Biology subjects

COLEINE, C.

Publications and source records attributed to COLEINE, C..

8 recordsLinked to original sources

bioRxiv2023

Metagenomics untangles metabolic adaptations of Antarctic endolithic 1 bacteria at the fringe of habitability

BackgroundEndolithic niches offer an ultimate refuge, supplying buffered conditions for microorganisms that dwell inside rock airspaces. Yet, survival and growth strategies of Antarctic endolithic microbes residing in Earths driest and coldest desert remains virtually unknown. ResultsFrom 109 endolithic microbiomes, 4,539 metagenome-assembled genomes were generated, 49.3% of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability. ConclusionsThese results represent the foundation to untangle adaptability at the edge of sustainability on Earth and on other dry Earth-like planetary bodies such as Mars.

microbiology↗

bioRxiv2023

Geography and environmental pressure are predictive of class-specific 1 radioresistance in black fungi

Black fungi are among the most resistant organisms to ionizing radiation on Earth. However, our current knowledge is based on studies on a few isolates, while the overall radioresistance limits across this microbial group and the relationship with local environmental conditions remains largely undetermined. To address this knowledge gap, we assessed the survival of 101 strains of black fungi isolated across a worldwide spatial distribution to gamma radiation doses up to 100 kGy. We found that intra and inter-specific taxonomy, UV radiation and precipitation levels primarily influence the radioresistance in black fungi. Altogether, this study provides insights into the adaptive mechanisms of black fungi to extreme environments and highlights the role of local adaptation in shaping the survival capabilities of these extreme-tolerant organisms. Originality statementAlthough previous studies showed the extraordinary ability of a few strains of black fungi to survive ionizing radiation, the overall radioresistance of this group of organisms has not been defined yet. Moreover, how and why radioresistance shifts across environmental gradients remain virtually unknown. Here, we collected black fungi from locations across the globe and found that biogeography shapes the responses of black fungi to environmental stress with UV light being significantly correlated with radiotolerance. Our study provides a clear picture of the boundaries of life for black fungi under ionizing radiation; further, we demonstrate, for the first time, that this ability in such microorganisms, not only is related to taxonomy, but also may be a consequence of their adaptation to various factors encountered in the environment where they live.

microbiology↗

bioRxiv2023

aweMAGs: a fully automated workflow for quality assessment and annotation of eukaryotic genomes from metagenomes

Metagenomics is one of the most promising approaches to identify and characterize novel microbial species from environmental samples. While a large amount of prokaryotic metagenome assembled genomes (MAGs) have been published, only a few examples of eukaryotic MAGs have been reported. This is in part due to the absence of dedicated and easy-to-use processing pipelines. Quality assessment, annotation and phylogenomic placement of eukaryotic MAGs involve the use of several computational tools and reference databases that are often difficult to collect and maintain. We present metashot/aweMAGs, a fully automated workflow capable of performing all these steps. metashot/aweMAGs can run out-of-the-box on any platform that supports Docker, Singularity and Nextflow, including computing clusters or batch systems in the cloud.

bioinformatics↗

bioRxiv2022

Environmental thresholds in the functional mycobiome of global drylands

Fungi are major drivers of ecosystem functions. Increases in aridity are known to negatively impact fungal communities in dryland ecosystems globally, however, much less is known on the potential influence of other environmental drivers. To fill this knowledge gap, we reanalyzed fungal data from 912 soil samples, providing the largest and most complete fungal community dataset from global drylands. We used machine learning tools to examine geographical patterns in community composition and spatial, edaphic, and climatic factors driving them. Further, we determined critical thresholds of community turnover along those gradients. Our analysis identifies UV index, climate seasonality, and sand content as the most important environmental predictors of community shifts, harbouring greatest association with the richness of putative plant pathogens and saprobes. Important nonlinear relationships existed with each of these fungal guilds, with increases in UV and temperature seasonality above 7.5 and 900 SD, respectively, being associated with an increased probability of plant pathogens and unspecified saprotrophs occurrence. Conversely, these environmental parameters had a negative relationship with litter and soil saprotrophs richness. Consequently, these functional groups might be differentially sensitive to environmental changes, which might result in an inevitable disturbance of current plant-soil dynamics in drylands.

ecology↗

bioRxiv2021

Rock traits drive complex microbial communities at the edge of life

Antarctic deserts are among the driest and coldest ecosystems of the planet; there, some microbes hang on to life under these extreme conditions inside porous rocks, forming the so-called endolithic communities. Yet, the contribution of distinct rock traits to support complex microbial assemblies remains poorly determined. Here, we combined an extensive Antarctic rock survey with rock microbiome sequencing and ecological networks, and found that contrasting combinations of microclimatic and rock traits such as thermal inertia, porosity, iron concentration and quartz cement can help explain the multiple complex and independent microbial assemblies found in Antarctic rocks. Our work highlights the pivotal role of rocky substrate heterogeneity in sustaining contrasting groups of microorganisms, which is essential to understand life at the edge on Earth, and for searching life on other rocky planets such as Mars.

microbiology↗

bioRxiv2019

Metabolic responses in opposite sun-exposed Antarctic cryptoendolithic communities.

Antarctic cryptoendolithic communities are self-supporting borderline ecosystems spreading across the extreme conditions of the Antarctic desert and represent the most predominant life-form in the ice-free desert of McMurdo Dry Valleys, accounted as the closest terrestrial Martian analogue. Components of these communities are very adapted extremophiles and extreme-tolerant microorganisms, among the most resistant known to date. Recent advances started to investigate the biodiversity and community composition in these microbial ecosystems but the metabolic activity of the metacommunity has never been investigated to date. In this study, we explored the stress-response, spreading in two different sites of the same location, subjected to increasing environmental pressure due to opposite sun exposure, to verify the effect of sunlight on settlement and adaptation strategies. Results indicated that the metabolic responses are shaped according to external conditions; in the overall 252 altered metabolites (56 and 196 unique for north and south, respectively), distinguished the two differently exposed communities. We also selected 10 metabolites and performed two-stage Receiver Operating Characteristic (ROC) analysis to test them as potential biomarkers. We focused further on melanin and allantoin as protective substances; their concentration was highly different in the community in the shadow or in the sun.

microbiology↗

bioRxiv2019

Sampling strategies to assess microbial diversity of Antarctic cryptoendolithic communities.

Describing the total biodiversity of an environmental metacommunity is challenging due to the presence of cryptic and rare species and incompletely described taxonomy. How many samples to collect is a common issue faces ecologists when designing fieldwork sampling: collecting many samples may indeed capture the whole metacommunity structure, but can be prohibitively costly and lead to an enormous amount of data to analyse. Conversely, too few samples may yield inadequate and incomplete data which can prohibit complete assessment of community diversity. High-throughput sequencing allows examination of large numbers of samples enabling comprehensive biodiversity assessments. In this study, we sought to estimate how the scale of sampling affects accuracy of community diversity description in order to develop strategies to exhaustively describe the microbial diversity of cryptoendolithic communities in the McMurdo Dry Valleys in Antarctica accounted as the closest Martian analogue on Earth, exhibiting extreme conditions such as low temperatures, wide thermal fluctuations, low nutrient availability and high UV radiation. We found that sampling effort, based on accumulation curves analysis, had a considerable impact on assessing species richness and composition in these ecosystems, confirming that a sampling as large as nine rock specimens was necessary to detect almost all fungal species present, but was not sufficient to capture whole bacterial assemblage.

microbiology↗

bioRxiv2019

Sun exposure drives Antarctic cryptoendolithic community structure and composition.

The harsh environmental conditions of the ice-free regions of Continental Antarctica are considered one of the closest Martian analogues on Earth. There, rocks play a pivotal role as substratum for life and endolithism represents a primary habitat for microorganisms when external environmental conditions become incompatible with active life on rock surfaces. Due to the thermal inertia of rock, the internal airspace of lithic substratum is where microbiota find a protected and buffered microenvironment, allowing life to spread throughout these regions with extreme temperatures and low water availability. The high degree of adaptation and specialization of the endolithic communities makes them highly resistant but scarsely resilient to any external perturbation and thus, any shifts in microbial community composition may serve as early-alarm systems of environmental perturbation, including climate change.\n\nPrevious research concluded that altitude and distance from sea do not play as driving factors in shaping microbial abundance and diversity, while sun exposure was hypothesized as significant parameter influencing endolithic settlement and development. This study aims to explore our hypothesis that changes in sun exposure translate to shifts in community composition and abundances of main biological compartments (fungi, algae and bacteria) in the Antarctic cryptoendolithic communities. We performed a preliminary molecular survey, based on DGGE and qPCR tecniques, of 48 rocks with varying sun exposure, collected in Victoria Land along an altitudinal transect from 834 to 3100 m a.s.l.\n\nOur findings demonstrate that differences in sun radiation between north and south exposure influence temperature of rocks surface, availability of water and metabolic activity and also have significant impact on community composition and microbial abundance.

microbiology↗