Responses of microbial communities to a gradient of pig manure amendment in red paddy soils

Li, Pengfa; Liu, Ming; Ma, Xiaoyan; Wu, Meng; Jiang, Chunyu; Liu, Kai; Liu, Jia; Li, Zhongpei

doi:10.1016/j.scitotenv.2019.135884

Cited by 51 publications

(29 citation statements)

References 51 publications

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“…The top 10 dominant phyla in all samples were, Proteobacteria (28.9-39.8%), Acidobacteria (9.3-16.6%), Chloroflexi (6.2-18.7%), Nitrospirae (2.8-12.7%), Bacteroidetes (2.0-8.9%), Gemmatimonadetes (1.9-4.4%), Planctomycetes (2.5-4.0%), Verrucomicrobia (1.9-3.9%), Chlorobi (1.9-3.9%) and Actinobacteria (1.2-2.2%). These phyla have also been reported in previous studies as dominant bacterial groups in paddy soil (Li et al, 2017;Zhen et al, 2019;Li et al, 2020a). Pollution-related changes in the relative abundance of the phyla were observed.…”

Section: Changes In Microbial Community Structuresupporting

confidence: 85%

Spatial Variation in Microbial Community in Response to As and Pb Contamination in Paddy Soils Near a Pb-Zn Mining Site

Zou¹,

Lu²,

Dai³

et al. 2021

Front. Environ. Sci.

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Mining activity is a growing environmental concern as it contributes to heavy metals (HMs) pollution in agricultural soils. Microbial communities play an important role in the biogeochemical cycling of HMs and have the potential to be used as bioindicators. Arsenic (As) and lead (Pb) are the most hazardous HMs and are mainly originated from mining activities. However, spatial variation in microbial community in response to As and Pb contamination in paddy soils remains overlooked. In this study, the biological and chemical properties of sixteen soil samples from four sites (N01, N02, N03, and N04) near a Pb-Zn mining site at different As and Pb levels were examined. The results showed that soil pH, total As and Pb, bioavailable As and Pb, nitrate-nitrogen (NO3−-N) and ammonia-nitrogen (NH4+-N) were the most important factors in shaping the bacterial community structure. In addition, significant correlations between various bacterial genera and As and Pb concentrations were observed, indicating their potential roles in As and Pb biogeochemical cycling. These findings provide insights into the variation of paddy soil bacterial community in soils co-contaminated with different levels of As and Pb.

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Section: Changes In Microbial Community Structuresupporting

confidence: 85%

Spatial Variation in Microbial Community in Response to As and Pb Contamination in Paddy Soils Near a Pb-Zn Mining Site

Zou¹,

Lu²,

Dai³

et al. 2021

Front. Environ. Sci.

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“…In statistical terms, the positive and negative linkage between species represents facilitative and antagonistic interactions, respectively [10,35]. In this study, we observed a higher PNCRM in the disease-suppressive (HB, 83.17%, Fig.…”

Section: Co-occurrence Pattern Among Ralstonia and Other Microbial Mesupporting

confidence: 51%

Soil Phosphorus Availability Determines the Invasion of Rhizospheric Microbial Networks and Peanut Infection by Ralstonia

Li¹,

Liu²,

Li³

et al. 2020

Preprint

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Background The soil disease-suppressiveness may depend on complex interactions between pathogens and microbiome in response to limiting nutrients. However, these interactions remain poorly understood. Thus, we investigated the significance of soil available phosphorus (AP) in modulating pathogen-microbiome interactions for the emergence or suppression of peanut wilt using receiver operating characteristic curve (ROC) analysis and structural equation modeling (SEM) approaches. Results We observed significant differences in the relative abundance of pathogenic and beneficial microbes, alpha- and beta-diversity indices between disease-conducive and -suppressive soils. The pathogenic ( Ralstonia) and beneficial ( Burkholderia and Bacillus ) taxa dominated the rhizosphere of wilted and healthy peanut plants. The rhizosphere of healthy rather than wilted plants showed significantly higher microbial biodiversity. Moreover, co-occurrences between Ralstonia and microbiome species were highly positive and negative in the disease-conducive and -suppressive soil, respectively, thus predicting facilitative ( Rudaea ) and suppressive ( Burkholderia , Enterobacter , Bacillus ) role of indigenous microbes in Ralstonia invasion in soil. Moreover, both ROC and SEM analyses revealed that Ralstonia invaded rhizospheric microbial networks and caused peanut wilt, very likely by competently utilizing soil phosphorus under copiotrophic (high AP) than oligotrophic (low AP) conditions. Conclusion Our results suggest the importance of soil phosphorus availability in altering the interactions between pathobiome and beneficial microbiome. Our study concludes that feeding soil with labile nutrients could deplete microbial biodiversity and interactions while paving the way for pathogen invasion.

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“…The patterns in our study suggested that the directional shifts in the stochastic-deterministic balance were mirrored by the spatial variations in soil pH and TP in the 0-to-10-cm and 10-to-20-cm layers. It has long been recognized that soil properties are crucial determinants of soil bacterial community assembly (32,33). For instance, soil pH has been identified as the key factor that mediates the relative influences of stochastic and deterministic processes of bacterial community assembly at a broad range of scales (7,32).…”

Section: Discussionmentioning

confidence: 99%

“…For instance, soil pH has been identified as the key factor that mediates the relative influences of stochastic and deterministic processes of bacterial community assembly at a broad range of scales (7,32). Manure fertilization supplies considerable quantities of organic P and effectively improves P-sorption capacity in acidic soils (33,34). A large shift in TP is expected to cause strong ecological selection to promote the compositional turnover of soil bacterial communities.…”

Section: Discussionmentioning

confidence: 99%

Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

et al. 2020

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Soil microbial community assembly is crucial for understanding the mechanisms of microbial communities that regulate ecosystem-level functioning. The relative contributions of stochastic and deterministic processes to microbial community assembly remain poorly defined, and major questions exist concerning the soil organic carbon (SOC) dynamics of microbial community assembly in deep soil. Here, the bacterial community assembly processes were explored across five soil profile depths (up to 80 cm) during a 15-year field experiment involving four fertilization regimes. We found that the bacterial community assembly was initially governed by deterministic selection in topsoil but was progressively structured by increasing stochastic dispersal with depth. The migration rate (m) and β-null deviation pattern supported the hypothesis of a relatively greater influence of dispersal in deep soil, which was correlated with bacterial community assembly by stochastic processes. These changes in the entire community assembly reflected consistent assembly processes of the two most dominant phyla, Acidobacteria and Chloroflexi. Structural equation modeling showed that soil features (pH and total phosphorus) and bacterial interactions (competition and network complexity) were significantly related to bacterial community assembly in the 0-to-10-cm and 10-to-20-cm layers. Partial Mantel tests, structural equation modeling, and random forest modeling consistently indicated a strong and significant correlation between bacterial community assemblages and SOC dynamics, implying that bacterial assembly processes would potentially suppress SOC metabolism and mineralization when the contributions of stochastic dispersal to communities increased in deeper layers. Our results have important implications for integrating bacterial community assembly processes into the predictions of SOC dynamics. IMPORTANCE We have provided a framework to better understand the mechanisms governing the balance between stochastic and deterministic processes and to integrate the shifts in community assembly processes with microbial carbon metabolism. Our study reinforced that environmental filtering and bacterial cooccurrence patterns influence the stochastic/deterministic continuum of soil bacterial community assembly and that stochasticity may act through deeper soil layers to influence carbon metabolism. Delineating theoretically the potential linkages between community assembly and SOC dynamics across a broad range of microbial systems represents an interesting topic for future research.

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Responses of microbial communities to a gradient of pig manure amendment in red paddy soils

Cited by 51 publications

References 51 publications

Spatial Variation in Microbial Community in Response to As and Pb Contamination in Paddy Soils Near a Pb-Zn Mining Site

Spatial Variation in Microbial Community in Response to As and Pb Contamination in Paddy Soils Near a Pb-Zn Mining Site

Soil Phosphorus Availability Determines the Invasion of Rhizospheric Microbial Networks and Peanut Infection by Ralstonia

Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

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