Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review

Abstract

Organic wastes have the potential to be used as soil organic amendments after undergoing a process of stabilization such as composting or as a resource of renewable energy by anaerobic digestion (AD). Both composting and AD are well-known, eco-friendly approaches to eliminate and recycle massive amounts of wastes. Likewise, the application of compost amendments and digestate (the by-product resulting from AD) has been proposed as an effective way of improving soil fertility. The study of microbial communities involved in these waste treatment processes, as well as in organically amended soils, is key in promoting waste resource efficiency and deciphering the features that characterize microbial communities under improved soil fertility conditions. To move beyond the classical analyses of metataxonomic data, the application of co-occurrence network approaches has shown to be useful to gain insights into the interactions among the members of a microbial community, to identify its keystone members and modelling the environmental factors that drive microbial network patterns. Here, we provide an overview of essential concepts for the interpretation and construction of co-occurrence networks and review the features of microbial co-occurrence networks during the processes of composting and AD and following the application of the respective end products (compost and digestate) into soil.

Long-term integrated soil-crop management improves soil microbial community structure to reduce GHG emission and increase yield

“…In addition, ISCM could significantly affect microbial network density and change with the crop growth stage ( Figure 2 ), which was closely related to the agronomic management practices in each period. The microorganism network density of T3 was the highest among the four treatments (except for the R6), which may be related to the fact that heavy fertilization accelerated the growth of soil microorganisms ( Siles et al, 2021 ), but too many microbes may lead to increased competition and increase more negative interactions between species ( Ratzke et al, 2020 ). However, Giovannoni et al (2014) showed that microorganisms tend to coexist in large numbers in low nutrient environments.…”

Long-Term Compost Amendment Changes Interactions and Specialization in the Soil Bacterial Community, Increasing the Presence of Beneficial N-Cycling Genes in the Soil

“…Moreover, the high number of correlations could be due to a greater number of niches in Org_C, which could allow a greater number of different habitats. However, this is not entirely in accordance with the increased network complexity of Org_C, which suggests that module members are less affected by environmental perturbations [56,57]. Total nitrogen correlated positively with a module from Org_C (OC7), and this module was composed of Nitrospirae, where members of Nitrospira show the capability to perform complete nitrification [58,59], or Actinobacteria, where genera like Streptomyces have been linked to some nitrogen-fixation genes [60,61].…”

Microbial community diversity and function analysis of Aconitum carmichaelii Debeaux in rhizosphere soil of farmlands in Southwest China

“…Modularity is another useful index to investigate the resistance of communities to disturbance ( Zhou et al, 2011 ), which are clusters of densely interconnected nodes ( Siles et al, 2021 ), and has been used to successfully predict the stability of networks of microbiomes ( Herren and McMahon, 2017 ; De Vries et al, 2018 ). Krause et al (2003) found that higher modularity was beneficial for increasing the stability of interaction networks and helping microbial communities resist environmental changes.…”