scholarly journals Reducing fluctuations in species composition facilitates artificial selection of microbial community function

2018 ◽  
Author(s):  
Li Xie ◽  
Wenying Shou
Keyword(s):  
Microbial Community ◽  
Species Composition ◽  
Microbial Communities ◽  
Cell Sorting ◽  
Maturation Time ◽  
Experimental Procedure ◽  
Community Function ◽  
Stochastic Fluctuations ◽  
Total Product ◽  
Selection Of

AbstractMulti-species microbial communities often display functions - biochemical activities unattainable by member species alone, such as fighting pathogens. To improve community function, we can artificially select communities by growing “Newborn” communities over “maturation time” into “Adult” communities, and selecting highest-functioning Adults to “reproduce” by diluting each into multiple Newborns of the next cycle. Community selection has been attempted a few times on complex communities, often generating mixed results that are difficult to interpret. Here, we ask how costly community function may be improved via mutations and community selection. We simulate selection of two-species communities where Helpers digest Waste and generate Byproduct essential to Manufacturers; Manufacturers divert a fraction of their growth to make Product. Community function, the total Product in an “Adult”, is sub-optimal even when both species have been pre-optimized as monocultures. If we dilute an Adult into Newborns by pipetting (a common experimental procedure), stochastic fluctuations in Newborn composition prevents community function from improving. Reducing fluctuations via cell sorting allows selection to work. Our conclusions hold regardless of whether H and M are commensal or mutualistic, or variations in model assumptions.

scholarly journals Understanding the evolution of interspecies interactions in microbial communities

2020 ◽  
Vol 375 (1798) ◽  
pp. 20190256 ◽  
Author(s):  
Florien A. Gorter ◽  
Michael Manhart ◽  
Martin Ackermann
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Interaction Strength ◽  
Quantitative Model ◽  
Systematic Effect ◽  
Interspecies Interactions ◽  
Fitness Effects ◽  
Indirect Fitness ◽  
Beneficial Traits ◽  
Selection Of

Microbial communities are complex multi-species assemblages that are characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength of interspecies interactions have important consequences for emergent community-level properties such as productivity and stability. It is not well understood how interspecies interactions change over evolutionary timescales. Here, we review the empirical evidence that evolution is an important driver of microbial community properties and dynamics on timescales that have traditionally been regarded as purely ecological. Next, we briefly discuss different modelling approaches to study evolution of communities, emphasizing the similarities and differences between evolutionary and ecological perspectives. We then propose a simple conceptual model for the evolution of interspecies interactions in communities. Specifically, we propose that to understand the evolution of interspecies interactions, it is important to distinguish between direct and indirect fitness effects of a mutation. We predict that in well-mixed environments, traits will be selected exclusively for their direct fitness effects, while in spatially structured environments, traits may also be selected for their indirect fitness effects. Selection of indirectly beneficial traits should result in an increase in interaction strength over time, while selection of directly beneficial traits should not have such a systematic effect. We tested our intuitions using a simple quantitative model and found support for our hypotheses. The next step will be to test these hypotheses experimentally and provide input for a more refined version of the model in turn, thus closing the scientific cycle of models and experiments. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

scholarly journals Cohesiveness in microbial community coalescence

2018 ◽  
Author(s):  
Nanxi Lu ◽  
Alicia Sanchez-Gorostiaga ◽  
Mikhail Tikhonov ◽  
Alvaro Sanchez
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Empirical Work ◽  
Invasion Success ◽  
Community Members ◽  
Interacting Species ◽  
Resource Interactions ◽  
Different Origins ◽  
Microbial Community Assembly ◽  
Selection Of

AbstractMicrobial invasions exhibit many unique properties; notably, entire microbial communities often invade one another, a phenomenon known as community coalescence. In spite of the potential importance of this process for the dynamics and stability of microbiome assembly, our understanding of it is still very limited. Recent theoretical and empirical work has proposed that large microbial communities may exhibit an emergent cohesiveness, as a result of collective consumer-resource interactions and metabolic feedbacks between microbial growth and the environment. A fundamental prediction of this proposal is the presence of ecological co-selection during community coalescence, where the invasion success of a given taxon is determined by its community members. To establish the generality of this prediction in experimental microbiomes, we have performed over one hundred invasion and coalescence experiments with environmental communities of different origins that had spontaneously and stably assembled in two different synthetic aerobic environments. We show that the dominant species of the coalesced communities can both recruit their community members (top-down co-selection) and be recruited by them (bottom-up co-selection) into the coalesced communities. Our results provide direct evidence that collective invasions generically produce ecological co-selection of interacting species, emphasizing the importance of community-level interactions during microbial community assembly.

scholarly journals Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

2017 ◽  
Vol 14 (23) ◽  
pp. 5403-5424 ◽  
Author(s):  
Minsu Kim ◽  
Dani Or
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Mechanistic Model ◽  
Soil Surface ◽  
Hydration Status ◽  
Carbon And Nitrogen ◽  
Community Function ◽  
Diurnal Cycles ◽  
Biogeochemical Fluxes ◽  
Biogeochemical Hotspots

Abstract. Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

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 Microbial Function and Hydrochemistry within a Stratified Anchialine Sinkhole: A Window into Coastal Aquifer Interactions

Water ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 972 ◽  
Author(s):  
Madison Davis ◽  
James Garey
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Coastal Aquifer ◽  
Sulfide Oxidation ◽  
Mixing Zone ◽  
Mixing Processes ◽  
Community Function ◽  
Bioinformatic Tools ◽  
Floridan Aquifer ◽  
Aquifer Systems

Anchialine sinkholes provide insight into coastal aquifer systems and coastal mixing processes. Aquifer microbial community function is usually inferred from hydrochemical information, but there are few direct studies of microbial communities in the Floridan Aquifer. Hospital Hole is a 43 m-deep stratified sinkhole under the Weeki Wachee River, FL, with three distinct brackish layers: a hypoxic layer, a chemocline and a sulfidic anoxic layer. Illumina sequencing and bioinformatic tools were used to reconstruct metabolic functions and interactions of microbial communities in each layer. Each layer appears to originate from different parts of the coastal mixing zone and has a distinct microbial community with unique functions, which are influenced by the respective hydrochemistry. Sulfide oxidation and nitrate reduction are the most abundant functions. Syntrophy between methane oxidizers, methanogens and sulfate reducers is present. Similarities between the hydrochemistry and potential connectivity of Hospital Hole and the Floridan Aquifer coastal mixing zone suggest that microbial communities of Hospital Hole could be a surrogate for the coastal mixing zone of the aquifer in the absence of direct studies. Understanding how groundwater microbial communities react to saltwater intrusion and nutrient flux will be useful in predicting how coastal aquifer regions might react to anthropogenic change.

scholarly journals Predicting the structure and function of coalesced microbial communities

2017 ◽  
Author(s):  
Pawel Sierocinski ◽  
Kim Milferstedt ◽  
Florian Bayer ◽  
Tobias Großkopf ◽  
Mark Alston ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Methane Production ◽  
Structure And Function ◽  
Recent Theory ◽  
Simple Method ◽  
Average Performance ◽  
Community Function ◽  
And Function

ABSTRACTMicrobial communities commonly coalesce in nature, but the consequences for resultant community structure and function is unclear. Consistent with recent theory, we demonstrate using methanogenic communities that the most productive communities in isolation dominated when communities were mixed. As a corollary of this dynamic, total methane production increased with the number of inoculated communities. The cohesion and dominance of single communities was explained by more “niche-packed” communities being both more efficient at exploiting resources and resistant to invasion, rather than a function of the average performance of component species. These results are likely to be relevant to the ecological dynamics of natural microbial communities, as well as demonstrating a simple method to predictably enhance microbial community function in biotechnology, health and agriculture.

scholarly journals Patterns of Microbially Driven Carbon Cycling in the Ocean: Links between Extracellular Enzymes and Microbial Communities

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Carol Arnosti
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Carbon Cycling ◽  
Large Scale ◽  
Extracellular Enzymes ◽  
Microbial Community Composition ◽  
Deep Ocean ◽  
Community Function ◽  
Enzymatic Function ◽  
Depth Gradients

Heterotrophic microbial communities play a central role in the marine carbon cycle. They are active in nearly all known environments, from the surface to the deep ocean, in the sediments, and from the equator to the Poles. In order to process complex organic matter, these communities produce extracellular enzymes of the correct structural specificity to hydrolyze substrates to sizes sufficiently small for uptake. Extracellular enzymatic hydrolysis thus initiates heterotrophic carbon cycling. Our knowledge of the enzymatic capabilities of microbial communities in the ocean is still underdeveloped. Recent studies, however, suggest that there may be large-scale patterns of enzymatic function in the ocean, patterns of community function that may be connected to emerging patterns of microbial community composition. Here I review some of these large-scale contrasts in microbial enzyme activities, between high-latitude and temperate surface ocean waters, contrasts between inshore and offshore waters, changes with depth gradients in the ocean, and contrasts between the water column and underlying sediments. These contrasting patterns are set in the context of recent studies of microbial communities and patterns of microbial biogeography. Focusing on microbial community function as well as composition and potential should yield clearer understanding of the factors driving carbon cycling in the ocean.

scholarly journals Steering ecological-evolutionary dynamics during artificial selection of microbial communities

2018 ◽  
Author(s):  
Li Xie ◽  
Wenying Shou
Keyword(s):  
Microbial Communities ◽  
Artificial Selection ◽  
Evolutionary Dynamics ◽  
Ecological Interactions ◽  
Evolutionary Trajectory ◽  
Community Function ◽  
Selection Strategies ◽  
Effective Selection ◽  
Orthogonal Components ◽  
Selection Of

AbstractMicrobial communities often perform important functions that arise from interactions among member species. Community functions can be improved via artificial selection: Many communities are repeatedly grown, mutations arise, and communities with the highest desired function are chosen to reproduce where each is partitioned into multiple offspring communities for the next cycle. Since selection efficacy is often unimpressive in published experiments and since multiple experimental parameters need to be tuned, we sought to use computer simulations to learn how to design effective selection strategies. We simulated community selection to improve a community function that requires two species and imposes a fitness cost on one of the species. This simplified case allowed us to distill community function down to two fundamental and orthogonal components: a heritable determinant and a nonheritable determinant. We then visualize a “community function landscape” relating community function to these two determinants, and demonstrate that the evolutionary trajectory on the landscape is restricted along a path designated by ecological interactions. This path can prevent the attainment of maximal community function, and trap communities in landscape locations where community function has low heritability. Exploiting these observations, we devise a species spiking approach to shift the path to improve community function heritability and consequently selection efficacy. We show that our approach is applicable to communities with complex and unknown function landscapes.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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