrient availability in topsoil (0-20 cm), especially TN, AK, and MBN. Meanwhile, biochar affected the enzymatic activity, especially the sucrase activity. Biochar affected the diversity and structure of the fungal community, of which HB treatment had the most obvious effect. Among these treatments, Aspergillus, unclassified_Chaetomiaceae, Mortierella, Spizellomyces, Penicillium, Fusarium, and unclassified_Chromista fungal genera were the highest. Moreover, biochar inhibited the growth of harmful pathogens and increased the abundance of beneficial fungi in soil, and the effect was enhanced with increasing biochar amount and soil depth. Redundancy analysis (RDA) showed that AK was an important factor in yellow soil, although the main environmental factors affecting the fungal community structure were different in different soil depths. Overall, biochar had a positive effect on improving the land productivity and micro-ecological environment of yellow soil in the karst area.
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Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China. Microorganisms 2022; 10:microorganisms10081507. [PMID: 35893564 PMCID: PMC9330434 DOI: 10.3390/microorganisms10081507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.
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Suppressive Effect of Soil Microbiomes Associated with Tropical Fruit Trees on Meloidogyne enterolobii. Microorganisms 2022; 10:microorganisms10050894. [PMID: 35630339 PMCID: PMC9144879 DOI: 10.3390/microorganisms10050894] [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] [Received: 03/18/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/16/2022] Open
Abstract
Plant-parasitic nematodes are one of the main biotic factors limiting agricultural production worldwide, with root-knot nematodes (Meloidogyne spp.) being the most damaging group. This study was conducted to evaluate the efficacy of soil microbiomes, associated with various subtropical fruit trees, on the management of a Meloidogyne enterolobii population. Of 14 soil microbiomes tested for nematode suppression, 9 samples in the first experiment and 10 samples in the repeat experiment had significantly (p ≤ 0.05) lower numbers of eggs and J2 compared to the untreated control. The highest nematode suppression was recorded for SA12 extracted from a papaya orchard with a 38% reduction in the nematode population density. In addition, the presence of some bacteria (Bacillus aryabhattai, B. funiculus and B. simplex) and fungi (Metarhizium marquandii, Acremonium sp. and Mortierella sp.) was correlated to a higher suppression potential in some samples. Substantial variations were observed for the diversity of bacterial and fungal isolates among the samples collected from various crop hosts and regions. This suggests that the nematode suppression potential of different soil microbiomes highly depends on the abundance and diversity of fungal and bacterial strains present in the soil. The study confirmed that among all variables, soil dryness, pH, Fe, Zn, organic matter, altitude, and crop cultivar strongly influenced the soil microbial composition.
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Su Y, Zi H, Wei X, Hu B, Deng X, Chen Y, Jiang Y. Application of Manure Rather Than Plant-Origin Organic Fertilizers Alters the Fungal Community in Continuous Cropping Tobacco Soil. Front Microbiol 2022; 13:818956. [PMID: 35516429 PMCID: PMC9063659 DOI: 10.3389/fmicb.2022.818956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Continuous cropping leads to the development of serious fungal diseases in tobacco plants and depleted yield of tobacco (Nicotiana tabacum), which can be mitigated by organic fertilization. Yet, we know little about how organic fertilizers affect the fungal community of continuous cropping tobacco soil. In this study, we investigated the soil fungal community after 11 years of tobacco planting with chemical fertilization (CF) or chemical fertilization combined with organic fertilizers obtained from plant or animal origin, including oil cake (CFO), straw (CFS), and farmyard fertilizer (CFM). The predominant phyla of Ascomycota (70%) and Mortierellomycota (15%) were identified in all the treatments. A significantly higher proportion of Pyrenochaetopsis and lower relative abundance of Sordariomycetes were observed in the CFM group compared to the controls. Compared to CF and non-fertilized control (CK), CFO and CFS led to higher species richness (P < 0.05), while CFM led to a less uniform fungal community, indicated by lower Shannon and higher Simpson diversity indices (P < 0.05). Pearson's correlation and redundancy analysis suggested that fertilizations primarily influenced the fungal community by altering the soil nutrient conditions, among which soil organic carbon and total phosphorus significantly correlated with the fungal diversity and community composition (P < 0.05). Notably, FUNGuild annotation suggested that while other treatments showed no significant effect on the fungal trophic modes, CFM strongly increased the abundance of saprotrophic fungi by more than 30% (P < 0.05), thus preventing the prevalence of potential pathotypes and symbionts. The results suggest that the type of organic fertilizers is essential to the long-term effects of organic application on the fungal community, and the animal-origin manure seems to be a better choice than plant-origin materials in continuous cropping tobacco fields.
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Affiliation(s)
- Yan Su
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Haiyun Zi
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xiaomeng Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Binbin Hu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Xiaopeng Deng
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Yi Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
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Influence of Intraspecific Competition Stress on Soil Fungal Diversity and Composition in Relation to Tree Growth and Soil Fertility in Sub-Tropical Soils under Chinese Fir Monoculture. SUSTAINABILITY 2021. [DOI: 10.3390/su131910688] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Soil microorganisms provide valuable ecosystem services, such as nutrient cycling, soil remediation, and biotic and abiotic stress resistance. There is increasing interest in exploring total belowground biodiversity across ecological scales to understand better how different ecological aspects, such as stand density, soil properties, soil depth, and plant growth parameters, influence belowground communities. In various environments, microbial components of belowground communities, such as soil fungi, respond differently to soil features; however, little is known about their response to standing density and vertical soil profiles in a Chinese fir monoculture plantation. This research examined the assemblage of soil fungal communities in different density stands (high, intermediate, and low) and soil depth profiles (0–20 cm and 20–40 cm). This research also looked into the relationship between soil fungi and tree canopy characteristics (mean tilt angle of the leaf (MTA), leaf area index (LAI), and canopy openness index (DIFN)), and general growth parameters, such as diameter, height, and biomass. The results showed that low-density stand soil had higher fungal alpha diversity than intermediate- and high-density stand soils. Ascomycota, Basidiomycota, Mucromycota, and Mortierellomycota were the most common phyla of the soil fungal communities, in that order. Saitozyma, Penicillium, Umbelopsis, and Talaromyces were the most abundant fungal genera. Stand density composition was the dominant factor in changing fungal community structure compared to soil properties and soil depth profiles. The most significant soil elements in soil fungal community alterations were macronutrients. In addition, the canopy openness index and fungal community structure have a positive association in the low-density stand. Soil biota is a nutrient cycling driver that can promote better plant growth in forest ecosystems by supporting nutrient cycling. Hence, this research will be critical in understanding soil fungal dynamics, improving stand growth and productivity, and improving soil quality in intensively managed Chinese fir plantations.
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Muneer MA, Huang X, Hou W, Zhang Y, Cai Y, Munir MZ, Wu L, Zheng C. Response of Fungal Diversity, Community Composition, and Functions to Nutrients Management in Red Soil. J Fungi (Basel) 2021; 7:jof7070554. [PMID: 34356933 PMCID: PMC8307627 DOI: 10.3390/jof7070554] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/23/2022] Open
Abstract
Soil fungi play a critical role in plant performance and soil nutrient cycling. However, the understanding of soil fungal community composition and functions in response to different nutrients management practices in red soils remains largely unknown. Here, we investigated the responses of soil fungal communities and functions under conventional farmer fertilization practice (FFP) and different nutrient management practices, i.e., optimization of NPK fertilizer (O) with soil conditioner (O + C), with lime and mushroom residue (O + L + M), and with lime and magnesium fertilizer (O + L + Mg). Illumina high-throughput sequencing was used for fungal identification, while the functional groups were inferred with FUNGuild. Nutrient management practices significantly raised the soil pH to 4.79–5.31 compared with FFP (3.69), and soil pH had the most significant effect (0.989 ***) on fungal communities. Predominant phyla, including Ascomycota, Basidiomycota, and Mortierellomycota were identified in all treatments and accounted for 94% of all fungal communities. The alpha diversity indices significantly increased under nutrients management practices compared with FFP. Co-occurrence network analysis revealed the keystone fungal species in the red soil, i.e., Ascomycota (54.04%), Basidiomycota (7.58%), Rozellomycota (4.55%), and Chytridiomycota (4.04%). FUNGuild showed that the relative abundance of arbuscular mycorrhizal fungi and ectomycorrhizal fungi was higher, while pathogenic fungi were lower under nutrient management practices compared with FFP. Our findings have important implications for the understanding of improvement of acidic soils that could significantly improve the soil fungal diversity and functioning in acidic soils.
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Affiliation(s)
- Muhammad Atif Muneer
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Xiaoman Huang
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Wei Hou
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Yadong Zhang
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Yuanyang Cai
- College of Plant Science, Jilin University, Changchun 130062, China;
| | - Muhammad Zeeshan Munir
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China;
| | - Liangquan Wu
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
| | - Chaoyuan Zheng
- College of Resources and Environment/International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.A.M.); (X.H.); (W.H.); (Y.Z.); (L.W.)
- Correspondence: ; Tel.: +86-177-5020-8499
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