Bacterial community structure in maize stubble-amended soils with different moisture levels estimated by bar-coded pyrosequencing

doi:10.1016/j.apsoil.2014.09.011

Applied Soil Ecology

Volume 86, February 2015, Pages 62-70

https://doi.org/10.1016/j.apsoil.2014.09.011 Get rights and content

Highlights

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Long-term straw amendment lessens the difference in bacterial community structure between the unfertilized soil and successive organic manure-fertilized soil.
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Moisture strongly affects bacterial distribution in the stubble-amended soils.
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Soil DOC, which drives the alternative dominance of two functional groups (copiotrophic and oligotrophic bacteria), is a critical property in shaping bacterial community composition in the amended soils.

Abstract

It is of ecological significance to investigate microbial communities in response to straw amendment and moisture in arable soils. However, in Chinese fluvo-aquic soils, these responses are still poorly understood. We designed an incubation experiment involving two soils with and without the addition of maize stubble at two moisture levels, and bacterial community structure at days 20, 80, and 200 after the start of incubation was assessed via bar-coded pyrosequencing of the 16S rDNA amplicons. In the presence of stubble with identical moisture level, we observed higher bacterial diversity and richness in long-term organic manure-fertilized soil compared with the unfertilized soil at days 20 and 80, which we attributed to the different quality and quantity of organic matter between the two soils. However, there was no significant difference in bacterial diversity and richness between the two soils at day 200, indicating that long-term straw amendment probably lessens the difference in bacterial community structure between the two soils. In the amended soils bacterial diversity, richness, and community composition at 25% of the water-holding capacity distinctly differed from those at 55% of the water-holding capacity, indicating that moisture strongly affects bacterial distribution in the amended soils. As stubble-C availability declined over time, the dominance of copiotrophic population weakened, and oligotrophic population was moderately abundant. Finally, our study suggests that dissolved organic carbon, which drives redistribution in copiotrophic and oligotrophic categories in response to the varying water and stubble-C availability, is a determinant of bacterial community composition in the amended soils.

Introduction

Microbiological processes are of significance for the ecological functions of arable soils. Of special importance in this respect is the effect of microorganisms on the input and output dynamics of soil organic matter (SOM) content. A loss of organic carbon (C) in agricultural soils due to mineralization and leaching can be balanced by the incorporation of crop straw (Perucci et al., 1997). Desiccated crop straw consists of cellulose, lignin, crude protein, low molecular carbohydrates, inorganic salts, etc. When crop straw is returned into the fields, it will be decomposed by soil microflora, which makes an important contribution to biogeochemical cycling of C and nitrogen (N) (Wakelin et al., 2007), and the maintenance of soil fertility (Derrien et al., 2014).

During straw decomposition microbial processes are affected by many abiotic factors, including straw quality and size (Bending and Turner, 1999), soil-straw contact (Henriksen and Breland, 2002), soil salinity (Muhammad et al., 2006), geographic location (Sun et al., 2013), straw intrinsic genotype (Becker et al., 2014), and so on. These factors can affect the accessibility of straw to soil microorganisms and the successive dynamics of microbial communities, and thus alter rates of colonization and patterns of decomposition. Among these factors, soil moisture is a critical factor in governing soil microbial activity, community composition, and function (Drenovsky et al., 2004, Geisseler et al., 2011, Brockett et al., 2012). Drenovsky et al. (2004) reported that soil moisture content was highly correlated with observed differences in microbial community composition across the straw-amended soils at four moisture levels (air dry, half field capacity, field capacity, and flooded condition). Geisseler et al. (2011) found that respiration and microbial biomass in a dry soil amended with oats-legume straw were reduced, while protease, beta glucosidase, beta glucosaminidase, and exocellulase activities were increased compared to an amended soil with higher moisture content.

Previous studies have described the succession of bacterial community in soils added with crop straw. For instance, Bastian et al. (2009) observed a magnitude of changes in bacterial community dynamics between the different soil zones (i.e. straw residues, detritusphere, and bulk soil). Pascault et al. (2013) reported that the dynamics and identity of the bacterial groups depend on the residues added; Firmicutes dominate in the wheat-amended treatment and Proteobacteria in the alfalfa-amended treatment. Many studies deal with the effects of straw residues and moisture level on soil bacterial community structure using some traditional approaches, such as phospholipid fatty acid (PLFA) analysis (Bossio and Scow, 1998, Drenovsky et al., 2004), DNA cloning and sequencing after denaturing gradient gel electrophoresis (DGGE) (Weber et al., 2001), and direct sequencing after RNA reverse transcription-polymerase chain reaction (RT-PCR) (Peltoniemi et al., 2012), although these methods provide little detail about the taxonomic composition and the phylogenetic structure of bacterial community.

The open burning of crop straw was ubiquitous in the North China Plain. At present with a concern for air pollution, a great deal of crop straw is returned back to the agricultural fields. Since soil microorganisms are a sensitive indicator of soil fertility and quality (He et al., 2008), it is therefore critical to monitor the effect of straw management on soil microbial communities for advancing the understanding of soil ecology. Up to now, in Chinese fluvo-aquic soils which are widely distributed in the North China Plain, bacterial community in response to straw amendment at different moisture levels is not well understood. Moreover, these soils are lack of fertility, and quality and productivity are low. Long-term application of organic manure can improve soil fertility and microbial properties (Ge et al., 2008). Likewise, we don't understand in long-term organic manure-fertilized soil how bacterial community responds to straw amendment and moisture level. To address these shortages, we simulated straw amendment experiment in a chamber, the unfertilized and long-term organic manure-fertilized soils with and without the addition of maize stubble were incubated at two moisture levels, and soil bacterial diversity and community composition were analyzed by a pyrosequencing-based approach. Due to microbial ecological functions are closely related to soil biochemical properties, we also determined basal soil biochemical properties, including available C and N, microbial biomass, and beta glucosidase activity, which is a limiting factor in the degradation of plant materials (Nannipieri et al., 2012). Finally, the objective of our study is to evaluate: (i) the effects of stubble amendment at different moisture levels on soil bacterial diversity and community composition; and (ii) the relationships of bacterial community composition with basal biochemical properties.

Section snippets

Site description

A long-term fertilization experiment was conducted at Fengqiu Agro-Ecological Experimental Station of Chinese Academy of Sciences in Fengqiu County (35°00′N, 114°24′E), Henan Province, China. The region had a temperate monsoon climate, with a mean annual precipitation of 615 mm and a mean annual temperature of 13.9 °C. The soil, with a profile of sandy loam (40.7% silt, 13.7% clay) in the plow layer and loam (55.8% silt, 35.9% clay) in the subsoil, has developed from alluvial sediments of the

Basal biochemical properties

Stubble amendment enhanced soil NH₄⁺–N, NO₃^––N, inorganic N, dissolved organic C (DOC), beta glucosidase activity (BGA), and Microbial biomass C (MBC) to varying degrees (Table 2). In the presence of stubble, NO₃^––N and inorganic N increased with increasing sampling time, and significantly increased at high moisture level at days 80 and 200; DOC decreased with increasing sampling time, and significantly increased at high moisture level (Table 2). The amended OrgMan soil had a higher (P < 0.05)

Discussion

In the current work we provided detailed information on bacterial community structure in stubble-amended soils as related to moisture level using a bar-coded pyrosequencing approach. Even though it is highly unlikely that we have surveyed the full extent of diversity in the treated soils, previous studies suggest that we can quantitatively compare overall community composition and general diversity patterns among different treatments using bar-coded pyrosequencing (Shaw et al., 2008, Chu et

Conclusion

In the presence of stubble, the significant differences in bacterial diversity and richness between the NoFer and OrgMan soils at the early stage of incubation is mainly ascribable to the different quality and quantity of organic matter in the two soils, whereas no statistical diversity difference between the two soils at the later stage of incubation suggests that long-term straw amendment probably lessens the inherent difference in bacterial community between the two soils. The effect of

Acknowledgements

The authors sincerely thank H.Y. Chu for advice and reagents required for molecular analyses, Y. Shi for help with the processing of pyrosequencing data, and two anonymous reviewers for their insightful comments on this manuscript. This work was supported by the National Basic Research Program (973 Program) of China (2011CB100506), the Knowledge Innovation Program of the Chinese Academy of Sciences (CXJQ120111), and China Agriculture Research System-Wheat.

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Bacterial community structure in maize stubble-amended soils with different moisture levels estimated by bar-coded pyrosequencing

Highlights

Abstract

Introduction

Section snippets

Site description

Basal biochemical properties

Discussion

Conclusion

Acknowledgements

Soil Biol. Biochem.

Soil Biol. Biochem.

Soil Biol. Biochem.

Appl. Soil Ecol.

Soil Biol. Biochem.

Pedosphere

Soil Biol. Biochem.

Soil Biol. Biochem.

Soil Biol. Biochem.

Biol. Conserv.

Soil Biol. Biochem.

Soil Biol. Biochem.

Soil Biol. Biochem.

Pedobiologia

Pedobiologia

J. Soils Sediments

FEMS Microbiol. Ecol.

Appl. Soil Ecol.

Soil Biol. Biochem.

Soil Biol. Biochem.

Soil Biol. Biochem.

Soil Biol. Biochem.

Soil Biol. Biochem.

Interaction of biochemical quality and particle size of crop residues and its effect on the microbial biomass and nitrogen dynamics following incorporation into soil

Biol. Fertil. Soils

Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques

Environ. Microbiol.

Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

Proc. Natl. Acad. Sci. U. S. A.

Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilization patterns

Microb. Ecol.

An ordination of the upland forest communities of southern Wisconsin

Ecol. Monogr.

Total nitrogen

Succession of microbiota estimated by phospholipid fatty acid analysis and changes in organic constituents during the composting process of rice straw

Soil Sci. Plant Nutr.

Dynamics and identification of soil microbial populations actively assimilating carbon from ¹³C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques