ArticleFrontiers in microbiology2016
A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?
Article in Frontiers in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 41 citations in OpenAlex.
- From Single Organisms to Communities: Modeling Methanotrophs and Their Satellites.Microorganisms · 2025Review
- Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes.FEMS microbiology reviews · 2025Review
- Expanding the C-S-R framework to incorporate microbial interactions: evidence from methane-consuming communities.Frontiers in microbiology · 2025Article
- Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity.Communications biology · 2024Article
- Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods.International journal of environmental research and public health · 2021Article
- From nature to nurture: Essence and methods to isolate robust methanotrophic bacteria.Synthetic and systems biotechnology · 2020Article
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- Article
- Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities.Frontiers in microbiology · 2020Article
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- Coculturing Bacteria Leads to Reduced Phenotypic Heterogeneities.Applied and environmental microbiology · 2019Article
- Interspecies Chemical Signaling in a Methane-Oxidizing Bacterial Community.Applied and environmental microbiology · 2019Article
- A pathway for biological methane production using bacterial iron-only nitrogenase.Nature microbiology · 2018Article
- Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems.Scientific reports · 2018Article
- Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution.Frontiers in genetics · 2018Article
- Experimental design and quantitative analysis of microbial community multiomics.Genome biology · 2017Review
- Communal metabolism of methane and the rare Earth element switch.Journal of bacteriology · 2017Article
- Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Resolving Species Level Changes in a Representative Soil Bacterial Community Using Microfluidic Quantitative PCR.Frontiers in microbiology · 2017Article
- Natural Selection in Synthetic Communities Highlights the Roles ofFrontiers in microbiology · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified co-occurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. These findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.
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