Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert

The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile

Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.

A review of factors affecting the soil microbial community structure in wetlands

Microbial community in wetland soils is crucial for maintaining the stability of the wetland ecosystem. Nevertheless, the soil microbial community is sensitive to the environmental stress in wetlands. This leads to the possibility that the microbial community structure may be influenced by environmental factors. To gain an in-depth understanding in the response of microbial community structure in wetland soils under different environmental factors, this review comprehensively explores the factors of natural conditions (e.g., different types of wetland, soil physical and chemical properties, climate conditions), biological factors (e.g., plants, soil animals), and human activities (e.g., land use, soil pollution, grazing). Those factors can affect microbial community structure and activities in wetland soils through different ways such as (i) affecting the wetland soil environment in which soil microorganisms survived in, (ii) influencing the available nutrients (e.g., carbon, nitrogen) required for microbial activity, and (iii) the direct effects on soil microorganisms (toxicity or promotion of resistant species). This review can provide references for the conservation of microbial diversity in wetland soils, the maintenance of wetland ecosystem balance, and the wetland ecological restoration.

Salinity affects microbial function genes related to nutrient cycling in arid regions

Introduction

Salinization damages soil system health and influences microbial communities structure and function. The response of microbial functions involved in the nutrient cycle to soil salinization is a valuable scientific question. However, our knowledge of the microbial metabolism functions in salinized soil and their response to salinity in arid desert environments is inadequate.

Methods

Here, we applied metagenomics technology to investigate the response of microbial carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling and the key genes to salinity, and discuss the effects of edaphic variables on microbial functions.

Results

We found that carbon fixation dominated the carbon cycle. Nitrogen fixation, denitrification, assimilatory nitrate reduction (ANRA), and nitrogen degradation were commonly identified as the most abundant processes in the nitrogen cycle. Organic phosphorus dissolution and phosphorus absorption/transport were the most enriched P metabolic functions, while sulfur metabolism was dominated by assimilatory sulfate reduction (ASR), organic sulfur transformation, and linkages between inorganic and organic sulfur transformation. Increasing salinity inhibited carbon degradation, nitrogen fixation, nitrogen degradation, anammox, ANRA, phosphorus absorption and transport, and the majority of processes in sulfur metabolism. However, some of the metabolic pathway and key genes showed a positive response to salinization, such as carbon fixation (facA, pccA, korAB), denitrification (narG, nirK, norBC, nosZ), ANRA (nasA, nirA), and organic phosphorus dissolution processes (pstABCS, phnCD, ugpAB). High salinity reduced the network complexity in the soil communities. Even so, the saline microbial community presented highly cooperative interactions. The soil water content had significantly correlations with C metabolic genes. The SOC, N, and P contents were significantly correlated with C, N, P, and S network complexity and functional genes. AP, NH4+, and NO3- directly promote carbon fixation, denitrification, nitrogen degradation, organic P solubilization and mineralization, P uptake and transport, ASR, and organic sulfur transformation processes.

Conclusion

Soil salinity in arid region inhibited multiple metabolic functions, but prompted the function of carbon fixation, denitrification, ANRA, and organic phosphorus dissolution. Soil salinity was the most important factor driving microbial functions, and nutrient availability also played important roles in regulating nutrient cycling.

Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem

Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.

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.

Salinity causes differences in stratigraphic methane sources and sinks

Methane metabolism, driven by methanogenic and methanotrophic microorganisms, plays a pivotal role in the carbon cycle. As seawater intrusion and soil salinization rise due to global environmental shifts, understanding how salinity affects methane emissions, especially in deep strata, becomes imperative. Yet, insights into stratigraphic methane release under varying salinity conditions remain sparse. Here we investigate the effects of salinity on methane metabolism across terrestrial and coastal strata (15-40 m depth) through in situ and microcosm simulation studies. Coastal strata, exhibiting a salinity level five times greater than terrestrial strata, manifested a 12.05% decrease in total methane production, but a staggering 687.34% surge in methane oxidation, culminating in 146.31% diminished methane emissions. Salinity emerged as a significant factor shaping the methane-metabolizing microbial community's dynamics, impacting the methanogenic archaeal, methanotrophic archaeal, and methanotrophic bacterial communities by 16.53%, 27.25%, and 22.94%, respectively. Furthermore, microbial interactions influenced strata system methane metabolism. Metabolic pathway analyses suggested Atribacteria JS1's potential role in organic matter decomposition, facilitating methane production via Methanofastidiosales. This study thus offers a comprehensive lens to comprehend stratigraphic methane emission dynamics and the overarching factors modulating them.

Microbial diversity and functions in saline soils: A review from a biogeochemical perspective

BACKGROUND

Soil salinization threatens food security and ecosystem health, and is one of the important drivers to the degradation of many ecosystems around the world. Soil microorganisms have extremely high diversity and participate in a variety of key ecological processes. They are important guarantees for soil health and sustainable ecosystem development. However, our understanding of the diversity and function of soil microorganisms under the change of increased soil salinization is fragmented.

AIM OF REVIEW

Here, we summarize the changes in soil microbial diversity and function under the influence of soil salinization in diverse natural ecosystems. We particularly focus on the diversity of soil bacteria and fungi under salt stress and the changes in their emerging functions (such as their mediated biogeochemical processes). This study also discusses how to use the soil microbiome in saline soils to deal with soil salinization for supporting sustainable ecosystems, and puts forward the knowledge gaps and the research directions that need to be strengthened in the future.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Due to the rapid development of molecular-based biotechnology (especially high-throughput sequencing technology), the diversity and community composition and functional genes of soil microorganisms have been extensively characterized in different habitats. Clarifying the responding pattern of microbial-mediated nutrient cycling under salt stress and developing and utilizing microorganisms to weaken the adverse effects of salt stress on plants and soil, which are of guiding significance for agricultural production and ecosystem management in saline lands.

Continuous planting of euhalophyte Suaeda salsa enhances microbial diversity and multifunctionality of saline soil

Halophyte-based remediation emerges as a novel strategy for ameliorating saline soils, offering a sustainable alternative to conventional leaching methods. While bioremediation is recognized for its ability to energize soil fertility and structure, the complex interplays among plant traits, soil functions, and soil microbial diversity remain greatly unknown. Here, we conducted a 5-year field experiment involving the continuous cultivation of the annual halophyte Suaeda salsa in saline soils to explore soil microbial diversity and their relationships with plant traits and soil functions. Our findings demonstrate that a decline in soil salinity corresponded with increases in the biomass and seed yield of S. salsa, which sustained a consistent seed oil content of approximately 22% across various salinity levels. Significantly, prolonged cultivation of halophytes substantially augmented soil microbial diversity, particularly from the third year of cultivation. Moreover, we identified positive associations between soil multifunctionality, seed yield, and taxonomic richness within a pivotal microbial network module. Soils enriched with taxa from this module showed enhanced multifunctionality and greater seed yields, correlating with the presence of functional genes implicated in nitrogen fixation and nitrification. Genomic analysis suggests that these taxa have elevated gene copy numbers of crucial functional genes related to nutrient cycling. Overall, our study emphasizes that the continuous cultivation of S. salsa enhances soil microbial diversity and recovers soil multifunctionality, expanding the understanding of plant-soil-microbe feedback in bioremediation.IMPORTANCEThe restoration of saline soils utilizing euhalophytes offers a viable alternative to conventional irrigation techniques for salt abatement and soil quality enhancement. The ongoing cultivation of the annual Suaeda salsa and its associated plant traits, soil microbial diversity, and functionalities are, however, largely underexplored. Our investigation sheds light on these dynamics, revealing that cultivation of S. salsa sustains robust plant productivity while fostering soil microbial diversity and multifunctionality. Notably, the links between enhanced soil multifunctionality, increased seed yield, and network-dependent taxa were found, emphasizing the importance of key microbial taxa linked with functional genes vital to nitrogen fixation and nitrification. These findings introduce a novel understanding of the role of soil microbes in bioremediation and advance our knowledge of the ecological processes that are vital for the rehabilitation of saline environments.

Effects of increasing soil moisture on Antarctic desert microbial ecosystems

Overgeneralization and a lack of baseline data for microorganisms in high-latitude environments have restricted the understanding of the microbial response to climate change, which is needed to establish Antarctic conservation frameworks. To bridge this gap, we examined over 17,000 sequence variants of bacteria and microeukarya across the hyperarid Vestfold Hills and Windmill Islands regions of eastern Antarctica. Using an extended gradient forest model, we quantified multispecies response to variations along 79 edaphic gradients to explore the effects of change and wind-driven dispersal on community dynamics under projected warming trends. We also analyzed a second set of soil community data from the Windmill Islands to test our predictions of major environmental tipping points. Soil moisture was the most robust predictor for shaping the regional soil microbiome; the highest rates of compositional turnover occurred at 10-12% soil moisture threshold for photoautotrophs, such as Cyanobacteria, Chlorophyta, and Ochrophyta. Dust profiles revealed a high dispersal propensity for Chlamydomonas, a microalga, and higher biomass was detected at trafficked research stations. This could signal the potential for algal blooms and increased nonendemic species dispersal as human activities increase in the region. Predicted increases in moisture availability on the Windmill Islands were accompanied by high photoautotroph abundances. Abundances of rare oligotrophic taxa, such as Eremiobacterota and Candidatus Dormibacterota, which play a crucial role in atmospheric chemosynthesis, declined over time. That photosynthetic taxa increased as soil moisture increased under a warming scenario suggests the potential for competition between primary production strategies and thus a more biotically driven ecosystem should the climate become milder. Better understanding of environmental triggers will aid conservation efforts, and it is crucial that long-term monitoring of our study sites be established for the protection of Antarctic desert ecosystems. Furthermore, the successful implementation of an improved gradient forest model presents an exciting opportunity to broaden its use on microbial systems globally.

Study of the Bacterial, Fungal, and Archaeal Communities Structures near the Bulgarian Antarctic Research Base "St. Kliment Ohridski" on Livingston Island, Antarctica

As belonging to one of the most isolated continents on our planet, the microbial composition of different environments in Antarctica could hold a plethora of undiscovered species with the potential for biotechnological applications. This manuscript delineates our discoveries after an expedition to the Bulgarian Antarctic Base "St. Kliment Ohridski" situated on Livingston Island, Antarctica. Amplicon-based metagenomics targeting the 16S rRNA genes and ITS2 region were employed to assess the metagenomes of the bacterial, fungal, and archaeal communities across diverse sites within and proximal to the research station. The predominant bacterial assemblages identified included Oxyphotobacteria, Bacteroidia, Gammaprotobacteria, and Alphaprotobacteria. A substantial proportion of cyanobacteria reads were attributed to a singular uncultured taxon within the family Leptolyngbyaceae. The bacterial profile of a lagoon near the base exhibited indications of penguin activity, characterized by a higher abundance of Clostridia, similar to lithotelm samples from Hannah Pt. Although most fungal reads in the samples could not be identified at the species level, noteworthy genera, namely Betamyces and Tetracladium, were identified. Archaeal abundance was negligible, with prevalent groups including Woesearchaeales, Nitrosarchaeum, Candidatus Nitrosopumilus, and Marine Group II.

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

Understanding 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.

Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments

Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.

Soil microbial responses to simulated climate change across polar ecosystems

The polar regions are among the most biologically constrained in the world, characterized by cold temperatures and reduced liquid water. These limitations make them among the most climate-sensitive regions on Earth. Despite the overwhelming constraints from low temperatures and resource availability, many polar ecosystems, including polar deserts and tundras across the Arctic and Antarctic host uniquely diverse microbial communities. Polar regions have warmed more rapidly than the global average, with continued warming predicted for the future, which will reduce constraints on soil microbial activity. This could alter polar carbon (C) cycles, increasing CO2 emissions into the atmosphere. The objective of this study was to determine how increased temperature and moisture availability impacts microbial respiration in polar regions, by focusing on a diversity of ecosystem types (polar desert vs. tundra) that are geographically distant across Antarctica and the Arctic. We found that polar desert soil microbes were co-limited by temperature and moisture, though C and nitrogen (N) mineralization were only stimulated at the coldest and driest of the two polar deserts. Only bacterial biomass was impacted at the less harsh of the polar deserts, suggesting microbial activity is limited by factors other than temperature and moisture. Of the tundra sites, only the Antarctic tundra was climate-sensitive, where increased temperature decreased C and N mineralization while water availability stimulated it. The greater availability of soil resources and vegetative biomass at the Arctic tundra site might lead to its lack of climate-sensitivity. Notably, while C and N dynamics were climate-sensitive at some of our polar sites, P availability was not impacted at any of them. Our results demonstrate that soil microbial processes in some polar ecosystems are more sensitive to changes in temperature and moisture than others, with implications for soil C and N storage that are not uniformly predictable across polar regions.

Dissolved organic compounds in shale gas extraction flowback water as principal disturbance factors of soil nitrogen dynamics

Flowback water, a by-product of shale gas extraction, represents an extremely complex industrial wastewater characterized by high organic compounds content and high salinity. The prospect of flowback water entering the soil through various approaches concerns regarding its ecological risk. Nitrogen mineralization (Nmin), a key rate-limiting step in the soil N cycle, might be adversely affected by flowback water. Nonetheless, no previous studies have examined the effects of flowback water on soil Nmin rates, let alone quantified the relative contributions of the major components of flowback water to changes in Nmin rates. Therefore, this study investigated the effects of flowback water and sterile flowback water at two different concentrations on the Nmin rates of three distinct soil types. This study aimed to elucidate the predominant influence of the key constituents within flowback water on the changes in soil Nmin rates. The results showed that soil soluble salt content, dissolved organic carbon (DOC) and dissolved nitrogen (DN) content significantly increased by 8.37 times, 9.5 % and 26.4 %, respectively, in soils contaminated by flowback water. In comparison with the control group, the introduction of flowback water resulted in a significant 25.9 % reduction in Nmin rate in sandy soils. Conversely, in clay and loam soils, there was a significant increase in Nmin rates by 44.9 % and 131.8 % respectively. Throughout the incubation period, leucine-aminopeptidase activity exhibited irregular fluctuations. Analysis of microbial communities demonstrated that flowback water only significant impacted soil rare microbial taxa, inducing a significant increase in alpha diversity for sandy, clay, and loamy soils by -16.9 %, 10.12 %, and 1.63 %, respectively. Linear regression and random forest analyses indicated that alterations in soil DOC:DN ratio and salt content were responsible for changes in soil Nmin rates within flowback water-contaminated soils. In contrast, only salt content significantly contributed to shifts in alpha diversity among soil rare microbial taxa. Structural equation modeling highlighted that the total effect of dissolved organic compounds (DOC and DN, λ = 0.64) from flowback water was greater than the total effect of salinity (λ = 0.24) on soil Nmin rates. In conclusion, our findings imply that dissolved organic compounds within flowback water play pivotal roles in determining soil Nmin rates. To the best of our knowledge, this is the first study to reveal the effects of major components in the flowback water on soil N mineralization rates.

Microbial successional pattern along a glacier retreat gradient from Byers Peninsula, Maritime Antarctica

The retreat of glaciers in Antarctica has increased in the last decades due to global climate change, influencing vegetation expansion, and soil physico-chemical and biological attributes. However, little is known about soil microbiology diversity in these periglacial landscapes. This study characterized and compared bacterial and fungal diversity using metabarcoding of soil samples from the Byers Peninsula, Maritime Antarctica. We identified bacterial and fungal communities by amplification of bacterial 16 S rRNA region V3-V4 and fungal internal transcribed spacer 1 (ITS1). We also applied 14C dating on soil organic matter (SOM) from six profiles. Physico-chemical analyses and attributes associated with SOM were evaluated. A total of 14,048 bacterial ASVs were obtained, and almost all samples had 50% of their sequences assigned to Actinobacteriota and Proteobacteria. Regarding the fungal community, Mortierellomycota, Ascomycota and Basidiomycota were the main phyla from 1619 ASVs. We found that soil age was more relevant than the distance from the glacier, with the oldest soil profile (late Holocene soil profile) hosting the highest bacterial and fungal diversity. The microbial indices of the fungal community were correlated with nutrient availability, soil reactivity and SOM composition, whereas the bacterial community was not correlated with any soil attribute. The bacterial diversity, richness, and evenness varied according to presence of permafrost and moisture regime. The fungal community richness in the surface horizon was not related to altitude, permafrost, or moisture regime. The soil moisture regime was crucial for the structure, high diversity and richness of the microbial community, specially to the bacterial community. Further studies should examine the relationship between microbial communities and environmental factors to better predict changes in this terrestrial ecosystem.

Wide divergence of fungal communities inhabiting rocks and soils in a hyper-arid Antarctic desert

Highly simplified microbial communities colonise rocks and soils of continental Antarctica ice-free deserts. These two habitats impose different selection pressures on organisms, yet the possible filtering effects on the diversity and composition of microbial communities have not hitherto been fully characterised. We hence compared fungal communities in rocks and soils in three localities of inner Victoria Land. We found low fungal diversity in both substrates, with a mean species richness of 28 across all samples, and significantly lower diversity in rocks than in soils. Rock and soil communities were strongly differentiated, with a multinomial species classification method identifying just three out of 328 taxa as generalists with no affinity for either substrate. Rocks were characterised by a higher abundance of lichen-forming fungi (typically Buellia, Carbonea, Pleopsidium, Lecanora, and Lecidea), possibly owing to the more protected environment and the porosity of rocks permitting photosynthetic activity. In contrast, soils were dominated by obligate yeasts (typically Naganishia and Meyerozyma), the abundances of which were correlated with edaphic factors, and the black yeast Cryomyces. Our study suggests that strong differences in selection pressures may account for the wide divergences of fungal communities in rocks and soils of inner Victoria Land.

The Salinity Survival Strategy of Chenopodium quinoa: Investigating Microbial Community Shifts and Nitrogen Cycling in Saline Soils

Quinoa is extensively cultivated for its nutritional value, and its exceptional capacity to endure elevated salt levels presents a promising resolution to the agricultural quandaries posed by salinity stress. However, limited research has been dedicated to elucidating the correlation between alterations in the salinity soil microbial community and nitrogen transformations. To scrutinize the underlying mechanisms behind quinoa's salt tolerance, we assessed the changes in microbial community structure and the abundance of nitrogen transformation genes across three distinct salinity thresholds (1 g·kg-1, 3 g·kg-1, and 6 g·kg-1) at two distinct time points (35 and 70 days). The results showed the positive effect of quinoa on the soil microbial community structure, including changes in key populations and its regulatory role in soil nitrogen cycling under salt stress. Choroflexi, Acidobacteriota, and Myxococcota were inhibited by increased salinity, while the relative abundance of Bacteroidota increased. Proteobacteria and Actinobacteria showed relatively stable abundances across time and salinity levels. Quinoa possesses the ability to synthesize or modify the composition of keystone species or promote the establishment of highly complex microbial networks (modularity index > 0.4) to cope with fluctuations in external salt stress environments. Furthermore, quinoa exhibited nitrogen (N) cycling by downregulating denitrification genes (nirS, nosZ), upregulating nitrification genes (Archaeal amoA (AOA), Bacterial amoA (AOB)), and stabilizing nitrogen fixation genes (nifH) to absorb nitrate-nitrogen (NO3-_N). This study paves the way for future research on regulating quinoa, promoting soil microbial communities, and nitrogen transformation in saline environments.

Soil microbial communities regulate the threshold effect of salinity stress on SOM decomposition in coastal salt marshes

Salinity stress is one of the critical environmental drivers of soil organic matter (SOM) decomposition in coastal ecosystems. Although the temperature sensitivity (Q10) of SOM decomposition has been widely applied in Earth system models to forecast carbon processes, the impact of salinity on SOM decomposition by restructuring microbial communities remains uncovered. Here, we conducted a microcosm experiment with soils collected from the coastal salt marsh in the Yellow River Estuary, which is subjected to strong dynamics of salinity due to both tidal flooding and drainage. By setting a gradient of salt solutions, soil salinity was adjusted to simulate salinity stress and soil carbon emission (CO2) rate was measured over the period. Results showed that as salinity increased, the estimated decomposition constants based on first-order kinetics gradually decreased at different temperatures. Below the 20‰ salinity treatments, which doubled the soil salinity, Q10 increased with increasing salinity; but higher salinity constrained the temperature-related response of SOM decomposition by inhibiting microbial growth and carbon metabolisms. Soil bacteria were more sensitive to salinity stress than fungi, which can be inferred from the response of microbial beta-diversity to changing salinity. Among them, the phylotypes assigned to Gammaproteobacteria and Bacilli showed higher salt tolerance, whereas taxa affiliated with Alphaproteobacteria and Bacteroidota were more easily inhibited by the salinity stress. Several fungal taxa belonging to Ascomycota had higher adaptability to the stress. As the substrate was consumed with the incubation, bacterial competition intensified, but the fungal co-occurrence pattern changed weakly during decomposition. Collectively, these findings revealed the threshold effect of salinity on SOM decomposition in coastal salt marshes and emphasized that salt stress plays a key role in carbon sequestration by regulating microbial keystone taxa, metabolisms, and interactions.

Sediment Bacteria in the Alpine Lake Sayram: Vertical Patterns in Community Composition

Bacterial communities inhabiting alpine lakes are essential to our understanding of ecosystem processes in a changing climate, but little has been reported about the vertical patterns of sediment bacterial communities in alpine lakes. To address this knowledge gap, we collected the 100 cm long sediment core from the center of Lake Sayram, the largest alpine lake in Xinjiang Uygur autonomous area, China, and used 16S rRNA gene-targeted amplicon sequencing to examine the bacterial populations. The results showed that bacterial diversity, as estimated by the Shannon index, was highest at the surface (6.9849 at 0-4 cm) and gradually decreased with depth up to 3.9983 at 68-72 cm, and then increased to 5.0927 at 96-100 cm. A total of 56 different phyla and 1204 distinct genera were observed in the sediment core of Lake Sayram. The bacterial community structure in the sediment samples from the various layers was dissimilar. The most abundant phyla in alpine Lake Sayram were Proteobacteria, Firmicutes, and Planctomycetes, accounting for 73%, 6%, and 4% of the total reads, respectively; the most abundant genera were Acinetobacter, Hydrogenophaga, and Pseudomonas, accounting for 18%, 12%, and 8% of the total reads, respectively. Furthermore, the relative abundance of Acinetobacter increased with sediment depth, while the relative abundance of Hydrogenophaga and Pseudomonas decreased with sediment depth. Our findings indicated that the nitrate-reducing bacteria (Acinetobacter, Hydrogenophaga, and Pseudomonas) may be prevalent in the sediment core of Lake Sayram. Canonical correspondence analysis showed that carbonate and total organic carbon (TOC) may be the main environmental factors affecting the vertical patterns of bacterial community composition (BCC) in the sediment of Lake Sayram. This work significantly contributes to our understanding of the BCC of sediments from alpine lakes in arid and semiarid regions.

The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea

Bacillota are widely distributed in various environments, owing to their versatile metabolic capabilities and remarkable adaptation strategies. Recent studies reported that Bacillota species were highly enriched in cold seep sediments, but their metabolic capabilities, ecological functions, and adaption mechanisms in the cold seep habitats remained obscure. In this study, we conducted a systematic analysis of the complete genome of a novel Bacillota bacterium strain M8S5, which we isolated from cold seep sediments of the South China Sea at a depth of 1151 m. Phylogenetically, strain M8S5 was affiliated with the genus Abyssisolibacter within the phylum Bacillota. Metabolically, M8S5 is predicted to utilize various carbon and nitrogen sources, including chitin, cellulose, peptide/oligopeptide, amino acids, ethanolamine, and spermidine/putrescine. The pathways of histidine and proline biosynthesis were largely incomplete in strain M8S5, implying that its survival strictly depends on histidine- and proline-related organic matter enriched in the cold seep ecosystems. On the other hand, strain M8S5 contained the genes encoding a variety of extracellular peptidases, e.g., the S8, S11, and C25 families, suggesting its capabilities for extracellular protein degradation. Moreover, we identified a series of anaerobic respiratory genes, such as glycine reductase genes, in strain M8S5, which may allow it to survive in the anaerobic sediments of cold seep environments. Many genes associated with osmoprotectants (e.g., glycine betaine, proline, and trehalose), transporters, molecular chaperones, and reactive oxygen species-scavenging proteins as well as spore formation may contribute to its high-pressure and low-temperature adaptations. These findings regarding the versatile metabolic potentials and multiple adaptation strategies of strain M8S5 will expand our understanding of the Bacillota species in cold seep sediments and their potential roles in the biogeochemical cycling of deep marine ecosystems.

Impact of altered groundwater depth on soil microbial diversity, network complexity and multifunctionality

Understanding the effects of groundwater depth on soil microbiota and multiple soil functions is essential for ecological restoration and the implementation of groundwater conservation. The current impact of increased groundwater levels induced by drought on soil microbiota and multifunctionality remains ambiguous, which impedes our understanding of the sustainability of water-scarce ecosystems that heavily rely on groundwater resources. This study investigated the impacts of altered groundwater depths on soil microbiota and multifunctionality in a semi-arid region. Three groundwater depth levels were studied, with different soil quality and soil moisture at each level. The deep groundwater treatment had negative impacts on diversity, network complexity of microbiota, and the relationships among microbial phylum unites. Increasing groundwater depth also changed composition of soil microbiota, reducing the relative abundance of dominant phyla including Proteobacteria and Ascomycota. Increasing groundwater depth led to changes in microbial community characteristics, which are strongly related to alterations in soil multifunctionality. Overall, our results suggest that groundwater depth had a strongly effect on soil microbiota and functionality.

Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient

INTRODUCTION

The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica.

METHODS

We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons.

RESULTS AND DISCUSSION

Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.

Explore the soil factors driving soil microbial community and structure in Songnen alkaline salt degraded grassland

Introduction

Saline-alkali degradation in grassland significantly affects plant community composition and soil physical and chemical properties. However, it remains unclear whether different degradation gradients affect soil microbial community and the main soil driving factors. Therefore, it is important to elucidate the effects of saline-alkali degradation on soil microbial community and the soil factors affecting soil microbial community in order to develop effective solutions to restore the degraded grassland ecosystem.

Methods

In this study, Illumina high-throughput sequencing technology was used to study the effects of different saline-alkali degradation gradients on soil microbial diversity and composition. Three different gradients were qualitatively selected, which were the light degradation gradient (LD), the moderate degradation gradient (MD) and the severe degradation gradient (SD).

Results

The results showed that salt and alkali degradation decreased the diversity of soil bacterial and fungal communities, and changed the composition of bacterial and fungal communities. Different degradation gradients had different adaptability and tolerance species. With the deterioration of salinity in grassland, the relative abundance of Actinobacteriota and Chytridiomycota showed a decreasing trend. EC, pH and AP were the main drivers of soil bacterial community composition, while EC, pH and SOC were the main drivers of soil fungal community composition. Different microorganisms are affected by different soil properties. The changes of plant community and soil environment are the main factors limiting the diversity and composition of soil microbial community.

Discussion

The results show that saline-alkali degradation of grassland has a negative effect on microbial biodiversity, so it is important to develop effective solutions to restore degraded grassland to maintain biodiversity and ecosystem function.

Bacterial Communities and Diversity of Western Ghats Soil: A Study of a Biodiversity Hotspot

The Western Ghats is one of India's mega-diversity hotspots and an ecologically and geologically important area for the diversity of endemic plants and animals. The present study provides insights into the aerobic bacterial diversity and composition of the soils of North Western Ghats located in Maharashtra state (NWGM), India. The samples for the culture-dependent study were collected from 6 different locations namely Malshej Ghat, Bhimashankar, Lonavala, Mulshi, Tail-Baila, and Mahabaleshwar. A total of 173 isolates were obtained from the different samples, which belonged to Proteobacteria (43%), Firmicutes (36%), and Actinobacteria (19%). Sequences of 15 strains shared ≤ 98.7% similarity (a species cut-off) which represent potential novel species. Metagenomic analysis revealed the presence of Actinobacteria and Proteobacteria as the most dominant phyla at both MB and MG. However, both sites showed variation in the composition of rare phyla and other dominant phyla. This difference in bacterial community composition could be due to differences in altitude or other physicochemical properties. The functional prediction from the amplicon sequencing showed the abundance of carbohydrate, protein, and lipid metabolism which was corroborated by screening the isolated bacterial strains for the same. The present study has a unique take on microbial diversity and defines the importance of community assembly processes such as drift, dispersal, and selection. Such processes are relatively important in controlling community diversity, distribution, as well as succession. This study has shown that the microbial community of NWGM is a rich source of polysaccharide degrading bacteria having biotechnological potential.

Effects of biodegradable and polyethylene film mulches and their residues on soil bacterial communities

To investigate the effects of plastic film mulches and their residual films after use on soil bacterial communities, mulching experiment and the subsequent residual film experiment were conducted on winter-planting potato field in two locations. During mulching experiment, treatments biodegradable film mulch (BM) and PE film mulch (PM) reduced soil nutrient regarding available nitrogen and available potassium, as well as microbial biomass carbon (MBC), but increased urease activity, as compared to treatment no film mulch (NM). Soil moisture was significantly elevated by mulching practices and correlated with more microbial phyla than the other tested soil properties, indicating its important role in shaping soil bacterial communities. In addition, mulching practices increased alpha diversity of soil bacteria, although location heterogeneity was observed. Network analyses showed that both treatments BM and PM promoted the interrelations within bacterial communities and harbored more keystone taxa than treatment NM. During residual film experiment, residual films from BM and PM were incorporated into soil after harvest of potato. Treatment residual biodegradable film (RBF) significantly increased the content of MBC and activity of β-glucosidase (BG) as compared to treatments residual PE film (RPF) and no residual film (NRF), and BG had the most correlations with microbial phyla among all the tested soil properties. Treatments RBF and RPF increased the relative abundance of some dominant bacterial phyla, including Bacteroidetes, Actinobacteria, and Chlorofexi, and enhanced the interrelations within bacterial community, whereas more keystone taxa were harbored by treatment RBF, due to the increase of keystone taxa in phyla Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. These results indicate that the indirect effects of biodegradable and PE film mulch as a soil surface barrier on soil are similar, whereas their direct effects via incorporation into soil as residual films show specificity.

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.

NosZI microbial community determined the potential of denitrification and nitrous oxide emission in river sediments of Qinghai-Tibetan Plateau

Denitrification in river sediments is the hotspot of nitrogen removal and nosZI gene is essential for reducing nitrous oxide (N₂O) emissions. However, few studies tried to link nosZI communities with variations of denitrification rates in sediments along the high-elevation rivers. Here, we investigated the spatial variation of potential denitrification rates of sediments along a section (hereafter YJ) of the middle reaches of the Yarlung Zangbo River in the Qinghai-Tibetan Plateau. We also used the real-time quantitative PCR (qPCR) and high-throughput sequencing techniques to evaluate the abundance and composition of nosZI-containing microbial groups. The influences of physicochemical factors and denitrifier communities on potential denitrification rates were further revealed through structural equation modeling. The obtained results indicated that potential denitrification rates and N₂O/(N₂O + N₂) ratio in the sediments along YJ section were greatly different. Moreover, the alpha diversity and composition of nosZI-containing microbial community in river sediments differed remarkably, mainly driven by the ammonia nitrogen (NH₄⁺-N), organic matter (OM) and pH in sediments. The relative abundances of Zoogloeaceae, Oxalobacteraceae, Rhodospirillaceae and Bradyrhizobiaceae significantly differed among five groups (P < 0.05). Structural equation modeling further suggested that nitrogen nutrients directly influenced the potential denitrification rates, while total phosphorus (TP) showed indirect effects on potential denitrification rates through modulating denitrifier abundances and nosZI community. The abundance and composition of nosZI community were powerful predictors in regulating denitrification rates and N₂O/(N₂O + N₂) ratio. Our findings highlight that the nosZI-containing microbial groups play a non-negligible role in nitrogen removal and N₂O mitigation in high-elevation river sediments.

Glacial Legacies: Microbial Communities of Antarctic Refugia

In the cold deserts of the McMurdo Dry Valleys (MDV) the suitability of soil for microbial life is determined by both contemporary processes and legacy effects. Climatic changes and accompanying glacial activity have caused local extinctions and lasting geochemical changes to parts of these soil ecosystems over several million years, while areas of refugia may have escaped these disturbances and existed under relatively stable conditions. This study describes the impact of historical glacial and lacustrine disturbance events on microbial communities across the MDV to investigate how this divergent disturbance history influenced the structuring of microbial communities across this otherwise very stable ecosystem. Soil bacterial communities from 17 sites representing either putative refugia or sites disturbed during the Last Glacial Maximum (LGM) (22-17 kya) were characterized using 16 S metabarcoding. Regardless of geographic distance, several putative refugia sites at elevations above 600 m displayed highly similar microbial communities. At a regional scale, community composition was found to be influenced by elevation and geographic proximity more so than soil geochemical properties. These results suggest that despite the extreme conditions, diverse microbial communities exist in these putative refugia that have presumably remained undisturbed at least through the LGM. We suggest that similarities in microbial communities can be interpreted as evidence for historical climate legacies on an ecosystem-wide scale.

Long-term cultivation alter soil bacterial community in a forest-grassland transition zone

Changes in land use types can significantly affect soil porperties and microbial community composition in many areas. However, the underlying mechanism of shift in bacterial communities link to soil properties is still unclear. In this study, Illumina high-throughput sequencing was used to analyze the changes of soil bacterial communities in different land use types in a forest-grassland transition zone, North China. There are two different land use types: grassland (G) and cultivated land (CL). Meanwhile, cultivated land includes cultivated of 10 years (CL10) or 20 years (CL20). Compared with G, CL decreased soil pH, SOC and TN, and significantly increased soil EC, P and K, and soil properties varied significantly with different cultivation years. Grassland reclamation increases the diversity of bacterial communities, the relative abundance of Proteobacteria, Gemmatimonadetes and Bacteroidetes increased, while that of Actinobacteria, Acidobacteria, Rokubacteria and Verrucomicrobia decreased. However, the relative abundance of Proteobacteria decreased and the relative abundance of Chloroflexi and Nitrospirae increased with the increase of cultivated land years. Mantel test and RDA analysis showed that TP, AP, SOC and EC were the main factors affecting the diversity of composition of bacterial communities. In conclusion, soil properties and bacterial communities were significantly altered after long-term cultivation. This study provides data support for land use and grassland ecological protection in this region.

Reduction of microbial diversity in grassland soil is driven by long-term climate warming

Anthropogenic climate change threatens ecosystem functioning. Soil biodiversity is essential for maintaining the health of terrestrial systems, but how climate change affects the richness and abundance of soil microbial communities remains unresolved. We examined the effects of warming, altered precipitation and annual biomass removal on grassland soil bacterial, fungal and protistan communities over 7 years to determine how these representative climate changes impact microbial biodiversity and ecosystem functioning. We show that experimental warming and the concomitant reductions in soil moisture play a predominant role in shaping microbial biodiversity by decreasing the richness of bacteria (9.6%), fungi (14.5%) and protists (7.5%). Our results also show positive associations between microbial biodiversity and ecosystem functional processes, such as gross primary productivity and microbial biomass. We conclude that the detrimental effects of biodiversity loss might be more severe in a warmer world.

Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach

Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils

Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.

Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient

Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.

Antibiotic resistance genes alternation in soils modified with neutral and alkaline salts: interplay of salinity stress and response strategies of microbes

Growing evidence points to the pivotal roles of salt accumulation in mediating antibiotic resistance genes (ARGs) spread in soil, whereas how salt mediates ARGs dissemination remains unknown. Herein, the effects of neutral or alkaline (Ne/Al) salt at low, moderate and high levels (Ne/Al-L, Ne/Al-M, Ne/Al-H) on the dissemination of ten typical ARGs in soils were explored, by simultaneously considering the roles of salinity stress and response strategies of microbes. In the soils amended with Ne/Al-L and Al-M salt, the dissemination of ARGs was negligible and the relative abundances of ARGs and mobile genetic elements (MGEs) were decreased. However, Ne-M and Al-H salt contributed to the dissemination of ARGs in soils, with the significantly increased absolute and relative abundances of ARGs and MGEs. In Ne-H soil, although the absolute abundance of ARGs declined drastically due to serious oxidative damage, their relative abundances were promoted. The facilitated ARGs transfer was potentially related to the excessive generation of intracellular reactive oxygen species and increased activities of DNA repair enzymes involved in SOS system. In addition, the activated intracellular protective response including quorum sensing and energy metabolism largely provided essential factors for ARGs dissemination. The co-occurrence of ARGs and over-expressed salt-tolerant genes in specific halotolerant bacteria further suggested the selection of salt stress on ARGs. Moreover, less disturbance of alkaline salt than neutral salt on ARGs evolution was observed, due to the lower abiotic stress and selective pressure on microbes. This study highlights that soil salinity-sodicity could dose-dependently reshape the dissemination of ARGs and community structure of microbes, which may increase the ecological risks of ARGs in agricultural environment.

Geochemically Defined Space-for-Time Transects Successfully Capture Microbial Dynamics Along Lacustrine Chronosequences in a Polar Desert

The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.

The role of the gut microbiota in the dietary niche expansion of fishing bats

Background

Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet.

Results

We first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish.

Conclusions

Our results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00137-w.

White Rann of Kachchh harbours distinct microbial diversity reflecting its unique biogeography

The understanding of sub-surface soil microbial diversity is limited at both saline and hypersaline ecosystems, even though salinity is found to affect the microbial community in aqueous and terrestrial environment. In this study, a phylo-taxonomy analysis as well as the functional characteristics of microbial community of flat salt basin of White Rann of Kachchh (WR), Gujarat, India was performed along the natural salinity gradient. The high throughput sequencing approach has revealed the numerical abundance of bacteria relative to the archaea. Salinity, TOC, EC and sulphate concentration might be the primary driver of the community distribution along the transect at WR. The much anticipated effect of salinity gradient on the microbial composition surprisingly turned out to be more speculative, with little variance in the community composition along the spatial distance of WR. The metabolic pathways involved in energy metabolism (like carbon, nitrogen, sulphur) along with environmental adaptive genes (like osmotic and oxidative stress response, heat and cold shock genes clusters) were abundantly annotated from shot-gun metagenomic study. The carbonic anhydrase harbouring bacteria Bacillus sp. DM4CA1 was isolated from WR, having a catalytic ability for converting the gaseous carbon dioxide in presence of calcium carbonate into calcite at 25 % higher rate as compared to non-harbouring strains. The enzyme has a role in multiple alternative pathways in microbial metabolism. With the array of results obtained, the study could become the new reference for understanding the diversity structure and functional characteristics of the microbial community of terrestrial saline environment.

Effects of plant growth regulator and chelating agent on the phytoextraction of heavy metals by Pfaffia glomerata and on the soil microbial community

Pfaffia glomerata is a candidate for the remediation of heavy metal-contaminated soil, but phytoremediation efficiency requires enhancement. In this study, we evaluated how application of DA-6, EDTA, or CA affected the growth and heavy metal accumulation of P. glomerata and soil microorganisms. We found that P. glomerata removed more Cd and Zn than Pb or Cu from contaminated soil. When compared to the control, application of DA-6, CA, or CA + DA-6 increased plant biomass and increased stem Cd concentration by 1.28-, 1.20-, and 1.31-fold respectively; increased leaf Cd concentration by 1.25-, 1.28-, and 1.20-fold, respectively; and increased the total quantity of Cd extracted by 1.37-, 1.37-, and 1.38-fold, respectively. When compared to the control, application EDTA or EDTA + DA-6 significantly increased the soil available metal and Na concentrations, which harmed plant growth. Application of EDTA or EDTA + DA-6 also significantly decreased the Cd concentration in roots and stems. 16S rRNA high-throughput sequencing analysis revealed that application of EDTA or CA alone to soil significantly reduced the richness and diversity of soil bacteria, while foliar spraying of DA-6 combined with EDTA or CA slightly alleviated this reduction. EDTA or CA addition significantly changed the proportion of Actinobacteria and Proteobacteria. In addition, EDTA or CA addition caused changes in soil properties (e.g. heavy metal availability, K concentration, Na concentration, soil pH, soil CEC, and soil DOC concentration) that were associated with changes in the bacterial community. EDTA addition mainly affected the soil bacterial community by changing soil DOC concentration, the soil available Pb and Na concentration, and CA addition mainly affected the soil bacterial community by changing the soil available Ca concentration.

Erosion reduces soil microbial diversity, network complexity and multifunctionality

While soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

Unraveling bacterial community structure and function and their links with natural salinity gradient in the Yellow River Delta

Salinization can change the soil environment and affect microbial processes. In this study, soil samples were collected from Zone A (Phragmites australis wetlands), Zone B (P. australis and Suaeda salsa wetlands), and Zone C (Spartina alterniflora wetlands) in the Yellow River Delta. The microbial community and functional potential along the natural salinity gradient were investigated. Total nitrogen, ammonia nitrogen, and soil organic matter presented a downward trend, and salinity first increased and then decreased from Zone A to Zone C. Nitrospira and norank_f_Nitrosomonadaceae were widely distributed throughout the zones. Denitrifying bacteria Alcanivorax, Marinobacterter, and Marinobacterium were abundant in Zone B and preferred high salinity levels. However, denitrifying bacteria Azoarcus, Flavobacterium, and Pseudomonas were mainly distributed in low-salinity Zones A and C, suggesting their high sensitivity to salinity. Dissimilatory nitrate reduction to ammonia (DNRA) bacteria Aeromonas and Geobacter dominated Zone C, whereas Caldithrix performed DNRA in Zone B. Interestingly, DNRA with organic matter as the electron donor (C-DNRA) occurred in Zone A; DNRA coupled with sulfide oxidation (S-DNRA) was dominant in Zone B; and C-DNRA and DNRA with divalent iron as electron donor and S-DNRA occurred simultaneously in Zone C. Salinity was the key factor distinguishing low and high salinity zones, and total nitrogen and total phosphorus had important effects at the phylum and genus levels. The abundance of genes encoding cell growth and death was relatively stable, indicating that the microbial community had good environmental adaptability. The genes related to the biodegradation of xenobiotics and the metabolism of terpenoids and polyketides were abundant in Zone B, revealing high metabolic potential for exogenous refractory substances. The microorganisms under low-salinity Zones A and C were more sensitive to environmental changes than those under Zone B. These results suggest that salinity plays important roles in microbial processes and shapes specific functional zones in coastal wetlands.

Growth Optimisation and Kinetic Profiling of Diesel Biodegradation by a Cold-Adapted Microbial Consortium Isolated from Trinity Peninsula, Antarctica

Simple Summary

Diesel fuel is very crucial for anthropogenic activities in Antarctica and the surges in annual demand mean higher likelihood of spillages from improper handling during transportation, storage and disposal processes. The impacts can be very extensive or well-contained depending on the scale of the spills as well as the terrain involved. Nevertheless, the freezing temperature and prolonged solar irradiance in the south pole greatly hampered the natural attenuation and photovolatilisation of petrogenic hydrocarbons, contributing to their persistency. The most susceptible groups are the soil microorganisms, mosses, seabirds and pinnipeds as they are easily found near the shore where hydrocarbons spillage is very common. Microbial bioremediation is a well-established approach in restoring many hydrocarbons-polluted areas, thus the current study focused on the optimisation and application of locally isolated microbial consortium to simulate the in situ diesel clean-up process in aqueous medium. This study highlights the ability of the selected consortium to degrade diesel almost completely at moderately low temperature, suggesting its potential application in Antarctic settings.

Abstract

Pollution associated with petrogenic hydrocarbons is increasing in Antarctica due to a combination of increasing human activity and the continent’s unforgiving environmental conditions. The current study focuses on the ability of a cold-adapted crude microbial consortium (BS24), isolated from soil on the north-west Antarctic Peninsula, to metabolise diesel fuel as the sole carbon source in a shake-flask setting. Factors expected to influence the efficiency of diesel biodegradation, namely temperature, initial diesel concentration, nitrogen source type and concentration, salinity and pH were studied. Consortium BS24 displayed optimal cell growth and diesel degradation activity at 1.0% NaCl, pH 7.5, 0.5 g/L NH₄Cl and 2.0% v/v initial diesel concentration during one-factor-at-a-time (OFAT) analyses. The consortium was psychrotolerant based on the optimum growth temperature of 10‒15 °C. In conventionally optimised media, the highest total petroleum hydrocarbons (TPH) mineralisation was 85% over a 7-day incubation. Further optimisation of conditions predicted through statistical response-surface methodology (RSM) (1.0% NaCl, pH 7.25, 0.75 g/L NH₄Cl, 12.5 °C and 1.75% v/v initial diesel concentration) boosted mineralisation to 95% over a 7-day incubation. A Tessier secondary model best described the growth pattern of BS24 in diesel-enriched medium, with maximum specific growth rate, μ_max, substrate inhibition constant, K_i and half saturation constant, K_s, being 0.9996 h⁻¹, 1.356% v/v and 1.238% v/v, respectively. The data obtained suggest the potential of microbial consortia such as BS24 in bioremediation applications in low-temperature diesel-polluted soils.

Variations in bacterial community structure and antimicrobial resistance gene abundance in cattle manure and poultry litter

Cattle manure and poultry litter are widely used as fertilizers as they are excellent sources of nutrients; however, potential adverse environmental effects exist during land applications, due to the release of zoonotic bacteria and antimicrobial resistance (AMR) genes. This study was conducted to understand linkages between physiochemical composition, bacterial diversity, and AMR gene presence of cattle manure and poultry litter using quantitative polymerase chain reaction to enumerate four AMR genes (ermB, sulI, intlI, and bla_ctx-m-32), Illumina sequencing of the 16 S region, and analysis of physical and chemical properties. Principal coordinate analysis of Bray-Curtis distance revealed distinct bacterial community structures between the two manure sources. Greater alpha diversity occurred in cattle manure compared to poultry litter (P < 0.05). Redundancy analysis showed a strong relationship between manure physiochemical and composition and bacterial abundance, with positive relationships occurring among electrical conductivity and carbon/nitrogen, and negative associations for total solids and soluble fractions of heavy metals. Cattle manure exhibited greater abundance of macrolide (ermB) and sulfonamide (sulI) resistant genes. Consequently, fresh cattle manure applications may result in greater potential spread of AMR genes to the soil-water environment (relative to poultry litter) and novel best management strategies (such as composting) may reduce the release of AMR genes to the soil-water environment.

Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand

Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines.

Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km²) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

Abiotic factors influencing soil microbial activity in the northern Antarctic Peninsula region

Microorganisms play a key role in the carbon (C) cycle through soil organic matter (SOM). The rate of SOM mineralization, the influence of abiotic factors on this rate and the potential behaviour of SOM are of particular interest in the northern Antarctic Peninsula and offshore islands. This is one of the most rapidly warming regions on Earth with numerous ice-free areas, some with abundant wildlife and with the greatest known soil organic carbon (SOC) storage in Antarctica. The latter implies extended Antarctic summer conditions promote increased terrestrial plant growth and soil microbial activity (SMA). SMA, determined by respirometry, is a measure of ecosystem function, and depends on microclimatic conditions and soil environmental properties. SMA and the effect of abiotic variables have been analysed in locations with different soil types, on Cierva Point (Antarctic Peninsula), Deception Island and Fildes Peninsula (King George Island). Soil microbial biomass carbon (SMBC) ranged from 5.66 to 196.6 mg SMBC kg^-1and basal respiration (BR) from 2.86 to 160.67 mg CO₂ kg^-1 d^-1. SMBC and BR values were higher in Cierva Point, followed by Fildes Peninsula and Deception Island, showing the same trend of SOM abundance_. Except for Cierva Point, low nitrogen, phosphorus and C concentrations were observed. SMBC/total organic carbon (TOC) levels indicated that SOC was recalcitrant and SOM content was closely related to the extent of vegetation cover observed in situ. High metabolic quotient values obtained at Cierva Point and Deception Island (median values 7.27 and 6.53 mg C-CO₂ g SMBC^-1 h^-1) and low SMBC/TOC in Cierva Point suggest a poor efficiency of the microbial populations in the consumption of the SOC. High SMBC/TOC values obtained in Deception Island indicates that SMBC may influence SOM stabilization. Mineralization rates were very low (negligible values to 1.44%) and sites with the lowest values had the highest SOM.

Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas

Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.

Salinity controls soil microbial community structure and function in coastal estuarine wetlands

Soil salinity acts as a critical environmental filter on microbial communities, but the consequences for microbial diversity and biogeochemical processes are poorly understood. Here, we characterized soil bacterial communities and microbial functional genes in a coastal estuarine wetland ecosystem across a gradient (~5 km) ranging from oligohaline to hypersaline habitats by applying the PCR-amplified 16S rRNA (rRNA) genes sequencing and microarray-based GeoChip 5.0 respectively. Results showed that saline soils in marine intertidal and supratidal zone exhibited higher bacterial richness and Faith's phylogenetic diversity than that in the freshwater-affected habitats. The relative abundance of taxa assigned to Gammaproteobacteria, Bacteroidetes and Firmicutes was higher with increasing salinity, while those affiliated with Acidobacteria, Chloroflexi and Cyanobacteria were more prevalent in wetland soils with low salinity. The phylogenetic inferences demonstrated the deterministic role of salinity filtering on the bacterial community assembly processes. The abundance of most functional genes involved in carbon degradation and nitrogen cycling correlated negatively with salinity, except for the hzo gene, suggesting a critical role of the anammox process in tidal affected zones. Overall, the salinity filtering effect shapes the soil bacterial community composition, and soil salinity act as a critical inhibitor in the soil biogeochemical processes in estuary ecosystems.

Microbial Nitrogen Cycling in Antarctic Soils

The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.