Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages

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Polish Journal of Microbiology

Polish Society of Microbiologists

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VOLUME 68 , ISSUE 2 (Jun 2019) > List of articles

Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages

LIN WANG * / ZHIYING LI / RUIRUI LIU / LULU LI / WEIWEI WANG

Keywords : soybean, growth stages, rhizosphere soil, bacterial community, Illumina high-throughput sequencing

Citation Information : Polish Journal of Microbiology. Volume 68, Issue 2, Pages 281-284, DOI: https://doi.org/10.33073/pjm-2019-023

License : (CC-BY-NC-ND 4.0)

Published Online: 28-June-2019

ARTICLE

ABSTRACT

Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends.

Graphical ABSTRACT

Rhizosphere microbes are important components of soil ecosystems. These organisms are closely related to soil fertility and are essential indicators for evaluating soil health. Soil microbial community and diversity can reflect changes in the soil environmental quality and reveal differences in microbial ecological functions, which are critical for maintaining soil quality and ecosystem stability (Gertini 2005). Rhizosphere microorganisms can absorb the hydrogen released by nitrogen-fixing nodules of leguminous plants lacking hydrogenase. Experiments have shown that bacteria remove hydrogen (Mclearn and Dong 2002), and these bacteria were beneficial to the growth of plants (Dong et al. 2003; Abdellatif et al 2017). Therefore, studying the rhizosphere microbial diversity of legumes will improve our understanding of microbes that promote the growth of legumes.

Accordingly, in this study, Illumina high-throughput sequencing was used to investigate the microbial communities of rhizosphere soil samples. The soybean field was located in Xianyang, Shaanxi, NW China (107°38’–109°10’ E, 34°11’–35°32’ N), which is a typical warm temperate continental monsoon climate. The soil is dominated by ash-calcium soil. The soybean rhizosphere soil samples, numbered as S, were collected on June 24, 2016, when after more than half of the cotyledons were breaking out, and also the soil samples, numbered as M, were collected on September 30, 2016. At this time, the leaves and beans were dehydrated, demonstrating the inherent traits of the varieties.

The five-point sampling method was used to collect the rhizosphere soil samples according to the shake-off method of Riley et al. (1969). The soil sample was divided into two portions after filtering through a 2-mm sieve. One portion was stored in an –80°C refrigerator for soil microbial diversity analysis and was sequenced using an Illumina HiSeq 2500 at Biomarker Technologies (Beijing, China). The primers used for sequencing were 338F (5’-ACTCCTACGGGAGGCAGCA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’) (Zhang et al. 2015); the other was naturally air-dried and sieved for soil physical and chemical properties analysis in a reference to Soil Agrochemical Analysis (Bao 2000).

Some physical and chemical properties of soil in different time are shown in Table I. There were significant differences in pH, available potassium, and soil temperature, whereas other indicators did not differ at the two sampling times. The contents of organic matter, total nitrogen, available phosphorus, and potassium, as well as the moisture in M soil samples were higher than those in S soil samples, and the pH and temperature increased in the M phase.

Table I

Changes in basic physical and chemical properties of soils at different sampling times.

10.33073_pjm-2019-023-tbl1.jpg

The coverage of each sample was greater than 99%, demonstrating that the sequencing results could reflect the real situation of the sample. The ACE (P = 0.453) index and the Chao1 (P = 0.909) index were higher at the S stage than at the M stage, indicating that the S stage soil samples were rich in microorganisms; however, the difference was not significant. The Shannon index of the S stage was larger than that of the M stage, and the P values between the S and M stages were the Shannon index (P = 0.00074) and Simpson index (P = 0.0037), respectively, indicating that the diversity of the bacteria were higher in the S stage.

As shown in Fig. 1, ten phyla including Actinobacteria, Acidobacteria, Proteobacteria, Gemmatimonadetes, Bacteroidetes, Chloroflexi, Verrucomicrobia, Nitrospirae, Planctomycetes, and Armatimonadetes were obtained from the six soil samples.

Fig. 1.

Microbial communities at the phylum level.

10.33073_pjm-2019-023-f001.jpg

The dominant phyla at the S and M stages were Actinobacteria, Acidobacteria, and Proteobacteria. At the S stage, Proteobacteria, Acidobacteria, and Actinobacteria accounted for 27.7%, 27.2%, and 14.3%, respectively; at the M stage, Proteobacteria, Actinobacteria, and Acidobacteria accounted for 17.0%, 38.1%, and 21.8%, respectively. Compared with the soil samples collected at the S stage, the number of Actinobacteria increased by 165.6%, and the numbers of Acidobacteria and Proteobacteria decreased by 20.1% and 38.6%, respectively.

Bacteria are important soil microbes, and their types and quantities have direct effects on soil biochemical properties and soil nutrients. The Illumina high-throughput sequencing is widely used in the study of soil microbial diversity owing to its rapid, convenient, and highly accurate results. In this study, we analyzed the community and diversity of bacteria in rhizosphere soil from two different growth stages. We found that microbial abundance and diversity at the S stage were higher than those at the M stage. Many factors influence microbial diversity (Lupwayi et al. 2001; Schutter and Dick 2002; Lipson 2007; Peralta et al. 2013). Rasche et al. (2011) suggested that humidity and temperature are the main environmental factors affecting soil microbes in temperate forests, similar to the results of the present study. The appropriate soil temperature affects the availability of nutrients in the soil and the growth environment of microorganisms, further stimulating the activity of soil microbes and function of soil microbial communities (Luo et al. 2001; Melillo et al. 2002). Suitable water can significantly change the microbial community and activity. A certain degree of humidity in the soil plays an important role in cultivating strong seedlings and improving the ability to resist drought in the later period. In June, the temperature and rainfall in Xianyang were appropriate, which led to increases in the number of nodules, the emission of hydrogen gas during nitrogen fixation, and enhancement of the number of hydrogen-oxidizing bacteria (Dong and Layzell 2001; Dong et al. 2003). This caused soil microbial diversity and abundance to be high in June. In September, the soil temperature rose significantly to 23°C, which was beneficial for microorganism growth; however, the diversity was lower in the M stage than in the S stage. The reason for this result may be that the appropriate temperature enhanced microbial metabolism, changing some specific flora into the main flora. These dominant bacteria had a competitive advantage over other microbiota, resulting in the proliferation of a few dominant phyla, whereas others were inhibited or eliminated during competition. At the same time, there was heavy rain in Xianyang in September 2016. Unger et al. (2009) also found that continuous flooding conditions reduced soil microbial biomass and affected the soil microbial community, causing microbial diversity and abundance to decrease.

Table II

Alpha diversity of samples.

10.33073_pjm-2019-023-tbl2.jpg

In this study, we found that compared with the S stage, the number of Actinobacteria increased, and both Proteobacteria and Acidobacteria decreased in the M stage. At the M stage, the nitrogen fixation capacity of soybean nodules is weakened, and the hydrogen concentration is lowered. Studies have shown that certain microorganisms in Actinobacteria (Constant et al. 2008; Constant et al. 2010) consume atmospheric tropospheric trace hydrogen at 0.553 ppmv. This may increase the number of Pseudonocardia and Nocardioides. Whether these two genera can absorb atmospheric trace hydrogen is worthy of further study. Li et al. (2018) found that in the original rhizosphere soil samples of Medicago sativa and the hydrogen-treated soil samples, changes in the abundances of Actinobacteria and Proteobacteria showed opposite trends. In this study, we found that soil samples from the rhizospheres of soybeans also showed similar trends. Further studies are needed to determine whether this trend exists in other legumes or other crops. Many studies have shown that the microbial community is related to the growth stage. For example, Duineveld et al. (2001) found that the microbial community structures of rhizosphere soils of young plants and mature plants differed. Additionally, Farina et al. (2012) found that the microbial community structure of canola differed accordingly to growth stage, with the greatest abundance during the rosette period. Xu et al. (2009) also found that the bacterial diversity in soybean rhizosphere increased primarily and then decreased; the increase was observed beginning from the flowering period, reached a maximum during the drum period, and was lowest during the maturity period.

In summary, the soybean growth period was found to have an important influence on the bacterial community in rhizosphere soil, and bacterial diversity was mainly affected by soil temperature and humidity. Changes in the abundances of Acidobacteria and Proteobacteria showed opposite trends. Our findings provided a theoretical basis for understanding the diversity and changes in the bacterial community in soybean rhizosphere soil.

Acknowledgments

This study is supported by the National Natural Science Foundation (Grant No. 41571243) and the project of young talents of science and technology association of Shaanxi province (Project Number: 20160232). We thank Biomarker Technologies for their excellent technical assistance.

Conflict of interest

The authors do not report any financial or personal connections with other persons or organizations, which might negatively affect the contents of this publication and/or claim authorship rights to this publication.

References


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    [PUBMED] [CROSSREF]
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    [CROSSREF]
  19. Schutter ME, Dick RP. Microbial community profiles and activities among aggregates of winter fallow and cover-cropped soil. Soil Sci Soc Am J. 2002;66(1):142–153. doi:10.2136/sssaj2002.1420
    [CROSSREF]
  20. Unger IM, Kennedy AC, Muzika RM. Flooding effects on soil microbial communities. Appl Soil Ecol. 2009 May;42(1):1–8. doi:10.1016/j.apsoil.2009.01.007
    [CROSSREF]
  21. Xu Y, Wang G, Jin J, Liu J, Zhang Q, Liu X. Bacterial communities in soybean rhizosphere in response to soil type, soybean genotype, and their growth stage. Soil Biol Biochem. 2009 May;41(5):919–925. doi:10.1016/j.soilbio.2008.10.027
    [CROSSREF]
  22. Zhang X, Tian X, Ma L, Feng B, Liu Q, Yuan L, Fan C, Huang H, Huang H, Yang Q. Biodiversity of the symbiotic bacteria associated with toxic marine dinoflagellate Alexandrium tamarense. J Biosci Med (Irvine). 2015;03(06):23–28. doi:10.4236/jbm.2015.36004
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FIGURES & TABLES

Fig. 1.

Microbial communities at the phylum level.

Full Size   |   Slide (.pptx)

REFERENCES

  1. Abdellatif L, Ben-Mahmoud OM, Yang C, Hanson KG, Gan Y, Hamel C. The H2-oxidizing rhizobacteria associated with field-grown lentil promote the growth of lentil inoculated with Hup+ rhizobium through multiple modes of action. J Plant Growth Regul. 2017 Jun;36(2):348–361. doi:10.1007/s00344-016-9645-7
    [CROSSREF]
  2. Bao SD. Soil Agricultural Chemistry analysis. Beijing (China): Agriculture Press; 2000.
  3. Constant P, Chowdhury SP, Pratscher J, Conrad R. Streptomy­cetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase. Environ Microbiol. 2010 Mar;12(3):821–829. doi:10.1111/j.1462-2920.2009.02130.x Medline
    [PUBMED] [CROSSREF]
  4. Constant P, Poissant L, Villemur R. Isolation of Streptomyces sp. PCB7, the first microorganism demonstrating high-affinity uptake of tropospheric H2. ISME J. 2008 Oct;2(10):1066–1076. doi:10.1038/ismej.2008.59 Medline
    [PUBMED] [CROSSREF]
  5. Dong Z, Layzell DB. H2 oxidation, O2 uptake and CO2 fixation in H2 treated soils. Plant Soil. 2001;229(1):1–12. doi:10.1023/A:1004810017490
    [CROSSREF]
  6. Dong Z, Wu L, Kettlewell B, Caldwell CD, Layzell DB. Hydrogen fertilization of soils – is this a benefit of legumes in rotation? Plant Cell Environ. 2003 Nov;26(11):1875–1879. doi:10.1046/j.1365-3040.2003.01103.x
    [CROSSREF]
  7. Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA. Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol. 2001 Jan 01;67(1):172–178. doi:10.1128/AEM.67.1.172-178.2001 Medline
    [PUBMED] [CROSSREF]
  8. Farina R, Beneduzi A, Ambrosini A, de Campos SB, Lisboa BB, Wendisch V, Vargas LK, Passaglia LMP. Diversity of plant growth-promoting rhizobacteria communities associated with the stages of canola growth. Appl Soil Ecol. 2012 Apr;55(1):44–52. doi:10.1016/j.apsoil.2011.12.011
    [CROSSREF]
  9. Gertini G. Effect on properties of forest soils: a review. Oecologia, 2005;143(1):l–10.
  10. Li Z, Liu X, Liu R, Li L, Wang L, Wang W. Insight into bacterial community diversity and monthly fluctuations of Medicago sativa rhizosphere soil in response to hydrogen gas using Illumina High-Throughput Sequencing. Curr Microbiol. 2018 Dec;75(12): 626–1633. doi:10.1007/s00284-018-1569-y Medline
  11. Lipson DA. Relationships between temperature responses and bacterial community structure along seasonal and altitudinal gradients. FEMS Microbiol Ecol. 2007 Feb;59(2):418–427. doi:10.1111/j.1574-6941.2006.00240.x Medline
    [PUBMED] [CROSSREF]
  12. Luo Y, Wan S, Hui D, Wallace LL. Acclimatization of soil respiration to warming in a tall grass prairie. Nature. 2001 Oct;413 (6856): 622–625. doi:10.1038/35098065 Medline
    [PUBMED] [CROSSREF]
  13. Lupwayi NZ, Arshad MA, Rice WA, Clayton GW. Bacterial diversity in water-stable aggregates of soils under conventional and zero tillage management. Appl Soil Ecol. 2001 Mar;16(3):251–261. doi:10.1016/S0929-1393(00)00123-2
    [CROSSREF]
  14. McLearn N, Dong Z. Microbial nature of the hydrogen-oxidizing agent in hydrogen-treated soil. Biol Fertil Soils. 2002 Jul 1; 35(6):465–469. doi:10.1007/s00374-002-0495-z
    [CROSSREF]
  15. Melillo JM, Steudler PA, Aber JD, Newkirk K, Lux H, Bowles FP, Catricala C, Magill A, Ahrens T, Morrisseau S. Soil warming and carbon-cycle feedbacks to the climate system. Science. 2002 Dec 13;298(5601):2173–2176. doi:10.1126/science.1074153 Medline
    [PUBMED] [CROSSREF]
  16. Peralta AL, Ludmer S, Kent AD. Hydrologic history influences microbial community composition and nitrogen cycling under experimental drying/wetting treatments. Soil Biol Biochem. 2013 Nov;66(11):29–37. doi:10.1016/j.soilbio.2013.06.019
    [CROSSREF]
  17. Rasche F, Knapp D, Kaiser C, Koranda M, Kitzler B, Zechmeister-Boltenstern S, Richter A, Sessitsch A. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. ISME J. 2011 Mar;5(3):389–402. doi:10.1038/ismej.2010.138 Medline
    [PUBMED] [CROSSREF]
  18. Riley D, Barber SA. Bicarbonate accumulation and pH changes at the soybean (Glycine max (L.) Merr.) root-soil interface. Soil Sci Soc Am J. 1969;33(6):905–908. doi:10.2136/sssaj1969.03615995003300060031x
    [CROSSREF]
  19. Schutter ME, Dick RP. Microbial community profiles and activities among aggregates of winter fallow and cover-cropped soil. Soil Sci Soc Am J. 2002;66(1):142–153. doi:10.2136/sssaj2002.1420
    [CROSSREF]
  20. Unger IM, Kennedy AC, Muzika RM. Flooding effects on soil microbial communities. Appl Soil Ecol. 2009 May;42(1):1–8. doi:10.1016/j.apsoil.2009.01.007
    [CROSSREF]
  21. Xu Y, Wang G, Jin J, Liu J, Zhang Q, Liu X. Bacterial communities in soybean rhizosphere in response to soil type, soybean genotype, and their growth stage. Soil Biol Biochem. 2009 May;41(5):919–925. doi:10.1016/j.soilbio.2008.10.027
    [CROSSREF]
  22. Zhang X, Tian X, Ma L, Feng B, Liu Q, Yuan L, Fan C, Huang H, Huang H, Yang Q. Biodiversity of the symbiotic bacteria associated with toxic marine dinoflagellate Alexandrium tamarense. J Biosci Med (Irvine). 2015;03(06):23–28. doi:10.4236/jbm.2015.36004

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