Influence of prokaryotic microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica

Response of bacterial ecological and functional properties to anthropogenic interventions during maturation of mine sand soil

Soil formation is a complex process that starts from the biological development. The ecological principles and biological function in soil are of great importance, whereas their response to anthropogenic intervention has been poorly understood. In this study, a 150-day microcosmic experiment was conducted with the addition of sludge and/or fermented wood chips (FWC) to promote the soil maturation. The results showed that, compared to the control (natural development without anthropogenic intervention), sludge, FWC, and their combination increased the availability of carbon, nitrogen, and potassium, and promoted the soil aggregation. They also enhanced the cellulase activity, microbial biomass carbon (MBC) and bacterial diversity, indicating that anthropogenic interventions promoted the maturation of sand soil. Molecular ecology network and functional analyses indicated that soil maturation was accomplished with the enhancement of ecosystem functionality and stability. Specifically, sludge promoted a transition in bacterial community function from denitrification to nitrification, facilitated the degradation of easily degradable organic matter, and enhanced the autotrophic nutritional mode. FWC facilitated the transition of bacterial function from denitrification to ammonification, promoted the degradation of recalcitrant organic matter, and simultaneously enhanced both autotrophic and heterotrophic nutritional modes. Although both sludge and FWC promoted the soil functionality, they showed distinct mechanistic actions, with sludge enhancing the physical structure, and FWC altering chemical composition. It is also worth emphasizing that sludge and FWC exhibited a synergistic effect in promoting biological development and ecosystem stability, thereby providing an effective avenue for soil maturation.

Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils

In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes.

Microbial impact on initial soil formation in arid and semiarid environments under simulated climate change

The microbiota is attributed to be important for initial soil formation under extreme climate conditions, but experimental evidence for its relevance is scarce. To fill this gap, we investigated the impact of in situ microbial communities and their interrelationship with biocrust and plants compared to abiotic controls on soil formation in initial arid and semiarid soils. Additionally, we assessed the response of bacterial communities to climate change. Topsoil and subsoil samples from arid and semiarid sites in the Chilean Coastal Cordillera were incubated for 16 weeks under diurnal temperature and moisture variations to simulate humid climate conditions as part of a climate change scenario. Our findings indicate that microorganism-plant interaction intensified aggregate formation and stabilized soil structure, facilitating initial soil formation. Interestingly, microorganisms alone or in conjunction with biocrust showed no discernible patterns compared to abiotic controls, potentially due to water-masking effects. Arid soils displayed reduced bacterial diversity and developed a new community structure dominated by Proteobacteria, Actinobacteriota, and Planctomycetota, while semiarid soils maintained a consistently dominant community of Acidobacteriota and Proteobacteria. This highlighted a sensitive and specialized bacterial community in arid soils, while semiarid soils exhibited a more complex and stable community. We conclude that microorganism-plant interaction has measurable impacts on initial soil formation in arid and semiarid regions on short time scales under climate change. Additionally, we propose that soil and climate legacies are decisive for the present soil microbial community structure and interactions, future soil development, and microbial responses.

Metagenomic insights into novel microbial lineages with distinct ecological functions in the Arctic glacier foreland ecosystems

Land-terminating glaciers are retreating globally, resulting in the expansion of the ice-free glacier forelands (GFs). These GFs act as a natural laboratory to study microbial community succession, soil formation, and ecosystem development. Here, we have employed gene-centric and genome-resolved metagenomic approaches to disseminate microbial diversity, community structure, and their associated biogeochemical processes involved in the carbon, nitrogen, and sulfur cycling across three GF ecosystems. Here, we present a compendium of draft Metagenome Assembled Genomes (MAGs) belonging to bacterial (n = 899) and archaeal (n = 4) domains. These MAGs were reconstructed using a total of 27 shotgun metagenomic datasets obtained from three different GFs, including Midtre Lovénbreen glacier (Svalbard), Russell glacier (Greenland), and Storglaciaren (Sweden). The taxonomic classification revealed that 98% of MAGs remained unclassified at species levels, suggesting the presence of novel microbial lineages. The abundance of metabolic genes associated with carbon, nitrogen, and sulfur cycling pathways varied between and within the samples collected across the three GF ecosystems. Our findings indicate that MAGs from different GFs share close phylogenetic relationships but exhibit significant differences in abundance, distribution patterns, and metabolic functions. This compendium of novel MAGs, encompassing autotrophic, phototrophic, and chemolithoautotrophic microbial groups reconstructed from GF ecosystems, represents a valuable resource for further studies.

New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain)

In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.

Measuring the effect of climate change in Antarctic microbial communities: toward novel experimental approaches

The Antarctic continent is undergoing a rapid warming, affecting microbial communities throughout its ecosystems. This continent is a natural laboratory for studying the effect of climate change, however, assessing the microbial communities' responses to environmental changes is challenging from a methodological point of view. We suggest novel experimental designs, including multivariable assessments that apply multiomics methods in combination with continuous environmental data recording and new warming simulation systems. Moreover, we propose that climate change studies in Antarctica should consider three main objectives, including descriptive studies, short-term temporary adaptation studies, and long-term adaptive evolution studies. This will help us to understand and manage the effects of climate change on the Earth.

Environmental micro-niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield

The pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50 m² area in the forefield of the Lobuche glacier (Himalayas, 5050 m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co-occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high-throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche-specific role of the micro-environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico-chemical and micro-climatic variations at the site-spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis.

Benthic Biofilms in Glacier-Fed Streams from Scandinavia to the Himalayas Host Distinct Bacterial Communities Compared with the Streamwater

Microbial life in glacier-fed streams (GFSs) is dominated by benthic biofilms which fulfill critical ecosystem processes. However, it remains unclear how the bacterial communities of these biofilms assemble in stream ecosystems characterized by rapid turnover of benthic habitats and high suspended sediment loads. Using16S rRNA gene amplicon sequence data collected from 54 GFSs across the Himalayas, European Alps, and Scandinavian Mountains, we found that benthic biofilms harbor bacterial communities that are distinct from the bacterial assemblages suspended in the streamwater. Our data showed a decrease in species richness in the benthic biofilms compared to the bacterial cells putatively free-living in the water. The benthic biofilms also differed from the suspended water fractions in terms of community composition. Differential abundance analyses highlighted bacterial families that were specific to the benthic biofilms and the suspended assemblages. Notably, source-sink models suggested that the benthic biofilm communities are not simply a subset of the suspended assemblages. Rather, we found evidence that deterministic processes (e.g., species sorting) shape the benthic biofilm communities. This is unexpected given the high vertical mixing of water and contained bacterial cells in GFSs and further highlights the benthic biofilm mode of life as one that is determined through niche-related processes. Our findings therefore reveal a "native" benthic biofilm community in an ecosystem that is currently threatened by climate-induced glacier shrinkage. IMPORTANCE Benthic biofilms represent the dominant form of life in glacier-fed streams. However, it remains unclear how bacterial communities within these biofilms assemble. Our findings from glacier-fed streams from three major mountain ranges across the Himalayas, the European Alps and the Scandinavian Mountains reveal a bacterial community associated with benthic biofilms that is distinct from the assemblage in the overlying streamwater. Our analyses suggest that selection is the underlying process to this differentiation. This is unexpected given that bacterial cells that are freely living or attached to the abundant sediment particles suspended in the water continuously mix with the benthic biofilms. The latter colonize loose sediments that are subject to high turnover owing to the forces of the water flow. Our research unravels the existence of a microbiome specific to benthic biofilms in glacier-fed streams, now under major threats due to global warming.

Impact of Climate and Slope Aspects on the Composition of Soil Bacterial Communities Involved in Pedogenetic Processes along the Chilean Coastal Cordillera

Soil bacteria play a fundamental role in pedogenesis. However, knowledge about both the impact of climate and slope aspects on microbial communities and the consequences of these items in pedogenesis is lacking. Therefore, soil-bacterial communities from four sites and two different aspects along the climate gradient of the Chilean Coastal Cordillera were investigated. Using a combination of microbiological and physicochemical methods, soils that developed in arid, semi-arid, mediterranean, and humid climates were analyzed. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes were found to increase in abundance from arid to humid climates, while Actinobacteria and Gemmatimonadetes decreased along the transect. Bacterial-community structure varied with climate and aspect and was influenced by pH, bulk density, plant-available phosphorus, clay, and total organic-matter content. Higher bacterial specialization was found in arid and humid climates and on the south-facing slope and was likely promoted by stable microclimatic conditions. The presence of specialists was associated with ecosystem-functional traits, which shifted from pioneers that accumulated organic matter in arid climates to organic decomposers in humid climates. These findings provide new perspectives on how climate and slope aspects influence the composition and functional capabilities of bacteria, with most of these capabilities being involved in pedogenetic processes.

Diazotrophic activity and denitrification in two long-term chronosequences of maritime Antarctica

The main goals of this study were to identify whether key processes involved in microbial soil nitrogen transformations, such as diazotrophic activity and denitrification, the chemical properties of limiting elements in the soil, and microbial community structure, differ in the different successional stages of two long term chronosequences in maritime Antarctica. Moreover, we expect the rates of diazotrophic activity and denitrification to be stimulated by increases in air temperature and moisture. To answer these questions, we selected three stages in the succession (early, mid and late) in each of two well established chronosequences: three raised beaches in Ardley Island; and the Barton Peninsula, which includes two cosmogenically dated sites and the forefield of the Fourcade glacier. In the Ardley chronosequence, higher diazotrophic activity was found in the older successional stages, concomitant with an increase in the abundance of Cyanobacteria. In the Barton chronosequence, Cyanobacteria were only present and abundant (Microcoleus) in the early successional stage, coinciding with the highest diazotrophic activity. Denitrification in the Barton chronosequence tended to be highest at the mid successional sites, associated with the highest abundance of Rhodanobacter. In the Ardley chronosequence, the lowest abundance of Rhodanobacter was linked to lower denitrification rates in the mid successional stage. In the Ardley chronosequence, significant positive effects of passive warming and water addition on diazotrophic activity were detected in the first and the second years of the study respectively. In the Barton chronosequence on the other hand, there was no response to either passive warming or water addition, probably a manifestation of the higher nutrient limitation in this site. Denitrification showed no response to either warming or water addition. Thus, the response of microbial nitrogen transformations to global change is highly dependent on the environmental setting, such as soil origin, age and climate regime.