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Dai W, Liu Y, Yao D, Wang N, Ye X, Cui Z, Wang H. Phylogenetic diversity of stochasticity-dominated predatory myxobacterial community drives multi-nutrient cycling in typical farmland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:161680. [PMID: 36682558 DOI: 10.1016/j.scitotenv.2023.161680] [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: 11/13/2022] [Revised: 01/03/2023] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
Predatory myxobacteria are keystone taxa in the soil microbial food web that potentially regulate soil microbial community structure and ecosystem functions. However, little is known about the community assembly processes of myxobacteria in typical farmland soils over large geographic scales, in addition to their relationship with soil multi-nutrient cycling. Here, we used high-throughput sequencing techniques and phylogenetic null modeling analysis to investigate the distribution patterns and assembly processes of myxobacteria communities, in addition to interactions between myxobacteria communities and soil multi-nutrient cycling. Anaeromyxobacter (28.5 %) and Haliangium (19.6 %) were the dominant myxobacteria genera in all samples, and myxobacteria community similarities exhibited distinct distance-decay relationships. Stochastic processes (~77.8 %) were the dominant ecological processes driving the assembly of predatory myxobacteria communities over large geographical scales and under three fertilization regimes. Myxobacteria community structure was influenced by geographic factors (location and climate), soil factors (soil pH, soil organic carbon, total nitrogen, and total potassium), and fertilization, with myxobacteria community assembly being more sensitive to geographic factors. Organic-inorganic combined fertilization (NPKM) increased the proportions of deterministic processes in myxobacteria community assembly. Moreover, myxobacteria community assembly and diversity were closely associated with soil multi-nutrient cycling. Hence, myxobacteria phylogenetic α-diversity represented by NTI index is a potential bioindicators for soil multi-nutrient cycling. Overall, our findings comprehensively reveal the mechanisms of assembly of myxobacteria communities in soils over large geographic scales, and provide a theoretical basis for further research on the role of predatory bacteria on soil nutrient cycling in agro-ecosystems.
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Affiliation(s)
- Wei Dai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Yang Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Dandan Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Ning Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China.
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Skariah S, Abdul-Majid S, Hay AG, Acharya A, Kano N, Al-Ishaq RK, de Figueiredo P, Han A, Guzman A, Dargham SR, Sameer S, Kim GE, Khan S, Pillai P, Sultan AA. Soil Properties Correlate with Microbial Community Structure in Qatari Arid Soils. Microbiol Spectr 2023; 11:e0346222. [PMID: 36847511 PMCID: PMC10100838 DOI: 10.1128/spectrum.03462-22] [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: 08/30/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
This is the first detailed characterization of the microbiota and chemistry of different arid habitats from the State of Qatar. Analysis of bacterial 16S rRNA gene sequences showed that in aggregate, the dominant microbial phyla were Actinobacteria (32.3%), Proteobacteria (24.8%), Firmicutes (20.7%), Bacteroidetes (6.3%), and Chloroflexi (3.6%), though individual soils varied widely in the relative abundances of these and other phyla. Alpha diversity measured using feature richness (operational taxonomic units [OTUs]), Shannon's entropy, and Faith's phylogenetic diversity (PD) varied significantly between habitats (P = 0.016, P = 0.016, and P = 0.015, respectively). Sand, clay, and silt were significantly correlated with microbial diversity. Highly significant negative correlations were also seen at the class level between both classes Actinobacteria and Thermoleophilia (phylum Actinobacteria) and total sodium (R = -0.82 and P = 0.001 and R = -0.86, P = 0.000, respectively) and slowly available sodium (R = -0.81 and P = 0.001 and R = -0.8 and P = 0.002, respectively). Additionally, class Actinobacteria also showed significant negative correlation with sodium/calcium ratio (R = -0.81 and P = 0.001). More work is needed to understand if there is a causal relationship between these soil chemical parameters and the relative abundances of these bacteria. IMPORTANCE Soil microbes perform a multitude of essential biological functions, including organic matter decomposition, nutrient cycling, and soil structure preservation. Qatar is one of the most hostile and fragile arid environments on earth and is expected to face a disproportionate impact of climate change in the coming years. Thus, it is critical to establish a baseline understanding of microbial community composition and to assess how soil edaphic factors correlate with microbial community composition in this region. Although some previous studies have quantified culturable microbes in specific Qatari habitats, this approach has serious limitations, as in environmental samples, approximately only 0.5% of cells are culturable. Hence, this method vastly underestimates natural diversity within these habitats. Our study is the first to systematically characterize the chemistry and total microbiota associated with different habitats present in the State of Qatar.
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Affiliation(s)
- Sini Skariah
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Sara Abdul-Majid
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Anthony G. Hay
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Anushree Acharya
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Noora Kano
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Raghad Khalid Al-Ishaq
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, Texas, USA
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, Texas, USA
| | - Adrian Guzman
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, Texas, USA
| | - Soha Roger Dargham
- Biostatistics, Epidemiology, & Biomathematics Research Core, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Saad Sameer
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Gi Eun Kim
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Sabiha Khan
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Priyamvada Pillai
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Ali A. Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
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Xu S, Yuan Y, Song P, Cui M, Zhao R, Song X, Cao M, Zhang Y, Yang J. The spatial patterns of diversity and their relationships with environments in rhizosphere microorganisms and host plants differ along elevational gradients. Front Microbiol 2023; 14:1079113. [PMID: 36910236 PMCID: PMC9996296 DOI: 10.3389/fmicb.2023.1079113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Identifying spatial patterns of biodiversity along elevational gradients provides a unified framework for understanding these patterns and predicting ecological responses to climate change. Moreover, microorganisms and plants are closely interconnected (e.g., via the rhizosphere) and thus may share spatial patterns of diversity and show similar relationships with environments. Methods This study compared diversity patterns and relationships with environments in host plants and rhizosphere microorganisms (including various functional groups) along elevational gradients across three climatic zones. Results We found that above-and belowground diversity decreased monotonically or showed a hump-shaped or U-shaped pattern along elevation gradients. However, the diversity patterns of plants, bacteria, and fungi varied depending on the taxon and climatic zone. Temperature and humidity strongly contribute to above-and belowground diversity patterns and community composition along elevational gradients. Nonetheless, soil factors might be important regulators of diversity patterns and the community composition of plants and microorganisms along these gradients. Structural equation modeling revealed that environmental factors had a stronger direct effect on rhizosphere microbial diversity than host plant diversity. Discussion In sum, spatial patterns of diversity and their relationships with environments in rhizosphere microorganisms and their host plants differed at the regional scale. Different functional groups (e.g., pathogen, mycorrhiza and nitrifier) of soil microorganisms may have divergent elevational patterns and environmental responses. These data improve our understanding of elevational diversity patterns, and provide new insights into the conservation of biodiversity and ecosystem management, especially under climate change.
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Affiliation(s)
- Shijia Xu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.,School of Ethnic Medicine, Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education of China, Yunnan Minzu University, Kunming, Yunnan, China
| | - Yan Yuan
- School of Ethnic Medicine, Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education of China, Yunnan Minzu University, Kunming, Yunnan, China
| | - Pengfei Song
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.,School of Ethnic Medicine, Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education of China, Yunnan Minzu University, Kunming, Yunnan, China
| | - Mufeng Cui
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.,School of Ethnic Medicine, Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education of China, Yunnan Minzu University, Kunming, Yunnan, China
| | - Rensheng Zhao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.,School of Ethnic Medicine, Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education of China, Yunnan Minzu University, Kunming, Yunnan, China
| | - Xiaoyang Song
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Min Cao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Yazhou Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Jie Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
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Zhu R, Liu C, Xu YD, He W, Liu J, Chen J, An Y, Shi S. Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks. Front Microbiol 2022; 13:968551. [PMID: 36160210 PMCID: PMC9493311 DOI: 10.3389/fmicb.2022.968551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Fertilization is the main strategy to accelerate vegetation restoration and improve the rhizosphere microbial community in the northeast China. However, the responses of rhizosphere microbial community structure, specific microbial community and symbiotic pattern to manure fertilization in grassland (alfalfa only) are not well clear. In this study, the variation of bacterial community structures in R_Manure (extracted liquid of fermented cow manure), E_Manure (extracted residue of fermented cow manure), F_Manure (full fermented cow manure), and Control (without fermented cow manure) collected from the rhizosphere microbial community of alfalfa were analyzed by the application of an Illumina HiSeq high-throughput sequencing technique. A total of 62,862 microbial operational taxonomic units (OTUs) were detected and derived from 21 phyla of known bacteria. The dominant bacteria in the rhizosphere include Proteobacteria (70.20%), Acidobacteria (1.24%), Actinobacteria (2.11%), Bacteroidetes (6.15%), Firmicutes (4.21%), and Chlorofexi (2.13%) accounting for 86% of the dominant phyla in all treatments. At the genus level, the dominant genus include NB1-j, Lysobacter, Alphaproteobacteria, Subgroup_6, Actinomarinales, Saccharimonadales, Aneurinibacillus, MO-CFX2, SBR1031, Caldilineaceae, and so on with the average relative abundance (RA) of 1.76%, 1.52%, 1.30%, 1.24%, 1.61%, 2.39%, 1.36%, 1.42%, 1.27%, and 1.03%, respectively. Bacterial diversities and community structures were significantly differentiated by different treatments of fertilization. The results of community structure composition showed that R_Manure treatment significantly increased the population abundance of Firmicutes, Chlorofexi, and Patescibacteria by 34.32%, 6.85%, and 2.70%, and decreased the population abundance of Proteobacteria and Actinobacteria by 16.83% and 1.04%, respectively. In addition, it showed that all treatments significantly resulted in an increase or decrease at the genus level. R_Manure had the higher richness and diversity of the bacterial community, with the greatest topology attributes of the co-occurrence networks. Through the analysis of the molecular ecological network (MENA), the co-occurrence networks had a shorter average path distance and diameter in R_Manure than in others, implying more stability to environmental changes. Redundancy analysis (RDA) showed that the ratio of carbon and nitrogen (C/N) was the main factor affecting rhizosphere microbial community composition while driving distinct rhizosphere bacterial community and its co-occurrence networks. The R_Manure associated with more C/N had relatively complex microbial co-occurrence network with a large number of nodes and edges, while the microbial network of others associated with less C/N had fewer taxa with loose mutual interactions. These results suggested that organic fertilizer with high C/N can regulate the rhizosphere microorganism, while high C/N can determine bacterial community structures, specific bacterial taxa, and their relationships with the nodule size of alfalfa. These significant changes can be used to evaluate soil fertility and fertilizer management in the artificial grassland system, while the potential biological indicators of the rhizosphere microbial community will play an important role in future eco-agriculture.
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Affiliation(s)
- Ruifen Zhu
- Pratacultural College, Gansu Agricultural University, Lanzhou, China
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
- Pratacultural Institute Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chang Liu
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Yuan Dong Xu
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Wei He
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Jielin Liu
- Pratacultural Institute Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jishan Chen
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Yajun An
- Gansu Yasheng Agricultural Research Institute Co., Ltd., Lanzhou, China
| | - Shangli Shi
- Pratacultural College, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Shangli Shi
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Liu H, Cheng J, Jin H, Xu Z, Yang X, Min D, Xu X, Shao X, Lu D, Qin B. Characterization of Rhizosphere and Endophytic Microbial Communities Associated with Stipa purpurea and Their Correlation with Soil Environmental Factors. PLANTS 2022; 11:plants11030363. [PMID: 35161345 PMCID: PMC8839079 DOI: 10.3390/plants11030363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022]
Abstract
This study was to explore the diversity of rhizosphere and endophytic microbial communities and the correlation with soil environmental factors of Stipa purpurea on the Qinghai-Tibetan Plateau. The bacterial phylum of Proteobacteria, Firmicutes and Bacteroidota, and the fungal phylum of Ascomycota, Basidiomycota and Zygomycota were dominant in microbial communities of S. purpurea in all three sampling sites. Multiple comparison analysis showed that there were significant differences in the composition of microbial communities in the roots, leaves and rhizosphere soil. Whether it is fungi or bacteria, the OTU abundance of rhizosphere soils was higher than that of leaves and roots at the same location, while the difference among locations was not obvious. Moreover, RDA analysis showed that Zygomycota, Cercozoa, Glomeromycota, Chytridiomycota and Rozellomycota possessed strongly positive associations with altitude, dehydrogenase, alkaline phosphatase, neutral phosphatase, available kalium and available phosphate, while Ascomycota was strongly negatively associated. Changes in ammonium nitrate, alkaline phosphatase, polyphenol oxidase, total phosphorus, and altitude had a significant impact on the bacterial communities in different habitats and altitudes. Taken together, we provide evidence that S. purpurea has abundant microbial communities in the alpine grassland of the Qinghai-Tibetan Plateau, whose composition and diversity are affected by various soil environmental factors.
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Affiliation(s)
- Haoyue Liu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinan Cheng
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Hui Jin
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
- Yantai Zhongke Research Institute of Advanced Materials and Green Chemical Engineering, Yantai 264006, China
- Correspondence: (H.J.); (B.Q.)
| | - Zhongxiang Xu
- Animal, Plant & Food Inspection Center of Nanjing Customs, Nanjing 210000, China;
| | - Xiaoyan Yang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
| | - Deng Min
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
| | - Xinxin Xu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
| | - Xiangfeng Shao
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China;
| | - Dengxue Lu
- Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China;
| | - Bo Qin
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources/Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; (H.L.); (X.Y.); (D.M.); (X.X.)
- Correspondence: (H.J.); (B.Q.)
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Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives. Microbiol Res 2021; 254:126901. [PMID: 34700186 DOI: 10.1016/j.micres.2021.126901] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022]
Abstract
In the light of intensification of cropping practices and changing climatic conditions, nourishing a growing global population requires optimizing environmental sustainability and reducing ecosystem impacts of food production. The use of microbiological systems to ameliorate the agricultural production in a sustainable and eco-friendly way is widespread accepted as a future key-technology. However, the multitude of interaction possibilities between the numerous beneficial microbes and plants in their habitat calls for systematic analysis and management of the rhizospheric microbiome. This review exploits present and future strategies for rhizospheric microbiome management with the aim to generate a comprehensive understanding of the known tools and techniques. Significant information on the structure and dynamics of rhizospheric microbiota of isolated microbial communities is now available. These microbial communities have beneficial effects including increased plant growth, essential nutrient acquisition, pathogens tolerance, and increased abiotic as well as biotic stress tolerance such as drought, temperature, salinity and antagonistic activities against the phyto-pathogens. A better and comprehensive understanding of the various effects and microbial interactions can be gained by application of molecular approaches as extraction of DNA/RNA and other biochemical markers to analyze microbial soil diversity. Novel techniques like interactome network analysis and split-ubiquitin system framework will enable to gain more insight into communication and interactions between the proteins from microbes and plants. The aim of the analysis tasks leads to the novel approach of Rhizosphere microbiome engineering. The capability of forming the rhizospheric microbiome in a defined way will allow combining several microbes (e.g. bacteria and fungi) for a given environment (soil type and climatic zone) in order to exert beneficial influences on specific plants. This integration will require a large-scale effort among academic researchers, industry researchers and farmers to understand and manage interactions of plant-microbiomes within modern farming systems, and is clearly a multi-domain approach and can be mastered only jointly by microbiology, mathematics and information technology. These innovations will open up a new avenue for designing and implementing intensive farming microbiome management approaches to maximize resource productivity and stress tolerance of agro-ecosystems, which in return will create value to the increasing worldwide population, for both food production and consumption.
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Cai L, Guo Z, Zhang J, Gai Z, Liu J, Meng Q, Liu X. No tillage and residue mulching method on bacterial community diversity regulation in a black soil region of Northeastern China. PLoS One 2021; 16:e0256970. [PMID: 34506513 PMCID: PMC8432829 DOI: 10.1371/journal.pone.0256970] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
Soil microorganisms are important components of agricultural ecosystems; they are important in agricultural soil nutrient cycle and are easily affected by soil tillage. The response of soil microbial community to tillage is very complex, and the effect of the no tillage and residue mulching method on soil microbial diversity remains unclear. In 2019, the soil was collected from an experimental field after 10 years of continuous cultivation in the black soil area of the Sanjiang Plain in Northeastern China. In this study, the diversity and composition of the soil bacterial community and their relationship with soil properties were explored via high-throughput sequencing under no tillage with four residue mulching treatments. No tillage with 60% residue mulching (NTR3) significantly increased the alpha diversity of the rhizosphere soil bacteria and changed the composition of the bacterial community-consistent with changes in soil physicochemical properties. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla in the sample soil. Soil physicochemical properties explained 80.6% of the changes in soil diversity and composition, of which soil organic carbon, soil pH, and soil temperature were the principal contributors. Our results suggest that no tillage and residue mulching is conducive to increasing soil organic carbon and soil nutrient content, which is a beneficial conservation tillage measure for black soil protection in Sanjiang Plain of Northeast China. The no tillage with residue mulching, especially 60% residue mulching, alters soil bacterial community and highlights the importance of soil physicochemical properties in shaping the diversity and composition of the soil bacterial community. Our findings contribute to a broad understanding of the effects of no tillage and residue mulching on bacterial community differences and provide a scientific basis for the optimization of no tillage measures and sustainable utilization of the black soil of the Sanjiang Plain in Northeastern China.
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Affiliation(s)
- Lijun Cai
- Department of Land and Environment, Shenyang Agricultural University, Shenyang, Liaoning, China
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, Heilongjiang, China
| | - Zhenhua Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, Heilongjiang, China
| | - Jingtao Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, Heilongjiang, China
| | - Zhijia Gai
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, Heilongjiang, China
| | - Jingqi Liu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, Heilongjiang, China
| | - Qingying Meng
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, Heilongjiang, China
| | - Xiaohu Liu
- Department of Land and Environment, Shenyang Agricultural University, Shenyang, Liaoning, China
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Looby CI, Martin PH. Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world. FEMS Microbiol Ecol 2021; 96:5891232. [PMID: 32780840 DOI: 10.1093/femsec/fiaa122] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/15/2020] [Indexed: 12/27/2022] Open
Abstract
Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.
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Affiliation(s)
- Caitlin I Looby
- Department of Ecology, Evolution and Behavior, University of Minnesota, Twin Cities, Saint Paul, MN 55108, USA
| | - Patrick H Martin
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
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Islam W, Noman A, Naveed H, Huang Z, Chen HYH. Role of environmental factors in shaping the soil microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:41225-41247. [PMID: 32829437 DOI: 10.1007/s11356-020-10471-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/10/2020] [Indexed: 05/09/2023]
Abstract
The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.
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Affiliation(s)
- Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Hassan Naveed
- College of Life Science, Leshan Normal University, Leshan, 614004, Sichuan, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
| | - Han Y H Chen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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10
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Lee SA, Kim JM, Kim Y, Joa JH, Kang SS, Ahn JH, Kim M, Song J, Weon HY. Different types of agricultural land use drive distinct soil bacterial communities. Sci Rep 2020; 10:17418. [PMID: 33060673 PMCID: PMC7562711 DOI: 10.1038/s41598-020-74193-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/20/2020] [Indexed: 01/11/2023] Open
Abstract
Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.
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Affiliation(s)
- Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Jeong Myeong Kim
- Water Supply and Sewerage Research Division, National Institute of Environmental Research, Incheon, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Jae-Ho Joa
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Seong-Soo Kang
- Soil and Fertilization Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea.
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11
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Microbial Diversity of Some Sabkha and Desert Sites in Saudi Arabia. Saudi J Biol Sci 2020; 27:2778-2789. [PMID: 32994737 PMCID: PMC7499299 DOI: 10.1016/j.sjbs.2020.06.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Several studies isolated fungal and bacterial species from extreme environments, such as Sabkha and hot deserts, as their natural habitat, some of which are of medicinal importance. Current research aimed investigating the microbial (fungi and bacteria) diversity and abundance in Sabkha and desert areas in Saudi Arabia. Soil samples from nine different geographical areas (Al-Aushazia lake, AlQasab, AlKasar, Tabuk, Al-Kharj, Al-Madina, Jubail, Taif and Abqaiq) were collected and cultured for microbial isolation. Isolated fungi and bacteria were identified by molecular techniques (PCR and sequencing). Based on 18S rDNA sequencing, 203 fungal species belonging to 33 genera were identified. The most common fungal genera were Fusarium, Alternaria, Chaetomium, Aspergillus Cochliobolus and Pencillium, while the most common species were Chaetomium globosum and Fusarium oxysporum. By 16S rDNA sequencing 22 bacterial species belonging to only two genera, Bacillus and Lactobacillus, were identified. The most commonly isolated bacterial species were Bacillus subtilis and Lactobacillus murinus. Some fungal species were confined to specific locations, such as Actinomyces elegans, Fusarium proliferatum, Gymnoascus reesii and Myzostoma spp. that were only isolated from Al-Aushazia soil. AlQasab soil had the highest microbial diversity among other areas with abundances of 23.5% and 4.4% of total fungi, and bacteria, respectively. Findings of this study show a higher degree of fungal diversity than that of bacteria in all studied areas. Further studies needed to investigate the connection between some isolated species and their habitat ecology, as well as to identify those of medicinal importance.
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12
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Analysis of the soil microbial communities in Pinus tabulaeformis Carr. and Bupleurum chinense plantations of the Xiaolongshan Mountain region, Gansu Province, China. ECOL INFORM 2019. [DOI: 10.1016/j.ecoinf.2019.100981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Adamczyk M, Hagedorn F, Wipf S, Donhauser J, Vittoz P, Rixen C, Frossard A, Theurillat JP, Frey B. The Soil Microbiome of GLORIA Mountain Summits in the Swiss Alps. Front Microbiol 2019; 10:1080. [PMID: 31156590 PMCID: PMC6529532 DOI: 10.3389/fmicb.2019.01080] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/29/2019] [Indexed: 01/03/2023] Open
Abstract
While vegetation has intensively been surveyed on mountain summits, limited knowledge exists about the diversity and community structure of soil biota. Here, we study how climatic variables, vegetation, parent material, soil properties, and slope aspect affect the soil microbiome on 10 GLORIA (Global Observation Research Initiative in Alpine environments) mountain summits ranging from the lower alpine to the nival zone in Switzerland. At these summits we sampled soils from all four aspects and examined how the bacterial and fungal communities vary by using Illumina MiSeq sequencing. We found that mountain summit soils contain highly diverse microbial communities with a total of 10,406 bacterial and 6,291 fungal taxa. Bacterial α-diversity increased with increasing soil pH and decreased with increasing elevation, whereas fungal α-diversity did not change significantly. Soil pH was the strongest predictor for microbial β-diversity. Bacterial and fungal community structures exhibited a significant positive relationship with plant communities, indicating that summits with a more distinct plant composition also revealed more distinct microbial communities. The influence of elevation was stronger than aspect on the soil microbiome. Several microbial taxa responded to elevation and soil pH. Chloroflexi and Mucoromycota were significantly more abundant on summits at higher elevations, whereas the relative abundance of Basidiomycota and Agaricomycetes decreased with elevation. Most bacterial OTUs belonging to the phylum Acidobacteria were indicators for siliceous parent material and several OTUs belonging to the phylum Planctomycetes were associated with calcareous soils. The trends for fungi were less clear. Indicator OTUs belonging to the genera Mortierella and Naganishia showed a mixed response to parent material, demonstrating their ubiquitous and opportunistic behaviour in soils. Overall, fungal communities responded weakly to abiotic and biotic factors. In contrast, bacterial communities were strongly influenced by environmental changes suggesting they will be strongly affected by future climate change and associated temperature increase and an upward migration of vegetation. Our results provide the first insights into the soil microbiome of mountain summits in the European Alps that are shaped as a result of highly variable local environmental conditions and may help to predict responses of the soil biota to global climate change.
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Affiliation(s)
- Magdalene Adamczyk
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Frank Hagedorn
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Sonja Wipf
- Community Ecology, WSL Institute for Snow and Avalanche Research SLF, Davos, Switzerland
| | - Johanna Donhauser
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pascal Vittoz
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Christian Rixen
- Community Ecology, WSL Institute for Snow and Avalanche Research SLF, Davos, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jean-Paul Theurillat
- Fondation J.-M. Aubert, Champex-Lac, Switzerland.,Department of Botany and Plant Biology, University of Geneva, Chambésy, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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14
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Profiling the Bacterial Diversity in a Typical Karst Tiankeng of China. Biomolecules 2019; 9:biom9050187. [PMID: 31091762 PMCID: PMC6572312 DOI: 10.3390/biom9050187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 01/31/2023] Open
Abstract
While karst tiankengs have a higher capacity to act as safe havens for biodiversity in changing climates, little is known about their soil microorganisms. To fill this gap, we investigate the distribution and driving factors of the bacterial community in karst tiankeng systems. There is a significant difference in the soil characteristics between the inside and the outside of a karst tiankeng. At the karst tiankeng considered in this study, the bacterial composition, in terms of the operational taxonomic unit (OTU), was found to be significantly different in different soil samples, taken from diverse sampling sites within the collapsed doline or the external area, and showed a high habitat heterogeneity. The dominant phylum abundances vary with the sampling sites and have their own indicator taxa from phylum to genus. Unlike the primary controlling factors of plant diversity, the microclimate (soil moisture and temperature), soil pH, and slope dominated the distribution of the bacterial community in karst tiankeng systems. Our results firstly showed the distribution characteristics of bacterial communities and then revealed the importance of microhabitats in predicting the microbial distribution in karst tiankeng systems.
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15
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Han D, Wang N, Sun X, Hu Y, Feng F. Biogeographical distribution of bacterial communities in Changbai Mountain, Northeast China. Microbiologyopen 2018; 7:e00529. [PMID: 29446229 PMCID: PMC5911996 DOI: 10.1002/mbo3.529] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/11/2017] [Accepted: 07/18/2017] [Indexed: 11/10/2022] Open
Abstract
The broad-leaved and Korean pine mixed forest in Changbai Mountain, China is an important component of boreal forest; the area is sensitive to global climate change. To understand spatial distribution patterns of soil bacterial community along elevation, we analyzed the soil bacterial community diversity and composition along an elevational gradient of 699-1177 m in a primitive Korean pine forest in Changbai Mountain using the high-throughput sequencing. In total, 149,519 optimized sequences were obtained. Bacterial Shannon index increased along elevation from 699 m to 937 m and started to decrease at the elevation of 1,044 m, showing a humpback curve along elevation. Evenness (ACE index) and richness (Chao index) of the soil bacterial community both decreased with elevation (the highest values of 770 and 762 at 699 m and the lowest values of 548 and 539 at 1,177 m, respectively), all the indices are significantly different between elevations. Bacterial composition at phylum and genus levels had some differences between elevations, but the dominant bacterial populations were generally consistent. Beta-diversity analysis showed a distance-decay pattern of bacterial community similarity at different samples. Soil physical and chemical properties explained 70.78% of the variation in bacterial community structure (soil pH explained 19.95%), and elevational distance only explained 8.42%. In conclusion, the contemporary environmental disturbances are the critical factors in maintaining the bacterial spatial distribution compared with historical contingencies.
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Affiliation(s)
- Dongxue Han
- Northeast Forestry University, Harbin, China.,Key Lab of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Ning Wang
- Northeast Forestry University, Harbin, China
| | - Xue Sun
- Northeast Forestry University, Harbin, China
| | - Yanbo Hu
- Northeast Forestry University, Harbin, China
| | - Fujuan Feng
- Northeast Forestry University, Harbin, China
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16
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Yao F, Yang S, Wang Z, Wang X, Ye J, Wang X, DeBruyn JM, Feng X, Jiang Y, Li H. Microbial Taxa Distribution Is Associated with Ecological Trophic Cascades along an Elevation Gradient. Front Microbiol 2017; 8:2071. [PMID: 29163383 PMCID: PMC5663944 DOI: 10.3389/fmicb.2017.02071] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 10/10/2017] [Indexed: 12/01/2022] Open
Abstract
The elevational pattern of soil microbial diversity along mountain slopes has received considerable interest over the last decade. An increasing amount of taxonomic data on soil microbial community composition along elevation gradients have been collected, however the trophic patterns and environmental drivers of elevational changes remain largely unclear. Here, we examined the distribution patterns of major soil bacterial and fungal taxa along the northern slope of Changbai Mountain, Northeast China, at five typical vegetation types located between 740 and 2,691 m above sea level. Elevational patterns of the relative abundance of specific microbial taxa could be partially explained by the oligotrophic-copiotrophic theory. Specifically, two dark-coniferous forests, located at mid-elevation sites, were considered to be oligotrophic habitats, with relatively higher soil C/N ratio and [Formula: see text]-N concentrations. As expected, oligotrophic microbial taxa, belonging to the bacterial phyla Acidobacteria and Gemmatimonadetes, and fungal phylum Basidiomycota, were predominant in the two dark-coniferous forests, exhibiting a mid-elevation maximum pattern. In contrast, the broad leaf-Korean pine mixed forest located at the foot of the mountain, Betula ermanii-dominated forest located below the tree line, and alpine tundra at the highest elevation were considered more copiotrophic habitats, characterized by higher substrate-induced-respiration rates and [Formula: see text]-N concentrations. Microbial taxa considered to be so called copiotrophic members, such as bacterial phyla Proteobacteria and Actinobacteria, and fungal phylum Ascomycota, were relatively abundant in these locations, resulting in a mid-elevation minimum pattern. At finer taxonomic levels, the two most abundant proteobacterial classes, alpha- and beta-Proteobacteria, along with Acidobacteria Gp1, 2, 3, 15, and the Basidiomycotal class of Tremellomycetes were classified with the copiotrophic group. Gamma- and delta-Proteobacteria, Acidobacteria Gp4, 6, 7, 16, and Basidiomycotal class of Agaricomycetes were classified as oligotrophic taxa. This work uses the oligotrophic-copiotrophic theory to explain the elevational distribution pattern of the relative abundance of specific microbial taxa, confirming some of the existing trophic classifications of microbial taxa and expanding on the theory to include a broader range of taxonomic levels.
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Affiliation(s)
- Fei Yao
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shan Yang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Zhirui Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji Ye
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xugao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Xue Feng
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yong Jiang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Hui Li
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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17
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Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains. FORESTS 2017. [DOI: 10.3390/f8100390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Kim JM, Roh AS, Choi SC, Kim EJ, Choi MT, Ahn BK, Kim SK, Lee YH, Joa JH, Kang SS, Lee SA, Ahn JH, Song J, Weon HY. Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea. J Microbiol 2016; 54:838-845. [DOI: 10.1007/s12275-016-6526-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/31/2016] [Indexed: 12/27/2022]
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19
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Siles JA, Margesin R. Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors? MICROBIAL ECOLOGY 2016; 72:207-220. [PMID: 26961712 PMCID: PMC4902835 DOI: 10.1007/s00248-016-0748-2] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/24/2016] [Indexed: 05/23/2023]
Abstract
Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.
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MESH Headings
- Altitude
- Archaea/classification
- Archaea/isolation & purification
- Bacteria/classification
- Bacteria/isolation & purification
- Biodiversity
- Chemical Phenomena
- DNA, Archaeal/genetics
- DNA, Archaeal/isolation & purification
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- Fungi/classification
- Fungi/isolation & purification
- Italy
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- Sequence Analysis, DNA
- Soil/chemistry
- Soil Microbiology
- Temperature
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Affiliation(s)
- José A Siles
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria.
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
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20
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Lanzén A, Epelde L, Blanco F, Martín I, Artetxe U, Garbisu C. Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient. Sci Rep 2016; 6:28257. [PMID: 27321429 PMCID: PMC4913321 DOI: 10.1038/srep28257] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/01/2016] [Indexed: 11/09/2022] Open
Abstract
Mountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diversity along elevational gradients were often limited by confounding variables such as vegetation, pH, and nutrients. Here, we utilised a transect in the Pyrenees established to minimise variation in such parameters, to examine prokaryotic, fungal, protist and metazoan communities throughout three consecutive years. We aimed to determine the influences of climate and environmental parameters on soil microbial community structure; as well as on the relationships between those microbial communities. Further, functional diversity of heterotrophic bacteria was determined using Biolog. Prokaryotic and fungal community structure, but not alpha-diversity, correlated significantly with elevation. However, carbon-to-nitrogen ratio and pH appeared to affect prokaryotic and protist communities more strongly. Both community structure and physicochemical parameters varied considerably between years, illustrating the value of long-term monitoring of the dynamic processes controlling the soil ecosystem. Our study also illustrates both the challenges and strengths of using microbial communities as indicators of potential impacts of climate change.
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Affiliation(s)
- Anders Lanzén
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
| | - Lur Epelde
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
| | - Fernando Blanco
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
| | - Iker Martín
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
| | - Unai Artetxe
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain
| | - Carlos Garbisu
- Soil Microbial Ecology Group, Department of Conservation of Natural Resources, NEIKER-Tecnalia, c/Berreaga 1, 48160 Derio, Spain
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21
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Nguyen NL, Kim YJ, Hoang VA, Subramaniyam S, Kang JP, Kang CH, Yang DC. Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time. PLoS One 2016; 11:e0155055. [PMID: 27187071 PMCID: PMC4871511 DOI: 10.1371/journal.pone.0155055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/24/2016] [Indexed: 12/12/2022] Open
Abstract
Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.
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Affiliation(s)
- Ngoc-Lan Nguyen
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Yeon-Ju Kim
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- * E-mail: (D-CY); (Y-JK)
| | - Van-An Hoang
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Sathiyamoorthy Subramaniyam
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jong-Pyo Kang
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Chang Ho Kang
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, JinJu-si, Gyeongsangnam-do, Republic of Korea
| | - Deok-Chun Yang
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- Graduation of Biotechnology, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- * E-mail: (D-CY); (Y-JK)
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Siles JA, Cajthaml T, Minerbi S, Margesin R. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils. FEMS Microbiol Ecol 2016; 92:fiw008. [PMID: 26787774 DOI: 10.1093/femsec/fiw008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated.
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Affiliation(s)
- José A Siles
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Tomas Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benatska 2, CZ-128 01 Prague 2, Czech Republic
| | - Stefano Minerbi
- Division Forestry, Autonomous Province of Bozen/Bolzano, Brennerstrasse 6, I-39100 Bozen/Bolzano, Italy
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
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Wang Y, Yang J, Liu L, Yu Z. Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:11010-11021. [PMID: 25787217 DOI: 10.1007/s11356-015-4308-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Bacterioplankton are important components of freshwater ecosystems and play essential roles in ecological functions and processes; however, little is known about their geographical distribution and the factors influencing their ecology, especially in stream ecosystems. To examine how geographical and environmental factors affect the composition of bacterioplankton communities, we used denaturing gradient gel electrophoresis and clone sequencing to survey bacterioplankton communities in 31 samples of streamwater from seven nature reserves in Fujian province, southeast China. Our results revealed that dominant bacterioplankton communities exhibited a distinct geographical pattern. Further, we provided evidence for distance decay relationships in bacterioplankton community similarity and found similar community gradients in response to elevation and latitude. Both redundancy analyses and Mantel tests showed that bacterioplankton community composition was significantly correlated with both environmental (electrical conductivity, total phosphorus, and PO4-P) and geographical factors (latitude, longitude, and elevation). Variance partitioning further showed that the joint effect of geographical and environmental factors explained the largest proportion of the variation in distribution of bacterioplankton communities (13.6 %), followed by purely geographical factors (11.2 %), and purely environmental factors (0.6 %). The Betaproteobacteria were the most common taxa in the streams, followed by Firmicutes and Gammaproteobacteria. Therefore, our results suggest that the biogeographical patterns of stream bacterioplankton communities across the Fujian nature reserves are more influenced by geographical factors than by local physicochemical properties.
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Affiliation(s)
- Yongming Wang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
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Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash. J Microbiol 2014; 52:995-1001. [PMID: 25467117 DOI: 10.1007/s12275-014-4129-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
Abstract
This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687-7,330 and 1,790-3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (p<0.05) and Shannon index (p<0.01). However, it showed the negative correlation with exchangeable aluminum contents (p<0.05). In conclusion, diversity of bacterial community in citrus orchard soil was affected by fertilization management, soil pH changes and characteristics of volcanic ash.
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Kim YE, Yoon H, Kim M, Nam YJ, Kim H, Seo Y, Lee GM, Ja Kim Y, Kong WS, Kim JG, Seu YB. Metagenomic analysis of bacterial communities on Dokdo Island. J GEN APPL MICROBIOL 2014; 60:65-74. [DOI: 10.2323/jgam.60.65] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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