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

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Li Xie ◽  
Wenying Shou
Keyword(s):  
Microbial Communities ◽  
Artificial Selection ◽  
Species Interactions ◽  
Evolutionary Dynamics ◽  
Species Coexistence ◽  
Evolutionary Trajectory ◽  
Community Function ◽  
Link Type ◽  
Selection Strategies ◽  
Effective Selection

AbstractMicrobial communities often perform important functions that depend on inter-species interactions. To improve community function via artificial selection, one can repeatedly grow many communities to allow mutations to arise, and “reproduce” the highest-functioning communities by partitioning each into multiple offspring communities for the next cycle. Since improvement is often unimpressive in experiments, we study how to design effective selection strategies in silico. Specifically, we simulate community selection to improve a function that requires two species. With a “community function landscape”, we visualize how community function depends on species and genotype compositions. Due to ecological interactions that promote species coexistence, the evolutionary trajectory of communities is restricted to a path on the landscape. This restriction can generate counter-intuitive evolutionary dynamics, prevent the attainment of maximal function, and importantly, hinder selection by trapping communities in locations of low community function heritability. We devise experimentally-implementable manipulations to shift the path to higher heritability, which speeds up community function improvement even when landscapes are high dimensional or unknown. Video walkthroughs: https://go.nature.com/3GWwS6j; https://online.kitp.ucsb.edu/online/ecoevo21/shou2/.

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.

scholarly journals Novel microbial syntrophies identified by longitudinal metagenomics

2021 ◽  
Author(s):  
Sebastien Raguideau ◽  
Anna Trego ◽  
Fred Farrell ◽  
Gavin Collins ◽  
Chris Quince ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Species Interactions ◽  
Novel Species ◽  
Sugar Transport ◽  
Operating Conditions ◽  
Functional Annotations ◽  
Community Function ◽  
Highly Correlated ◽  
Longitudinal Dataset ◽  
Syntrophic Associations

Identifying species interactions in a microbial community and how this relates to community function is a key challenge. Towards addressing this challenge, we present here an extensive genome-resolved, longitudinal dataset and associated metadata. We collected weekly samples of microbial communities and recorded operating conditions from industrial methane producing anaerobic digestion reactors for a year. This allowed us to recover 2240 dereplicated metagenome assembled genomes (dMAGs), together with their coverage dynamics and functional annotations from which functional traits were inferred. Of these dMAGs, 1910 were novel species, with 22 representing novel orders and classes. Methanogenic communities are expected to be strongly structured by syntrophic and other associations between the methanogens and syntrophs that produce their substrates. We identified 450 potential syntrophic dMAGs by searching for pairs of methanogenic and non-methanogenic dMAGs that had highly correlated time-series. Genomes of potential syntrophs were enriched for oxidoreductases and sugar transport genes and there was a strong taxonomic signal in their associations with methanogens. Of particular note, we found that Bathyarchaeiea associated specifically with methanogens from the Thermoplasmata, and Thermococci classes. Same syntrophic associations were only rarely observed across multiple reactors, suggesting that syntrophies might be facultative, with particular strains within a species forming syntrophic associations only sometimes and not necessarily always with the same methanogenic partner. The presented results show that longitudinal metagenomics is a highly valuable approach for identifying species and their interactions in microbial communities.

scholarly journals The importance of species interactions in eco-evolutionary community dynamics under climate change

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Anna Åkesson ◽  
Alva Curtsdotter ◽  
Anna Eklöf ◽  
Bo Ebenman ◽  
Jon Norberg ◽  
...  
Keyword(s):  
Climate Change ◽  
Species Interactions ◽  
Community Dynamics ◽  
Evolutionary Dynamics ◽  
Negative Impact ◽  
Trophic Levels ◽  
Temperature Dependent ◽  
Modeling Framework ◽  
Impact Of Climate Change ◽  
The Impact

AbstractEco-evolutionary dynamics are essential in shaping the biological response of communities to ongoing climate change. Here we develop a spatially explicit eco-evolutionary framework which features more detailed species interactions, integrating evolution and dispersal. We include species interactions within and between trophic levels, and additionally, we incorporate the feature that species’ interspecific competition might change due to increasing temperatures and affect the impact of climate change on ecological communities. Our modeling framework captures previously reported ecological responses to climate change, and also reveals two key results. First, interactions between trophic levels as well as temperature-dependent competition within a trophic level mitigate the negative impact of climate change on biodiversity, emphasizing the importance of understanding biotic interactions in shaping climate change impact. Second, our trait-based perspective reveals a strong positive relationship between the within-community variation in preferred temperatures and the capacity to respond to climate change. Temperature-dependent competition consistently results both in higher trait variation and more responsive communities to altered climatic conditions. Our study demonstrates the importance of species interactions in an eco-evolutionary setting, further expanding our knowledge of the interplay between ecological and evolutionary processes.

scholarly journals Topographic Effects on the Spatial Species Associations in Diverse Heterogeneous Tropical Evergreen Forests

2021 ◽  
Vol 13 (5) ◽  
pp. 2468
Author(s):  
Nguyen Hong Hai ◽  
Yousef Erfanifard ◽  
Van Bac Bui ◽  
Trinh Hien Mai ◽  
Any Mary Petritan ◽  
...  
Keyword(s):  
Species Interactions ◽  
Species Coexistence ◽  
Spatial Scales ◽  
Interspecific Interactions ◽  
Spatial Association ◽  
Topographic Effects ◽  
Habitat Association ◽  
Important Species ◽  
Evergreen Forests ◽  
Partial Overlap

Studying spatial patterns and habitat association of plant communities may provide understanding of the ecological mechanisms and processes that maintain species coexistence. To conduct assessments of correlation between community compositions and habitat association, we used data from two topographically different plots with 2 ha area in tropical evergreen forests with the variables recorded via grid systems of 10 × 10 m subplots in Northern-Central Vietnam. First, we tested the relationship between community composition and species diversity indices considering the topographical variables. We then assessed the interspecific interactions of 20 dominant plant species using the nearest-neighbor distribution function, Dij(r), and Ripley’s K-function, Kij(r). Based on the significant spatial association of species pairs, indices of interspecific interaction were calculated by the quantitative amounts of the summary statistics. The results showed that (i) community compositions were significantly influenced by the topographic variables and (ii) almost 50% significant pairs of species interactions were increased with increasing spatial scales up to 10–15 m, then declined and disappeared at scales of 30–40 m. Segregation and partial overlap were the dominant association types and disappeared at larger spatial scales. Spatial segregation, mixing, and partial overlap revealed the important species interactions in maintaining species coexistence under habitat heterogeneity in diverse forest communities.

scholarly journals Evolution of a predator-induced, nonlinear reaction norm

2017 ◽  
Vol 284 (1861) ◽  
pp. 20170859 ◽  
Author(s):  
Mauricio J. Carter ◽  
Martin I. Lind ◽  
Stuart R. Dennis ◽  
William Hentley ◽  
Andrew P. Beckerman
Keyword(s):  
Evolutionary Dynamics ◽  
Daphnia Pulex ◽  
Reaction Norm ◽  
Maximum Response ◽  
Selective Predation ◽  
Evolutionary Trajectory ◽  
Defensive Reaction ◽  
Selection Gradients ◽  
Hunting Strategies ◽  
Evolutionary Response

Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the micro-evolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients, we show how in the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex .

scholarly journals Deciphering the evolution of microbial interactions: in silico studies of two-member microbial communities

2022 ◽  
Author(s):  
Gayathri Sambamoorthy ◽  
Karthik Raman
Keyword(s):  
Microbial Communities ◽  
In Silico ◽  
Microbial Interactions ◽  
Interaction Patterns ◽  
Wild Type ◽  
Community Function ◽  
Evolutionary Forces ◽  
In Silico Studies ◽  
Wide Range ◽  
In The Wild

Microbes thrive in communities, embedded in a complex web of interactions. These interactions, particularly metabolic interactions, play a crucial role in maintaining the community structure and function. As the organisms thrive and evolve, a variety of evolutionary processes alter the interactions among the organisms in the community, although the community function remains intact. In this work, we simulate the evolution of two-member microbial communities in silico to study how evolutionary forces can shape the interactions between organisms. We employ genomescale metabolic models of organisms from the human gut, which exhibit a range of interaction patterns, from mutualism to parasitism. We observe that the evolution of microbial interactions varies depending upon the starting interaction and also on the metabolic capabilities of the organisms in the community. We find that evolutionary constraints play a significant role in shaping the dependencies of organisms in the community. Evolution of microbial communities yields fitness benefits in only a small fraction of the communities, and is also dependent on the interaction type of the wild-type communities. The metabolites cross-fed in the wild-type communities appear in only less than 50% of the evolved communities. A wide range of new metabolites are cross-fed as the communities evolve. Further, the dynamics of microbial interactions are not specific to the interaction of the wild-type community but vary depending on the organisms present in the community. Our approach of evolving microbial communities in silico provides an exciting glimpse of the dynamics of microbial interactions and offers several avenues for future investigations.

scholarly journals Genotype-Species Interactions in Neighbourhoods of Forest Tree Communities

2007 ◽  
Vol 56 (1-6) ◽  
pp. 101-110 ◽  
Author(s):  
Chr. Wehenkel ◽  
F. Bergmann ◽  
H.-R. Gregorius
Keyword(s):  
Species Interactions ◽  
Species Coexistence ◽  
Biotic Interactions ◽  
Forest Tree ◽  
Target Species ◽  
Species Identity ◽  
Enzymatic Function ◽  
Genotype Frequencies ◽  
Tree Communities ◽  
Large Survey

Abstract Studies on plant communities of various annual species suggest that there are particular biotic interactions among individuals from different species which could be the basis for long-term species coexistence. In the course of a large survey on species-genetic diversity relationships in several forest tree communities, it was found that statistically significant differences exist among isozyme genotype frequencies of conspecific tree groups, which differ only by species identity of their neighbours. Based on a specific measure, the association of the neighbouring species with the genotypes of the target species or that of the genotypes with the neighbouring species was quantified. Since only AAT and HEK of the five analysed enzyme systems differed in their genotype frequencies among several tree groups of the same target species, a potential involvement of their enzymatic function in the observed differences was discussed. The results of this study demonstrate a fine-scale genetic differentiation within single tree species of forest communities, which may be the result of biotic interactions between the genetic structure of a species and the species composition of its community. This observation also suggests the importance of intraspecific genetic variation for interspecific adaptation.

scholarly journals Metabolic Symbiosis Facilitates Species Coexistence and Generates Light-Dependent Priority Effects

2021 ◽  
Vol 8 ◽  
Author(s):  
Veronica Hsu ◽  
Holly V. Moeller
Keyword(s):  
Carbon Source ◽  
Community Composition ◽  
Green Algae ◽  
Species Interactions ◽  
Species Coexistence ◽  
Priority Effects ◽  
Competitive Interactions ◽  
Paramecium Bursaria ◽  
Mutual Benefit ◽  
Cascading Effects

Metabolic symbiosis is a form of symbiosis in which organisms exchange metabolites, typically for mutual benefit. For example, acquired phototrophs like Paramecium bursaria obtain photosynthate from endosymbiotic green algae called Chlorella. In addition to facilitating the persistence of P. bursaria by providing a carbon source that supplements P. bursaria’s heterotrophic digestion of bacteria, symbiotic Chlorella may impact competitive interactions between P. bursaria and other bacterivores, with cascading effects on community composition and overall diversity. Here, we tested the effects of metabolic symbiosis on coexistence by assessing the impacts of acquired phototrophy on priority effects, or the effect of species arrival order on species interactions, between P. bursaria and its competitor Colpidium. Our results suggest light-dependent priority effects. The acquired phototroph benefited from metabolic symbiosis during sequential arrival of each organism in competition, and led to increased growth of late-arriving Colpidium. These findings demonstrate that understanding the consequences of priority effects for species coexistence requires consideration of metabolic symbiosis.

Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities

Microbiology ◽  
2021 ◽  
Vol 167 (10) ◽  
Author(s):  
Aarón Barraza ◽  
Juan J. Montes-Sánchez ◽  
M. Goretty Caamal-Chan ◽  
Abraham Loera-Muro
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Plant Communities ◽  
Large Intestine ◽  
Bacterial Communities ◽  
Sonoran Desert ◽  
Rainy Season ◽  
Native Plant ◽  
Content Type ◽  
Link Type

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

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