From diversity to complexity: Microbial networks in soils

Guseva, Ksenia; Darcy, Sean; Simon, Eva; Alteio, Lauren; Montesinos‐Navarro, Alicia; Kaiser, Christina

doi:10.1016/j.soilbio.2022.108604

Cited by 128 publications

(45 citation statements)

References 135 publications

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“…The studies of ecological theory showed that competitive interactions could promote stability of ecological networks ( Coyte et al, 2015 ). It is worth noting that interspecific interactions within microbial community are highly complex, further studies with more experimental evidence are needed to compensate for the limitations of co-occurrence network analysis only ( Banerjee et al, 2018 ; Guseva et al, 2022 ; Jin et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Short-term application of chicken manure under different nitrogen rates alters structure and co-occurrence pattern but not diversity of soil microbial community in wheat field

et al. 2022

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Manure application is an effective way to improve the utilization efficiency of organic resources and alleviate the adverse effects of long-term application of chemical fertilizers. However, the impact of applying manure under different nitrogen rates on soil microbial community in wheat field remains unclear. Treatments with and without chicken manure application under three nitrogen rates (N 135, 180 and 225 kg⋅hm–2) were set in wheat field. Soil organic carbon, available nutrients, and abundance, diversity, structure and co-occurrence pattern of soil microbial community at wheat maturity were investigated. Compared with no manure application, chicken manure application increased the soil organic carbon and available phosphorus, while the effects on soil mineral nitrogen and available potassium varied with different nitrogen rates. Chicken manure application significantly increased soil bacterial abundance under the nitrogen fertilization of 135 and 225 kg⋅hm–2, increased soil fungal abundance under the nitrogen fertilization of 135 kg⋅hm–2, but decreased soil fungal abundance under the nitrogen fertilization of 180 and 225 kg⋅hm–2 (P < 0.05). There was no significant difference in alpha diversity indices of soil microbial communities between treatments with and without chicken manure application under different nitrogen rates (P > 0.05). Chicken manure application and its interaction with nitrogen rate significantly changed soil bacterial and fungal community structures (P < 0.05). There were significantly different taxa of soil microbial communities between treatments with and without chicken manure application. Chicken manure application reduced the ecological network complexity of soil bacterial community and increased that of soil fungal community. In summary, the responses of soil available nutrients and microbial abundance to applying chicken manure varied with different nitrogen rates. One growing season application of chicken manure was sufficient to alter the soil microbial community structure, composition and co-occurrence pattern, whereas not significantly affected soil microbial community diversity.

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Section: Discussionmentioning

confidence: 99%

Short-term application of chicken manure under different nitrogen rates alters structure and co-occurrence pattern but not diversity of soil microbial community in wheat field

et al. 2022

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“…In this paper, we deconvoluted a highly disordered immune and structural landscape to provide accurate annotations and abundance metrics for the cellular landscape and then leveraged mathematical techniques to describe co -location and cell contact-based network construction. Our mathematical tools encompassed a range of spatial statistics and methods from network science; some transposed from ecology (Baddeley et al, 2014;Guseva et al, 2022;Morueta-Holme et al, 2016). The pipeline uncovered a hitherto undescribed physical partnership between immature neutrophils and CD8 T cells in COVID-19 lungs linked to proliferating alveolar epithelium in areas with diffuse alveolar damage.…”

Section: Discussionmentioning

confidence: 99%

Unbiased single cell spatial analysis localises inflammatory clusters of immature neutrophils-CD8 T cells to alveolar progenitor cells in fatal COVID-19 lungs

Weeratunga

Denney

Bull

et al. 2022

Preprint

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Single cell spatial interrogation of the immune-structural interactions in COVID -19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we developed a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method revealed a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and cytotoxic CD8 T cells, was found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings provide new insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline [Spatial Omics Oxford Pipeline (SpOOx)] and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.

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“…Most network analyses of soil microbial communities rely on a statistical inference of association metrics based on pairwise correlations of taxa across a sufficiently large number of soil samples (i.e. co-occurrence networks) 76 . This is necessary because it is impossible to directly quantify small-scale microbial interactions, in the relatively large size of soil samples.…”

Section: Methodsmentioning

confidence: 99%

Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities

et al. 2022

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Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.

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From diversity to complexity: Microbial networks in soils

Cited by 128 publications

References 135 publications

Short-term application of chicken manure under different nitrogen rates alters structure and co-occurrence pattern but not diversity of soil microbial community in wheat field

Short-term application of chicken manure under different nitrogen rates alters structure and co-occurrence pattern but not diversity of soil microbial community in wheat field

Unbiased single cell spatial analysis localises inflammatory clusters of immature neutrophils-CD8 T cells to alveolar progenitor cells in fatal COVID-19 lungs

Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities

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