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Abstract Horizontal gene transfer (HGT) is a fundamental ecological and evolutionary process involving the movement of genetic material across taxa within a single generation. While traditionally studied at the level of individual genes with encoded adaptive functions, recent advances in genomics and metagenomics highlight the need for a broader, integrative framework. Here, we expand the concept of the “ecology of DNA transfer,” which conceptualizes HGT as a multi-layered process spanning the genome, cell, and ecological context. We further explore how the fate and expression of transferred DNA vary over evolutionary timescales, from recently acquired, transcriptionally silenced sequences to ancient, fully integrated genes. Together, this framework underscores HGT as a dynamic, context-dependent process shaped by interactions across biological scales. 

Abstract The genusPaulinellarepresents a rare, independent case of primary endosymbiosis, providing a unique system to study the early stages of organelle evolution. Here, we expand current understanding of primary plastid endosymbiosis through the discovery and characterization of two novel photosynthetic amoebae,Paulinella maraesp. nov. andPaulinella murrayisp. nov., isolated from a brackish water habitat in North Carolina, United States. Complete chromatophore genomes and mitochondrial data revealed conserved gene content but notable structural variation, including genome rearrangements and inversion events. Phylogenetic analyses uncovered significant discordance between nuclear and organelle datasets, likely driven by substitution saturation, limited taxon sampling, and differing evolutionary signals across loci. Ecological observations over multiple years indicate that both species are in low abundance but consistently present, and when coupled with hobbyist data, support the hypothesis that photosyntheticPaulinellaspecies are globally distributed yet under‐sampled. These results increase known species diversity within the clade from four to six and highlight the importance of integrating field‐based observations with genomic approaches. Overall, this work advancesPaulinellaas a model for studying ongoing primary endosymbiosis, lineage divergence, and the ecological strategies of low‐abundance microbial eukaryotes. 

Summary The unicellular red algae, Cyanidiophyceae, that diverged early during Archaeplastida (algal and plant) evolution, occupy a variety of extreme habitats that are inhospitable for most other eukaryotes. With the use of modern genomics and genetics methods, Cyanidiophyceae show a remarkable taxonomic diversity, share haplodiplophasic life cycles, and are engaged in complex trophic interactions with microbes that occupy geothermal niches. Amenable to molecular engineering, Cyanidiophyceae are excellent models for understanding evolutionary mechanisms that underpin their extremophilic lifestyles. Their unique growth conditions make these choice red algae of high interest for biotechnological exploitation in environments unsuitable for crops. 

The genus Paulinella represents a rare, independent case of primary endosymbiosis, providing a unique system to study the early stages of organelle evolution. Here, we expand current understanding of primary plastid endosymbiosis through the discovery and characterization of two novel photosynthetic amoebae, Paulinella marae sp. nov. and Paulinella murrayi sp. nov., isolated from a brackish water habitat in North Carolina, USA. Complete chromatophore genomes and mitochondrial data reveal conserved gene content but notable structural variation, including genome rearrangements and inversion events. Phylogenetic analyses uncover significant discordance between nuclear and organelle datasets, likely driven by substitution saturation, limited taxon sampling, and differing evolutionary signals across loci. Ecological observations over multiple years indicate that both species are in low abundance but consistently present, and when coupled with hobbyist data, support the hypothesis that photosynthetic Paulinella species are globally distributed yet under-sampled. These findings increase known species diversity within the clade from four to six and highlight the importance of integrating field-based observations with genomic approaches. Overall, this work advances Paulinella as a model for studying ongoing primary endosymbiosis, lineage divergence, and the ecological strategies of low-abundance microbial eukaryotes. 

Horizontal gene transfer (HGT) generates genetic variation in populations across all domains of life; however, most studies focus on individual transfers and functional information derived therefrom. This is useful but does not consider DNA transfer more broadly, that is, nongene transfers, donor–recipient dynamics, or trends and background levels that may help infer ecological information. Here, we review the mechanistic underpinnings of DNA transfer, literature from diverse fields that addresses HGT on a community basis and the associated methodological challenges, and propose a framework for conceptualizing the process of DNA transfer, highlighting DNA mobility as a feature of community ecology and DNA itself as a public good. These ideas coalesce to support DNA transfer as a fundamental ecological phenomenon that remains largely unmeasured. 

Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reduction in Cyanidiophyceae and enabled the neofunctionalization of genes in multi-enzyme pathways. Utilizing arsenic detoxification as a model, we discuss how the sharing of gene functions by other members of the microbial assemblage weakened selection on homologs in the Cyanidiophyceae, allowing long-term gene persistence via the putative gain of novel functions. This hypothesis, referred to as the Integrated Horizontal Gene Transfer (HGT) Model (IHM), attempts more generally to explain how extremophilic eukaryotes may have transitioned from 'hot start' milieus by functional innovations driven by the duplication and divergence of HGT-derived genes.