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Geographic distance and amorphous iron affect the abundance and distribution of Geobacteraceae in paddy soils in China

  • Soils, Sec 1 • Soil Organic Matter Dynamics and Nutrient Cycling • Research Article
  • Published:
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Abstract

Purpose

Geobacteraceae are important dissimilatory Fe (III)-reducing microorganisms, influencing the cycling of metals, nutrients as well as the degradation of organic contaminants. However, little is known about their distribution, diversity, and abundance of Geobacteraceae and the effects of environment factors and geographic distance on the distribution and diversity of Geobacteraceae in paddy soils remain unclear. Therefore, the objectives of this study were to investigate the distribution, diversity, and abundance of Geobacteraceae in paddy soils and to determine key factors in shaping the Geobacteraceae distribution, environmental factors, geographic distance, or both and to quantify their contribution to Geobacteraceae variation.

Materials and methods

Illumina sequencing and quantitative real-time PCR using a primer set targeting 16S rRNA genes of bacteria affiliated with the family Geobacteraceae were employed to measure the community composition, diversity, and abundance patterns of 16S rRNA genes of Geobacteraceae in 16 samples collected from north to south of China. MRT, Mantel test, and VPA were used to analyze the relationship between communities of Geobacteraceae and environmental factors and geographic distance.

Results and discussion

Quantitative PCR showed that the abundance of 16S rRNA genes of Geobacteraceae ranged from (1.20 ± 0.18) × 108 to 1.13 × 109 ± 2.25 × 108 copies per gram of soil (dry weight) across different types of soils. Illumina sequencing results showed Geobacter was the dominant genus within the family of Geobacteraceae. Multivariate regression tree (MRT) analysis showed that soil amorphous iron contributed more (22.46 %) to the variation of dominant species of Geobacteraceae than other examined soil chemical factors such as pH (14.52 %), ammonium (5.12 %), and dissolved organic carbon (4.74 %). Additionally, more geographically distant sites harbored less similar communities. Variance partitioning analysis (VPA) showed that geographic distance contributed more to the variation of Geobacteraceae than any other factor, although the environmental factors explained more variation when combined. So, we detected the uneven distribution of Geobacteraceae in paddy soils of China and demonstrated that Geobacteraceae community composition was strongly associated with geographic distance and soil chemical factors including aFe, pH, Fe, DOC, C:N, and NO3 −-N. These results greatly expand the knowledge of the distribution of Geobacteraceae in environments, particularly in terrestrial ecosystems.

Conclusions

Our results showed that geographic distance and amorphous iron played important roles in shaping Geobacteraceae community composition and revealed that both geographic distance and soil properties governed Geobacteraceae biogeography in paddy soils. Our findings will be critical in facilitating the prediction of element cycling by incorporating information on functional microbial communities into current biogeochemical models.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (41430858) and the Strategic Priority Research Program of Chinese Academy of Sciences (XDB15020402).

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Authors and Affiliations

  1. State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People’s Republic of China

    Hai-Yan Yuan, Long-Jun Ding, Song-Can Chen, Ye Deng, Xiao-Ming Li & Yong-Guan Zhu

  2. University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China

    Hai-Yan Yuan, Song-Can Chen & Xiao-Ming Li

  3. Institute of Agricultural Resources and Environments, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People’s Republic of China

    Ning Wang

  4. CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People’s Republic of China

    Ye Deng

  5. Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People’s Republic of China

    Yong-Guan Zhu

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  1. Hai-Yan Yuan
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  2. Long-Jun Ding
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Correspondence to Yong-Guan Zhu.

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Responsible editor: Zhihong Xu

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Yuan, HY., Ding, LJ., Wang, N. et al. Geographic distance and amorphous iron affect the abundance and distribution of Geobacteraceae in paddy soils in China. J Soils Sediments 16, 2657–2665 (2016). https://doi.org/10.1007/s11368-016-1462-x

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  • DOI: https://doi.org/10.1007/s11368-016-1462-x

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