More Like this

1. The impact of phage and phage resistance on microbial community dynamics

   https://doi.org/10.1371/journal.pbio.3002346  

   Alseth, Ellinor O; Custodio, Rafael; Sundius, Sarah A; Kuske, Rachel A; Brown, Sam P; Westra, Edze R (April 2024, PLOS Biology)

   Barr, Jeremy J (Ed.)

   Where there are bacteria, there will be bacteriophages. These viruses are known to be important players in shaping the wider microbial community in which they are embedded, with potential implications for human health. On the other hand, bacteria possess a range of distinct immune mechanisms that provide protection against bacteriophages, including the mutation or complete loss of the phage receptor, and CRISPR-Cas adaptive immunity. While our previous work showed how a microbial community may impact phage resistance evolution, little is known about the inverse, namely how interactions between phages and these different phage resistance mechanisms affect the wider microbial community in which they are embedded. Here, we conducted a 10-day, fully factorial evolution experiment to examine how phage impact the structure and dynamics of an artificial four-species bacterial community that includes eitherPseudomonas aeruginosawild-type or an isogenic mutant unable to evolve phage resistance through CRISPR-Cas. Additionally, we used mathematical modelling to explore the ecological interactions underlying full community behaviour, as well as to identify general principles governing the impacts of phage on community dynamics. Our results show that the microbial community structure is drastically altered by the addition of phage, withAcinetobacter baumanniibecoming the dominant species andP.aeruginosabeing driven nearly extinct, whereasP.aeruginosaoutcompetes the other species in the absence of phage. Moreover, we find that aP.aeruginosastrain with the ability to evolve CRISPR-based resistance generally does better when in the presence ofA.baumannii, but that this benefit is largely lost over time as phage is driven extinct. Finally, we show that pairwise data alone is insufficient when modelling our microbial community, both with and without phage, highlighting the importance of higher order interactions in governing multispecies dynamics in complex communities. Combined, our data clearly illustrate how phage targeting a dominant species allows for the competitive release of the strongest competitor while also contributing to community diversity maintenance and potentially preventing the reinvasion of the target species, and underline the importance of mapping community composition before therapeutically applying phage. 

   more » « less
2. Resources do not limit compensatory response of a tallgrass prairie plant community to the loss of a dominant species

   https://doi.org/10.1111/1365-2745.13741  

   Chaves, Francis A.; Smith, Melinda D. (August 2021, Journal of Ecology)

   Abstract The effect of species loss on ecosystem productivity is determined by both the functional contribution of the species lost, and the response of the remaining species in the community. According to the mass ratio hypothesis, the loss of a dominant plant species, which has a larger proportionate contribution to productivity, is expected to exert an overwhelming effect on this important ecosystem function. However, via competitive release, loss of a dominant species can provide the opportunity for other plant species to establish, thrive and become abundant in the community, potentially compensating for the function lost. Furthermore, if resource limitation is removed, then the compensatory response of function to the loss of a dominant species should be greater and more rapid than if resources are more limiting.To evaluate how resources may limit compensation of above‐ground productivity to the loss of a dominant plant species, we experimentally removed the C₄perennial tallgrass,Andropogon gerardii, from intact plant communities. We added water for 4 years, as well as nitrogen in the fourth year, to test the effect of resource limitation on the compensatory response.Overall, above‐ground biomass production increased in the remaining community with both water and nitrogen addition. However, this increase in biomass production was not sufficient to fully compensate for the loss ofA. gerardii, indicating water and nitrogen were not limiting short‐term compensation in this community.Following the removal of the dominant species, there was reordering of species abundances in the community, rather than changes in species richness. The C₄grassBouteloua curtipendulawas the most responsive species, increasing by 57.9% in abundance with water addition and 91.0% with both water and nitrogen addition. Despite this dramatic increase in abundance, its short stature and lower per capita biomass production prevented this species from compensating for the loss ofA. gerardii.Synthesis. Short‐term compensation after the loss of a dominant plant species can be hastened by increased resource availability, but ultimately full compensation appears to be limited by the presence and abundance of species in the remaining community that possess traits that allow them compensate for the species lost. 

   more » « less
3. Gene communities in co-expression networks across different tissues

   https://doi.org/10.1371/journal.pcbi.1011616  

   Russell, Madison; Aqil, Alber; Saitou, Marie; Gokcumen, Omer; Masuda, Naoki (November 2023, PLOS Computational Biology)

   Fu, Feng (Ed.)

   With the recent availability of tissue-specific gene expression data, e.g., provided by the GTEx Consortium, there is interest in comparing gene co-expression patterns across tissues. One promising approach to this problem is to use a multilayer network analysis framework and perform multilayer community detection. Communities in gene co-expression networks reveal groups of genes similarly expressed across individuals, potentially involved in related biological processes responding to specific environmental stimuli or sharing common regulatory variations. We construct a multilayer network in which each of the four layers is an exocrine gland tissue-specific gene co-expression network. We develop methods for multilayer community detection with correlation matrix input and an appropriate null model. Our correlation matrix input method identifies five groups of genes that are similarly co-expressed in multiple tissues (a community that spans multiple layers, which we call a generalist community) and two groups of genes that are co-expressed in just one tissue (a community that lies primarily within just one layer, which we call a specialist community). We further found gene co-expression communities where the genes physically cluster across the genome significantly more than expected by chance (on chromosomes 1 and 11). This clustering hints at underlying regulatory elements determining similar expression patterns across individuals and cell types. We suggest thatKRTAP3-1,KRTAP3-3, andKRTAP3-5share regulatory elements in skin and pancreas. Furthermore, we find thatCELA3AandCELA3Bshare associated expression quantitative trait loci in the pancreas. The results indicate that our multilayer community detection method for correlation matrix input extracts biologically interesting communities of genes. 

   more » « less
4. Press–pulse interactions and long‐term community dynamics in a Chihuahuan Desert grassland

   https://doi.org/10.1111/jvs.12881  

   Collins, Scott L.; Chung, Y. Anny; Baur, Lauren E.; Hallmark, Alesia; Ohlert, Timothy J.; Rudgers, Jennifer A.; Valencia, ed., Enrique (May 2020, Journal of Vegetation Science)

   Abstract QuestionsReordering of dominant species is an important mechanism of community response to global environmental change. We asked how wildfire (apulseevent) interacts with directional changes in climate (environmentalpresses) to affect plant community dynamics in a Chihuahuan Desert grassland. LocationSevilleta National Wildlife Refuge, Socorro County, New Mexico, USA. MethodsVegetation cover by species was measured twice each year from 1989 to 2019 along two permanently located 400‐m long line intercept transects, one in Chihuahuan Desert grassland, and the second in the ecotone between Chihuahuan Desert and Great Plains grasslands. Trends in community structure were plotted over time, and climate sensitivity functions were used to predict how changes in the Pacific Decadal Oscillation (PDO) affected vegetation dynamics. ResultsCommunity composition was undergoing gradual change in the absence of disturbance in the ecotone and desert grassland. These changes were related to the reordering of abundances between two foundation grasses,Bouteloua eriopodaandB. gracilis, that together account for >80% of above‐ground primary production. However, reordering varied over time in response to wildfire (apulse) and changes in the PDO (apress). Community dynamics were initially related to the warm and cool phases of the PDO, but in the ecotone these relationships changed following wildfire, which reset the system. ConclusionSpecies reordering is an important component of community dynamics in response to ecological presses. However, reordering is a complex, non‐linear process in response to ecological presses that may change over time and interact with pulse disturbances. 

   more » « less
5. Disturbance–diversity relationships of microbial communities change based on growth substrate

   https://doi.org/10.1128/msystems.00887-23  

   Hoang, Don Q; Wilson, Lindsay R; Scheftgen, Andrew J; Suen, Garret; Currie, Cameron R (January 2024, mSystems)

   Gibbons, Sean M (Ed.)

   ABSTRACT Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances and how those responses can vary is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that the community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the generaCellvibrio,Lacunisphaera, andAsticcacaulisare the most abundant microbes. However,Lacunisphaerais only abundant in the lower disturbance frequency treatments, whileAsticcacaulisis more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are twoPseudomonassequence variants and aCohnellasequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (1.95–7.33 Hill 1 diversity) that peaks at the intermediate disturbance frequency treatment or one disturbance every 3 days. Communities grown on glucose, however, ranged from 1.63 to 5.19 Hill 1 diversity with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency and may potentially explain the variety of diversity–disturbance relationships observed in microbial systems. IMPORTANCEA generalizable diversity–disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial community’s response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment. 

   more » « less