Biology subjects

Morais, D.

Publications and source records attributed to Morais, D..

8 recordsLinked to original sources

bioRxiv2025

Long-term evolution of prokaryotic genomes in a chemolithotrophic cave over 5.5 million years of isolation

Fluctuating conditions drive adaptive evolution, yet understanding how genomes evolve under stable conditions over extended periods remains a major challenge, since most research on microbial evolution relies on short-term experiments or phylogenetic comparisons. The Movile Cave, isolated from external influences 5.5 million years, offers a unique opportunity to explore microbial evolution under prolonged environmental stability. Here, we analyzed metagenome-assembled genomes from this cave, revealing that prokaryotes exhibit lower gene diversity and higher levels of pseudogenization compared to those from non-isolated environments, mainly affecting housekeeping functions involved in translation. Functional redundancy across genomes remained comparable to related habitats. Our results suggest that pseudogenization may serve as a fine-tuning mechanism to reduce excess redundancy. Although horizontal gene transfer is limited overall, the cave virome seems to contribute to microbial adaptation through the transfer of auxiliary metabolic genes. Movile microorganisms harbor fewer phage-defense systems than counterparts in related environments, suggesting a long-term adaptation to a relatively stable virosphere. Our findings indicate that prolonged isolation under stable selective pressures does not necessarily lead to major genomic divergence, but rather promotes adaptive gene loss. This study provides key insights into how long-term stability shapes microbial genome evolution and ecosystem function.

microbiology↗

bioRxiv2020

GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultural and wild plants and pathogenicity. The high importance of fungi in the ecosystem processes contrasts with the incompleteness of understanding of the patterns of fungal biogeography and the environmental factors that drive it. To close this gap of knowledge, we have here collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at http://globalfungi.com. The GlobalFungi database contains over 650 million observations of fungal sequences across >20 000 samples with geographical locations and additional metadata contained in 207 original studies with millions of unique sequence variants of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. As it is, the study represents the most comprehensive atlas of fungal distribution on the global scale open to further additions.

ecology↗

bioRxiv2019

Gene copy normalization of the 16S rRNA gene cannot outweigh the methodological biases of sequencing

The 16S rRNA gene is the golden standard target of sequencing to uncover the composition of bacterial communities but the presence of multiple copies of the gene makes gene copy normalization (GCN) inevitable. Even though GCN resulted in abundances closer to the metagenome, it should be validated by communities with known composition as both amplicon and shotgun sequencing are prone to methodological biases. Here we compared the composition of three mock communities to the composition derived from 16S sequencing without and with GCN. In all of them, the 16S composition was different from the mock community and GCN improved the picture only in the community with the lowest Shannon diversity. Albeit with low abundance, half of the identified genera were not present in the mock communities. Our approach provides empirical evidence to the methodological biases introduced by sequencing that was only counteracted by GCN in the case of low -diversity, potentially due to the small number of bacterial taxa with known gene copy numbers. We thus cannot recommend the use of GCN moving forward and it is questionable whether a complete catalogue of 16S rRNA copy numbers can outweigh the methodological biases of sequencing.

microbiology↗

bioRxiv2019

The total fungal microbiome functionality

Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here we used a meta-analysis of 377 completely annotated and taxonomically different fungal genomes to predict the total fungal microbiome functionality on Earth with all known functions from level 3 of KEGG Orthology using both parametric and non-parametric estimations. The unsaturated model described the accumulation of functions with increasing species richness significantly better (P-value < 2.2e-16) than the saturated model suggesting the presence of widespread and rare functions. Consistent with the parametric approach, the non-parametric Chao-1 estimator that assumes a maximum functional richness did not reach a plateau. Based on previous estimates of fungal species richness on Earth, we propagated the unsaturated model to predict a total fungal microbiome functionality of 42.4 million. Of those, only 0.06% are known today since the vast majority belongs to yet unknown rare functions. Logically, our approach not only highlighted the presence of two types of functions but pointed towards the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.

ecology↗

bioRxiv2018

GenPipes: an open-source framework for distributed and scalable genomic analyses

With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High Performance Computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA-Seq, ChIP-Seq, DNA-Seq, Methyl-Seq, Hi-C, capture Hi-C, metagenomics and PacBio long read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has been already configured on several servers and a docker image is also available to facilitate additional installations. In summary, GenPipes offers genomic researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.

bioinformatics↗

bioRxiv2018

The gill-associated symbiont microbiome is a main source of woody-plant polysaccharide hydrolase genes and secondary metabolite gene clusters in Neoteredo reynei, a unique shipworm from south Atlantic mangroves.

Teredinidae is a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the symbiotic gammaproteobacterial community of gills of different N. reynei specimens, indicating closely related bacterial types are shared, while intestine and digestive glands presented related, and more diverse microbiomes that did not overlap with gills. Annotation of assembled metagenomic contigs revealed that the symbiotic community of N. reynei gills was a hotspot of woody-polysaccharides degrading hydrolase genes, and Biosynthetic Gene Clusters (BGCs), while in contrast, the digestive tract microbiomes seems to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae \"clade I\" strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as unbinned gill-derived gammaproteobacteria contigs, code for novelty including an endo-{beta}-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating {beta}-branching on complex polyketides. Multivariate analyzes have shown that the secondary metabolome encoded on the genomes of Teredinibacter representatives, including the genomes binned from N. reynei gills metagenomes, stand out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results grouped here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.

microbiology↗

bioRxiv2017

Stability in the genetic structure of a Zymoseptoria tritici population from epidemic to interepidemic stages at a small spatial scale

Subpopulations of the wheat pathogen Zymoseptoria tritici (26 sample groups composed of 794 strains) were collected in two nearby wheat fields in the Paris basin, during both epidemic and inter-epidemic periods of three successive years (2009-2013). In addition to the type of inoculum (ascospores vs. pycnidiospores), the alternative presence of wheat debris allowed taking into account its putative origin (local vs. distant). We used a molecular epidemiology approach, based on population genetic indices derived from SSR marker analysis, to describe putative changes in the structure and genotypic diversity of these subpopulations over three years, at a spatiotemporal scale consistent with epidemiological observations. Genetic structure was stable over time (within and between years) and between fields. All subpopulations displayed very high levels of gene and genotypic diversity. The low levels of linkage disequilibrium and the very low clonal fraction at all stages were consistent with the regular occurrence of sexual reproduction in the two fields. A significant increase of the MAT1-1/MAT1-2 ratio was observed over the course of the epidemics, suggesting a competitive advantage of MAT1-1 strains consistently with their greater pathogenicity reported in the literature. Finally, we found that the period, the type of inoculum and its putative origin had little effect on the short term evolution of the local population of Z. tritici. Fungal population size and diversity are apparently large enough to prevent genetic drift at this fine spatiotemporal scale, and more likely short distance migration contributes strongly to the stabilization of genetic diversity among and within plots.

epidemiology↗

bioRxiv2017

Trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen population

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100039). The efficiency of plant resistance to fungal pathogen populations is expected to decrease over time, due to its evolution with an increase in the frequency of virulent or highly aggressive strains. This dynamics may differ depending on the scale investigated (annual or pluriannual), particularly for annual crop pathogens with both sexual and asexual reproduction cycles. We assessed this time-scale effect, by comparing aggressiveness changes in a local Zymoseptoria tritici population over an eight-month cropping season and a six-year period of wheat monoculture. We collected two pairs of subpopulations to represent the annual and pluriannual scales: from leaf lesions at the beginning and end of a single annual epidemic, and from crop debris at the beginning and end of a six-year period. We assessed two aggressiveness traits - latent period and lesion size - on sympatric and allopatric host varieties. A trend toward decreased latent period concomitant with a significant loss of variability was established during the course of the annual epidemic, but not over the six-year period. Furthermore, a significant cultivar effect (sympatric vs. allopatric) on the average aggressiveness of the isolates revealed host adaptation, arguing that the observed patterns could result from selection. We thus provide an experimental body of evidence of an epidemiological trade-off between the intra- and inter-annual scales in the evolution of aggressiveness in a local plant pathogen population. More aggressive isolates were collected from upper leaves, on which disease severity is usually lower than on the lower part of the plants left in the field as crop debris after harvest. We suggest that these isolates play little role in sexual reproduction, due to an Allee effect (difficulty finding mates at low pathogen densities), particularly as the upper parts of the plant are removed from the field, explaining the lack of transmission of increases in aggressiveness between epidemics.

epidemiology↗