Carbon and nutrient inputs are required to stimulate the formation and mineralization of soil organic carbon (SOC) through processes related to microbial growth and priming effects (PEs). PEs are thought to affect microbial life strategies, however, the mechanisms underlying their role in SOC formation and microbial dynamics remain largely unknown, particularly in paddy soils. Here, we examined the underlying strategies and response mechanisms of microorganisms in regulating PEs and C accumulation in flooded paddy soil. Levels and stoichiometric ratios of resources were evaluated over a 60-day incubation period. Low (equivalent to 50% soil microbial biomass C [MBC]) and high (500% MBC) doses of 13C-labeled glucose were added to the soil, along with mineral N, P, and S (NPS) fertilizers at five concentrations. Glucose mineralization increased linearly with NPS concentration under both low and high glucose inputs. However, glucose addition without nutrients induced the preferential microbial utilization of the readily available C, leading to negative PEs. Under high-glucose input, the intensity of negative PEs increased with increasing NPS addition (PE: from −460 to −710 mg C kg−1 soil). In contrast, under low-glucose inputs, the intensity of positive PEs increased with increasing NPS addition (PE: 60–100 mg C kg−1 soil). High-glucose input with NPS fertilization favored high-yield microbial strategists (Y-strategists), increasing glucose-derived SOC accumulation. This phenomenon was evidenced by the large quantities of 13C detected in microbial biomass and phospholipid fatty acids (PLFAs), increasing the soil net C balance (from 0.76 to 1.2 g C kg−1). In contrast, low levels of glucose and NPS fertilization shifted the microbial community composition toward dominance of resource-acquisition strategists (A-strategists), increasing SOC mineralization. This was evidenced by 13C incorporation into the PLFAs of gram-positive bacteria, increased activity of N- and P-hydrolases, and positive PEs for acquiring C and nutrients from soil organic matter. Consequently, the soil net C balance decreased from 0.31 to 0.01 g C kg−1 soil. In conclusion, high C input (i.e., 500% MBC), particularly alongside hig NPS addition, increases SOC content via negative priming and microbial-derived C accumulation due to the shift toward Y-strategist communities which efficiently utilize resources. This study highlights the importance of mineral fertilization management when incorporating organic supplements in paddy soils to stimulate microbial turnover and C sequestration.

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the scientific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.

How soil microorganisms respond to global warming is key to infer future soil-climate feedbacks, yet poorly understood. Here, we applied metatranscriptomics to investigate microbial physiological responses to medium-term (8 years) and long-term (>50 years) subarctic grassland soil warming of +6°C. Besides indications for a community-wide up-regulation of centralmetabolic pathways and cell replication, we observed a down-regulation of the bacterial protein biosynthesis machinery in the warmed soils, coinciding with a lower microbial biomass, RNA, and soil substrate content. We conclude that permanently accelerated reaction rates at higher temperatures and reduced substrate concentrations result in cellular reduction of ribosomes, the macromolecular complexes carrying out protein biosynthesis. Later efforts to test this, including a short-term warming experiment (6 weeks, +6°C), further supported our conclusion. Down-regulating the protein biosynthesis machinery liberates energy and matter, allowing soil bacteria to maintain high metabolic activities and cell division rates even after decades of warming.