Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems

Jiao, Shuo; Qi, Jiejun; Jin, Chujie; Liu, Yu; Wang, Yan; Pan, Haibo; Chen, Shi; Liang, Chunling; Peng, Ziyi; Chen, Beibei; Qian, Xiaoqing; Wei, Gehong

doi:10.1111/gcb.16387

Cited by 52 publications

(18 citation statements)

References 118 publications

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“…First, core taxa drove the nutrient cycling in both surface and bottom waters. This may be because core taxa maintain nutrient cycling by facilitating the community stability to environmental changes, consistent with a previous study in the soil environment (Jiao et al, 2022b). Second, core taxa facilitated nutrient cycling by maintaining community abundance.…”

Section: Discussionsupporting

confidence: 88%

“…Compared with satellite taxa, core taxa had wider niche breadths and could adapt to a wide range of environmental niches (Mo et al, 2021). Core taxa can play key roles in enhancing the community resistance of soil microbiome (Jiao et al, 2022b). Satellite taxa, analogous to rare taxa, may be more influenced by environmental changes and maintain community stability (Wang et al, 2023; Xiong et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing

Xue,

Chen,

Xiao

et al. 2023

Environ Microbiol Rep

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Microeukaryotes are key for predicting the change of ecosystem processes in the face of a disturbance. However, their vertical responses to multiple interconnected factors caused by water mixing remain unknown. Here, we conducted a 12‐month high‐frequency study to compare the impacts of mixing disturbances on microeukaryotic community structure and stability over different depths in a stratified reservoir. We demonstrate that core and satellite microeukaryotic compositions and interactions in surface waters were not resistant to water mixing, but significantly recovered. This was because the water temperature rebounded to the pre‐mixing level. Core microeukaryotes maintained community stability in surface waters with high recovery capacity after water mixing. In contrast, the changes in water temperature, chlorophyll‐a, and nutrients resulted in steep and prolonged variations in the bottom core and satellite microeukaryotic compositions and interactions. Under low environmental fluctuation, the recovery of microbial communities did not affect nutrient cycling in surface waters. Under high environmental fluctuation, core and satellite microeukaryotic compositions in bottom waters were significantly correlated with the multi‐nutrient cycling index. Our findings shed light on different mechanisms of plankton community resilience in reservoir ecosystems to a major disturbance over depths, highlighting the role of bottom microeukaryotes in nutrient cycling.

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Section: Discussionsupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing

Xue,

Chen,

Xiao

et al. 2023

Environ Microbiol Rep

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“…Core bacteria can enhance protection from abiotic factors and maintain ecosystem multifunction; thereby, they were often considered key to improving agricultural sustainability and productivity [ 12 ]. The relationships between bacterial abundance and soil properties are observed with Spearman correlation analysis ( Figure 4 b,c).…”

Section: Discussionmentioning

confidence: 99%

“…In agricultural ecosystems, anthropogenic interference, for example, fertilization and nutrient source selection, has profound effects on soil property, soil microbial diversity and ecosystem service [ 12 ]. Soil microbes are the most active and sensitive components in a soil ecosystem and are highly involved in organic matter decomposition, nutrient cycling and soil aggregation [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

Positive Effects of Organic Substitution in Reduced-Fertilizer Regimes on Bacterial Diversity and N-Cycling Functionality in Greenhouse Ecosystem

Sun

Wang

Sun

et al. 2022

IJERPH

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Conventional fertilization in the greenhouses of North China used excessive amounts of chemical and organic fertilizer, resulting in soil degradation and severe agricultural non-point source pollution. A nine-year study was conducted on a loamy clay soil in Shijiazhuang, Hebei province, to investigate the effects of reduced-fertilizer input regimes on soil property, bacterial diversity, nitrogen (N) cycling and their interactions. There were four treatments, including high organic + chemical fertilizer application rate and three reduced-fertilizer treatments with swine manure, maize straw or no substitution of 50% chemical N. Treatments with reduced-fertilizer input prevented soil salinization and acidification as in local conventional fertilization after being treated for nine years. In comparison to chemical fertilizer only, swine manure or maize straw substitution maintained higher nutrient availability and soil organic C contents. Fertilizer input reduction significantly increased bacterial richness and shifted bacterial community after nine years, with decisive factors of EC, Olsen P and C/N ratio of applied fertilizer. Soil chemical characteristics (EC, pH and nutrients), aggregation and C/N ratio of applied fertilizer selected certain bacterial groups, as well as N-cycling functions. Reduced-fertilizer input decreased the potential nitrification and denitrification functioning of bacterial community, but only in organic substitution treatments. The results of this study suggested that fertilizer input reduction combined with organic C input has potential in reducing non-point source pollution and increasing N-use efficiency in greenhouse vegetable production in North China.

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“…In agricultural fields, the relative importance of deterministic versus stochastic processes in soil microbiome assembly is significantly affected by crop type, plant developmental stage and microbial sub-community (e.g. abundant or rare species; Jiao et al, 2020Jiao et al, , 2022Liu, Zhu, et al, 2023;Xiong et al, 2021). However, the deterministic and stochastic processes of the BS and RS soil microbial community remains controversial in agricultural fields (Thiergart et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

The core microbiota as a predictor of soil functional traits promotes soil nutrient cycling and wheat production in dryland farming

et al. 2023

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Host plants and the microbiota living in the rhizosphere are interdependent, mutually reinforced and mutually beneficial but the assembly, functions and microbial interactions of the host‐associated microbiota are still unclear. Herein, winter wheat was selected as a test plant to explore the assembly process of total bacteria from bulk soil (BS) and rhizosphere soil (RS), and phoD‐harbouring bacteria in RS at a long‐term (14 years) trial site. We also identified core microbes that are potentially relevant to soil carbon (C), nitrogen (N) and phosphorus (P) cycling genes and soil biogeochemical properties, and investigated the relationships between soil variables, functional genes and wheat productivity. The results showed that the microhabitat of the plant, rather than P fertilizer input, was the main factor affecting the microbial diversity, composition and co‐occurrence networks. The BS bacterial community was driven by deterministic processes but the RS and phoD bacterial communities were dominated by stochastic processes. The influence of deterministic processes decreased with increasing soil nutrient content. A core microbial community consisted of 10 OTUs in different microhabitats and was significantly related to soil functional genes and properties. In the rhizosphere soil, significant correlations were found between soil variables, soil functional bacteria and genes, and crop productivity. Synthesis and applications. This study provides empirical evidence that the assembly process of the microbial community is governed by environmental factors in various soil environments and provides new perspectives on the sustainable improvement of crop productivity. Read the free Plain Language Summary for this article on the Journal blog.

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Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems

Cited by 52 publications

References 118 publications

Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing

Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing

Positive Effects of Organic Substitution in Reduced-Fertilizer Regimes on Bacterial Diversity and N-Cycling Functionality in Greenhouse Ecosystem

The core microbiota as a predictor of soil functional traits promotes soil nutrient cycling and wheat production in dryland farming

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