Changes in the Microbial Community Structure and Soil Chemical Properties of Vertisols Under Different Cropping Systems in Northern China

Song, Xiuli; Tao, Bo; Guo, Jing; Li, Jingjing; Chen, Guofeng

doi:10.3389/fenvs.2018.00132

Cited by 43 publications

(27 citation statements)

References 48 publications

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“…In addition, soil-derived determinants could be important indicators that correlate with soil bacterial communities, as shown by RDA analysis (Figure 6A,B). Our results agree with previous studies [36,53], suggesting that significant changes in soil nutrient and biological functions are likely associated with changes in bacterial community composition and diversity. In this study, we found that soil pH was the main factor, and a slight change in pH significantly correlated with several core phyla (Gemmatimonadetes, Acidobacteria, and Actinobacteria).…”

Section: Discussionsupporting

confidence: 93%

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Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China

Ali

Ghani

et al. 2019

IJMS

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Cover crops are key determinants of the ecological stability and sustainability of continuous cropping soils. However, their agro-ecological role in differentially reshaping the microbiome structure and functioning under a degraded agroecosystem remains poorly investigated. Therefore, structural and metabolic changes in soil bacterial community composition in response to diverse plant species were assessed. Winter catch leafy vegetables crops were introduced as cover plants in a cucumber-fallow period. The results indicate that cover crop diversification promoted beneficial changes in soil chemical and biological attributes, which increased crop yields in a cucumber double-cropping system. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community composition and diversity changed through changes in the soil properties. Principal component analysis (PCA) coupled with non-metric multidimensional scaling (NMDS) analysis reveals that the cover planting shaped the soil microbiome more than the fallow planting (FC). Among different cropping systems, spinach–cucumber (SC) and non-heading Chinese cabbage–cucumber (NCCC) planting systems greatly induced higher soil nutrient function, biological activity, and bacterial diversity, thus resulting in higher cucumber yield. Quantitative analysis of linear discriminant analysis effect size (LEfSe) indicated that Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were the potentially functional and active soil microbial taxa. Rhizospheres of NCCC, leaf lettuce–cucumber (LLC), coriander–cucumber (CC), and SC planting systems created hotspots for metabolic capabilities of abundant functional genes, compared to FC. In addition, the predictive metabolic characteristics (metabolism and detoxification) associated with host–plant symbiosis could be an important ecological signal that provides direct evidence of mediation of soil structure stability. Interestingly, the plant density of non–heading Chinese cabbage and spinach species was capable of reducing the adverse effect of arsenic (As) accumulation by increasing the function of the arsenate reductase pathway. Redundancy analysis (RDA) indicated that the relative abundance of the core microbiome can be directly and indirectly influenced by certain environmental determinants. These short-term findings stress the importance of studying cover cropping systems as an efficient biological tool to protect the ecological environment. Therefore, we can speculate that leafy crop diversification is socially acceptable, economically justifiable, and ecologically adaptable to meet the urgent demand for intensive cropping systems to promote positive feedback between crop–soil sustainable intensification.

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Section: Discussionsupporting

confidence: 93%

“…Previous reports suggested that many bacterial activities, such as ammonia oxidization and phosphate solubilization, are pH-dependent [54,55]. Acidobacteria contain many taxa that have physiological functions that are pH-dependent [36,53], which might explain the large impact of pH on those bacteria.…”

Section: Discussionmentioning

confidence: 99%

Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China

Ali

Ghani

et al. 2019

IJMS

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“…To our knowledge, this is one of the first studies investigating subsoil and bulk soil microbial diversity using high-throughput sequencing in an agriculturally managed Vertosol, in the southern hemisphere [31,68,69]. Whilst our data have followed trends observed in studies from the northern hemisphere (i.e., decline in diversity with increasing depth), there have been a few surprises [30,70].…”

Section: Discussionsupporting

confidence: 50%

Subsoil Microbial Diversity and Stability in Rotational Cotton Systems

et al. 2020

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Microbial diversity has been well documented for the top 0–0.30 m of agricultural soils. However, spatio-temporal research into subsoil microbial diversity and the effects of agricultural management remains limited. Soil type may influence subsoil microbial diversity, particularly Vertosols. These soils lack distinct horizons and are known to facilitate the downward movement of organic matter, potentially supporting subsoil microbiota, removed from the crop root system (i.e., bulk soils). Our research used the MiSeq Illumina Platform to investigate microbial diversity down the profile of an agricultural Australian Vertosol to 1.0 m in bulk soils, as influenced by crop system (continuous cotton and cotton–maize) and sample time (pre- and in-crop samples collected over two seasons). Overall, both alpha- (Chao1, Gini–Simpson Diversity and Evenness indices) and beta-diversity (nMDS and Sørensen’s Index of Similarity) metrics indicated that both bacterial (16S) diversity and fungal (ITS) diversity decreased with increasing soil depth. The addition of a maize rotation did not significantly influence alpha-diversity metrics until 0.70–1.0 m depth in the soil, where bacterial diversity was significantly higher in this system, with beta-diversity measures indicating this is likely due to root system differences influencing dissolved organic carbon. Sample time did not significantly affect bacterial or fungal diversity over the two seasons, regardless of the crop type and status (i.e., crop in ground and post crop). The relatively stable subsoil fungal and overall microbial diversity in bulk soils over two crop seasons suggests that these microbiota have developed a tolerance to prolonged agricultural management.

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“…The assessment of soil health and quality under different cropping systems may be based on soil bacterial assemblages ( Song et al., 2018 ). Using vetch and rye as cover crops increased soil microbial biomass in the rhizosphere of tomato ( Buyer et al., 2010 ).…”

Section: Impact Of Cropping Systems and Climate Change On Soil Microbial Communitiesmentioning

confidence: 99%

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Lahlali

Ibrahim

Belabess

et al. 2021

Heliyon

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Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.

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Changes in the Microbial Community Structure and Soil Chemical Properties of Vertisols Under Different Cropping Systems in Northern China

Cited by 43 publications

References 48 publications

Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China

Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China

Subsoil Microbial Diversity and Stability in Rotational Cotton Systems

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

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