About this Research Topic
Marine microbes play a fundamental role in sustaining global food webs by generating organic matter from CO2 and breaking down living cells and dead organic matter to release nutrients. While modern sequencing technologies provide means to easily assess microbial community profiles from ecosystems, we are lagging behind in functional and mechanistic understanding of these communities. This becomes evident, for example, when cultured microbial strains behave differently than expected from in vivo observations. Ecosystems are more than the sum of their individual parts, and we need models to find out how the parts interact to generate the observed ecosystem behavior. Ecological interactions such as predation and parasitism have been recognized as crucial factors shaping marine microbial ecosystems, but environmental conditions (pH, salinity, nutrient availability) are equally important. To achieve a holistic view of these systems, physicochemical data should be integrated with microbial profiles. A variety of modeling approaches can be applied to achieve this goal, ranging from network representations to metabolic models covering the whole ecosystem or parts thereof.
For this Research Topic, we encourage submissions taking up one or several of the following challenges:
- Providing functional and/or mechanistic insights into ecosystem dynamics or functions on small or large scales, including deciphering interactions between individuals of the same species, of different species and models that encompass the whole community and environmental parameters.
- Modeling the interplay between planktonic and sessile or particle attached microorganisms: how they interact and how their interactions influence community functions.
- How can we better understand the metabolic workings of microbial communities? Can we infer metabolic strategies and their impact on interactions from sequence data? Can we integrate metabolic capabilities and/or strategies in the models to explain ecosystem dynamics and resilience?
- How well do models based on traits or functions describe marine ecosystems? Does the integration of functional aspects improve population models? How can we reliably quantify the relevant traits?
- Methodological advances: What are alternatives to generating relative abundance data and how can they be implemented (new library preparation techniques, spike-ins, flow cytometry, high-throughput imaging techniques, ...)? How can we best experimentally validate species interactions? How can we measure efficiently model parameters such as growth rates and nutrient uptake kinetics?
For this Research Topic, we encourage submissions taking up one or several of the following challenges:
- Providing functional and/or mechanistic insights into ecosystem dynamics or functions on small or large scales, including deciphering interactions between individuals of the same species, of different species and models that encompass the whole community and environmental parameters.
- Modeling the interplay between planktonic and sessile or particle attached microorganisms: how they interact and how their interactions influence community functions.
- How can we better understand the metabolic workings of microbial communities? Can we infer metabolic strategies and their impact on interactions from sequence data? Can we integrate metabolic capabilities and/or strategies in the models to explain ecosystem dynamics and resilience?
- How well do models based on traits or functions describe marine ecosystems? Does the integration of functional aspects improve population models? How can we reliably quantify the relevant traits?
- Methodological advances: What are alternatives to generating relative abundance data and how can they be implemented (new library preparation techniques, spike-ins, flow cytometry, high-throughput imaging techniques, ...)? How can we best experimentally validate species interactions? How can we measure efficiently model parameters such as growth rates and nutrient uptake kinetics?
Keywords: microbial ecosystem modeling, marine systems biology, marine microbial ecology, metabolic bases of species interactions, network modeling
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
