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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.

    

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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)

   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.

    

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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.

    

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4. Arbuscular mycorrhizal diversity increases across a plant productivity gradient driven by soil nitrogen availability

   https://doi.org/10.1002/pei3.70002  

   McPherson, Morgan_R ; Zak, Donald_R ; Ibáñez, Inés ; Upchurch, Rima_A ; Argiroff, William_A ( August 2024 , Plant-Environment Interactions)

   Arbuscular mycorrhizal fungi (AMF) are widespread obligate symbionts of plants. This dynamic symbiosis plays a large role in successful plant performance, given that AMF help to ameliorate plant responses to abiotic and biotic stressors. Although the importance of this symbiosis is clear, less is known about what may be driving this symbiosis, the plant's need for nutrients or the excess of plant photosynthate being transferred to the AMF, information critical to assess the functionality of this relationship. Characterizing the AMF community along a natural plant productivity gradient is a first step in understanding how this symbiosis may vary across the landscape. We surveyed the AMF community diversity at 12 sites along a plant productivity gradient driven by soil nitrogen availability. We found that AMF diversity in soil environmental DNA significantly increased along with the growth of the host plantsAcerrubrumandA. saccharum., a widespread tree genus. These increases also coincided with a natural soil inorganic N availability gradient. We hypothesize photosynthate from the increased tree growth is being allocated to the belowground AMF community, leading to an increase in diversity. These findings contribute to understanding this complex symbiosis through the lens of AMF turnover and suggest that a more diverse AMF community is associated with increased host–plant performance.

    

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5. Expanding the invasion footprint: Ventenata dubia and relationships to wildfire, environment, and plant communities in the Blue Mountains of the Inland Northwest, USA

   https://doi.org/10.1111/avsc.12511  

   Tortorelli, Claire_M ; Krawchuk, Meg_A ; Kerns, Becky_K ; Fraser, ed., Lauchlan ( August 2020 , Applied Vegetation Science)

   A recently introduced non‐native annual grass,Ventenata dubia, is challenging previous conceptions of community resistance in forest mosaic communities in the Inland Northwest. However, little is known of the drivers and potential ecological impacts of this rapidly expanding species. Here we (1) identify abiotic and biotic habitat characteristics associated with theV. dubiainvasion and examine how these differ betweenV. dubiaand other problematic non‐native annual grasses,Bromus tectorumandTaeniatherum caput‐medusae; and (2) determine how burning influences relationships betweenV. dubiaand plant community composition and structure to address potential impacts on Inland Northwest forest mosaic communities.

   Blue Mountains of the Inland Northwest, USA.

   We measured environmental and plant community characteristics in 110 recently burned and nearby unburned plots. Plots were stratified to capture a range ofV. dubiacover, elevations, biophysical classes, and fire severities. We investigated relationships betweenV. dubia, wildfire, environmental, and plant community characteristics using non‐metric multidimensional scaling and linear regressions.

   Ventenata dubiawas most abundant in sparsely vegetated, basalt‐derived rocky scablands interspersed throughout the forested landscape. Plant communities most heavily invaded byV. dubiawere largely uninvaded by other non‐native annual grasses.Ventenata dubiawas abundant in both unburned and burned areas, but negative relationships betweenV. dubiacover and community diversity were stronger in burned plots, where keystone sagebrush species were largely absent after fire.

   Ventenata dubiais expanding the overall invasion footprint into previously uninvaded communities. Burning may exacerbate negative relationships betweenV. dubiaand species richness, evenness, and functional diversity, including in communities that historically rarely burned. Understanding the drivers and impacts of theV. dubiainvasion and recognizing how these differ from other annual grass invasions may provide insight into mechanisms of community invasibility, grass‐fire feedbacks, and aid the development of species‐specific management plans.

    

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