Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils

Exploring prokaryotic diversity in permafrost-affected soils of Ladakh's Changthang region and its geochemical drivers

Global warming due to climate change has substantial impact on high-altitude permafrost affected soils. This raises a serious concern that the microbial degradation of sequestered carbon can result in alteration of the biogeochemical cycles. Therefore, the characterization of permafrost affected soil microbiomes, especially of unexplored high-altitude, low oxygen arid region, is important for predicting their response to climate change. This study presents the first report of the bacterial diversity of permafrost-affected soils in the Changthang region of Ladakh. The relationship between soil pH, organic carbon, electrical conductivity, and available micronutrients with the microbial diversity was investigated. Amplicon sequencing of permafrost affected soil samples from Jukti and Tsokar showed that Proteobacteria and Actinobacteria were the dominant phyla in all samples. The genera Brevitalea, Chthoniobacter, Sphingomonas, Hydrogenispora, Clostridium, Gaiella, Gemmatimonas were relatively abundant in the Jukti samples whereas the genera Thiocapsa, Actinotalea, Syntrophotalea, Antracticibcterium, Luteolibacter, Nitrospirillum dominated the Tsokar sample. Correlation analyses highlighted the influence of soil geochemical parameters on the bacterial community structure. PCoA analyses showed that the bacterial beta diversity varied significantly between the sampling locations (PERMANOVA test (F-value: 2.3316; R2 = 0.466, p = 0.001) and similar results were also obtained while comparing genus abundance data using the ANOSIM test (R = 0.345, p = 0.007).

Study of Archaeal Diversity in the Arctic Meltwater Lake Region

Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two lakes were sequenced with high throughput. At the phylum level, the intertidal zone was dominated by Crenarchaeota and the subtidal zone was dominated by Halobacter; at the genus level, the intertidal zone was dominated by Nitrososphaeraceae_unclassified and Candidatus_Nitrocosmicus, while the subtidal zone was dominated by Methanoregula. The soil physicochemical factors pH, moisture content (MC), total organic carbon (TOC), total organic nitrogen (TON), nitrite nitrogen (NO₂^--N), and nitrate nitrogen (NO₃^--N) were significantly different in the intertidal and subtidal zones of the lake. By redundancy analysis, the results indicated that NH₄⁺-N, SiO₃^2--Si, MC, NO₃^--N, and NO₂^--N have had highly significant effects on the archaeal diversity and distribution. A weighted gene co-expression network analysis (WGCNA) was used to search for hub archaea associated with physicochemical factors. The results suggested that these physicochemical factors play important roles in the diversity and structure of the archaeal community at different sites by altering the abundance of certain hub archaea. In addition, Woesearchaeales was found to be the hub archaea genus at every site.

The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador

A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40  years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.

Soil Microbial Communities Associated with Three Arctic Plants in Different Local Environments in Ny-Ålesund, Svalbard

Understanding soil microbial community structure in the Arctic is essential for predicting the impact of climate change on interactions between organisms living in polar environments. The hypothesis of the present study was that soil microbial communities and soil chemical characteristics would vary depending on their associated plant species and local environments in Arctic mature soils. We analyzed soil bacterial communities and soil chemical characteristics from soil without vegetation (bare soil) and rhizosphere soil of three Arctic plants (Cassiope tetragona [L.] D. Don, Dryas octopetala L. and Silene acaulis [L.] Jacq.) in different local environments (coal-mined site and seashore-adjacent site). We did not observe any clear differences in microbial community structure in samples belonging to different plant rhizospheres; however, samples from different environmental sites had distinct microbial community structure. The samples from coal-mined site had a relatively higher abundance of Bacteroidetes and Firmicutes. On the other hand, Acidobacteria was more prevalent in seashore-adjacent samples. The relative abundance of Proteobacteria and Acidobacteria decreased toward higher soil pH, whereas that of Bacteroidetes and Firmicutes was positively correlated with soil pH. Our results suggest that soil bacterial community dissimilarity can be driven by spatial heterogeneity in deglaciated mature soil. Furthermore, these results indicate that soil microbial composition and relative abundance are more affected by soil pH, an abiotic factor, than plant species, a biotic factor.

Temperature sensitivity of Antarctic soil-humic substance degradation by cold-adapted bacteria

Heteropolymer humic substances (HS) are the largest constituents of soil organic matter and are key components that affect plant and microbial growth in maritime Antarctic tundra. We investigated HS decomposition in Antarctic tundra soils from distinct sites by incubating samples at 5°C or 8°C (within a natural soil thawing temperature range of -3.8°C to 9.6°C) for 90 days (average Antarctic summer period). This continuous 3-month artificial incubation maintained a higher total soil temperature than that in natural conditions. The long-term warming effects rapidly decreased HS content during the initial incubation, with no significant difference between 5°C and 8°C. In the presence of Antarctic tundra soil heterogeneity, the relative abundance of Proteobacteria (one of the major bacterial phyla in cold soil environments) increased during HS decomposition, which was more significant at 8°C than at 5°C. Contrasting this, the relative abundance of Actinobacteria (another major group) did not exhibit any significant variation. This microcosm study indicates that higher temperatures or prolonged thawing periods affect the relative abundance of cold-adapted bacterial communities, thereby promoting the rate of microbial HS decomposition. The resulting increase in HS-derived small metabolites will possibly accelerate warming-induced changes in the Antarctic tundra ecosystem.

Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile

Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.

Foxes fertilize the subarctic forest and modify vegetation through denning

Ecosystem engineers modify habitats through processes other than trophic interactions, such as by regulating soil nutrients, and can influence resource availability and quality for other organisms. Predator-mediated elemental cycling may be especially important in determining plant diversity and growth in ecosystems where soil fertility and primary productivity are low. Red foxes (Vulpes vulpes L.), top predators in the Subarctic, could engineer local ecosystems through denning, which could create biogeochemical hotspots of nutrients due to continual input of feces, urine and prey remains. We examined soil and vegetation characteristics on red fox dens and paired control sites in woodland habitats near the Arctic treeline in Manitoba, Canada. The organic soil layer on den sites had 81% more inorganic nitrogen and 250% more extractable phosphorus than in control areas. Denning also increased soil respiration and pH in the organic layer, suggesting improved soil quality and nutrient availability for plants. By enriching nutrients and disturbing soils through digging, den sites had a higher plant species ß-diversity and a greater cover of erect woody shrubs (Salix spp.), grasses (Leymus mollis (Trinius) Pilger) and weedy ephemerals compared to control sites, resulting in a regional increase in plant species richness. Our research highlights the importance of considering impacts of predators other than through their consumption of prey, and provides insight into the role of red foxes in modifying plant diversity and productivity in the Subarctic.

Insights on comparative bacterial diversity between different arid zones of Cholistan Desert, Pakistan

The present study was conducted to analyze bacterial diversity profile of Cholistan desert located in Pakistan. The study investigates the influence of physicochemical parameters of soil on distribution of different bacteria at all taxonomic levels and also study the distribution pattern between different desert environments, particularly rhizospheric and bulk desert sands. Species richness showed phyla Proteobacteria and Chloroflexi as the dominant OTUs in all the samples. Besides the two phyla, the rhizospheric soils with root remnants were dominated by Firmicutes, Deinococcus-Thermus, Actinobacteria and Acidobacteri, while phylum Thermotogae was present in significant quantity in rhizosheaths devoid of roots. In non-rhizospheric desert soils, a considerable number of OTUs belonged to phyla Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. An important finding from this study is that a bulk portion of the OTUs were assigned to unclassified taxa, indicating a large repertoire of unexplored taxa in the desert ecology of Pakistan. Distribution of taxonomic groups among various regions of the desert was collaborating well with the physicochemical parameters of the sites. The findings of this study establish the fundamental relationships between desert ecosystem, specific native plant and the total bacterial flora. This is the first study of microbial community analysis of any desert in Pakistan and thus, will serve as a future platform to explore further on desert ecosystem functioning by employing the ever-changing biotechnological tools.

Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils

BACKGROUND

Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season.

RESULTS

The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted.

CONCLUSIONS

We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.

Microbial diversity and biogeography in Arctic soils

Microorganisms dominate terrestrial environments in the polar regions and Arctic soils are known to harbour significant microbial diversity, far more diverse and numerous in the region than was once thought. Furthermore, the geographic distribution and structure of Arctic microbial communities remains elusive, despite their important roles in both biogeochemical cycling and in the generation and decomposition of climate active gases. Critically, Arctic soils are estimated to store over 1500 Pg of carbon and, thus, have the potential to generate positive feedback within the climate system. As the Arctic region is currently undergoing rapid change, the likelihood of faster release of greenhouse gases such as CO₂ , CH₄ and N₂ O is increasing. Understanding the microbial communities in the region, in terms of their diversity, abundance and functional activity, is key to producing accurate models of greenhouse gas release. This review brings together existing data to determine what we know about microbial diversity and biogeography in Arctic soils.

Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation

Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyzed transcriptomes extracted from Pseudomonas sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate O-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA.

High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia

A wide variety of terrestrial ecosystems in tundra have a ground vegetation cover composed of reindeer lichens (genera Cladonia and Cetraria). The microbial communities of two lichen-dominated ecosystems typical of the sub-arctic zone of northwestern Siberia, that is a forested tundra soil and a shallow acidic peatland, were examined in our study. As revealed by molecular analyses, soil and peat layers just beneath the lichen cover were abundantly colonized by bacteria from the phylum Planctomycetes. Highest abundance of planctomycetes detected by fluorescence in situ hybridization was in the range 2.2-2.7 × 107 cells per gram of wet weight. 16S rRNA gene fragments from the Planctomycetes comprised 8-13% of total 16S rRNA gene reads retrieved using Illumina pair-end sequencing from the soil and peat samples. Lichen-associated assemblages of planctomycetes displayed unexpectedly high diversity, with a total of 89,662 reads representing 1723 operational taxonomic units determined at 97% sequence identity. The soil of forested tundra was dominated by uncultivated members of the family Planctomycetaceae (53-71% of total Planctomycetes-like reads), while sequences affiliated with the Phycisphaera-related group WD2101 (recently assigned to the order Tepidisphaerales) were most abundant in peat (28-51% of total reads). Representatives of the Isosphaera-Singulisphaera group (14-28% of total reads) and the lineages defined by the genera Gemmata (1-4%) and Planctopirus-Rubinisphaera (1-3%) were present in both habitats. Two strains of Singulisphaera-like bacteria were isolated from studied soil and peat samples. These planctomycetes displayed good tolerance of low temperatures (4-15°C) and were capable of growth on a number of polysaccharides, including lichenan, a characteristic component of lichen-derived phytomass.

Microbial Communities in a High Arctic Polar Desert Landscape

The High Arctic is dominated by polar desert habitats whose microbial communities are poorly understood. In this study, we used next generation sequencing to describe the α- and β-diversity of microbial communities in polar desert soils from the Kongsfjorden region of Svalbard. Ten phyla dominated the soils and accounted for 95% of all sequences, with the Proteobacteria, Actinobacteria, and Chloroflexi being the major lineages. In contrast to previous investigations of Arctic soils, relative Acidobacterial abundances were found to be very low as were the Archaea throughout the Kongsfjorden polar desert landscape. Lower Acidobacterial abundances were attributed to characteristic circumneutral soil pHs in this region, which has resulted from the weathering of underlying carbonate bedrock. In addition, we compared previously measured geochemical conditions as possible controls on soil microbial communities. Phosphorus, pH, nitrogen, and calcium levels all significantly correlated with β-diversity, indicating landscape-scale lithological control of available nutrients, which in turn, significantly influenced soil community composition. In addition, soil phosphorus and pH significantly correlated with α-diversity, particularly with the Shannon diversity and Chao 1 richness indices.

Temporal changes in soil bacterial diversity and humic substances degradation in subarctic tundra soil

Humic substances (HS), primarily humic acids (HA) and fulvic acids (FA), are the largest constituent of soil organic matter. In microcosm systems with subarctic HS-rich tundra soil (site AK 1-75; approximately 5.6 °C during the thawing period) from Council, Alaska, the HA content significantly decreased to 48% after a 99-day incubation at 5 °C as part of a biologically mediated process. Accordingly, levels of FA, a putative byproduct of HA degradation, consistently increased to 172% during an identical incubation process. Culture-independent microbial community analysis showed that during the microcosm experiments, the relative abundance of phyla Proteobacteria (bacteria) and Euryarchaeota (archaea) largely increased, indicating their involvement in HS degradation. When the indigenous bacteria in AK 1-75 were enriched in an artificial mineral medium spiked with HA, the changes in relative abundance were most conspicuous in Proteobacteria (from 60.2 to 79.0%), specifically Betaproteobacteria-related bacteria. One hundred twenty-two HA-degrading bacterial strains, primarily from the genera Paenibacillus (phylum Firmicutes) and Pseudomonas (class Gammaproteobacteria), were cultivated from AK 1-75 and nearby sites. Through culture-dependent analysis with these bacterial isolates, we observed increasing HS-degradation rates in parallel with rising temperatures in a range of 0 °C to 20 °C, with the most notable increase occurring at 8 °C compared to 6 °C. Our results indicate that, although microbial-mediated HS degradation occurs at temperature as low as 5 °C in tundra ecosystems, increasing soil temperature caused by global climate change could enhance HS degradation rates. Extending the thawing period could also increase degradation activity, thereby directly affecting nearby microbial communities and rhizosphere environments.

Assessment of microbial diversity bias associated with soil heterogeneity and sequencing resolution in pyrosequencing analyses

It is important to estimate the true microbial diversities accurately for a comparative microbial diversity analysis among various ecological settings in ecological models. Despite drastically increasing amounts of 16S rRNA gene targeting pyrosequencing data, sampling and data interpretation for comparative analysis have not yet been standardized. For more accurate bacterial diversity analyses, the influences of soil heterogeneity and sequence resolution on bacterial diversity estimates were investigated using pyrosequencing data of oak and pine forest soils with focus on the bacterial 16SrRNA gene. Soil bacterial community sets were phylogenetically clustered into two separate groups by forest type. Rarefaction curves showed that bacterial communities sequenced from the DNA mixtures and the DNAs of the soil mixtures had midsize richness compared with other samples. Richness and diversity estimates were highly variable depending on the sequence read numbers. Bacterial richness estimates (ACE, Chao 1 and Jack) of the forest soils had positive linear relationships with the sequence read number. Bacterial diversity estimates (NPShannon, Shannon and the inverse Simpson) of the forest soils were also positively correlated with the sequence read number. One-way ANOVA shows that sequence resolution significantly affected the α-diversity indices (P<0.05), but the soil heterogeneity did not (P>0.05). For an unbiased evaluation, richness and diversity estimates should be calculated and compared from subsets of the same size.

Stoichiometric imbalances between terrestrial decomposer communities and their resources: mechanisms and implications of microbial adaptations to their resources

Terrestrial microbial decomposer communities thrive on a wide range of organic matter types that rarely ever meet their elemental demands. In this review we synthesize the current state-of-the-art of microbial adaptations to resource stoichiometry, in order to gain a deeper understanding of the interactions between heterotrophic microbial communities and their chemical environment. The stoichiometric imbalance between microbial communities and their organic substrates generally decreases from wood to leaf litter and further to topsoil and subsoil organic matter. Microbial communities can respond to these imbalances in four ways: first, they adapt their biomass composition toward their resource in a non-homeostatic behavior. Such changes are, however, only moderate, and occur mainly because of changes in microbial community structure and less so due to cellular storage of elements in excess. Second, microbial communities can mobilize resources that meet their elemental demand by producing specific extracellular enzymes, which, in turn, is restricted by the C and N requirement for enzyme production itself. Third, microbes can regulate their element use efficiencies (ratio of element invested in growth over total element uptake), such that they release elements in excess depending on their demand (e.g., respiration and N mineralization). Fourth, diazotrophic bacteria and saprotrophic fungi may trigger the input of external N and P to decomposer communities. Theoretical considerations show that adjustments in element use efficiencies may be the most important mechanism by which microbes regulate their biomass stoichiometry. This review summarizes different views on how microbes cope with imbalanced supply of C, N and P, thereby providing a framework for integrating and linking microbial adaptation to resource imbalances to ecosystem scale fluxes across scales and ecosystems.