Biology subjects

Orlando, J.

Publications and source records attributed to Orlando, J..

3 recordsLinked to original sources

bioRxiv2025

A structure-guided pipeline to uncover the underexplored beta-lactamases from Antarctic and Subantarctic soil microbiota

As the One Health approach points out, the environment can significantly affect human health, particularly having diverse and profound implications in the ongoing antimicrobial resistance crisis. One central aspect is the potential role of environmental microorganisms as a source of resistance genes that could emerge among pathogens aided by horizontal transfer. In this context, previous reports showed that the Antarctic soil microbiota hosts a rich resistome, including putative beta-lactamases conferring resistance to beta-lactams, the most widely used antibiotics for treating bacterial infections worldwide. However, the diversity of beta-lactamases across different areas of Antarctica and Subantarctic islands and their associated microbiota remains largely unexplored. In this study, we analyzed an extensive collection of Antarctic soil metagenomes, applying a novel bioinformatic pipeline based on combining sequence identity and structural similarity criteria to search for bona fide distant beta-lactamase orthologs. We found several classes and families, with a notable predominance of class-B metallo-beta-lactamases, including proposed novel families and variants of known families. The beta-lactamase diversity and dominant classes varied across sites following changes in the microbial community, observing three main sample groups: 1) Subantarctic islands, 2) Antarctic Peninsula and surrounding islands; and 3) Cold-desert environments. The most prevalent beta-lactamases corresponded to subclass B3. We reconstructed more than 3500 metagenome-assembled genomes (MAGs) and searched for beta-lactamases among them. The main taxa encoding the beta-lactamases were Pseudomonadota and Bacteroidota. Moreover, a certain proportion of beta-lactamases was associated with mobile genetic elements, especially integrons and insertion sequences, suggesting their potential dissemination by horizontal transference. This evidence reinforces the role of the environment, and especially (sub)Antarctic soils, as a reservoir of resistance genes, in particular, beta-lactamases.

bioinformatics↗

bioRxiv2023

Unveiling the co-phylogeny signal between plunderfish Harpagifer spp. and their gut microbiomes across the Southern Ocean.

Understanding the factors that sculpt fish gut microbiome is challenging, especially in natural populations characterized by high environmental and host genomic complexity. Yet, closely related hosts are valuable models for deciphering the contribution of host evolutionary history to microbiome assembly, through the underscoring of phylosymbiosis and co-phylogeny patterns. Here, we hypothesized that the recent allopatric speciation of Harpagifer across the Southern Ocean (1.2-0.8 Myr) will promote the detection of robust phylogenetic congruence between the host and its microbiome. We characterized the gut mucosa microbiome of 77 individuals from four field-collected species of the plunderfish Harpagifer (Teleostei, Notothenioidei), distributed across three biogeographic regions of the Southern Ocean. We found that seawater physicochemical properties, host phylogeny and geography collectively explained 35% of the variation in bacterial community composition in Harpagifer gut mucosa. The core microbiome of Harpagifer spp. gut mucosa was characterized by a low diversity, mostly driven by selective processes, and dominated by a single Aliivibrio taxon detected in more than 80% of the individuals. Almost half of the core microbiome taxa, including Aliivibrio, harbored co-phylogeny signal at microdiversity resolution with Harpagifer phylogeny. This suggests an intimate symbiotic relationship and a shared evolutionary history with Harpagifer. The robust phylosymbiosis signal emphasizes the relevance of the Harpagifer model to understanding the contribution of fish evolutionary history to the gut microbiome assembly. We propose that the recent allopatric speciation of Harpagifer across the Southern Ocean may have generated the diversification of Aliivibrio into patterns recapitulating the host phylogeny. ImportanceAlthough challenging to detect in wild populations, phylogenetic congruence between marine fish and its microbiome is critical, as it allows highlighting potential intimate associations between the hosts and ecologically relevant microbial symbionts. Through a natural system consisting of closely related fish species of the Southern Ocean, our study provides foundational information about the contribution of host evolutionary trajectory on gut microbiome assembly, that represents an important yet underappreciated driver of the global marine fish holobiont. Notably, we unveiled striking evidence of co-diversification between Harpagifer and its microbiome, demonstrating both phylosymbiosis of gut bacterial communities, and co-phylogeny of specific bacterial symbionts, in patterns that mirror the host diversification. Considering the increasing threats that fish species are facing in the Southern Ocean, understanding how the host evolutionary history could drive its microbial symbiont diversification represents a major challenge to better predict the consequences of environmental disturbances on microbiome and host fitness.

microbiology↗

bioRxiv2021

Exploring the microdiversity within marine bacterial taxa: Towards an integrated biogeography in the Southern Ocean

The phylogeography traditionally correlates the genetic relationships among individuals within a macroorganism species, to their spatial distribution. Most microbial phylogeographic studies so far have been restricted to narrow geographical regions, mainly focusing on isolated strains, either obtained by culture or single-strain natural enrichments. However, the laborious culture-based methodology imposes a low number of studied individuals, leading to poor resolution of haplotype frequency estimation, making difficult a realistic evaluation of the genetic structure of natural microbial populations in the environment. To tackle this limitation, we present a new approach to unravel the phylogeographic patterns of bacteria combining (i) community-wide survey by 16S rRNA gene metabarcoding, (ii) intra-species resolution through the oligotyping method, and (iii) genetic and phylogeographic indices, as well as migration parameters, estimated from populational molecular data as traditionally developed for macroorganisms as models. As a proof-of-concept, we applied this methodology to the bacterial genus Spirochaeta, classically reported as a gut endosymbiont of various invertebrates inhabiting the Southern Ocean (SO), but also described in marine sediment and in open waters. For this purpose, we centered our sampling into three biogeographic provinces of the SO; maritime Antarctica (King George Island), sub-Antarctic Islands (Kerguelen archipelago) and Patagonia in southern South America. Each targeted OTU was chaLRracterized by substantial intrapopulation microdiversity, a significant genetic differentiation and a robust phylogeographic structure among the three distant biogeographic provinces. Patterns of gene flow in Spirochaeta populations support the role of the Antarctic Polar Front (APF) as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current (ACC) appears as the main driver of connectivity between geographically distant sub-Antarctic areas such as Patagonia and Kerguelen archipelago, and between Kerguelen archipelago and maritime Antarctica. Additionnally, we found that historical processes (drift and dispersal limitation) together govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach represents a substantial first attempt to bridge the gap between microbial and macrobial ecology by unifying the way to study phylogeography. We revealed that strong congruency with macroorganisms patterns at the populational level shaped by the same oceanographic structures and ecological processes.

microbiology↗