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Investigation of rhizospheric microbial communities in wheat, barley and two rice varieties at the seedling stage Tao Lu, Mingjing Ke, W.J.G.M. Peijnenburg, Youchao Zhu, Meng Zhang, Liwei Sun, Zhengwei Fu, and Haifeng Qian J. Agric. Food Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jafc.7b06155 • Publication Date (Web): 23 Feb 2018 Downloaded from http://pubs.acs.org on February 24, 2018
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Journal of Agricultural and Food Chemistry
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Investigation of rhizospheric microbial communities in wheat, barley and two
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rice varieties at the seedling stage
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Tao Lu1, Mingjing Ke1, W.J.G.M. Peijnenburg 2,3, Youchao Zhu1, Meng Zhang1, Liwei
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Sun1, Zhengwei Fu4, Haifeng Qian1,5,*
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1
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R. of China
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The Netherlands
College of Environment, Zhejiang University of Technology, Hangzhou 310032, P.
Institute of Environmental Sciences (CML), Leiden University, 2300 RA, Leiden,
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of Substances and Products, P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
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Hangzhou 310032, P. R. of China
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Academy of Sciences, Urumqi 830011, P. R. of China
National Institute of Public Health and the Environment (RIVM), Center for Safety
College of Biotechnology and Bioengineering, Zhejiang University of Technology,
Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Chinese
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*
Correspondence Author: Tel.:+86 5718832 0742, Fax: +86 571 8832 0599, E-mail address:
[email protected] 1
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Abstract
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The plant rhizosphere microbiota plays multiple roles in plant growth. We
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investigated the taxonomic and functional variations in the rhizosphere microbial
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community, examining both prokaryotes and eukaryotes, of four crops at the seedling
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stage: wheat, barley and two rice varieties (indica and japonica) seeded in paddy soil.
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The diversity of rhizosphere communities in these four species were determined.
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Results showed that wheat and barley had much stronger selection effects than rice
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for the rhizosphere microbial community. Functional metagenomic profiling indicated
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that a series of sequences related to glycan, limonene and pinene degradation
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pathways, as well as some relatively rare functions related to N or S metabolism, were
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enriched in the rhizosphere soil. We conclude that the four tested crops induced the
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formation of microbial community with specific features which may influence the
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plant growth, but the stochastic processes also appreciably influenced the functional
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selection.
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Keywords: Rhizosphere microbiome; Taxonomic selection; Metagenomics;
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Functional selection
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Journal of Agricultural and Food Chemistry
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Introduction
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Soil microorganisms play an important role in regulating soil fertility, carbon and
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nitrogen cycling, plant health and productivity.1-3 Soil microbial communities consist
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of numerous microorganisms, including bacteria, fungi, actinomycetes, algae, viruses
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and archaea.4 Most of these microorganisms utilize large quantities of nutrients (e.g.,
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exudates, border cells, and mucilage) that are released from plant roots. Specific
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microbiomes that assemble near these roots are composed of rhizosphere
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microorganisms and are some of the most complex ecosystems on Earth.5 However,
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the impact of underground root-associated microbes on plant species and their growth
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is less well understood. Some plant-associated microbes are known and well-studied,
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including symbiotic, nitrogen-fixing Rhizobium leguminosarum6 and both beneficial
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and pathogenic Pseudomonas spp.7 Plants may regulate the rhizosphere microbiome
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by selectively stimulating microorganisms with traits that are beneficial to plant
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growth and health.8 Soybean selected for instance a specific microbial community that
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included Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria. These
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microbes inhabit the rhizosphere because of their functional traits, which might be
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beneficial to plant nutrient absorption and growth.3, 9, 10 Plant root microbiomes vary
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by soil type and host genotype because of interactions between the host plant and the
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rhizosphere microbiomes.11 However, information regarding the relationship between
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plant genotypes and rhizosphere microorganism communities is mostly lacking.
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Each gram of soil harbors more than 50,000 species of microorganisms,12 but the vast 3
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majority of plant-associated microorganisms are uncultured due to an unobserved
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lifestyle.13 Sequencing of polymerase chain reaction (PCR)-amplified 16S rRNA gene
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has been extensively used to examine bacterial communities.14 In contrast, PCR
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amplification of genomic DNA is inherently biased by primer design15 and is
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somewhat limited to prokaryotic targets, especially bacteria. In addition, it is difficult
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to know how the functional capabilities of soil microbial communities change
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between plants, although individual soil microbial process (e.g., N2 fixation) and
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specific extracellular enzymes are well-studied. Metagenomics sequencing is
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expected to clarify correlations between taxonomic composition and the functional
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attributes of soil microbial communities.
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In the present study, wheat, barley and two rice varieties (indica and japonica) were
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cultured for 15 d in paddy soil from Hangzhou, China. The effects of four different
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crops at their seedling stage on soil rhizosphere bacterial communities were tested at
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the metagenomic level. The four crops mentioned above are the major worldwide
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food staples. In Asia, the main crop is rice and most cultivated land is paddy soil,
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while wheat and barley are also farmed widely in this area. Although all of these crops
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belong to the class of Poaceae, we hypothesized that there still exist many differences
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in their microbiota selection. The composition and structure of the rhizosphere
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community in different plant species were determined by using 16S rRNA gene and
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internal transcribed spacer (ITS) high-throughput sequencing. The functional
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metagenomic profiles of root-associated microorganisms (including both prokaryotes 4
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and eukaryotes) of four plant hosts were analyzed.
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Methods and materials
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Plant growth and sampling
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Wheat, barley, indica and japonica were cultivated in a paddy soil (5 to 20 cm depth)
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which was collected in a paddy field near Zhejiang University (Hangzhou, China) (N:
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30°15’36’’; E: 120°11’24’’). The soil (pH 7.2) contained 1.41% organic carbon and
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0.4% total soluble salts. The available potassium, nitrogen and phosphorus of the soil
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was 115.8, 25.2 and 58.5 mg/kg, respectively. The soil was air-dried, homogenized,
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sieved (
