Biology subjects

Aguirre de Carcer, D.

Publications and source records attributed to Aguirre de Carcer, D..

9 recordsLinked to original sources

bioRxiv2026

Drift-driven microbiome simplification generates reconstructable and ecologically cohesive microbial communities

Engineering simplified microbial communities that retain function and ecological cohesiveness remains a major challenge because the taxa and interactions required for community establishment are rarely known a priori. Here, we experimentally evaluated drift-driven microbiome simplification as an alternative strategy for generating reduced and reconstructable microbial consortia. Using the tomato rhizosphere as a model system, three source microbial communities were subjected to different dilution bottlenecks and serial propagation. Increasing dilution was the main determinant of community composition and simplification, while repeated passage produced additional reductions in ASV richness, phylogenetic diversity, and evenness. Importantly, diversity loss was not accompanied by a uniform deterioration in bacterial colonization or plant performance, indicating that substantial simplification can occur without a parallel collapse in these system-level properties. Candidate Minimal Microbiome prototypes were selected from endpoint communities, reconstructed as synthetic communities, and their ecological cohesiveness was evaluated through invasion experiments. The reconstructed communities strongly restricted the establishment of the original complex microbial fractions, although invasion success depended markedly on invader identity. The drift-derived communities were at least as resistant to invasion as an independently designed bottom-up synthetic community. Together, these results provide experimental support for drift-driven simplification as a strategy to generate reduced microbial communities whose dominant members can be isolated, reconstructed, and experimentally evaluated. By allowing ecological assembly to generate candidate community configurations before cultivation and reconstruction, this approach provides a complementary route to rational bottom-up design and function-directed top-down microbiome engineering.

microbiology↗

bioRxiv2026

Combinatorial community coalescence in early tomato assembly reveals a rhizosphere attractor in composition and abundance architecture

The rhizosphere microbiome plays fundamental roles in plant health and productivity, yet the ecological rules governing microbiome assembly remain poorly understood. Here, we investigated early rhizosphere community assembly in tomato using a replicated combinatorial community coalescence framework, in which seven distinct natural bacterial communities were inoculated individually and in all possible pairwise and triplet combinations. Single-inoculum communities clustered according to inoculum identity, indicating a strong effect of source community composition on assembly trajectories. However, when all communities were analyzed jointly, samples formed a continuous compositional landscape with no clear evidence of discrete community states. Despite major differences in source community composition, rhizosphere communities consistently converged toward a highly similar uneven rank-abundance structure, with two ASVs accounting for 50% and a median of nineteen ASVs for 90% of total abundance. While assembly was dominated by a very small number of Pseudomonas ASVs, limited evidence of alternative dominant states was observed. Increasing inoculum complexity did not increase stochasticity but instead promoted stronger convergence toward a global rhizosphere compositional centroid. Moreover, dominance hierarchies emerging from community coalescence closely mirrored the distance of source communities to this centroid. The two most dominant communities originated from orchard soils, suggesting that historical contingency and prior adaptation to horticultural crop rhizospheres may influence competitive success. Together, these results are consistent with the existence of a canonical rhizosphere attractor in composition and abundance architecture, with patterns consistent with assembly occurring under a limited number of dominant ecological niches imposed by the tomato rhizosphere.

microbiology↗

bioRxiv2026

Early rhizosphere assembly during the onset of photosynthesis reveals inoculum-constrained succession with increased phylogenetic clustering, filtering and diversity

The rhizosphere microbiome, one of the most diverse and metabolically active microbial ecosystems known, plays fundamental roles in plant health and productivity. However, the ecological dynamics occurring during the transition between germination and the establishment of the first true leaves, a developmental window associated with the onset of active photosynthesis and rapid root expansion, remain poorly understood. Here, we investigated rhizosphere microbiome assembly during the first four weeks of tomato development by sampling communities arising from seven distinct natural soil inocula twice weekly to obtain fine-scale temporal resolution. Bacterial load, richness, evenness and phylogenetic diversity all increased significantly during plant development, indicating progressive increases in rhizosphere ecosystem complexity. In addition, diverse initial microbial communities differentially influenced both host plant development and the bacterial carrying capacity of the resulting rhizosphere ecosystem. Although temporal effects on rhizosphere microbiome composition were significant, assembly trajectories remained strongly constrained by the initial inoculum. Temporal analysis nevertheless revealed significant taxonomic turnover despite limited global compositional restructuring. In particular, Proteobacteria and Pseudomonadaceae decreased over time, whereas Actinobacteria, Acidobacteria and Streptomycetaceae increased. However, communities did not become progressively more similar or divergent over time. Altogether, our results indicate that early rhizosphere microbiome assembly involves rapid ecological succession within inoculum-constrained compositional trajectories, with early copiotrophic Proteobacteria progressively giving rise to more diverse and phylogenetically structured communities. These findings suggest that the first weeks of plant development may represent a critical ecological window for microbiome-based manipulation strategies in agriculture.

microbiology↗

bioRxiv2025

Computational simulation of ecological drift for generating functional minimal microbiomes identifies key experimental and biotic factors influencing success

We describe a top-down engineering approach that leverages ecological drift to generate Minimal Microbiomes; microbial consortia that are relatively simple, cohesive, and functionally complete. This process can be applied to any microbial ecosystem, provided that the target microbiome can be experimentally mimicked. Empirical support for this approach has emerged from multiple independent studies. Here, we use simulations across diverse scenarios, significantly varying niche structures and biotic interactions, to explore the experimental conditions and source microbiome characteristics that favor successful outcomes. Our results indicate that the effectiveness of this approach is constrained by several factors, and that perfect outcomes should not be routinely expected. Nevertheless, despite its drawbacks, this strategy remains a powerful tool for simplifying microbiomes and isolating key co-adapted populations, enabling the construction of low-diversity consortia that retain community function and present ecological cohesion.

microbiology↗

bioRxiv2025

Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex microbiomes

Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high-throughput isolation of microbiome members thus represents a core resource in this field of research. Here, we present and test a culturomics pipeline based on the use of the limiting dilution method with multi-well plates, an optical plate reader, and barcoded sequencing for phylogenetic identification, and offer modularity by proposing different protocols and possibilities along the pipeline. Most importantly, we provide all scripts required for process automation using an affordable pipetting robot, along with associated estimates of financial and labor costs.

microbiology↗

bioRxiv2024

Coupled phylogenetic and functional enrichment in the tomato rhizosphere microbiome

Plant-microbe interactions occur mainly in the rhizosphere, a hot spot of microbial activity and diversity. Given that the outcome of such interactions can significantly impact plant productivity, we require a better understanding of the rhizosphere microbiome if knowledge-based microbiome modification strategies are to be successfully deployed in the future. Here, we aimed to gain a better understanding of the assembly process of the tomato rhizosphere microbiome and its potential composition-function relationships. Among other things, we studied community assembly through the lens of a conceptual framework for the phylogenetically constrained assembly of microbial communities, while assessing community function based on the predicted minimal metagenome of the microbial ecosystem. We observed a systematic enrichment in terms of phylogeny and predicted functional content in the rhizosphere and were able to delimit phylogenetic signal in the ecosystem with 12 functionally coherent phylogenetic groups present in all samples which together accounted for a large fraction of the total community. Our analyses indicated that these groups included a significantly larger content of the ecosystems minimal metagenome than expected by chance. Thus, our study suggests that community assembly followed coupled phylo-functional selection independent of host genetics, and we expect the same phenomenon to occur in other rhizosphere microbiomes. This knowledge provides a thrust in our understanding of how community composition-phylogeny-function relationships drive the assembly process of the rhizosphere microbiome and should help guide the design of synthetic rhizosphere microbiomes for both research and commercial purposes.

microbiology↗

bioRxiv2020

Detection of phylogenetic core groups in diverse microbial ecosystems

The detection and subsequent analysis of phylogenetic core groups (PCGs) in a microbial ecosystem has been recently proposed as a potentially important analytical framework with which to increase our understanding of its structure and function. However, it was still unclear whether PCGs represented an infrequent phenomenon in nature. Here we provide evidence of PCGs in a large and diverse array of environments, which seems to indicate that their existence is indeed a predominant feature of microbial ecosystems. Moreover, we offer dedicated scripts to examine the presence and characteristics of PCGs in other microbial community datasets.

microbiology↗

bioRxiv2019

A comprehensive human minimal gut metagenome extends the host’s metabolic potential

Accumulating evidence suggests that humans should be considered as holobionts in which the gut microbiota plays essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis, and present in all healthy individuals. Despite its interest, this concept has received little attention following its initial description in terms of various ubiquitous pathways in Western cohorts. This study analyzes the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3,412 gene clusters, mapping to 1,856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.

microbiology↗

bioRxiv2019

Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy

In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxa and taxonomic rank. Subsequently, we employ the same data to delimit the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. IMPORTANCEWhile bacterial taxonomy and phylogeny resources as well as related bioinformatic tools continue to improve, the question remains as to how they should best be employed in studies using 16S rRNA gene surveys to assess bacteria-ecosystem relationships, a widespread approach. The results contained herein lead to the recommendation that all ranks from genus to class/phylum be employed if using taxonomic binning in the analysis of 16S rRNA gene surveys. With regards to the use of phylogeny or clustering-based approaches, single or arbitrary tree topology or sequence distance thresholds should not be employed. Instead, the results presented here can be used to obtain more meaningful results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data.

microbiology↗