Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Abstract

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria

“…We selected 110 bacterial isolates from the same ORFRC field site for this study and compared the growth of the isolates in both NLDM and R2A. Notably, most isolations (35%) were made using R2A ( Supplementary Table 3 ; Thorgersen et al, 2015 ; Hemme et al, 2016 ; Liu et al, 2018 ; Price et al, 2018 ; Carlson et al, 2019 ; Vuono et al, 2019 ; Lui et al, 2021 ). It was found that only 2 out of the 110 isolates did not display significant growth in NLDM, whereas 6 out of the 110 isolates did not display significant growth in R2A medium ( Figure 1 and Supplementary Tables 3 , 7A–C ).…”

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

“…Microbial processes in soil are complicated by the physically and chemically structured environment, which is characterized by the porous soil architecture, diverse components and interfacial properties, coupled with the heterogeneous distribution of water, solutes, gases, and microbes. ,, Mechanistic understanding of the diversity, functions, and global ecological significance of soil microbes are still lack . Microfluidics is rapidly transforming the study of microbiology. − Multiple features make microfluidics a promising technology for exploring soil microbial processes .…”

“…The microenvironments, such as temperature, oxygen, flows, and chemical gradients, can be precisely manipulated as being constant or oscillating, homogeneous or heterogeneous. Therefore, microfluidics can serve as an experimental platform that addresses the challenge to link field (in situ) experiments and conventional laboratory culture-based methods for microbial studies . In this section, we review how soil microbial processes on-a-chip platforms facilitate soil microbiology studies from three aspects: (1) Microbe-environment interactions, which mainly deal with the question of how soil microbes adapt to environmental factors and how microbial activities reshape the soil environments; (2) Microbe-microbe interactions, which occur in microbial communities; and (3) Microbe-plant interactions, which dominate the processes in the rhizosphere.…”

Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer

“…The existence of abundant metal resistance genes in Rhodanobacter strains has been demonstrated by metagenomic data of the ORR site groundwater samples ( 8 ). As most studies have been based on metagenomic sequencing, studies with culture-dependent methods (i.e., isolation and growth) are needed to understand the growth, physiology, and mechanisms of adaptation for discrete but related populations ( 9 ).…”