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Luo W, Wang Y, Cahill JF, Luan F, Zhong Y, Li Y, Li B, Chu C. Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest. Ecology 2024; 105:e4189. [PMID: 37877169 DOI: 10.1002/ecy.4189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/25/2023] [Indexed: 10/26/2023]
Abstract
Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains largely unknown. As β diversity can reflect the degree of community-wide biotic homogenization, such information is crucial for better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0-30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw ) and mean nearest neighbor distance (Dnn ) to quantify species ecological differences, we first tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.
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Affiliation(s)
- Wenqi Luo
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Youshi Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fucheng Luan
- Guangdong Chebaling National Nature Reserve, Shaoguan, China
| | - Yonglin Zhong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhi Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Buhang Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Huang Z, Su Y, Lin S, Wu G, Cheng H, Huang G. Elevational patterns of microbial species richness and evenness across climatic zones and taxonomic scales. Ecol Evol 2023; 13:e10594. [PMID: 37818244 PMCID: PMC10560872 DOI: 10.1002/ece3.10594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Understanding the elevational patterns of soil microbial diversity is crucial for microbial biogeography, yet the elevational patterns of diversity across different climatic zones, trophic levels, and taxonomic levels remain unclear. In this study, we investigated the elevational patterns of species richness, species evenness and the relationship between species richness and evenness (RRE) in the forest soil bacterial and fungal communities and individual phyla across three climatic zones (tropical, subtropical, and cold temperate). Our results revealed that soil bacterial richness (alpha diversity) decreased with elevation, while fungal richness exhibited a hump-shaped pattern in the tropical and cold-temperate forests. Elevational patterns of evenness in bacterial and fungal communities showed the hump-shaped pattern across climatic zones, except for bacterial evenness in the tropical forest. Both bacterial and fungal richness and evenness were positively correlated in the subtropical and cold-temperate forests, while negatively correlated for bacteria in the tropical forest. The richness and evenness of soil microorganisms across different regions were controlled by climatic and edaphic factors. Soil pH was the most important factor associated with the variations in bacterial richness and evenness, while mean annual temperature explained the major variations in fungal richness. Our results addressed that the varieties of elevational patterns of microbial diversity in climatic zones and taxonomic levels, further indicating that richness and evenness may respond differently to environmental gradients.
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Affiliation(s)
- Zhengyi Huang
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Yangui Su
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Sinuo Lin
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Guopeng Wu
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Hao Cheng
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
| | - Gang Huang
- School of Geographical Sciences, School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhouChina
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3
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López-Angulo J, Matesanz S, Illuminati A, Pescador DS, Sánchez AM, Pías B, Chacón-Labella J, de la Cruz M, Escudero A. Ecological drivers of fine-scale distribution of arbuscular mycorrhizal fungi in a semiarid Mediterranean scrubland. ANNALS OF BOTANY 2023; 131:1107-1119. [PMID: 36976581 PMCID: PMC10457037 DOI: 10.1093/aob/mcad050] [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: 01/24/2023] [Accepted: 03/27/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND AIMS Arbuscular mycorrhizal (AM) fungi enhance the uptake of water and minerals by the plant hosts, alleviating plant stress. Therefore, AM fungal-plant interactions are particularly important in drylands and other stressful ecosystems. We aimed to determine the combined and independent effects of above- and below-ground plant community attributes (i.e. diversity and composition), soil heterogeneity and spatial covariates on the spatial structure of the AM fungal communities in a semiarid Mediterranean scrubland. Furthermore, we evaluated how the phylogenetic relatedness of both plants and AM fungi shapes these symbiotic relationships. METHODS We characterized the composition and diversity of AM fungal and plant communities in a dry Mediterranean scrubland taxonomically and phylogenetically, using DNA metabarcoding and a spatially explicit sampling design at the plant neighbourhood scale. KEY RESULTS The above- and below-ground plant community attributes, soil physicochemical properties and spatial variables explained unique fractions of AM fungal diversity and composition. Mainly, variations in plant composition affected the AM fungal composition and diversity. Our results also showed that particular AM fungal taxa tended to be associated with closely related plant species, suggesting the existence of a phylogenetic signal. Although soil texture, fertility and pH affected AM fungal community assembly, spatial factors had a greater influence on AM fungal community composition and diversity than soil physicochemical properties. CONCLUSIONS Our results highlight that the more easily accessible above-ground vegetation is a reliable indicator of the linkages between plant roots and AM fungi. We also emphasize the importance of soil physicochemical properties in addition to below-ground plant information, while accounting for the phylogenetic relationships of both plants and fungi, because these factors improve our ability to predict the relationships between AM fungal and plant communities.
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Affiliation(s)
- Jesús López-Angulo
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
- Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich (ETH), 8092 Zurich, Switzerland
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Angela Illuminati
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - David S Pescador
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Ana M Sánchez
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Beatriz Pías
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | | | - Marcelino de la Cruz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
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Kong W, Qiu L, Ishii S, Jia X, Su F, Song Y, Hao M, Shao M, Wei X. Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems. ISME COMMUNICATIONS 2023; 3:81. [PMID: 37596350 PMCID: PMC10439144 DOI: 10.1038/s43705-023-00286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Soil microbiomes play important roles in supporting agricultural ecosystems. However, it is still not well-known how soil microbiomes and their functionality respond to fertilization in various cropping systems. Here we examined the effects of 36 years of phosphorus, nitrogen, and manure application on soil bacterial communities, functionality and crop productivity in three contrasting cropping systems (i.e., continuous leguminous alfalfa (AC), continuous winter wheat (WC), and grain-legume rotation of winter wheat + millet - pea - winter wheat (GLR)) in a highland region of China's Loess Plateau. We showed that long-term fertilization significantly affected soil bacterial communities and that the effects varied with cropping system. Compared with the unfertilized control, fertilization increased soil bacterial richness and diversity in the leguminous AC system, whereas it decreased those in the GLR system. Fertilization, particularly manure application, enlarged the differences in soil bacterial communities among cropping systems. Soil bacterial communities were mostly affected by the soil organic carbon and nitrogen contents in the WC and GLR systems, but by the soil available phosphorous content in the AC system. Crop productivity was closely associated with the abundance of fertilization-responsive taxa in the three cropping systems. Our study highlights that legume and non-legume cropping systems should be disentangled when assessing the responses of soil microbial communities to long-term fertilizer application.
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Affiliation(s)
- Weibo Kong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Liping Qiu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, 55108, USA
| | - Xiaoxu Jia
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fuyuan Su
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Yu Song
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Mingde Hao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Mingan Shao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, Shaanxi, China
| | - Xiaorong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China.
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, Shaanxi, China.
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Wang C, Sun D, Junaid M, Xie S, Xu G, Li X, Tang H, Zou J, Zhou A. Effects of tidal action on the stability of microbiota, antibiotic resistance genes, and microplastics in the Pearl River Estuary, Guangzhou, China. CHEMOSPHERE 2023; 327:138485. [PMID: 36966930 DOI: 10.1016/j.chemosphere.2023.138485] [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: 01/28/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
In this study, the 16S rRNA gene amplicon sequencing technique was used to explore the microbial diversity and differences in the water environment of the Pearl River Estuary in Nansha District with various land use types such as the aquaculture area, industrial area, tourist area, agricultural plantation, and residential area. At the same time, the quantity, type, abundance, and distribution of two types of emerging environmental pollutants, antibiotic resistance genes (ARGs) and microplastics (MPs), are explored in the water samples from different functional areas. The results show that the dominant phyla in the five functional regions are Proteobacteria, Actinobacteria and Bacteroidetes, and the dominant genera are Hydrogenophaga, Synechococcus, Limnohabitans and Polynucleobacter. A total of 248 ARG subtypes were detected in the five regions, belonging to nine classes of ARGs (Aminoglycoside, Beta_Lactamase, Chlor, MGEs, MLSB, Multidrug, Sul, Tet, Van). Blue and white were the dominant MP colors in the five regions; 0.5-2 mm was the dominant MP size, and cellulose, rayon, and polyester comprised the highest proportion of the plastic polymers. This study provides the basis for understanding the environmental microbial distribution in estuaries and the prevention of environmental health risks from ARGs and microplastics.
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Affiliation(s)
- Chong Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Di Sun
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Muhammad Junaid
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Shaolin Xie
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 16 510070, China.
| | - Xiang Li
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A5T1, Canada.
| | - Huijuan Tang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Jixing Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Aiguo Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A5T1, Canada.
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Xu H, Wei X, Cheng X. Fungal diversity dominates the response of multifunctionality to the conversion of pure plantations into two-aged mixed plantations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161384. [PMID: 36621475 DOI: 10.1016/j.scitotenv.2022.161384] [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: 09/20/2022] [Revised: 12/31/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
Plantation forests are essential in driving global biogeochemical cycling and mitigating climate change. Biodiversity and environmental factors can shape multiple forest ecosystem functions simultaneously (i.e., multifunctionality). However, their effect on multifunctionality when pure plantations are converted into two-aged plantations remains underexplored. Therefore, we assessed above- and below-ground biodiversity and environmental factors and 11 ecosystem functions in different plantation types in subtropical China. The two-aged mixed plantations exhibited higher multifunctionality than did a pure plantation, primarily due to soil fungal diversity and secondarily due to tree diversity, based on the coefficient of variation for tree diameter at breast height (CVD) and community-weighted specific leaf area (CWMSLA). Further analysis revealed saprotrophy as the key soil fungal trophic mode in maintaining multifunctionality. Moreover, structural equation modeling confirmed that soil environmental factors, namely the soil water content and pH, had no direct association with multifunctionality, but were indirectly related to multifunctionality via elevated CVD and CWMSLA, respectively. Our results indicate that the tree and soil fungal diversity, as well as soil environmental factors, resulting from the conversion of pure plantations to two-aged mixed plantations, can enhance multifunctionality, and provide a better comprehensive understanding of the driving mechanisms of multifunctionality, leading to the sustainable management of subtropical plantation forest ecosystems.
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Affiliation(s)
- Haidong Xu
- East China Coastal Forest Ecosystem Research Station, Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China; Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, Shandong 256603, China
| | - Xiaomeng Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Resource and Environment, Northwest A&F University, Yangling, China
| | - Xiangrong Cheng
- East China Coastal Forest Ecosystem Research Station, Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China.
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Chung YA. The temporal and spatial dimensions of plant-soil feedbacks. THE NEW PHYTOLOGIST 2023; 237:2012-2019. [PMID: 36604846 DOI: 10.1111/nph.18719] [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: 10/04/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Feedbacks between plants and soil microbes form a keystone to terrestrial community and ecosystem dynamics. Recent advances in dissecting the spatial and temporal dynamics of plant-soil feedbacks (PSFs) have challenged longstanding assumptions of spatially well-mixed microbial communities and exceedingly fast microbial assembly dynamics relative to plant lifespans. Instead, PSFs emerge from interactions that are inherently mismatched in spatial and temporal scales, and explicitly considering these spatial and temporal dynamics is crucial to understanding the contribution of PSFs to foundational ecological patterns. I propose a synthetic spatiotemporal framework for future research that pairs experimental and modeling approaches grounded in mechanism to improve predictability and generalizability of PSFs.
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Affiliation(s)
- Y Anny Chung
- Departments of Plant Biology and Plant Pathology, University of Georgia, Athens, GA, 30602, USA
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Benucci GMN, Beschoren da Costa P, Wang X, Bonito G. Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche. Environ Microbiol 2023; 25:352-366. [PMID: 36354216 PMCID: PMC10099798 DOI: 10.1111/1462-2920.16269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome.
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Affiliation(s)
- Gian Maria Niccolò Benucci
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, USA
| | - Pedro Beschoren da Costa
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Xinxin Wang
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Gregory Bonito
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
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He X, Hanusch M, Ruiz-Hernández V, Junker RR. Accuracy of mutual predictions of plant and microbial communities vary along a successional gradient in an alpine glacier forefield. FRONTIERS IN PLANT SCIENCE 2023; 13:1017847. [PMID: 36714711 PMCID: PMC9880484 DOI: 10.3389/fpls.2022.1017847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Receding glaciers create virtually uninhabited substrates waiting for initial colonization of bacteria, fungi and plants. These glacier forefields serve as an ideal ecosystem for studying transformations in community composition and diversity over time and the interactions between taxonomic groups in a dynamic landscape. In this study, we investigated the relationships between the composition and diversity of bacteria, fungi, and plant communities as well as environmental factors along a successional gradient. We used random forest analysis assessing how well the composition and diversity of taxonomic groups and environmental factors mutually predict each other. We did not identify a single best indicator for all taxonomic and environmental properties, but found specific predictors to be most accurate for each taxon and environmental factor. The accuracy of prediction varied considerably along the successional gradient, highlighting the dynamic environmental conditions along the successional gradient that may also affect biotic interactions across taxa. This was also reflected by the high accuracy of predictions of plot age by all taxa. Next to plot age, our results indicate a strong importance of pH and temperature in structuring microbial and plant community composition. In addition, taxonomic groups predicted the community composition of each other more accurately than environmental factors, which may either suggest that these groups similarly respond to other not measured environmental factors or that direct interactions between taxa shape the composition of their communities. In contrast, diversity of taxa was not well predicted, suggesting that community composition of one taxonomic group is not a strong driver of the diversity of another group. Our study provides insights into the successional development of multidiverse communities shaped by complex interactions between taxonomic groups and the environment.
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Affiliation(s)
- Xie He
- Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Maximilian Hanusch
- Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Victoria Ruiz-Hernández
- Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Robert R. Junker
- Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Salzburg, Austria
- Evolutionary Ecology of Plants, Department of Biology, Philipps University of Marburg, Marburg, Germany
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Ni B, Zhao W, Zuo X, You J, Li Y, Li J, Du Y, Chen X. Deyeuxia angustifolia Kom. encroachment changes soil physicochemical properties and microbial community in the alpine tundra under climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152615. [PMID: 34963583 DOI: 10.1016/j.scitotenv.2021.152615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/18/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Plant encroachment in alpine regions, caused by global changes and human activities, has been well documented. However, our knowledge of the effects of plant encroachment on belowground microbial communities is limited. Here, we investigated soil physicochemical properties and microbial community structures under the impact of plant encroachment along an elevation gradient in the alpine tundra of the Changbai Mountain, China. We found that plant encroachment had insignificant (P > 0.05) and inconsistent effects on the α-diversity (number of observed OTUs, Shannon, Chao1, Faith's PD) of soil microbial communities. Plant encroachment indirectly influenced soil microbial community structures by altering soil physicochemical properties, which differed between elevations and plant types (P < 0.05). In all, 40 bacterial indicator taxa and 57 fungal indicator taxa significantly shifted in response to plant encroachment, some of which were involved in soil biogeochemical cycle. Overall, our results documented the impacts of plant encroachment on soil microbial diversity and community composition, and provided a scientific basis for predicting future changes in alpine ecosystem structure and function and its subsequent feedbacks to global change.
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Affiliation(s)
- Biao Ni
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, Jilin University, Changchun 130012, China; School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wei Zhao
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, Jilin University, Changchun 130012, China; School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xianghua Zuo
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, Jilin University, Changchun 130012, China; School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jian You
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, Jilin University, Changchun 130012, China; School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yulong Li
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, Jilin University, Changchun 130012, China; School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jiangnan Li
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, Jilin University, Changchun 130012, China; School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yingda Du
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xia Chen
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, Jilin University, Changchun 130012, China; School of Life Sciences, Jilin University, Changchun 130012, China.
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11
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Lu P, Jiang K, Hao YQ, Chu WY, Xu YD, Yang JY, Chen JL, Zeng GH, Gu ZH, Zhao HX. Profiles of Bacillus spp. Isolated from the Rhizosphere of Suaeda glauca and Their Potential to Promote Plant Growth and Suppress Fungal Phytopathogens. J Microbiol Biotechnol 2021; 31:1231-1240. [PMID: 34261851 PMCID: PMC9706026 DOI: 10.4014/jmb.2105.05010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022]
Abstract
Members of the genus Bacillus are known to play an important role in promoting plant growth and protecting plants against phytopathogenic microorganisms. In this study, 21 isolates of Bacillus spp. were obtained from the root micro-ecosystem of Suaeda glauca. Analysis of the 16S rRNA genes indicated that the isolates belong to the species Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus subtilis, Bacillus pumilus, Bacillus aryabhattai and Brevibacterium frigoritolerans. One of the interesting findings of this study is that the four strains B1, B5, B16 and B21 are dominant in rhizosphere soil. Based on gyrA, gyrB, and rpoB gene analyses, B1, B5, and B21 were identified as B. amyloliquefaciens and B16 was identified as B. velezensis. Estimation of antifungal activity showed that the isolate B1 had a significant inhibitory effect on Fusarium verticillioides, B5 and B16 on Colletotrichum capsici (syd.) Butl, and B21 on Rhizoctonia cerealis van der Hoeven. The four strains grew well in medium with 1-10% NaCl, a pH value of 5-8, and promoted the growth of Arabidopsis thaliana. Our results indicate that these strains may be promising agents for the biocontrol and promotion of plant growth and further study of the relevant bacteria will provide a useful reference for the development of microbial resources.
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Affiliation(s)
- Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Ya-Qiao Hao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China,Experimental Teaching Center, College of Life Science, Shenyang Normal University, Shenyang 110034, P.R. China
| | - Wan-Ying Chu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Yu-Dong Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Jia-Yao Yang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Jia-Le Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Guo-Hong Zeng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Zhou-Hang Gu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China,
Z.H. Gu E-mail:
| | - Hong-Xin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China,Corresponding authors H.X. Zhao E-mail:
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12
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Iversen CM, McCormack ML. Filling gaps in our understanding of belowground plant traits across the world: an introduction to a Virtual Issue. THE NEW PHYTOLOGIST 2021; 231:2097-2103. [PMID: 34405907 DOI: 10.1111/nph.17326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - M Luke McCormack
- Center for Tree Science, The Morton Arboretum, Liesle, IL, 60515, USA
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13
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Teng J, Tian J, Barnard R, Yu G, Kuzyakov Y, Zhou J. Aboveground and Belowground Plant Traits Explain Latitudinal Patterns in Topsoil Fungal Communities From Tropical to Cold Temperate Forests. Front Microbiol 2021; 12:633751. [PMID: 34177822 PMCID: PMC8222577 DOI: 10.3389/fmicb.2021.633751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
Soil fungi predominate the forest topsoil microbial biomass and participate in biogeochemical cycling as decomposers, symbionts, and pathogens. They are intimately associated with plants but their interactions with aboveground and belowground plant traits are unclear. Here, we evaluated soil fungal communities and their relationships with leaf and root traits in nine forest ecosystems ranging from tropical to cold temperate along a 3,700-km transect in eastern China. Basidiomycota was the most abundant phylum, followed by Ascomycota, Zygomycota, Glomeromycota, and Chytridiomycota. There was no latitudinal trend in total, saprotrophic, and pathotrophic fungal richness. However, ectomycorrhizal fungal abundance and richness increased with latitude significantly and reached maxima in temperate forests. Saprotrophic and pathotrophic fungi were most abundant in tropical and subtropical forests and their abundance decreased with latitude. Spatial and climatic factors, soil properties, and plant traits collectively explained 45% of the variance in soil fungal richness. Specific root length and root biomass had the greatest direct effects on total fungal richness. Specific root length was the key determinant of saprotrophic and pathotrophic fungal richness while root phosphorus content was the main biotic factor determining ectomycorrhizal fungal richness. In contrast, spatial and climatic features, soil properties, total leaf nitrogen and phosphorus, specific root length, and root biomass collectively explained >60% of the variance in fungal community composition. Soil fungal richness and composition are strongly controlled by both aboveground and belowground plant traits. The findings of this study provide new evidence that plant traits predict soil fungal diversity distribution at the continental scale.
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Affiliation(s)
- Jialing Teng
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Romain Barnard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche Comté, Dijon, France
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany.,Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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14
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Stefan L, Hartmann M, Engbersen N, Six J, Schöb C. Positive Effects of Crop Diversity on Productivity Driven by Changes in Soil Microbial Composition. Front Microbiol 2021; 12:660749. [PMID: 33936016 PMCID: PMC8081861 DOI: 10.3389/fmicb.2021.660749] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Intensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant-microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and activity, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (three times larger) or soil moisture (three times larger). Furthermore, these processes were context-dependent: in Spain, where resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes and emphasizing the context-dependence of crop-microbe relationships.
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Affiliation(s)
- Laura Stefan
- Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
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15
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Teng J, Tian J, Yu G, Kuzyakov Y. Soil properties and root traits jointly shape fine-scale spatial patterns of bacterial community and metabolic functions within a Korean pine forest. PeerJ 2021; 9:e10902. [PMID: 33680578 PMCID: PMC7919533 DOI: 10.7717/peerj.10902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/13/2021] [Indexed: 11/20/2022] Open
Abstract
Spatial heterogeneity of soil bacterial community depends on scales. The fine-scale spatial heterogeneity of bacterial community composition and functions remains unknown. We analyzed the main driving factors of fine-scale spatial patterns of soil bacterial community composition and carbon metabolic functions across a 30 m × 40 m plot within a Korean pine forest by combining Illumina 16S rRNA sequencing with Biolog Ecoplates based on 53 soil samples. Clear spatial patterns in bacterial community composition and metabolic functions were observed in the forest soil. The bacterial community composition and metabolic functions both showed distance-decay of similarity within a distance of meters. Structural equation model analysis revealed that environmental variables and geographic distance together explained 37.9% and 63.1% of community and metabolic functions, respectively. Among all environmental factors, soil organic carbon (SOC) and root biomass emerged as the most important drivers of the bacterial community structure. In contrast, soil pH explained the largest variance in metabolic functions. Root biomass explained the second-largest variance in soil bacterial community composition, but root traits made no difference in metabolic functions variance. These results allow us to better understand the mechanisms controlling belowground diversity and plant-microbe interactions in forest ecosystems.
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Affiliation(s)
- Jialing Teng
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Tian
- College of Resources and Environmental Sciences; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany.,Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
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16
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Maldonado S, Rodríguez A, Ávila B, Morales P, González MP, Araya Angel JPA, Olalde V, Bravo J, Jana C, Sierra C, Stoll A. Enhanced Crop Productivity and Sustainability by Using Native Phosphate Solubilizing Rhizobacteria in the Agriculture of Arid Zones. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.607355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The importance of phosphate solubilizing rhizobacteria (PSB) has been well-document as an option for enhancing sustainable agriculture. As a particular group of plant growth promoting rhizobacteria (PGPR), PSB play an important role in the soil phosphorus cycle, increasing the bioavailability for growth and plant development. This study analyses the plant growth promoting effects of 5 strains (BN0009, BN0013, BN0015, BN0024, and BN0035) out of 180 isolated from Jarava frigida (Phil.) F.Rojas (Poaceae), a native grass from the Andean Atacama desert from North of Chile. The five bacterial isolated (BN strains) were identified as non-pathogenic Erwinia sp. and show a high phosphate solubilization capacity for Ca(PO4) ranging from 608.9 to 781.4 mg/L. Strains IAA production varies between 23.5 and 35.9 mg/L, siderophores, phosphatase (alkaline and acid) production was also observed, but none of the five isolated presented antagonism against plant pathogens Botrytis sp. and Sclerotinia sp. All isolates enhanced seed germination in Lactuca sativa and Solanum lycopersicum (excepting BN009). Additionally, all strains stimulated the early root elongation and seedling development in lettuce and tomato. Pot experiments displayed that BN0015, BN0024, and BN0035 significantly promote plant growth regarding root and leaf area, root and leaf weight, as well as leaf number compared with non-treated plants. In a field experiment with lettuce and two fertilization treatments (50 and 100% of the recommended crop fertilization), BN0024 application improved crop productivity compared to respective control. P content in plants with bacterial inoculations increased significantly compared to control in either fertilization treatment, suggesting an improved nutrient uptake. Also, lettuce with 50% fertilization and inoculation with BN0024 equate productivity with the control 100% fertilization. Finally, we discuss these results in the context of applicability to enhance the agroecosystem productivity in arid and semiarid zones.
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