Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale

Zhang, Baogang; Zhang, Jun; Liu, Yao; Shi, Peng; Wei, Gehong

doi:10.1016/j.soilbio.2017.12.011

Cited by 294 publications

(168 citation statements)

References 64 publications

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“…In a co‐occurrence network, positive and negative interactions are regarded as mutualistic and antagonistic relationships among the microbial species, respectively (Xun et al ., ; Zhang et al ., ). Here, we found that the positive interaction in the fungal network was significantly higher than that in the bacterial network, especially at the upstream and midstream sites (Table ), implying that occurrence of mutualism or commensalism among interspecies in the fungal community might be enhanced in these sites.…”

Section: Discussionmentioning

confidence: 97%

“…These relative changes in Firmicutes and Bacteroidetes levels might be explained by the concept of ecological succession, assuming that the dominance of r‐strategists like Bacteroidetes in the upstream samples could be replaced by the k‐strategists towards the downstream during the succession process (Read et al ., ; Savio et al ., ). For the fungi, the higher relative abundance of the phylum Ascomycota in the midstream and downstream samples may be due to its critical ecological functions relating to ecosystem succession (Zhang et al ., ). Additionally, several studies have reported that the abundance of Ascomycota increases in environments with high levels of nutrients (Xu et al ., ; Guo et al ., ).…”

Section: Discussionmentioning

confidence: 99%

“…Given that the complexity and connectivity of microbial network were reported to be region‐dependent (Zhang et al ., ), it would be expected that the bacterial and fungal interaction varied among different river sections. In this study, both bacterial and fungal communities had higher network connectivity and stronger biotic interaction in downstream than in other two river sections, as expected.…”

Section: Discussionmentioning

confidence: 99%

“…Here, we found that the positive interaction in the fungal network was significantly higher than that in the bacterial network, especially at the upstream and midstream sites (Table ), implying that occurrence of mutualism or commensalism among interspecies in the fungal community might be enhanced in these sites. One possible explanation is that some fungal taxa have a greater ability to degrade organic matter and transfer nutrient elements, which in turn facilitates the growth of other taxa via an ecological interaction of commensalism or mutualism (Zhang et al ., ). Remarkably, the positive interaction was higher for the bacterial network (99.5%) but lower for the fungal network (89.1%) at the downstream sites compared to the other sites, possibly relating to a complex competition or antagonism relationship between the bacteria and fungi (He et al ., ; Zheng et al ., ); however, this idea needs to be tested in future studies.…”

Section: Discussionmentioning

confidence: 99%

“…Several recent studies have indicated that the microbial co-occurrence network in aquatic systems generally has a non-random pattern and modular structure, which is mainly governed by the taxonomic relatedness of the co-occurring species (Kara et al, 2013;Aylward et al, 2015;Jones et al, 2018). Some keystone species in an ecological network have also been shown to play irreplaceable roles in maintaining the structure and function of the whole microbial community (Xiao et al, 2018;Zhang et al, 2018a). However, most existing studies have focused on only one microbial group in soil (Fan et al, 2017), lakes (Kara et al, 2013) or oceans (Aylward et al, 2015), and there is still a lack of studies that inspect and compare the structural changes of the co-occurrence network between bacteria and fungi in riverine sediments.…”

Section: Introductionmentioning

confidence: 99%

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Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river

Juan

Wang

et al. 2019

Environmental Microbiology

133

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Summary Despite the essential functions of sedimentary bacterial and fungal communities in biogeochemical cycling, little is known about their biogeographic patterns and driving processes in large rivers. Here we investigated the biogeographic assemblies and co‐occurrence patterns of sedimentary bacterial and fungal communities in the Jinsha River, one of the largest rivers in southwestern China. The mainstream of river was divided into upstream, midstream and downstream. The results showed that both bacterial and fungal communities differed significantly among three sections. For both communities, their composition variations in all sites or each river section were controlled by the combination of dispersal limitation and environmental selection, and dispersal limitation was the dominant factor. Compared with bacteria, fungi had stronger dispersal limitation. Co‐occurrence network analyses revealed higher network connectivity but a lower proportion of positive interaction in the bacterial than fungal network at all sites. In particular, the keystone species belonging to bacterial phyla Proteobacteria and Firmicutes and fungal phyla Ascomycota and Chytridiomycota may play critical roles in maintaining community function. Together, these observations indicate that fungi have a stronger dispersal limitation influence and less network connectivity than bacteria, implying different community assembly mechanisms and ecological functions between bacteria and fungi in large rivers.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river

Juan

Wang

et al. 2019

Environmental Microbiology

133

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Characterization of soil microbes associated with a grazing‐tolerant grass species, Stipa breviflora, in the Inner Mongolian desert steppe

Chen

Saixi

et al. 2020

Ecology and Evolution

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The soil microbial community plays an important role in grassland ecosystem dynamics and has a crucial influence upon plant ecophysiological traits (Andres et al., 2017; Ford, Rousk, Garbutt, Jones, & Jones, 2013). A major challenge in applied ecology is to understand response mechanisms of those complex microbial communities to grazing, especially for those associated with grass species tolerant of grazing. Many studies have demonstrated that herbivores largely determine aboveground biomass, and also directly and indirectly affect the belowground soil microbial community through their impact on plants and soil properties (Dawson, Grayston, & Paterson, 2000; Yang et al., 2013). In this interaction, a common response of grazed grass plants to browsing is the stimulation of microbial processes and nitrogen availability within their rhizospheres, and the reallocation of belowground resources to aboveground structures (Bardgett,

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Comparison of soil microbial community structure and function for karst tiankeng with different degrees of degradation

Jiang

Zeng

2022

Ecology and Evolution

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Karst tiankengs are oases in degraded karst landscapes and act as repositories for biodiversity conservation; however, knowledge about the bacterial and fungal structure and function of the karst tiankeng ecosystems is limited. This study investigated the microbial communities in three different tiankeng (nondegraded, moderately degraded, and heavily degraded tiankeng) by Illumina NovaSeq sequencing. We found that the degradation of karst tiankeng can lead to changes in microbial community structure and functions, while there are differences in bacterial and fungal responses. There were significant differences in bacterial and fungal community composition and beta diversity in the three tiankeng soils. Random molecular ecological network analysis results indicated that a more complex and stable bacterial network existed in nondegraded tiankeng, while more complex fungal networks existed in moderately degraded tiankeng. The keystones of Proteobacteria , Actinobacteria , Acidobacteria , Ascomycota , and Basidiomycota played essential roles in maintaining soil function and stability. The functional profiles revealed that tiankeng habitat changes may affect microbial survival strategies, such as increasing gene abundance associated with the carbon cycle. To our knowledge, this is the first report on bacterial and fungal communities in different degrees of karst tiankeng, which provides crucial insights into our understanding of the microbial communities' structure and potential function in karst tiankeng ecosystems.

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Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale

Cited by 294 publications

References 64 publications

Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river

Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river

Characterization of soil microbes associated with a grazing‐tolerant grass species, Stipa breviflora, in the Inner Mongolian desert steppe

Comparison of soil microbial community structure and function for karst tiankeng with different degrees of degradation

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