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Kohout P, Sudová R, Odriozola I, Kvasničková J, Petružálková M, Hadincová V, Krahulec F, Pecháčková S, Skálová H, Herben T. Accumulation of pathogens in soil microbiome can explain long-term fluctuations of legumes in a grassland community. THE NEW PHYTOLOGIST 2024. [PMID: 39101271 DOI: 10.1111/nph.20031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 07/18/2024] [Indexed: 08/06/2024]
Abstract
All plant populations fluctuate in time. Apart from the dynamics imposed by external forces such as climate, these fluctuations can be driven by endogenous processes taking place within the community. In this study, we aimed to identify potential role of soil-borne microbial communities in driving endogenous fluctuations of plant populations. We combined a unique, 35-yr long abundance data of 11 common plant species from a species-rich mountain meadow with development of their soil microbiome (pathogenic fungi, arbuscular mycorrhizal fungi and oomycetes) observed during 4 yr of experimental cultivation in monocultures. Plant species which abundance fluctuated highly in the field (particularly legumes) accumulated plant pathogens in their soil mycobiome. We also identified increasing proportion of mycoparasitic fungi under highly fluctuating legume species, which may indicate an adaptation of these species to mitigate the detrimental effects of pathogens. Our study documented that long-term fluctuations in the abundance of plant species in grassland communities can be explained by the accumulation of plant pathogens in plant-soil microbiome. By contrast, we found little evidence of the role of mutualists in plant population fluctuations. These findings offer new insights for understanding mechanisms driving both long-term vegetation dynamics and patterns of species coexistence and richness.
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Affiliation(s)
- Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Faculty of Science, Charles University in Prague, Albertov 6, 128 00, Prague, Czechia
| | - Radka Sudová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czechia
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Markéta Petružálková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Věroslava Hadincová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - František Krahulec
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Sylvie Pecháčková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Hana Skálová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Tomáš Herben
- Faculty of Science, Charles University in Prague, Albertov 6, 128 00, Prague, Czechia
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
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Giri A, Pant D, Chandra Srivastava V, Kumar M, Kumar A, Goswami M. Plant -microbe assisted emerging contaminants (ECs) removal and carbon cycling. BIORESOURCE TECHNOLOGY 2023:129395. [PMID: 37380038 DOI: 10.1016/j.biortech.2023.129395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/22/2023] [Accepted: 06/24/2023] [Indexed: 06/30/2023]
Abstract
Continuous increase in the level of atmospheric CO2 and environmental contaminates has aggravated various threats resulting from environmental pollution and climate change. Research into plant -microbe interaction has been a central concern of ecology for over the year. However, despite the clear contribution of plant -microbe to the global carbon cycle, the role of plant -microbe interaction in carbon pools, fluxes and emerging contaminants (ECs) removal are still a poorly understood. The use of plant and microbes in ECs removal and carbon cycling is an attractive strategy because microbes operate as biocatalysts to remove contaminants and plant roots offer a rich niche for their growth and carbon cycling. However, bio-mitigation of CO2 and removal of ECs is still under research phase because of the CO2 capture and fixation efficiency is too low for industrial purposes and cutting-edge removal methods have not been created for such emerging contaminants.
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Affiliation(s)
- Anand Giri
- School of Civil and Environmental Engineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175005, India
| | - Deepak Pant
- Departments of Environmental Sciences, Central University of Himachal Pradesh, Dharamshala 176215, India.
| | - Vimal Chandra Srivastava
- Department of Chemical Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttrakhand 247667, India
| | - Manoj Kumar
- Indian Oil Corporation R&D Centre, Sector 13, Faridabad, India
| | - Ashok Kumar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, India
| | - Meera Goswami
- Department of Zoology and Environmental Science, Gurukul Kangri (Deemed to Be University), Haridwar 249404, Uttarakhand, India
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Liang S, Wang W, Zeng X, Wu R, Chen W. Enhanced suppression of saprotrophs by ectomycorrhizal fungi under high level of nitrogen fertilization. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.974449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ectomycorrhizal fungi (EMF) are widespread in northern conifer forests. By competing with the free-living saprotrophic fungal and bacterial communities for limited soil nitrogen, EMF are expected to suppress litter decomposition and thus drive soil carbon accumulation. The EMF may also stimulate rhizosphere microbial growth through inputs of labile plant carbon, and subsequently contribute to the soil carbon pool via microbial necromass. Here we examined the relative strength of these two potential EMF effects in a northern conifer plantation of the Saihanba Forest, the largest plantation in China. The soil fungal and bacterial biomass, as well as their respiration, were quantified within the two types of soil cores that either allow or exclude the ingrowth of EMF. We also set up a nitrogen fertilization gradient (0, 5, 10, 15 g N m–2 y–1) in this plantation to quantify the influence of external inorganic nitrogen on the EMF effects. We found evidence that EMF inhibit the overall fungal and bacteria biomass, confirming the suppression of saprotrophs by EMF. In addition, high levels of external nitrogen fertilization (15 g N m–2 y–1) might further enhance the suppression by EMF. In contrast, the presence of EMF consistently increased soil microbial respiration across all nitrogen fertilization levels, indicating that the carbon allocated to EMF could have been largely consumed by microbial respiration and contributed minimally to the accumulation of microbial biomass. Our results also indicated that the suppression of saprotrophs by EMF may play a critical role in driving continuous soil carbon accumulation in this northern pine plantation under atmospheric nitrogen deposition.
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Liu Q, Zhang L, Wang L, Wu Q, Li K, Guo X. Autotoxin affects the rhizosphere microbial community structure by influencing the secretory characteristics of grapevine roots. Front Microbiol 2022; 13:953424. [PMID: 35958141 PMCID: PMC9360756 DOI: 10.3389/fmicb.2022.953424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Autotoxins secreted by roots into the soil can trigger rhizosphere microecological imbalances and affect root secretory properties resulting in conditions such as replanting disease. However, information on the effect of autotoxins on root secretion characteristics and regulation of the composition of rhizosphere microorganisms by altered root exudates is limited. In this study, autotoxin ρ-hydroxybenzoic acid (4-HBA) was added to the soil of potted grapevine seedlings, CO2 pulse-labeling, and DNA stable isotope probing were used to track the rhizosphere microbiome that assimilates root exudates. Bacterial and fungal microbiomes that assimilated plant-derived carbon were identified by high-throughput sequencing. Results showed that 4-HBA treatment altered bacterial and fungal communities in 13C-labeled organisms, with a lower abundance of beneficial bacteria (e.g., Gemmatimonas, Streptomyces, and Bacillus) and a higher abundance of potential pathogen fungi (e.g., Fusarium, Neocosmospora, Gibberella, and Fusicolla) by changing the composition of root exudates. The exogenous addition of upregulated compound mixtures of root exudates reduced the abundance of beneficial bacterial Bacillus and increased the abundance of potential pathogen fungi Gibberella. These results suggest that 4-HBA can alter root secretion properties and altered root exudates may enrich certain potential pathogens and reduce certain beneficial bacteria, thereby unbalancing the structure of the rhizosphere microbial community.
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Affiliation(s)
- Qianwen Liu
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Liheng Zhang
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Dalian Academy of Agricultural Sciences, Dalian, China
| | - Lu Wang
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Qingchun Wu
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Kun Li
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Kun Li,
| | - Xiuwu Guo
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Xiuwu Guo,
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Effects of Plant Fine Root Functional Traits and Soil Nutrients on the Diversity of Rhizosphere Microbial Communities in Tropical Cloud Forests in a Dry Season. FORESTS 2022. [DOI: 10.3390/f13030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The composition and diversity of rhizosphere microbial communities may be due to root–soil–microbial interactions. The fine root functional traits and rhizosphere soil environmental factors of 13 representative plants in the Bawangling tropical cloud forest of Hainan Island were measured, to assess the key factors driving plant rhizosphere microbial communities. Illumina MiSeq sequencing technology was used to sequence the v3-V4 region of the 16SrDNA gene of 13 plant rhizosphere soil bacteria and the ITS1 region of the fungal ITSrDNA gene. Results showed that there were 355 families, 638 genera, and 719 species of rhizosphere soil bacteria as well as 29 families, 31 genera, and 31 species of rhizosphere soil fungi in the tropical cloud forests. The fine root traits, such as root phosphorus content, the specific root length and specific root area, were significantly negatively correlated with the Faith-pd indices of the bacterial community but were not correlated with the diversity of fungi communities. The soil pH was significantly and positively correlated with the Chao1 index, OTUs, Faith-pd and Simpson indices of the bacteria and fungi communities. The soil available phosphorus content was significantly and negatively correlated with the bacteria Simpson and the fungus Faith-pd indices. ABT analysis showed that soil pH and soil available phosphorus were the most important environmental conditions contributing to the rhizosphere bacterial and fungi communities, respectively. Our findings demonstrate that the soil environments had more influence on rhizosphere soil microbial diversity than the fine root functional traits.
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Rupawalla Z, Robinson N, Schmidt S, Li S, Carruthers S, Buisset E, Roles J, Hankamer B, Wolf J. Algae biofertilisers promote sustainable food production and a circular nutrient economy - An integrated empirical-modelling study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148913. [PMID: 34328895 DOI: 10.1016/j.scitotenv.2021.148913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Agriculture has radically changed the global nitrogen (N) cycle and is heavily dependent on synthetic N-fertiliser. However, the N-use efficiency of synthetic fertilisers is often only 50% with N-losses from crop systems polluting the biosphere, hydrosphere and atmosphere. To address the large carbon and energy footprint of N-fertiliser synthesis and curb N-pollution, new technologies are required to deliver enhanced energy efficiency, decarbonisation and a circular nutrient economy. Algae fertilisers (AF) are an alternative to synthetic N-fertiliser (SF). Here microalgae were used as biofertiliser for spinach production. AF production was evaluated using life-cycle analyses. Over 4 weeks, AF released 63.5% of N as bioavailable ammonium and nitrate, and 25% of phosphorous (P) as phosphate to the growth substrate; SF released 100% N and 20% P. To maximise crop N-use and minimise N-leaching, we explored AF and SF dose-response-curves with spinach in glasshouse conditions. AF-grown spinach produced 36% less biomass than SF-grown plants due to AF's slower and linear N-release; SF exhibited 5-times higher N-leaching than AF. Optimised AF:SF blends yielded greater synchrony between N-release and crop-uptake, boosting crop yields and minimising N-loss. Additional benefits of AF included greener leaves, lower leaf nitrate concentration, and higher microbial diversity and water holding capacity of the growth substrate. An integrated techno-economic and life-cycle-analysis of scaled-up microalgae systems (+/- wastewater) normalised to the application dose showed that replacing the most effective SF-dose with AF lowered the annual carbon footprint of fertiliser production from 3.644 kg CO2 m-2 (C-producing) to -6.039 kg CO2 m-2 (C-assimilation). N-loss from growth substrate was lowered by 54%. Embodied energy for AF:SF blends could be reduced by 29% when cultivating microalgae on wastewater. Conclusions: (i) microalgae offer a sustainable alternative to synthetic N-fertiliser for spinach production and potentially other crop systems, (ii) microalgae biofertilisers support the circular-nutrient-economy and several UN-Sustainable-Development-Goals.
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Affiliation(s)
- Zeenat Rupawalla
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nicole Robinson
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susanne Schmidt
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sijie Li
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Selina Carruthers
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Elodie Buisset
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - John Roles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Juliane Wolf
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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Lofgren LA, Stajich JE. Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes. Curr Biol 2021; 31:R1312-R1325. [PMID: 34637742 PMCID: PMC8516061 DOI: 10.1016/j.cub.2021.06.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
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Persistence of plant-mediated microbial soil legacy effects in soil and inside roots. Nat Commun 2021; 12:5686. [PMID: 34584090 PMCID: PMC8478921 DOI: 10.1038/s41467-021-25971-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/25/2021] [Indexed: 01/04/2023] Open
Abstract
Plant-soil feedbacks are shaped by microbial legacies that plants leave in the soil. We tested the persistence of these legacies after subsequent colonization by the same or other plant species using 6 typical grassland plant species. Soil fungal legacies were detectable for months, but the current plant effect on fungi amplified in time. By contrast, in bacterial communities, legacies faded away rapidly and bacteria communities were influenced strongly by the current plant. However, both fungal and bacterial legacies were conserved inside the roots of the current plant species and their composition significantly correlated with plant growth. Hence, microbial soil legacies present at the time of plant establishment play a vital role in shaping plant growth even when these legacies have faded away in the soil due the growth of the current plant species. We conclude that soil microbiome legacies are reversible and versatile, but that they can create plant-soil feedbacks via altering the endophytic community acquired during early ontogeny. Legacies of past plant communities are likely to influence plant-soil interactions. Here, the authors report a reciprocal transplant experiment showing that soil microbial legacies shaped by previous plants persist for soil fungi and root endophytes but can be reversed by a next generation of plants for soil bacteria.
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Yuan MM, Kakouridis A, Starr E, Nguyen N, Shi S, Pett-Ridge J, Nuccio E, Zhou J, Firestone M. Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches. mBio 2021; 12:e03509-20. [PMID: 33879589 PMCID: PMC8092305 DOI: 10.1128/mbio.03509-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.IMPORTANCE Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.
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Affiliation(s)
- Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
| | - Anne Kakouridis
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
| | - Evan Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Nhu Nguyen
- Department of Tropical Plants and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Shengjing Shi
- AgResearch Ltd., Lincoln Science Centre, Christchurch, New Zealand
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Erin Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mary Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
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Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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Song K, Sun Y, Qin Q, Sun L, Zheng X, Terzaghi W, Lv W, Xue Y. The Effects of Earthworms on Fungal Diversity and Community Structure in Farmland Soil With Returned Straw. Front Microbiol 2020; 11:594265. [PMID: 33391211 PMCID: PMC7773728 DOI: 10.3389/fmicb.2020.594265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/16/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND To promote the decomposition of returned straw, reduce the incidence of soil-borne diseases caused by returned straw, and accelerate the conversion of straw carbon into soil carbon, we inoculated earthworms into fields with returned straw. The earthworms accelerated straw degradation and promoted carbon conversion. However, the impact of externally inoculated earthworms on the farmland soil ecosystem, especially the structure and the function of its microbial community, remains unclear. METHODS We analyzed the effects of straw return and earthworms on the diversity of fungal populations and the community structure of dominant fungal taxa in soil by quantifying fungal population size and community composition via PCR amplification of internal transcribed spacer genes and 18S rRNA gene sequencing. RESULTS The results showed that earthworm inoculation significantly accelerated the degradation of rice straw and promoted the conversion of straw carbon to soil carbon. Both fungal abundance and α-diversity (Sobs and Shannon indices) were higher in the plots with surface straw but without earthworms than in those inoculated with earthworms and in the CK. Principal component analysis indicated that straw return increased the diversity and the abundance of the fungal community, whereas earthworms inhibited this expansion of the fungal community caused by straw return. Interestingly, the overall differences in fungal community composition were smallest in plots with straw return, while the dominant fungal community features in plots inoculated with earthworms were closer to those of the CK. CONCLUSION Generally, straw return stimulated unclassified_K_fungi, Pseudeurotium, and Fusarium with strong cellulolytic ability. In contrast, the abundances of Stachybotrys, unclassified_c_Sordariomycetes, unclassified_f_Lasiosphaeriaceae, and Schizothecium were higher in the plots inoculated with earthworms and in the CK. Furthermore, evolutionary analysis showed that the evolution of soil fungal communities tended to diverge after straw return, and the evolutionary directions of fungal species in the plots inoculated with earthworms were similar to those in the CK.
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Affiliation(s)
- Ke Song
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yafei Sun
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qin Qin
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lijuan Sun
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xianqing Zheng
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, PA, United States
| | - Weiguang Lv
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yong Xue
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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