scholarly journals Ecological landscapes guide the assembly of optimal microbial communities

2021 ◽  
Author(s):  
Ashish B. George ◽  
Kirill S. Korolev
Keyword(s):  
Microbial Communities ◽  
Heuristic Search ◽  
Niche Overlap ◽  
Biofuel Production ◽  
Microbial Consortia ◽  
Search Performance ◽  
High Performing ◽  
Soil Microbial ◽  
Community Function ◽  
Distribution Of Resources

Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.

scholarly journals Anaerobic Decomposition of Switchgrass by Tropical Soil-Derived Feedstock-Adapted Consortia

mBio ◽  
2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Kristen M. DeAngelis ◽  
Julian L. Fortney ◽  
Sharon Borglin ◽  
Whendee L. Silver ◽  
Blake A. Simmons ◽  
...  
Keyword(s):  
Microbial Community ◽  
Tropical Forest ◽  
Microbial Communities ◽  
Forest Soils ◽  
Cloud Forest ◽  
Electron Acceptors ◽  
Biofuel Production ◽  
Microbial Consortia ◽  
Microbial Community Function ◽  
Community Function

ABSTRACTTropical forest soils decompose litter rapidly with frequent episodes of anoxic conditions, making it likely that bacteria using alternate terminal electron acceptors (TEAs) play a large role in decomposition. This makes these soils useful templates for improving biofuel production. To investigate how TEAs affect decomposition, we cultivated feedstock-adapted consortia (FACs) derived from two tropical forest soils collected from the ends of a rainfall gradient: organic matter-rich tropical cloud forest (CF) soils, which experience sustained low redox, and iron-rich tropical rain forest (RF) soils, which experience rapidly fluctuating redox. Communities were anaerobically passed through three transfers of 10 weeks each with switchgrass as a sole carbon (C) source; FACs were then amended with nitrate, sulfate, or iron oxide. C mineralization and cellulase activities were higher in CF-FACs than in RF-FACs. Pyrosequencing of the small-subunit rRNA revealed members of theFirmicutes,Bacteroidetes, andAlphaproteobacteriaas dominant. RF- and CF-FAC communities were not different in microbial diversity or biomass. The RF-FACs, derived from fluctuating redox soils, were the most responsive to the addition of TEAs, while the CF-FACs were overall more efficient and productive, both on a per-gram switchgrass and a per-cell biomass basis. These results suggest that decomposing microbial communities in fluctuating redox environments are adapted to the presence of a diversity of TEAs and ready to take advantage of them. More importantly, these data highlight the role of local environmental conditions in shaping microbial community function that may be separate from phylogenetic structure.IMPORTANCEAfter multiple transfers, we established microbial consortia derived from two tropical forest soils with different native redox conditions. Communities derived from the rapidly fluctuating redox environment maintained a capacity to use added terminal electron acceptors (TEAs) after multiple transfers, though they were not present during the enrichment. Communities derived from lower-redox soils were not responsive to TEA addition but were much more efficient at switchgrass decomposition. Though the communities were different, diversity was not, and both were dominated by many of the same species of clostridia. This reflects the inadequacy of rRNA for determining the function of microbial communities, in this case the retained ability to utilize TEAs that were not part of the selective growth conditions. More importantly, this suggests that microbial community function is shaped by life history, where environmental factors produce heritable traits through natural selection over time, creating variation in the community, a phenomenon not well documented for microbes.

scholarly journals Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Kateryna Zhalnina ◽  
Karsten Zengler ◽  
Dianne Newman ◽  
Trent R. Northen
Keyword(s):  
Microbial Communities ◽  
Metabolic Networks ◽  
Soil Microbial Communities ◽  
Microbial Interactions ◽  
Microbial Consortia ◽  
Cellular Biology ◽  
Model Organisms ◽  
Soil Microbial ◽  
Integrative Framework ◽  
Genome Annotations

ABSTRACTThe chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.

scholarly journals High-order interactions dominate the functional landscape of microbial consortia

2018 ◽  
Author(s):  
Alicia Sanchez-Gorostiaga ◽  
Djordje Bajić ◽  
Melisa L. Osborne ◽  
Juan F. Poyatos ◽  
Alvaro Sanchez
Keyword(s):  
Species Interactions ◽  
Species Traits ◽  
High Order ◽  
Microbial Consortia ◽  
Order Effects ◽  
High Performing ◽  
Community Function ◽  
Functional Interactions ◽  
Complex Interactions ◽  
And Function

AbstractUnderstanding the link between community composition and function is a major challenge in microbial ecology, with implications for the management of natural microbiomes and the design of synthetic consortia. For this purpose, it is critical to understand the extent to which community functions and properties can be predicted from species traits and what role is played by complex interactions. Inspired by the study of complex genetic interactions and fitness landscapes, here we have examined how the amylolytic function of combinatorial assemblages of seven starch-degrading soil bacteria depends on the functional contributions from each species and their interactions. Filtering our experimental results through the theory of enzyme kinetics, we show that high-order functional interactions dominate the amylolytic rate of our consortia, even though this function is biochemically simple, redundantly distributed in the community, and additive in the absence of inter-species interactions. As the community grows in size, the contribution of high-order functional interactions grows too, making the community function increasingly unpredictable. We can explain the prevalence of high order effects and their sign from the redundancy of ecological interactions in the network, in particular from redundant facilitation towards a high-performing community member. Our results suggest that even simple functions can be dominated by complex interactions, posing challenges for the predictability and bottom-up engineering of ecosystem function in complex multi-species communities.

scholarly journals Interactions in self-assembled microbial communities saturate with diversity

2018 ◽  
Author(s):  
Xiaoqian Yu ◽  
Martin F. Polz ◽  
Eric J. Alm
Keyword(s):  
Microbial Communities ◽  
Niche Overlap ◽  
Detectable Effect ◽  
Negative Effects ◽  
Community Function ◽  
Carbon Use Efficiency ◽  
Large Numbers ◽  
Wide Range ◽  
Use Efficiency ◽  
Self Assembled

AbstractHow the diversity of organisms competing for or sharing resources influences community production is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. To parse the effect of different types of organismal interactions, we developed relative total function (RTF) as an index for positive or negative effects of diversity on community function. Our analysis identified three overall regimes with increasing diversity. At low richness (<12 taxa), potential positive and negative effects of interactions are both weak, while at moderate richness (12-20 taxa), community resource uptake increases but the carbon use efficiency decreases. Finally, beyond 20 taxa, there was no net change in community function indicating a saturation of potential interactions. These data suggest that although more diverse communities had overall greater access to resources, individual taxa within these communities had lower resource availability and reduced carbon use efficiency, indicating that competition due to niche overlap increases with diversity but that these interactions saturate at a specific threshold.

scholarly journals The effect of resource history on the functioning of soil microbial communities is maintained across time

2011 ◽  
Vol 8 (1) ◽  
pp. 1643-1667 ◽  
Author(s):  
A. D. Keiser ◽  
M. S. Strickland ◽  
N. Fierer ◽  
M. A. Bradford
Keyword(s):  
Microbial Communities ◽  
Rapid Evolution ◽  
Soil Microbial Communities ◽  
Loss Of Function ◽  
Decomposition Rates ◽  
Soil Microbial ◽  
Community Function ◽  
History Of ◽  
Experimental History ◽  
Litter Environment

Abstract. Historical resource conditions appear to influence microbial community function. With time, historical influences might diminish as populations respond to the contemporary environment. Alternatively, they may persist given factors such as contrasting genetic potentials for adaptation to a new environment. Using experimental microcosms, we test competing hypotheses that function of distinct soil microbial communities in common environments (H1a) converge or (H1b) remain dissimilar over time. Using a 6 × 2 (soil community inoculum × litter environment) full-factorial design, we compare decomposition rates in experimental microcosms containing grass or hardwood litter environments. After 100 days, communities that develop are inoculated into fresh litters and decomposition followed for another 100 days. We repeat this for a third, 100-day period. In each successive, 100-day period, we find higher decomposition rates (i.e. functioning) suggesting communities function better when they have an experimental history of the contemporary environment. Despite these functional gains, differences in decomposition rates among initially distinct communities persist, supporting the hypothesis that dissimilarity is maintained across time. In contrast to function, community composition is more similar following a common, experimental history. We also find that "specialization" on one experimental environment incurs a cost, with loss of function in the alternate environment. For example, experimental history of a grass-litter environment reduced decomposition when communities were inoculated into a hardwood-litter environment. Our work demonstrates experimentally that despite expectations of fast growth rates, physiological flexibility and rapid evolution, initial functional differences between microbial communities are maintained across time. These findings question whether microbial dynamics can be omitted from models of ecosystem processes if we are to predict reliably global change effects on biogeochemical cycles.

scholarly journals Nutrient availability shifts the biosynthetic potential of soil-derived microbial communities

2021 ◽  
Author(s):  
Marc Chevrette ◽  
Bradley Himes ◽  
Camila Carlos-Shanley
Keyword(s):  
Secondary Metabolites ◽  
Microbial Communities ◽  
Nutrient Availability ◽  
Biological Activities ◽  
Gene Clusters ◽  
Microbial Consortia ◽  
Pharmaceutical Drugs ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Soil Microbial

Secondary metabolites produced by microorganisms are the main source of antimicrobials other pharmaceutical drugs. Soil microbes have been the primary discovery source for these secondary metabolites, often producing complex organic compounds with specific biological activities. Research suggests that secondary metabolism broadly shapes microbial ecological interactions, but little is known about the factors that shape the abundance, distribution, and diversity of biosynthetic gene clusters in the context of microbial communities. In this study, we investigate the role of nutrient availability on the abundance of biosynthetic gene clusters in soil-derived microbial consortia. We found that soil microbial consortia enriched in medium with 150 mg/L of glucose and 200 mg/L of trehalose (here defined as high sugar) had more biosynthetic gene cluster and higher inhibitory activity than soil microbial consortia enriched in medium with 15 mg/L of glucose + 20 mg/L of trehalose (here defined as low sugar). Our results demonstrate that laboratory microbial communities are a promising tool to study ecology of specialized metabolites.

scholarly journals The effect of resource history on the functioning of soil microbial communities is maintained across time

2011 ◽  
Vol 8 (6) ◽  
pp. 1477-1486 ◽  
Author(s):  
A. D. Keiser ◽  
M. S. Strickland ◽  
N. Fierer ◽  
M. A. Bradford
Keyword(s):  
Microbial Communities ◽  
Rapid Evolution ◽  
Soil Microbial Communities ◽  
Loss Of Function ◽  
Decomposition Rates ◽  
Soil Microbial ◽  
Community Function ◽  
History Of ◽  
Experimental History ◽  
Litter Environment

Abstract. Historical resource conditions appear to influence microbial community function. With time, historical influences might diminish as populations respond to the contemporary environment. Alternatively, they may persist given factors such as contrasting genetic potentials for adaptation to a new environment. Using experimental microcosms, we test competing hypotheses that function of distinct soil microbial communities in common environments (H1a) converge or (H1b) remain dissimilar over time. Using a 6 × 2 (soil community inoculum × litter environment) full-factorial design, we compare decomposition rates in experimental microcosms containing grass or hardwood litter environments. After 100 days, communities that develop are inoculated into fresh litters and decomposition followed for another 100 days. We repeat this for a third, 100-day period. In each successive, 100-day period, we find higher decomposition rates (i.e. functioning) suggesting communities function better when they have an experimental history of the contemporary environment. Despite these functional gains, differences in decomposition rates among initially distinct communities persist, supporting the hypothesis that dissimilarity is maintained across time. In contrast to function, community composition is more similar following a common, experimental history. We also find that "specialization" on one experimental environment incurs a cost, with loss of function in the alternate environment. For example, experimental history of a grass-litter environment reduced decomposition when communities were inoculated into a hardwood-litter environment. Our work demonstrates experimentally that despite expectations of fast growth rates, physiological flexibility and rapid evolution, initial functional differences between microbial communities are maintained across time. These findings question whether microbial dynamics can be omitted from models of ecosystem processes if we are to predict reliably global change effects on biogeochemical cycles.

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