Uncovering the uncultivated majority in Antarctic soils : toward a synergistic approach

Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent

Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica

peer reviewedUnderstanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet (“Dry Valley”). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.MICROBIA

Drivers of the terrestrial cyanobacterial community composition in the Sør Rondane Mountains, East Antarctica

The sparse ice-free regions of Antarctica harbor diverse microbial communities that can vary significantly between regions and micro-climatic conditions. The factors responsible for the diversity and community structure in inland nunataks of East Antarctica are still poorly understood. During the BELSPO MICROBIAN project, three sampling campaigns took place in the Sør Rondane Mountains during the austral summers of 2018, 2019 and 2020, resulting in more than 100 samples ranging from different types of barren bedrock to substrates covered by biofilms and well-developed biological soil crusts including lichens, mosses, microalgae and/or cyanobacteria. Cyanobacterial diversity was assessed by amplicon sequencing targeting the V3-V4 variable region of the 16S rRNA gene with cyanobacteria-specific primers using the Illumina MiSeq platform (2x300 bp). The recently developed CyanoSeq database was used for the taxonomic affiliation of the OTUs (99% similarity threshold). Whilst favorable habitats, such as sheltered spots in rocky areas, enhance the development of different kinds of cyanobacterial crusts, cyanobacteria were present even in the most extreme ones. Granitic soils were dominated by very diverse cyanobacterial crusts, mostly composed by filamentous cyanobacteria of the Leptolynbyaceae, Oculatellaceae and Microcoleaceae families, and by Nostocaceae. Most abundant OTUs on gneiss bedrock were from the Cyanothecaceae and Microcoleaceae. In contrast, marble soils were dominated almost exclusively by the Chroococcidiopsaceae family. Moraine samples from very dry areas were mainly characterized by members of the Gomontiellaceae family whereas moraine samples taken close to a lake were rich in filamentous taxa as well, mostly belonging to the Leptolynbyaceae, Oculatellaceae and Gomontiellaceae families. Next to bedrock type, other abiotic variables such as pH, NO3 and TOC were especially important drivers of the community composition in each sampled site.MICROBIAN15. Life on lan

MICROBIAN : Microbial diversity in the Sør Rondane Mountains in a context of climate change

The Sør Rondane Mountains (SRM) represent a c. 900 km² large mountain range, encompassing a large range of terrestrial habitats differing in geology and soil characteristics, exposure time and microclimatic conditions. The objectives of the BelSPO project MICROBIAN are to (i) use a combination of remote sensing (Digital Elevation Model) and close-range field observation techniques to map physical habitat characteristics and the presence/extent of biological crust communities in the region of the Princess Elisabeth Station Antarctica (PEA), (ii) generate a comprehensive inventory of the taxonomic and functional diversity of microbial communities in these habitats by amplicon sequencing of the 16S and 18S rRNA genes and metagenomics, (iii) use mesocosm field experiments (Open Top Chambers and snow fences) to mimic the possible effects of future climate change on the taxonomic diversity of these microbial ecosystems, and (iv) conduct field experiments to inform policy-makers in view of decision making regarding environmental protection and prevention measures to reduce the introduction and spread of non-native species and to avoid cross-contamination between sites. The proposed research will provide a proof of concept to use high resolution satellite images for identifying regions of particular biological interest in East Antarctica and more broadly make a significant contribution to understanding Antarctic terrestrial microbial ecology.MICROBIA

The science-policy link in practice: how to propose an Antarctic Specially Protected Area (ASPA)?

The BelSPO projects ANTAR-IMPACT, BELDIVA and MICROBIAN and literature data concerning the biodiversity in the inland biotopes of the Western Sør Rondane Mountains (Dronning Maud Land) indicated a very rich and unique terrestrial biodiversity on the nunataks in the surroundings of Princess Elisabeth Station, including biofilms and Biological Soil Crusts. However, there is potential for negative impacts due to visits and (human) disturbances, mainly driven by the presence of infrastructures in the vicinity. Therefore, the involved scientists initiated the process of creating an ASPA in collaboration with the relevant ministries (Foreign Affairs, Environment and Science Policy). The first step was the submission of a Working Paper (WP42) at CEP XX (2017) with a Preliminary assessment of the values to be protected, using the template of Appendix 4 to the CEP XX report. Other countries scrutinized the document and raised useful comments and questions. The Information Paper (IP42) submitted at CEP XXI (2018) contained the answers to these questions. The next step was the writing of a Management Plan, based on a Guide that includes all the elements to describe (annex to Resolution 2 (2011)). Several versions were discussed, also with the station operator. The WP15 was finally presented to CEP XXIV that forwarded it to the Subsidiary Group on Management Plan, where it will be further improved during the intersessional period. The process was a learning experience for the scientists, from creating the maps to developing management options, and lastly communicating the importance of the area to policy- and decision-makers.MICROBIAN15. Life on lan

The Importance of Socio-Economic Versus Environmental Risk Factors for Reported Dengue Cases in Java, Indonesia

Background: Dengue is a major mosquito-borne viral disease and an important public health problem. Identifying which factors are important determinants in the risk of dengue infection is critical in supporting and guiding preventive measures. In South-East Asia, half of all reported fatal infections are recorded in Indonesia, yet little is known about the epidemiology of dengue in this country. Methodology/Principal findings: Hospital-reported dengue cases in Banyumas regency, Central Java were examined to build Bayesian spatial and spatio-temporal models assessing the influence of climatic, demographic and socio-economic factors on the risk of dengue infection. A socio-economic factor linking employment type and economic status was the most influential on the risk of dengue infection in the Regency. Other factors such as access to healthcare facilities and night-time temperature were also found to be associated with higher risk of reported dengue infection but had limited explanatory power. Conclusions/Significance: Our data suggest that dengue infections are triggered by indoor transmission events linked to socio-economic factors (employment type, economic status). Preventive measures in this area should therefore target also specific environments such as schools and work areas to attempt and reduce dengue burden in this community. Although our analysis did not account for factors such as variations in immunity which need further investigation, this study can advise preventive measures in areas with similar patterns of reported dengue cases and environmen

Towards physical habitat characterisation in the Antarctic Sor Rondane Mountains using satellite remote sensing

Ice-free areas occupy less than 0.25% of the Antarctic surface, and mainly occur along coastlines, or as inland nunataks protruding from the extensive ice sheet. Their extreme environment and geographical isolation have contributed to the evolution of highly adapted, and largely endemic terrestrial biota. Physical habitat mapping is important to identify the main drivers of spatial variation in soil biodiversity, to predict its response to climate change and to help conservation planning. In this paper we retrieved remotely sensed Land Surface Temperature (LST) and Digital Surface Models (DSM) for the Sor Rondane Mountains in East Antarctica from respectively the Thermal InfraRed Sensor (TIRS) on Landsat 8 and the Pl eiades constellation of high resolution optical imagers. Satellite data were combined with ground truth temperature and elevation measurements with the aim to assess the performance of these remotely sensed data. Over a 2 year period, satellite derived LST corresponded to in situ temperature with Mean Average Difference (MAD) of 2.5 K, and Root Mean Squared Difference (RMSD) of - 6.3 K. Lower biases were observed for periods when the data loggers were frozen or snow covered (MAD 1.8K) compared to intervals where the devices were not frozen (MAD 4 K), with larger scatter (RMSD 7 K) being observed during the latter. These larger MAD and RMSD are caused by the differential heating of the top of the gravel/rocks as observed by the satellite compared to their underside, where the loggers were installed, and are also impacted by the time step of the in situ logging (3 h) and the non-linear heating of the surface. In addition, for the different study sites different biases were observed as a result of the spatial resolution of the TIRS, depending on the composition, structure, geomorphology, and the surroundings of the logger position. Sites on a narrow rock outcrop (e.g. the Perlebandet and Utsteinen nunataks) show a negative bias due to the surrounding ice fields decreasing the satellite pixel average temperature compared to the in situ measured temperatures. For sites with a more extensive rock and gravel composition further away from the ice sheet (Dry and Yuboku Valleys), a positive bias was found as a result of the temperature differential between the exposed top and covered bottom of the rocks and gravel. The DSM derived from Pl ' eiades (without bias correction) showed in general a bias of - 6 m (MAD) and scatter of - 9 m (RMSD) when compared to the Reference Elevation Model of Antarctica and IceSAT-1 LIDAR data. Lowest errors were also found here for the extensive Dry and Yuboku Valley sites (respectively - 5 and 3 m MAD, 7 and 4 m RMSD). Correspondence with in situ logged GPS positions was slightly worse, with a positive bias of 12 m (MAD) and scatter of 15 m (RMSD) across the sites. An analysis on the basis of these LST and DSM datasets, show a clear separability of sites by their average temperature and solar exposition (in terms of slope and aspect) at the time of Landsat overpass. Due to the Landsat overpass times, the LST datasets are however strongly biased, and further work is needed for a better understanding of the light and temperature climate in the ice-free regions. This could for example be achieved by coupling the DSM to a solar irradiance and terrain shadowing model

Disentangling terrestrial microbial community composition in the Sør Rondane Mountains, East Antarctica

The sparse ice-free regions of Antarctica are the coldest deserts on Earth. Yet, ice-free soils harbor substantial microbial communities that can vary significantly in response to environmental and micro-climatic conditions. The factors responsible for driving the microbial diversity and community structure in inland nunataks of East Antarctica are still poorly understood. Within the MICROBIAN project, two sampling campaigns took place in the Sør Rondane Mountains during the austral summers of 2018 and 2019, resulting in more than 100 samples ranging from different types of barren bedrock to well-developed biological soil crusts. Bacterial and eukaryotic diversity was assessed by amplicon sequencing targeting the V1-V3 variable region of the 16S rRNA gene and the V4 region of the 18S rRNA gene with general bacterial and eukaryotic primers using the Illumina MiSeq v3 platform. To investigate the responses of these communities to soil driven geochemical variables (such as pH, TN, TOC, NH4-N, etc.) across the sampled bedrock types (gneiss, granite, marble and moraine) we coupled a Spearman co-occurrence network of ASVs (ρ > 0.7 and p-value < 0.01) to random forest variable ranking and correlations with Spearman and Pearson statistics. A total of 13 clusters (modules) were observed, of which 8 gathered 82% of the ASVs and 97% of the reads in the network. Modules of ASVs that mostly occurred in granitic soils were dominated by filamentous Cyanobacteria and correlated well with increasing NH4-N concentrations while unicellular Cyanobacteria dominated modules occurring in marble samples which correlated well with increasing pH values. One module occurring in gneiss soils was dominated by Proteobacteria and correlated with increasing TOC concentrations, whereas Actinobacteria dominated modules occurring in moraine samples which correlated with increasing TN concentrations. Chlorophyta was the most ubiquitous eukaryotic Phylum, and Metazoa were surprisingly found in the dry and oligotrophic moraine soils as well

Understanding the microbiome diversity through a combination of remote sensing and close-range field observation techniques in the Sør Rondane Mountains, East Antarctica

The sparse ice-free regions of Antarctica are the coldest arid deserts on Earth. Yet, ice-free soils harbor substantial and diverse microbial communities that can vary significantly between the regions and the micro-climatic conditions. The factors responsible for driving the microbial diversity and community structure in inland nunataks of East Antarctica, like the Sør Rondane Mountains, are still poorly understood. Within the BELSPO MICROBIAN project, three sampling campaigns took place in a 70 km radius around the Belgian Princess Elisabeth Station during the Austral summers of 2018, 2019 and 2020, resulting in the biggest sampling effort for microbial analysis in the region. Samples ranged from different kind of barren bedrock to substrates covered by biofilms and well-developed biological soil crusts consisting of lichens, mosses and cyanobacterial/microalgal mats. In this study, long-term microenvironmental monitoring data show that temperature and soil humidity regimes vary with the elevation, slope, aspect, wind exposure and daily irradiance regimes of the surveyed nunataks. Bacterial and eukaryotic diversity were assessed by amplicon sequencing targeting 16S and 18S regions of the rRNA genes with the Illumina MiSeq platform (2x300 bp). Preliminary multivariate analysis indicate that habitat characteristics derived from remote sensing and data loggers give important insights about the distribution of bacteria, cyanobacteria and eukaryotes in these unique environments. Further analyses are ongoing on chemical characterization of the soils and on potential biotic interactions to better understand the terrestrial microbial ecology of Antarctic ice-free regions.MICROBIA