Biology subjects

Cabrol, L.

Publications and source records attributed to Cabrol, L..

6 recordsLinked to original sources

bioRxiv2026

Comparing DNA Extraction Protocols for Freshwater Prokaryotic Communities: Impacts on Yield and Microbial Profiling

DNA extraction from aquatic samples is a critical process that influences the quantity and purity of the DNA obtained. This can have profound effects on the accuracy of the community depiction. In this study, DNA extraction workflows of seven commercial kits (Qiagen: DNeasy PowerLyzer PowerSoil, DNeasy PowerSoil Pro, DNeasy PowerSoil, DNeasy PowerMax Soil; Macherey-Nagel: NucleoSpin Soil; Zymo: ZymoBIOMICS DNA; MP Biomedicals: FastDNA SPIN), along with several modifications of manufacturer's protocols focusing on the lysis and elution steps, were tested, accounting for a total of 18 different protocols. For each protocol, DNA yield (quantity, replicability and quality), richness and compositional reproducibility based on 16S rRNA gene sequencing, as well as processing time and cost were assessed. The standard protocols recommended by the manufacturer showed comparable DNA yield results. Shared ASVs between all protocols accounted for >90% of the reads and were mostly abundant ASVs, indicating consistent detection of dominant taxa across all protocols. Adding supplementary lysis and elution steps to the manufacturer's protocols yielded up to ~4x more DNA. However, total read counts and ASV richness were lower as total DNA increased. Manufacturer's protocols therefore showed higher values than their modified versions, although these effects were not significant on community composition. We conclude that the choice of a protocol is the balance between recovering sufficient DNA of good quality versus potential effects on downstream sequencing output (reads and ASVs).

microbiology↗

bioRxiv2025

Drone Survey Reveals a Severe Chinstrap Penguin Decline and a Novel Gentoo Colony in an Antarctic Specially Protected Area

Seabird populations in Antarctica are sensitive indicators of environmental change and understanding their dynamics is crucial for assessing the health and future of the Antarctic ecosystems. This study provides an updated population assessment for three key seabird species - the Antarctic Shag (Leucocarbo bransfieldensis), Gentoo Penguin (Pygoscelis papua), and Chinstrap Penguin (P. antarcticus) - within the Antarctic Specially Protected Area (ASPA) 133 on Nelson Island. Using drone-based imagery and photogrammetric analysis, we conducted comprehensive nest counts to evaluate current population size in comparison with historical data. Our results reveal a pronounced 57% decline in the Chinstrap Penguin population at Harmony Point since the 1990s, with 38,080 nests counted compared to historical estimates of nearly 90,000. In contrast, Gentoo Penguin numbers at Harmony Point (3,659 nests) appear stable following a previously documented increase. We also provide the first population estimate for a large Gentoo Penguin colony located on a small peninsula south of Harmony Point, known as the Toe, where 4,641 nests were recorded. Additionally, we report an 84% increase in Antarctic Shags, with 127 nests recorded at Harmony Point. These findings are consistent with regional species-level trends and provide critical baseline data for monitoring the impacts of rapid environmental change on Antarctic seabird communities.

ecology↗

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

Temperature increase affects acetate-derived methane production in Alaskan lake sediments and wetland soils

Under climate change framework, methanogens activity is expected to be strongly affected, eventually resulting in positive feedback on global climate, with higher greenhouse gas (GHG) emissions in the Arctic. This work aimed to evaluate the effect of increasing temperature on methane production rate and archaeal community of lake sediments and wetland soils from Denali to Toolik regions in Alaska (USA). For that, anaerobic acetate-amended microcosms were incubated at 5, 10, 15 and 20 {degrees}C. The acetate-derived methanogenic rate was determined and the methanogenic communities were analyzed by qPCR and 16S rRNA sequencing. Warmer temperatures yielded 4-6 times higher methane production rates and organic matter content (OM) showed significant positive correlation to methane production. Different patterns were observed in the archaeal communities after incubation at higher temperatures, with an increase in Methanosarcina abundance for most of the samples and Methanosaeta in one of the lakes tested, showing the adaptation of key acetoclastic groups among different temperatures. Our results demonstrate the impact of increasing temperature on methane production, bringing insights on key drivers involved in the process of acetoclastic methanogenic potential occurring in these ecosystems in Alaska.

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↗

bioRxiv2019

Widespread microbial mercury methylation genes in the global ocean

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, yet only anaerobic microorganisms have been identified so far as efficient methylmercury producers in anoxic environments. The microaerophilic nitrite oxidizing bacteria Nitrospina has been previously suggested as a possible mercury methylator in Antarctic sea ice. However, the microorganisms processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here we show metagenomic evidence from open ocean for widespread microbial methylmercury production in oxic subsurface waters. We find high abundances of the key mercury methylating genes hgcAB across all oceans corresponding to taxonomic relatives of known mercury methylators from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread key player for methylmercury production in the oxic subsurface waters of the global ocean.

genomics↗