Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter

Microbial carbon use efficiency (CUE) is a critical regulator of soil organic matter dynamics and terrestrial carbon fluxes, with strong implications for soil biogeochemistry models. While ecologists increasingly appreciate the importance of CUE, its core concepts remain ambiguous: terminology is inconsistent and confusing, methods capture variable temporal and spatial scales, and the significance of many fundamental drivers remains inconclusive. Here we outline the processes underlying microbial efficiency and propose a conceptual framework that structures the definition of CUE according to increasingly broad temporal and spatial drivers where (1) CUEP reflects population-scale carbon use efficiency of microbes governed by species-specific metabolic and thermodynamic constraints, (2) CUEC defines community-scale microbial efficiency as gross biomass production per unit substrate taken up over short time scales, largely excluding recycling of microbial necromass and exudates, and (3) CUEE reflects the ecosystem-scale efficiency of net microbial biomass production (growth) per unit substrate taken up as iterative breakdown and recycling of microbial products occurs. CUEE integrates all internal and extracellular constraints on CUE and hence embodies an ecosystem perspective that fully captures all drivers of microbial biomass synthesis and decay. These three definitions are distinct yet complementary, capturing the capacity for carbon storage in microbial biomass across different ecological scales. By unifying the existing concepts and terminology underlying microbial efficiency, our framework enhances data interpretation and theoretical advances

Variability and Host Density Independence in Inductions-based Estimates of Environmental Lysogeny

Temperate bacterial viruses (phages) may enter a symbiosis with their host cell, forming a unit called a lysogen. Infection and viral replication are disassociated in lysogens until an induction event such as DNA damage occurs, triggering viral-mediated lysis. The lysogen–lytic viral reproduction switch is central to viral ecology, with diverse ecosystem impacts. It has been argued that lysogeny is favoured in phages at low host densities. This paradigm is based on the fraction of chemically inducible cells (FCIC) lysogeny proxy determined using DNA-damaging mitomycin C inductions. Contrary to the established paradigm, a survey of 39 inductions publications found FCIC to be highly variable and pervasively insensitive to bacterial host density at global, within-environment and within-study levels. Attempts to determine the source(s) of variability highlighted the inherent complications in using the FCIC proxy in mixed communities, including dissociation between rates of lysogeny and FCIC values. Ultimately, FCIC studies do not provide robust measures of lysogeny or consistent evidence of either positive or negative host density dependence to the lytic–lysogenic switch. Other metrics are therefore needed to understand the drivers of the lytic–lysogenic decision in viral communities and to test models of the host density-dependent viral lytic–lysogenic switch

Influence of incubation conditions on bacterial production estimates in an estuarine system

This study aimed to assess the influence of incubation conditions in the determination of bacterial production (BP). In order to achieve that goal, experimental setups were performed in situ and in the laboratory under both dark and light conditions. To test spatial and seasonal variations and the different natural light exposure of microorganisms, sampling was performed in two distinct zones of the estuary Ria de Aveiro (Portugal), typifying the marine and brackish water zones of the estuarine system. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments was used to monitor possible alterations in bacterial community composition induced by the incubation conditions. The results showed that BP determined in situ conditions significantly differed from in the laboratory. In the marine zone, a defined pattern of variation was detected, with consistent higher values of BP in laboratory dark conditions. This trend was not present in the brackish water zone. The seasonal and spatial variability of BP observed in field incubations was related to the physical–chemical proprieties of the water column, irradiance levels and the original community composition. The metabolic active profiles of bacteria were substantially different in the several incubation conditions, suggesting that methodological procedure influences the bacterial community composition, and the values of BP reported for aquatic ecosystems could be quite different from the real ones. In the light of these results, we suggest that BP determinations should be conducted under in situ conditions. However, due to execution limitations, BP needs to be frequently determined in the laboratory, and in this case, dark incubations provide more approximate values. This is the method routinely used, and although this incubation condition can cause stimulation of BP, the structure of the bacterial community is more similar to the one obtained with the in situ incubations