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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. 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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3. 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. 

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4. Sea-ice and macrozooplankton distribution as determinants of top predator community structure in Antarctic winter

   https://doi.org/10.3354/meps14609  

   Czapanskiy, MF; Santora, JA; Dietrich, KS; Cimino, MA; Hazen, EL; Reiss, CS; Veit, RR (June 2024, Marine Ecology Progress Series)

   NA (Ed.)

   The Antarctic Peninsula marine ecosystem is highly productive, with large populations of commercially and ecologically important species including Antarctic krillEuphausia superba, Adélie penguinsPygoscelis adeliae, and crabeater sealsLobodon carcinophagus. The ecology of the peninsula is rapidly changing due to accelerating climate change and fishing pressure. Systematic ecosystem surveys have focused on austral spring and summer, leaving an information gap on winter ecosystem dynamics. Using data from 5 consecutive ecosystem surveys, we quantified the composition and distribution of winter predator communities and investigated the physical and biological influences on community structure. Seabirds and marine mammals clustered into 3 communities: an ice-associated community represented by Adélie penguins and crabeater seals; a diverse marginal ice zone community dominated by fur seals and several species of seabirds including 3 petrels, kelp gullsLarus dominicanus, and Antarctic ternsSterna vittata; and an open water community consisting of southern fulmarsFulmarus glacialoidesand 4 species of petrels. These communities were distributed along an environmental gradient ranging from ice-covered, cold, saline water to ice-free, warmer, and fresher water with greater chlorophyll concentrations. Predator communities were also associated with different communities of macrozooplankton: ice-associated predators with an extremely diverse assemblage of typically mesopelagic zooplankton; marginal ice zone predators with a community of large-bodied euphausiids (E. superba, E. crystallorophias); and open water predators with a community of small-bodied euphausiids (Thysanoessa macrura). Our synthesis of integrated winter predator and macrozooplankton communities relative to sea-ice concentration provides reference points for future ecosystem assessments within this rapidly changing region. 

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5. Apicomplexan and non-metazoan microeukaryotes in the thermosensitive reef-building coral Acropora hyacinthus shift in abundance throughout an extreme coral bleaching event

   https://doi.org/10.3389/fmars.2025.1626071  

   Peterson, Athena; Patton, Sunni; Schmeltzer, Emily R; Grupstra, Carsten_G B; Howe-Kerr, Lauren I; Klinges, J Grace; Maher, Rebecca L; Messyasz, Adriana; Seabrook, Sarah; Thurber, Andrew R; et al (September 2025, Frontiers in Marine Science)

   Coral reefs play vital roles in global marine systems and are currently facing increased threats of bleaching. Coral bleaching is heavily influenced by the host-associated microeukaryote community – most notably the dinoflagellate family Symbiodiniaceae. The apicomplexan family Corallicolidae, is the second most abundant member of the microeukaryote community, yet their role in coral health is largely unknown. To explore the role that this apicomplexan and the greater non-metazoan microeukaryotic community play in coral health, samples of a thermally sensitive scleractinian coral,Acropora hyacinthus, were collected over the course of a severe coral bleaching event and its aftermath. Through 18S rRNA gene sequencing analysis, we found that taxa within the family Corallicolidae were relatively enriched in corals during, and immediately after, the severe bleaching event as compared to before or one year after. Although utilizing 18S rRNA gene sequencing methods is not the standard for Symbiodiniaceae community profiling, we were able to observe symbiont shuffling among the Symbiodiniaceae communities, as the dominant algal symbiont shifted from the genusCladocopiumto the genusSymbiodiniumfollowing the bleaching event. Furthermore, the non-metazoan microeukaryote community displayed a general shift towards a state of dysbiosis; evidenced by substantial changes in both microeukaryote community composition and dispersion. These results offer insight into the dynamics of apicomplexans throughout the course of an increasingly common global coral reef stressor. 

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