Biology subjects

Ferrari, B. C.

Publications and source records attributed to Ferrari, B. C..

6 recordsLinked to original sources

bioRxiv2026

Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions

Asgard archaea are the closest known relatives of eukaryotes and are central to models of eukaryogenesis involving archaeal bacterial symbiosis, yet the contribution of viruses remains unexplored. Here, for the first time, we visualised unique viruses associated with Asgard archaeal cells. Additionally, we identified the first putative Asgard-archaeal virus satellite, which exhibited genomic interactions involving a bacterium, Stromatodesulfovibrio nilemahensis, providing evidence of a virus-mediated interaction between an Asgard archaeon and a bacterium. Additionally, novel proviruses of S. nilemahensis displayed distinct genomic features where predictions of alternate recombination sites suggested the acquisition of horizontally acquired genes associated with biofilm formation. Further, we comprehensively characterise (pro)viruses associated with this co-culture using high resolution cryo-electron tomography, proximity ligation (Hi-C), and metagenomics. Together, these findings expand the known diversity of Asgard archaeal viruses and establish a foundation for investigating the role of viruses in microbial symbiosis relevant to the emergence of eukaryotic life.

microbiology↗

bioRxiv2026

Trace gas oxidation supports sub-surface microbial communities across Namib Desert fog and aridity gradients

Widely accepted climate predictions indicate that drylands will expand to cover more than half of the Earths terrestrial surface by the end of the 21st century. In these environments, harsh conditions including nutrient and water limitations restrict plant and animal life, thereby increasing the importance of soil microbial communities in nutrient cycling and ecosystem functioning. The Namib Desert is a distinctive dryland ecosystem characterised by a steep natural aridity gradient, transitioning from a coastal hyperarid zone influenced by frequent fog deposition to an inland arid region receiving seasonal rainfall. This study investigates the impact of water availability and moisture regime on microbial trace gas oxidation and community composition across this aridity gradient. Quantitative analyses revealed that total microbial abundance and activity indicators, including ATP concentrations and respiration rates, were significantly (p < 0.005) reduced in hyperarid soils compared to their arid counterparts. In contrast, hyperarid fog-dominated soils exhibited significantly (p < 0.0005) elevated rates of atmospheric hydrogen oxidation, even in the absence of water inputs. We propose that sustained high-affinity hydrogen oxidation, coupled with rapid microbial resuscitation following wetting events, supports shallow sub-surface microbial communities in the Namib Desert, particularly in the coastal hyperarid zone. Together, these findings challenge current understanding of the lower limits of microbial activity and reveal alternate metabolic pathways that enable microbial persistence in hyperarid hot desert soils. ImportanceDrylands are expanding globally, yet the mechanisms that allow microbial life to persist under extreme and sustained water limitation remain poorly understood. This study demonstrates that atmospheric trace gas oxidation, particularly high-affinity hydrogen oxidation, supports active and resilient microbial communities in hyperarid soils of the Namib Desert, even in the absence of liquid water inputs. By revealing how microbes may couple trace gas metabolism to energy and water generation, our findings provide new insight into the lower limits of microbial activity in dry hot desert soils and highlight the need to investigate how microbes persist and sustain soil ecosystem functioning.

microbiology↗

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↗

bioRxiv2021

Tracing boundaries in Eastern Antarctica: Multi-scale drivers of soil microbial communities across the hyperarid Vestfold Hills

Microorganisms are key to sustaining core ecosystem processes across terrestrial Antarctica but they are rarely considered in conservation frameworks. Whilst greater advocacy has been made towards the inclusion of microbial data in this context, there is still a need for better tools to quantify multispecies responses to environmental change. Here, we extend the scope of Gradient Forest modelling beyond macroorganisms and small datasets to the comprehensive polar soil microbiome encompassing >17, 000 sequence variants for bacteria, micro-eukarya and archaea throughout the hyperarid Vestfold Hills of Eastern Antarctica. Quantification of microbial diversity against 79 physiochemical variables revealed that whilst rank-order importance differed, predictors were broadly consistent between domains, with greatest sharing occurring between bacteria and micro-eukarya. Moisture was identified as the most robust predictor for shaping the regional soil microbiome, with highest compositional turnover or "splits" occurring within the 10 - 12 % moisture content range. Often the most responsive taxa were rarer lineages of bacteria and micro-eukarya with phototrophic and nutrient-cycling capacities such as Cyanobacteria (up to 61.81 % predictive capacity), Chlorophyta (62.17 %) and Ochrophyta (57.81 %). These taxa groups are thus at greater risk of biodiversity loss or gain to projected climate trajectories, which will inevitably disturb current ecosystem dynamics. Better understanding of these threshold tipping points will positively aid conservation efforts across Eastern Antarctica. Furthermore, the successful implementation of an improved Gradient Forest model also presents an exciting opportunity to broaden its use on microbial systems globally.

microbiology↗

bioRxiv2019

Novel Quorum Sensing Activity in East Antarctic Soil Bacteria

Antarctica, being the coldest, driest and windiest continent on Earth, represents the most extreme environment a living organism can thrive in. Under constant exposure to harsh environmental threats, terrestrial Antarctica remains home to a great diversity of microorganisms, indicating that the soil bacteria must have adapted a range of survival strategies that require cell-to-cell communication. Survival strategies include secondary metabolite production, biofilm formation, bioluminescence, symbiosis, conjugation, sporulation and motility, all of which are often regulated by quorum sensing (QS), a type of bacterial communication. Up to now, such mechanisms have not been explored in terrestrial Antarctica. Here, for the first time, LuxI/LuxR-based quorum sensing (QS) activity was delineated in soil bacterial isolates recovered from Adams Flat, in the Vestfold Hills region of East Antarctica. Interestingly, we identified the production of potential homoserine lactones (HSLs) ranging from medium to long chain length in 19 bacterial species using three biosensors, namely Agrobacterium tumefaciens NTL4, Chromobacterium violaceum CV026 and Escherichia coli MT102, in conjunction with thin layer chromatography (TLC). The majority of detectable HSLs were from gram-positive microorganisms not previously known to produce HSLs. This discovery further expands our understand of the microbial community capable of this type of communication, as well as providing insights into physiological adaptations of microorganisms that allow them to survive in the harsh Antarctic environment.\n\nIMPORTANCEQuorum sensing, a type of bacterial communication, is widely known to regulate many processes including those that confer survival advantage. However, little is known about communication by bacteria thriving within Antarctic soils. Employing a combination of bacteria biosensors, analytical techniques, and genome mining, we found a variety of Antarctic soil bacteria speaking a common language, via the LuxI/LuxR-based quorum sensing, thus potentially supporting survival in a mixed microbial community. This is the first report of quorum sensing activity in Antarctic soils and has provided a platform for studying physiological adaptations of microorganisms that allow them to not just survive but thrive in the harsh Antarctic environment.

microbiology↗

bioRxiv2019

Extreme niche partitioning promotes a remarkably high diversity of soil microbiomes across eastern Antarctica.

Terrestrial Antarctica, a predominantly microbial realm, encompasses some of the most unique environments on Earth where resident soil microbiota play key roles in the sustainability and evolution of the ecosystem. Yet the fundamental ecological processes that govern the assemblage of these natural communities remain unclear. Here, we combined multivariate analyses, co-occurrence networks and fitted species abundance distributions of amplicon sequencing data to disentangle community assemblage patterns of polar soil microbiomes across two ice-free deserts (Windmill Islands and Vestfold Hills) situated along the coastline of eastern Antarctica. Our findings report that communities were predominantly structured by non-neutral processes, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. In contrast, both eukaryotic and archaeal communities exhibited multimodal distributions, indicating the potential emergence of neutrality. Between the three microbial domains, polar soil bacterial communities consistently demonstrated the greatest taxonomic diversity, estimated richness, network connectivity and linear response to contemporary environmental soil parameters. We propose that reduced niche overlap promotes greater phylogenetic diversity enabling more bacterial species to co-exist and essentially thrive under adversity. However, irrespective of overall relative abundance, consistent and robust associations between co-existing community members from all three domains of life highlights the key roles that diverse taxa play in ecosystem dynamics. SignificanceIn the face of a warming Antarctica, contemporary dynamics between polar soil microbial communities will inevitably change due to the climate-induced expansion of new ice-free areas. Increasing concern about disturbance and rapid biodiversity loss has intensified the need to better understand microbial community structure and function in high-latitude soils. We have taken an integrated approach to elucidate domain-level assemblage patterns across east Antarctic soil microbiomes. These assemblage patterns will be available to feed into policy management and conservation planning frameworks to potentially mitigate future biodiversity loss.

microbiology↗