Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

Ren Bai,Kai Feng,Li-Mei Zhang,Ji-Zheng He,Ye Deng,Jun-Tao Wang

doi:10.3389/fmicb.2017.00945

Abstract

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Highlights

Soils cover most of the natural and artificial habitats of terrestrial ecosystems
Some studies suggested that certain microbial taxa would prefer to specific soil types, and soil bacterial community composition was distinct among soil types but could be hardly explained by a single soil chemical parameter (Nie et al, 2012; Tripathi et al, 2012)
By combining Illumina Mi-Seq sequencing with Geochip techniques, the study demonstrated manifest separation of bacterial and archaeal community and function structure among soil types, and visible but relatively slight shift of community structure along soil depth within each soil type, suggesting the overwhelming effect of soil parent material characteristics mainly via determination of soil pH, even under uniform rice cultivation management

Summary

Introduction

Soils cover most of the natural and artificial habitats of terrestrial ecosystems. Due to the high spatial heterogeneity in soil particles and large variation of soil physiochemical properties among soil types, soils are considered harboring the most diverse microbial groups in comparison with other ecosystems (Schimel and Schaeffer, 2012). Soil scientists have noticed that the soil natural properties determined by soil parent materials during soil formation period, such as pH, texture, and base saturation, etc., sustain soil biodiversity in nature and greatly affect the basic fertility and productivity of soil to a large degree (Anderson, 1988) Anthropogenic activities such as tillage, fertilization, irrigation, and cultivation, etc., in soils exert considerable influence on the structure and functional performance of microbial communities via changing the soil properties, subsequently influence soil quality in the long term (Tripathi et al, 2015). The current knowledge on the differentiation of soil microorganism among various soil types and their potential significance are still very limited and deserved to be well depicted, considering the large body of pedodiversity and microbial diversity

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