Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

Abstract

Plant response to drought stress involves fungi and bacteria that live on and in plants and in the rhizosphere, yet the stability of these myco- and micro-biomes remains poorly understood. We investigate the resistance and resilience of fungi and bacteria to drought in an agricultural system using both community composition and microbial associations. Here we show that tests of the fundamental hypotheses that fungi, as compared to bacteria, are (i) more resistant to drought stress but (ii) less resilient when rewetting relieves the stress, found robust support at the level of community composition. Results were more complex using all-correlations and co-occurrence networks. In general, drought disrupts microbial networks based on significant positive correlations among bacteria, among fungi, and between bacteria and fungi. Surprisingly, co-occurrence networks among functional guilds of rhizosphere fungi and leaf bacteria were strengthened by drought, and the same was seen for networks involving arbuscular mycorrhizal fungi in the rhizosphere. We also found support for the stress gradient hypothesis because drought increased the relative frequency of positive correlations.

Soil bacterial community response to cover crop introduction in a wheat-based dryland cropping system

“…Consistent with previous findings (Banerjee et al, 2019;Gao et al, 2022), our work suggests that the number of taxa within a community is less important in determining network complexity than the number of associations among taxa with more associations leading to greater resilience in the community. Our work suggests that incorporating cover crops in a cropping system can in some cases increase the network complexity which should in theory make the system more robust to environmental perturbations, however more work is needed to empirically determine the biological relevance of network components (Faust and Raes, 2012).…”

Fungal plastiphily and its link to generic virulence traits makes environmental microplastics a global health factor

“…As expected, both networks contained predominantly positive edges (Fig. 6a), which is consistent with the stress gradient hypothesis 43,76 , according to which facilitation and niche sharing prevail over competition in harsher environments such as the investigated low-water, oligotrophic, and UV-irradiated ferralsols 77 . Positive networks, however, are unstable due to possible fitness interdependences, resulting in rapid regime shifts and low resilience of both MCs when perturbated 76 .…”

“…On the other hand, network-based studies have highlighted the importance of biotic interactions such as competition and facilitation, as well as so-called keystone taxa in the formation of microbial biofilms on environmental plastics 41,42 , and polymer type was considered as a deterministic driver in plastisphere bacteriome development 11 . Selective factors play a crucial role in structuring mycobiomes during colonisation of extreme habitats 43 and the succession of dysbiotic mycobiota 44 , which are inevitably linked to pathogenicity outcomes.…”

Prolonged drought regulates the silage quality of maize (Zea mays L.): Alterations in fermentation microecology

“…Water is an effective tool to modify nutrient availability, plant physiological processes and microbial communities (Tan et al, 2021). The moisture content regulates the microbial abundance (Gao et al, 2022). In addition, fungus is more likely to colonize and develop at higher moisture levels.…”