Liming does not counteract the influence of long-term fertilization on soil bacterial community structure and its co-occurrence pattern

Ma, Bin; Lv, Xiaofei; Cai, Yanjiang; Chang, Scott X.; Dyck, Miles

doi:10.1016/j.soilbio.2018.05.003

Cited by 73 publications

(39 citation statements)

References 43 publications

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“…promote both co-operation and competition in bacterial networks. Accordingly, microbial networks were found to be less complex under limed and N-fertilized conditions than under control conditions [52]. In this study, NO 3 − fertilization resulted in less complex bacterial networks in all soil compartments, probably because NO 3 − application provided more favorable conditions in terms of higher soil pH and N nutrition.…”

Section: Nitrogen Form and Maize Rhizosphere In Uenced Bacterial Co-omentioning

confidence: 53%

“…Although the NH 4 + treatment provided su cient N in the soil environment, the soil pH was decreased to 4.5 due to NH 4 + absorption and nitri cation. This may have enhanced niche sharing and intensi ed competition and cooperation among bacterial taxa [52]. The bacterial networks were more complex in the maize root zone and its adjacent soil compartments (0.5-1 cm) than in the outer compartments in both the NH 4 + and NO 3 − treatments, indicative of more complex bacterial networks in the maize rhizosphere than in bulk soil.…”

Section: Nitrogen Form and Maize Rhizosphere In Uenced Bacterial Co-omentioning

confidence: 98%

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Ammonium and Nitrate Shift the Spatial Distribution of Soil Bacterial Communities and Association Networks Along a Distance from Maize Roots in an Acidic Red Soil

Zhang

Zhao

Shi

et al. 2020

Preprint

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Background: Ammonium (NH4+) and nitrate (NO3−) are two major inorganic nitrogen (N) forms available for plant growth. Soil microbes affect the availability and transformation of these N forms in the rhizosphere, and this affects the N-use efficiency of plants. However, little is known about the responses of the rhizosphere bacterial community structure to NH4+ and NO3−. Here, a rhizobox containing a root zone (root growing area) and various soil compartments (0–0.5 cm, 0.5–1 cm, 1–2 cm, 2–4 cm, and 4–9 cm from the root zone) was designed to investigate the spatial distribution of bacterial diversity, community structure, and co-occurrence patterns along a distance from maize (Zea mays L.) roots with the addition of 15N-labeled NH4+ or NO3− in an acidic red soil.Results: Addition of NH4+ and NO3− reduced soil bacterial diversity in the maize root zone. The structures of soil bacterial communities differed between NH4+ and NO3− in the root zone and 0.5 cm away from the root zone. Soil pH was the major driver of bacterial community assembly during plant uptake of N. Maize roots recruited potentially beneficial acidophilic bacteria (e.g. Acidibacter, Burkholderia, and Catenulispora) under NH4+ treatment, and recruited growth-promoting bacteria that prefer higher pH (e.g. Sphingomonas, Sphingobium, Azospirillum, and Novosphingobium) under NO3− treatment. In the N-fertilization treatments, the soil bacterial networks were more complex in the root zone and its adjacent 0.5–1 cm zone than in other soil compartments. The soil bacterial networks were more complex under NH4+ treatment than under NO3−. More bacterial taxa in the networks responded positively and negatively to soil residual NH4+ than to NO3− in all zones in the rhizobox.Conclusions: The combined effects of the N form and the rhizosphere influenced the spatial patterns and co-occurrence network of soil bacterial communities at different distances from the maize root zone, mainly because of changes in soil pH during the uptake of NH4+ and NO3− by maize roots. Regulating microbial communities by adjusting soil pH through NH4+ and NO3− supply may be an environmentally friendly option for promoting soil microbial functions in intensively managed agro-ecosystems.

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Section: Nitrogen Form and Maize Rhizosphere In Uenced Bacterial Co-omentioning

confidence: 53%

Section: Nitrogen Form and Maize Rhizosphere In Uenced Bacterial Co-omentioning

confidence: 98%

Ammonium and Nitrate Shift the Spatial Distribution of Soil Bacterial Communities and Association Networks Along a Distance from Maize Roots in an Acidic Red Soil

Zhang

Zhao

Shi

et al. 2020

Preprint

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“…In particular, significant relationships suggested that the soil pH determined the topological features of the co-occurrence network for soil microbiota in the Tibetan alpine grasslands. One possible explanation for this is that soil pH could affect soil microbial interactions via regulating the availability of soil nutrients [45,46]. Based on the strong relationships between soil pH versus SOM, TN, AN (NH 4 + and NO 3 − ), TP, and AP, soil pH was likely to influence the interactions among soil bacterial and archaeal taxa via changing the C, P, and N availability in the alpine grasslands (Additional file 2: Fig S10).…”

Section: Discussionmentioning

confidence: 99%

Increasing soil pH enhances the network interactions among bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau

Chen

Luo

et al. 2019

Preprint

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Background: Soil functioning and processes are driven by complex microbial interactions. It is therefore critical to understand the co-occurrence patterns of soil microbiota, especially in fragile alpine ecosystems. Here we explored the geographic patterns of the topological features and the major drivers shaping the topological structure of the co-occurrence network for bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau based on high-throughput sequencing.Results: Soil pH was the most important environmental variable for predicting the topological features of the microbial network at both network and node levels. Associations among soil microbiota were enhanced with increasing pH (5.17-8.92), and the network was the most stable at neutral pH (7).Node-level topological features suggested that taxa of the high-pH cluster had more important roles in maintaining complex network connections than taxa of the low-pH cluster. Network-level features revealed closer relationships among soil microbiota in the steppe ecosystem than in the meadow ecosystem. Archaeal operational taxonomic units (OTUs) with higher values for node-level topological features appeared to be more important than bacterial OTUs in maintaining complex connections. The co-occurrence patterns of bacterial OTUs with lower node-level feature values followed a power-law distribution, whereas those of archaeal OTUs did not.Conclusions: Soil pH plays a decisive role in determining the complex interactions among soil microbiota in alpine grassland ecosystems of the Tibetan Plateau, with a more stable co-occurrence network at neutral pH. Bacterial and archaeal taxa, which occupy distinct network niches, have closer relationships in alpine steppe than in alpine meadow ecosystems.

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“…The discrepancy in driving factors for environmental selection from soils to leaves suggests that divergent environmental selection processes are active in the compartments. It is not surprising to find that soil pH, the best predictor of soil bacterial and archaeal community composition across global [46], regional [47] and local scales [48], is an important driver for microbiomes in both the rhizosphere and bulk soil. In addition to soil pH, soil organic carbon quality and quantity and nitrogen and phosphorus availability also have notable influences on soil microbial community structure [49].…”

Section: Community Assembly Mechanisms Of C Sinensis Microbiomes Fromentioning

confidence: 99%

Trade-off between stochastic and deterministic processes shifts from soil to leaf microbiome of tea plant

Xu¹,

Stirling²,

Wen-bing³

et al. 2020

Preprint

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Background : Plant microbiome plays an important role in promoting plant health and production. However, even though the microbiomes in various compartments have been widely investigated, the association across plant compartments from soil to leaf remain unclear. Tea is a globally popular beverage due to its flavor and health benefits associating with secondary metabolites; the microbiomes of tea plant ( Camellia sinensis ) play a significant role in the production of these secondary metabolites. Here, we sequenced the microbiomes of bulk and rhizosphere soils, roots and leaves of C. sinensis collected from tea plantations across over 2000 km to investigate the association and driving mechanisms for microbiomes in the compartments. Results : Camellia sinensis microbiomes differed between the compartments with α-diversity gradually decreasing from soils to roots and leaves. The core leaf microbiome comprised Bacilli, Sphingobacteriia and α-Proteobacteria, which we suggest might ascendingly migrate from soils to leaves. Microbial community assembly processes were dominated by deterministic processes in bulk and rhizosphere soils; these assembly processes were dominated by stochastic processes in roots and leaves. Dispersal limitation was stronger in old leaves than in other compartments. Amino acids were also critical drivers for environmental selection. The microbiomes in C. sinensis roots and leaves possessed a lower intensity of microbial associations and more negative microbial associations than in bulk and rhizosphere soils, suggesting that the contribution of microbial interactions varied in different compartments. Conclusion : In summary, there is a trade-off between stochastic and deterministic processes in microbiomes community assembly along from soil to leaf of C. sinensis . These results provide valuable information for understanding the associations and driving mechanism of microbiomes in various C. sinensis compartments, which could be used to predict C. sinensis microbiome and harness its power to improve tea production and quality.

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Liming does not counteract the influence of long-term fertilization on soil bacterial community structure and its co-occurrence pattern

Cited by 73 publications

References 43 publications

Ammonium and Nitrate Shift the Spatial Distribution of Soil Bacterial Communities and Association Networks Along a Distance from Maize Roots in an Acidic Red Soil

Ammonium and Nitrate Shift the Spatial Distribution of Soil Bacterial Communities and Association Networks Along a Distance from Maize Roots in an Acidic Red Soil

Increasing soil pH enhances the network interactions among bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau

Trade-off between stochastic and deterministic processes shifts from soil to leaf microbiome of tea plant

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