Model microbial communities for ecosystems biology

Blasche, Sonja; Kim, Yongkyu; Oliveira, Ana Paula de; Patil, Kiran R.

doi:10.1016/j.coisb.2017.09.002

Cited by 48 publications

(40 citation statements)

References 63 publications

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“…By studying bacteria in complex, spatially structured communities instead of homogeneous planktonic populations, we have advanced the understanding of emergent properties and interactions (Tan et al, 2017;Madsen et al, 2018). When studying multi-species biofilms, it is of great importance to choose the right consortium for the research inquiry (for example processes, spatial patterns and mechanisms) and determine whether to consider the community as a unit or evaluate activity, fitness and functional contribution of individual species (Johns et al, 2016;Liu et al, 2016;Blasche et al, 2017;Tan et al, 2017). Many studies investigating the fundamental mechanisms behind interactions use model strains, such as Escherichia coli and Pseudomonas aeruginosa, which have been adapted to laboratory growth conditions and are easily genetically engineered.…”

Section: Synthetic Communities and Choice Of Model Systemmentioning

confidence: 99%

Unravelling interspecies interactions across heterogeneities in complex biofilm communities

Røder

Olsen

Whiteley

et al. 2019

Environmental Microbiology

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The importance of microbial biofilms has been wellrecognized for several decades, and focus is now shifting towards investigating multispecies biofilm communities rather than mono-or dual-species biofilms. Therefore, the demand for techniques that provide a sufficient amount of information at adequate resolution is increasing. One major challenge for multispecies studies is that diversity and spatial organization often lead to a high degree of spatial and chemical heterogeneity. Many current approaches do not account for such heterogeneity and therefore only provide average information (−omics techniques in particular), which could obscure important information about the community. Here, we bring attention to the issues of heterogeneity when analysing synthetic multi-species biofilms, in vitro, and the importance of multi-scale approaches. We provide an overview of current and newer approaches that can be applied to biofilm communities, in order to elucidate interactions at the appropriate scale.

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Section: Synthetic Communities and Choice Of Model Systemmentioning

confidence: 99%

Unravelling interspecies interactions across heterogeneities in complex biofilm communities

Røder

Olsen

Whiteley

et al. 2019

Environmental Microbiology

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“…Laboratory studies therefore remain crucial for understanding the mechanistic basis of stable coexistence. Experiments with synthetic assemblies or communities with genetically engineered members have helped in, for example, providing empirical evidence for stability at higher species richness (Pennekamp et al, 2018), discover assembly rules (Friedman et al, 2017), and, more mechanistically, in discovering stabilizing interactions like cross-feeding (Blasche et al, 2017a;Dubey and Ben-Yehuda, 2011;Ponomarova et al, 2017;Wintermute and Silver, 2010).…”

Section: Introductionmentioning

confidence: 99%

Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning

Blasche¹,

Kim²,

Mars³

et al. 2019

Preprint

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Microbial communities in nature often feature complex compositional dynamics yet also stable coexistence of diverse species. The mechanistic underpinnings of such dynamic stability remain unclear as system-wide studies have been limited to small engineered communities or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community, realizes stable coexistence through spatio-temporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a dynamic fashion with early members opening metabolic niches for the followers. Through large-scale mapping of metabolic preferences and inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate the community through metabolic cooperation and uneven partitioning between the grain and the liquid phase. Overall, our findings reveal how spatio-temporal dynamics promote stable coexistence and have implications for deciphering and modulating complex microbial ecosystems.

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“…The use of microcosms eliminates the spatial heterogeneity in edaphic factors that routinely confounds attempts to attribute carbon fate to microbial community features in field studies. Proof-of-principle studies with laboratory ecosystems can justify and guide more targeted validation studies in natural ecosystems (5, 6).…”

Section: Introductionmentioning

confidence: 99%

Microbial community-level features linked to divergent carbon flows during early litter decomposition in a constant environment

Johansen

Albright

Lopez

et al. 2019

Preprint

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27During plant litter decomposition in soils, carbon has two general fates: return to the atmosphere 28 via microbial respiration or transport into soil where long-term storage may occur. Discovering 29 microbial community features that drive carbon fate from litter decomposition may improve 30 modeling and management of soil carbon. This concept assumes there are features (or 31 underlying processes) that are widespread among disparate communities, and therefore amenable 32 to modeling. We tested this assumption using an epidemiological approach in which two 33 contrasting patterns of carbon flow in laboratory microcosms were delineated as functional states 34 and diverse microbial communities representing each state were compared to discover shared 35 features linked to carbon fate. Microbial communities from 206 soil samples from the 36 southwestern United States were inoculated on plant litter in microcosms, and carbon flow was 37 measured as cumulative carbon dioxide (CO2) and dissolved organic carbon (DOC) after 44 38 days. Carbon flow varied widely among the microcosms, with a 2-fold range in cumulative CO2 39 efflux and a 5-fold range in DOC quantity. Bacteria, not fungi, were the strongest drivers of 40 DOC variation. The most significant community-level feature linked to DOC abundance was 41 bacterial richness-the same feature linked to carbon fate in human-gut microbiome studies. 42 This proof-of-principle study under controlled conditions suggests common features driving 43 carbon flow in disparate microbial communities can be identified, motivating further exploration 44 of underlying mechanisms that may influence carbon fate in natural ecosystems. 45 46

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Model microbial communities for ecosystems biology

Cited by 48 publications

References 63 publications

Unravelling interspecies interactions across heterogeneities in complex biofilm communities

Unravelling interspecies interactions across heterogeneities in complex biofilm communities

Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning

Microbial community-level features linked to divergent carbon flows during early litter decomposition in a constant environment

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