Biology subjects

Rodriguez-Gijon, A.

Publications and source records attributed to Rodriguez-Gijon, A..

5 recordsLinked to original sources

bioRxiv2025

Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales

Model bacteria are fundamental for research, but knowledge about their ecology and evolution is often limited. Here we establish evolutionary and ecological context for the model organism Caulobacter crescentus--an alphaproteobacterium intensively studied for its dimorphic lifecycle. By analyzing the species relationships and genetic potential of hundreds of Caulobacterales species, we reveal striking diversity regarding their environmental distribution, morphology, cell development, and metabolism. Our work provides insights into the evolutionary history of morphological features such as the cell curvature determinant crescentin and uncovers a striking case of convergent loss of traits for cellular dimorphism among close relatives of C. crescentus. Moreover, we find that genes for phototrophy are widespread across Caulobacterales and that the new genus Acaudatibacter, described here, includes the first reported Caulobacterales lineage with photoautotrophic potential. Our study advances our understanding of an environmentally widespread bacterial order and sheds light onto the evolution of fundamental prokaryotic features.

microbiology↗

bioRxiv2025

Microbial model communities reveal widespread auxotrophies in abundant bacteria

Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity - ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than 3 species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, biosynthetic genes were distributed across genomes within the same model community, indicating metabolic interdependencies. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.

microbiology↗

bioRxiv2025

The ecological success of freshwater microorganisms is mediated by streamlining and biotic interactions

Genome size is known to reflect aspects of the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to microbial prevalence, relative abundance and co-occurrence in the environment. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems, including 80,561 medium-to-high quality genomes. We identified 9,028 species (defined by ANI >95%) across a manually curated dataset of 636 freshwater metagenomes and calculated their relative abundance. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, and a greater prevalence than expected based on their mean abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, our network analysis revealed that prokaryotes with reduced genomes are found in co-occurrent groups comprising up to 295 species. The species in these groups potentially possess a diminished capacity for synthesizing essential metabolites such as vitamins, amino acids and nucleotides, which may foster complex metabolic interdependencies within the community. Moreover, the fitness advantage of losing biosynthetic functions appears to be frequency dependent: while nucleotide biosynthesis is the most retained biosynthetic function, amino acid and then vitamin biosynthesis are more frequently lost. Our study finds that genome size is linked to microbial community structure and ecological adaptation to freshwaters. Our results underscore genome streamlining as a central ecological and evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.

microbiology↗

bioRxiv2022

Genome size variation between pelagic and benthic communities across prokaryotic taxonomy and environmental gradients in the Baltic Sea

While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.

microbiology↗

bioRxiv2021

A genomic perspective on genome size distribution across Earth's microbiomes reveals a tendency to gene loss

Our view of genome size in Archaea and Bacteria has remained skewed as the data used to paint its picture has been dominated by genomes of microorganisms that can be cultivated under laboratory settings. However, the continuous effort to catalog the genetic make-up of Earths microbiomes specifically propelled by recent extensive work on uncultivated microorganisms, provides a unique opportunity to revise our perspective on genome size distribution. Capitalizing on a recently released extensive catalog of tens of thousands of metagenome-assembled genomes, we provide a comprehensive overview of genome size distributions. We observe that the known phylogenetic diversity of environmental microorganisms possesses significantly smaller genomes than the collection of laboratory isolated microorganisms. Aquatic microorganisms average 3.1 Mb, host-associated microbial genomes average 3.0 Mb, terrestrial microorganism average 3.7 Mb and isolated microorganisms average 4.3 Mb. While the environment where the microorganisms live can certainly be linked to genome size, in some cases, evolutionary phylogenetic history can be a stronger predictor. Moreover, ecological strategies such as auxotrophies have a direct impact on genome size. To better understand the ecological drivers of genome size, we expand on the known and the overlooked factors that influence genome size in different environments, phylogenetic groups and trophic strategies.

microbiology↗