Microbial Adaptation and Diversity In The High-Elevation Extreme Cryosphere: Implications For Astrobiology

Life on Earth has been found in every extreme environment explored to date where liquid water is at least occasionally available. The discovery of extreme environments and organisms inhabiting them has provided valuable insights into the search for life beyond our own planet. Terrestrial analogues are environments on Earth exhibiting a subset of conditions similar to those found on other planetary surfaces such as Mars, the best candidate for harboring life in our solar system. A number of environments of the Earth's cryosphere are analogues of the three main climatic stages of Mars and may help in assessing the habitability of past and present Mars. Here I describe previously unexplored analogue environments and show how they support thriving microbial communities, as well as discuss potential strategies microbes use to survive and grow in these extreme systems. In chapter 2, I present the first study of microbial diversity in ice and soils from the top of Mt. Kilimanjaro, a terrestrial analogue of the middle age of Mars, and demonstrate that this site supports both cosmopolitan and endemic microbial communities. In chapter 3, I demonstrate that the dominant microeukaryote (Naganishia friedmannii) at high elevations (5100 to 6300 m.a.s.l.) on several Atacama volcanoes (analogues of the third epoch of Mars), is able to grow rapidly during extreme diurnal freeze-thaw cycles and is metabolically versatile. In chapter 4, I show that high-elevation transient ice structures known as &ldquo;nieves penitentes&rdquo; are oases that support thriving communities of snow algae and other microbes on Volc&aacute;n Llullaillaco, one of the Atacama volcanoes and the second tallest volcano on Earth. In chapter 5, I present work from microcosm and field experiments showing that extremophilic communities can respond to water and nutrient amendments in soils from Volc&aacute;n Llullaillaco. In chapter 6, I describe the draft genome of Naganishia friedmannii isolated from tephra soils at an elevation of 6030 m.a.s.l. on Volc&aacute;n Llullaillaco. I show it has a streamlined genome compared to closely related fungi and possesses genes known to play a role in coping with environmental stressors prevalent at extreme elevations.</p

The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities

Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genus Polaromonas emphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation &ldquo;island of the cryosphere&rdquo; before the glaciers of Kilimanjaro disappear forever.</p

Clarification and guidance on the use of the Socio-Economic Impact Classification for Alien Taxa (SEICAT) framework

Understanding the ways in which alien taxa threaten human well-being, beyond purely monetary costs, can be difficult as impacts differ vastly across social, cultural, and economic contexts. Failure to capture impacts outside of monetary costs means that impacts are unfairly weighted towards those that can be easily monetised, which is unlikely to be a realistic measure of how alien species truly affect human well-being. To address this issue, the Socio-Economic Impact Classification for Alien Taxa (SEICAT) was developed with the intention to facilitate standardised classifications and comparisons of the impacts of alien taxa on human well-being and livelihood. The framework measures impacts by assessing to what extent alien taxa have altered human activities, so has application across a broad range of reported impacts associated with different constituents of human well-being. Although in their original paper, Bacher et al. (2018) provided an overview of the SEICAT framework, comprehensive guidelines that enable assessors to overcome potential ambiguities were, until now, unavailable. This may be preventing the broad application of the framework due to reduced usability. Here, we provide clarification and guidance for the application of SEICAT to facilitate standardised, consistent assessments. In particular, we address uncertainties stemming from unclear definitions of impacted communities and activities, as well as the spatial and temporal scales of relevance. We clarify these key issues and give explicit recommendations, whilst encouraging the collection of additional contextual information to be recorded for each assessed impact report, to generate more practical information for end-users of SEICAT data. Further, we recommend adopting an alternative terminology for the impact categories to reduce the potential misuse of the current descriptors. The intended outcome of this work is to aid the broad application of the SEICAT framework in a consistent and transparent manner

The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity

Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions

The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity

Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions.Agencia Estatal de Investigación PCI2018-092939, PCI2018-092986Swiss National Science Foundation 31003A_179491, 31BD30_184114Austrian Fonds zur Förderung der Wissenschaftlichen Forschung 4011-B32German Bundesministerium für Bildung und Forschung 16LC1803A, 01LC1807CFrench National Research Agency ANR-18-EBI4-0001-06US National Science Foundation ICER-1852060National Research Foundation of South Africa 89967Australian Research Council DP200101680UK Natural Environment Research Council NE/V007548/1Hellenic Foundation for Research and Innovation (H.F.R.I.) HFRIFM17-159

Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica

Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem

Microbial Species–Area Relationships in Antarctic Cryoconite Holes Depend on Productivity

The island species&ndash;area relationship (ISAR) is a positive association between the number of species and the area of an isolated, island-like habitat. ISARs are ubiquitous across domains of life, yet the processes generating ISARs remain poorly understood, particularly for microbes. Larger and more productive islands are hypothesized to have more species because they support larger populations of each species and thus reduce the probability of stochastic extinctions in small population sizes. Here, we disentangled the effects of &ldquo;island&rdquo; size and productivity on the ISAR of Antarctic cryoconite holes. We compared the species richness of bacteria and microbial eukaryotes on two glaciers that differ in their productivity across varying hole sizes. We found that cryoconite holes on the more productive Canada Glacier gained more species with increasing hole area than holes on the less productive Taylor Glacier. Within each glacier, neither productivity nor community evenness explained additional variation in the ISAR. Our results are, therefore, consistent with productivity shaping microbial ISARs at broad scales. More comparisons of microbial ISARs across environments with limited confounding factors, such as cryoconite holes, and experimental manipulations within these systems will further contribute to our understanding of the processes shaping microbial biogeography.</p

Comparison of Microbial Communities in the Sediments and Water Columns of Frozen Cryoconite Holes in the McMurdo Dry Valleys, Antarctica

Although cryoconite holes, sediment-filled melt holes on glacier surfaces, appear small and homogenous, their microbial inhabitants may be spatially partitioned. This partitioning could be particularly important for maintaining biodiversity in holes that remain isolated for many years, such as in Antarctica. We hypothesized that cryoconite holes with greater species richness and biomass should exhibit greater partitioning between the sediments and water, promoting greater biodiversity through spatial niche partitioning. We tested this hypothesis by sampling frozen cryoconite holes along a gradient of biomass and biodiversity in the Taylor Valley, Antarctica, where ice-lidded cryoconite holes are a ubiquitous feature of glaciers. We extracted DNA and chlorophyll a from the sediments and water of these samples to describe biodiversity and quantify proxies for biomass. Contrary to our expectation, we found that cryoconite holes with greater richness and biomass showed less partitioning of phylotypes by the sediments versus the water, perhaps indicating that the probability of sediment microbes being mixed into the water is higher from richer sediments. Another explanation may be that organisms from the water were compressed by freezing down to the sediment layer, leaving primarily relic DNA of dead cells to be detected higher in the frozen water. Further evidence of this explanation is that the dominant sequences unique to water closely matched organisms that do not live in cryoconite holes or the Dry Valleys (e.g., vertebrates); so this cryptic biodiversity could represent unknown microbial animals or DNA from atmospheric deposition of dead biomass in the otherwise low-biomass water. Although we cannot rule out spatial niche partitioning occurring at finer scales or in melted cryoconite holes, we found no evidence of partitioning between the sediments and water in frozen holes. Future work should include more sampling of cryoconite holes at a finer spatial scale, and characterizing the communities of the sediments and water when cryoconite holes are melted and active

Supporting information: The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity [dataset]

Supporting information A in S1 File. Glossary of additional key terms. Supporting information B in S1 File. Table reporting contrasting arguments and approaches used to define how alien taxa are considered and should be managed in accordance with different conservation values/motivations. As multiple values/motivations exist and determine which entities we are interested in (see also Supporting information A), distinct conservation targets can be identified. Note that here, we only consider conservation values/motivations that are expressed regardless of any nature’s instrumental (utilitarian) value, i.e., regardless of nature’s contributions to human well-being (see “nature for itself” framing [9]). Also, note that such contrasting arguments and approaches are not necessarily mutually exclusive and have been occasionally combined to find a middle ground to achieve broader conservation goals [10–13]. Supporting information C in S1 File. Circumstances under which the prevention/mitigation of a decreasing change is considered as a positive change under EICAT+. In EICAT+, we also consider as positive impacts (i.e., increasing changes) cases in which an alien species prevents/mitigates decreasing changes, e.g., when the performance of a native individual, the size of a native population, or the occupancy of a native species would have decreased, or decreased to a greater extent, if the alien species had not been introduced. Although some of these positive impacts can be inferred, the prevention of a decreasing change should be assessed under EICAT+ only when there is convincing evidence that a certain biodiversity attribute (e.g., population size) would have decreased, or decreased to a greater extent, in the absence of the alien species. In the case of extinction prevention, for instance, it must be clear that (i) the population was locally heading toward extinction before the introduction of the alien; and (ii) the alien taxon prevented, through a specific impact mechanism, an extinction that would have occurred in its absence [41,42] (Fig 2b). Other cases where an alien species may prevent or mitigate decreasing changes are, for instance, those in which the abundance (i.e., a proxy for population size) of a native species declined in the uninvaded (i.e., control) plots but not, or to a lesser extent, in the plots invaded by the alien. Note that positive impacts associated with the prevention/mitigation of a decreasing change will generally be more difficult to study and identify than those associated with actual increasing changes, as the former require extensive data regarding the temporal trend of individual performance, population size, or area of occupancy. Supporting information D in S1 File. EICAT+ mechanisms and submechanisms by which an alien taxon can cause positive impacts on native biodiversity attributes and examples of positive impacts sourced from the literature and assessed under EICAT+ (ML+ = Minimal positive impact, MN+ = Minor positive impact, MO+ = Moderate positive impact, MR+ = Major positive impact, MV+ = Massive positive impact). Rationales behind the formulation of the mechanisms and submechanisms can be found in the main text and in Supporting information G, H, and J. Supporting information E in S1 File. Table reporting examples sourced from the literature and classified as information that cannot be classified under EICAT+, but that contain information about mechanisms and might set the stage for future studies. Although these studies described the existence of mechanisms by which alien taxa may cause positive impacts on native taxa, such literature is considered as nonrelevant, as it did not measure, or provide information on, biodiversity attributes used in EICAT+ (e.g., performance of individuals or population size). Rationales behind the formulation of the mechanisms and submechanisms can be found in the main text and in Supporting information G, H, and J. Supporting information F in S1 File. How to attribute a confidence score in EICAT+. Supporting information G in S1 File. Additional information around the rationale behind the formulation of the EICAT+ mechanisms and submechanisms. Supporting information H in S1 File. Additional information about how alien species can cause positive impacts on native biodiversity through overcompensation. Supporting information J in S1 File. Additional information about how alien species can cause positive impacts on native biodiversity through hybridization. Supporting information K in S1 File. References used in the Supporting information.Peer reviewe

Limited Response of Indigenous Microbes to Water and Nutrient Pulses in High-Elevation Atacama Soils: Implications for the Cold–Dry Limits of Life on Earth

Soils on the world&rsquo;s highest volcanoes in the Atacama region represent some of the harshest ecosystems yet discovered on Earth. Life in these environments must cope with high UV flux, extreme diurnal freeze&ndash;thaw cycles, low atmospheric pressure and extremely low nutrient and water availability. Only a limited spectrum of bacterial and fungal lineages seems to have overcome the harshness of this environment and may have evolved the ability to function in situ. However, these communities may lay dormant for most of the time and spring to life only when enough water and nutrients become available during occasional snowfalls and aeolian depositions. We applied water and nutrients to high-elevation soils (5100 meters above sea level) from Volc&aacute;n Llullaillaco, both in lab microcosms and in the field, to investigate how microbial communities respond when resource limitations are alleviated. The dominant taxon in these soils, the extremophilic yeast Naganishia sp., increased in relative sequence abundance and colony-forming unit counts after water + nutrient additions in microcosms, and marginally in the field after only 6 days. Among bacteria, only a Noviherbaspirillum sp. (Oxalobacteraceae) significantly increased in relative abundance both in the lab and field in response to water addition but not in response to water and nutrients together, indicating that it might be an oligotroph uniquely suited to this extreme environment. The community structure of both bacteria and eukaryotes changed significantly with water and water + nutrient additions in the microcosms and taxonomic richness declined with amendments to water and nutrients. These results indicate that only a fraction of the detected community is able to become active when water and nutrients limitations are alleviated in lab microcosms, and that water alone can dramatically change community structure. Our study sheds light on which extremophilic organisms are likely to respond when favorable conditions occur in extreme earthly environments and perhaps in extraterrestrial environments as well