Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska

Dynamic soil columns simulate Arctic redox biogeochemistry and carbon release during changes in water saturation

Thawing Arctic permafrost can induce hydrologic change and alter redox conditions, shifting the balance of soil organic matter (SOM) decomposition. There remains uncertainty about how soil saturation and redox transitions impact dissolved and gas phase carbon fluxes, and efforts to link hydrobiogeochemical processes to ecosystem-scale models are limited. This study evaluates SOM decomposition of Arctic tundra soils using column experiments, water chemistry measurements, microbial community analysis, and a PFLOTRAN reactive transport model. Soil columns from a thermokarst channel (TC) and an upland tundra (UC) were exposed to cycles of saturation and drainage, which controlled carbon emissions. During saturation, an outflow of dissolved organic carbon from the UC soil correlated with elevated reduced iron and decreased pH; during drainage, UC carbon dioxide fluxes were 70% higher than TC fluxes. Intermittent methane release was observed for TC, consistent with higher methanogen abundance. Slower drainage in the TC soil correlated with more subtle biogeochemical changes. PFLOTRAN simulations captured experimental trends in soil carbon fluxes, oxygen concentrations, and water contents. The model was then used to evaluate additional soil water drainage rates. This study emphasizes the importance of considering hydrologic change when evaluating and simulating SOM decomposition in dynamic Arctic tundra environments.

Potential risks of bacterial plant pathogens from thawing permafrost in the Alaskan tundra

Global warming-induced permafrost thawing raises concerns about the release of dormant microbes, including potentially harmful plant pathogens. However, the potential pathogenic risks associated with the thawing of permafrost remain poorly understood. Here, we conducted a 90-day soil incubation experiment at 4 °C to mimic extended permafrost thawing in Alaskan tundra soils stratified into active (A), transitional (T), and permanently frozen (P) layers. Following incubation, we examined the changes in bacterial abundance and community composition and tested the reactivation and pathogenicity of dormant plant pathogenic bacteria. Bacterial abundance, measured by colony-forming units and 16S rRNA gene copies, distinctly increased in the T and P layers after thawing. These layers also exhibited substantial shifts in bacterial community structure, with Fe-cycling taxa becoming more abundant and permafrost-dominant taxa decreasing in abundance. Notably, we isolated 52 strains with proteolytic activity, and our pathogenicity tests confirmed that Pseudomonas spp. isolates caused potato soft rot symptoms. Some Pseudomonas pathogens were undetectable in the amplicon sequencing data before thawing and emerged only in the thawed T and P layers. Our findings illustrate that permafrost acts as a reservoir of potential plant pathogens, and their resurgence upon thawing poses a potential risk to Arctic ecosystems.

Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N)

Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ∼6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.

Land use/cover drive functional patterns of bacterial communities in sediments of a subtropical river, China

The bacterial community in sediment serves as an important indicator for assessing the environmental health of river ecosystems. However, the response of bacterial community structure and function in river basin sediment to different land use/cover changes has not been widely studied. To characterize changes in the structure, composition, and function of bacterial communities under different types of land use/cover, we studied the bacterial communities and physicochemical properties of the surface sediments of rivers. Surface sediment in cropland and built-up areas was moderately polluted with cadmium and had high nitrogen and phosphorus levels, which disrupted the stability of bacterial communities. Significant differences in the α-diversity of bacterial communities were observed among different types of land use/cover. Bacterial α-diversity and energy sources were greater in woodlands than in cropland and built-up areas. The functional patterns of bacterial communities were shown that phosphorus levels and abundances of pathogenic bacteria and parasites were higher in cropland than in the other land use/cover types; Urban activities have resulted in the loss of the denitrification function and the accumulation of nitrogen in built-up areas, and bacteria in forested and agricultural areas play an important role in nitrogen degradation. Differences in heavy metal and nutrient inputs driven by land use/cover result in variation in the composition, structure, and function of bacterial communities.

Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone

Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.

Response of microbial community to different land-use types, nutrients and heavy metals in urban river sediment

Nutrients and heavy metals (HM) in the sediment have an impact on microbial diversity and community structure. In this study, the distribution characteristics of nutrients, HM, and microbial community in the sediments along the Longsha River, a tributary of the Pearl River (or Zhu Jiang), China were investigated by analyzing samples from 11 sites. On the basis of the HM-contamination level, the 11 sampling sites were divided into three groups to explore the changes in microbial communities at different ecological risk levels. Results indicated that nutrient concentrations were higher near farmlands and residential lands, while the ecological risk of HM at the 11 sampling sites was from high to low as S10 > S2 > S9 > S6 > S11 > S7 > S5 > S8 > S3 > S4 > S1. Among these HM, Cu, Cr, and Ni had intense ecological risks. In addition, the results of Variance Partitioning Analysis (VPA) revealed a higher contribution of HM (35.93%) to microbial community variation than nutrients (12.08%) and pH (4.08%). Furthermore, the HM-tolerant microbial taxa (Clostridium_sensu_stricto_1, Romboutsia, norank_o__Gaiellales, and etc.) were the dominant genera, and they were more dynamic around industrial lands, while microbes involved in the C, N, and S cycles (e.g., Smithella, Thiobacillus, Dechloromonas, Bacter oidetes_vadinHA17, and Syntrophorhabdus) were inhibited by HM, while their abundance was lower near industrial lands and highway but higher around residential lands. A three-unit monitoring program of land-use types, pollutants, and microbial communities was proposed. These results provide a new perspective on the control of riparian land-use types based on contaminants and microbes, and different microbial community response patterns may provide a reference for contaminant control in sediments with intensive industrial activities.

The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types

Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer-degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.

Spatial Variation of Microbial Community Structure and Its Driving Environmental Factors in Two Forest Types in Permafrost Region of Greater Xing′an Mountains

Climate warming is accelerating permafrost degradation. Soil microorganisms play key roles in the maintenance of high-latitude permafrost regions and forest ecosystems’ functioning and regulation of biogeochemical cycles. In this study, we used Illumina MiSeq high-throughput sequencing to investigate soil bacterial community composition at a primeval Larix gmelinii forest and a secondary Betula platyphylla forest in a permafrost region of the Greater Xing’an Mountains. The Shannon diversity index tended to decrease and then increase with increasing soil depth, which was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 40–60 cm. Proteobacteria (19.86–29.68%), Acidobacteria (13.59–31.44%), Chloroflexi (11.04–27.19%), Actinobacteria (7.05–25.57%), Gemmatimonadetes (1.76–9.18%), and Verrucomicrobia (2.03–7.00%) were the predominant phyla of the bacterial community in two forest types. The relative abundance of Proteobacteria showed a decreasing trend in the B. platyphylla forest and an increasing trend in the L. gmelinii forest, whereas that of Chloroflexi increased and then decreased in the B. platyphylla forest and decreased in the L. gmelinii forest with increasing soil depth. The relative abundance of Acidobacteria was significantly higher in the B. platyphylla forest than in the L. gmelinii forest at 0–20 cm depth, whereas that of Actinobacteria was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 0–20 cm and 40–60 cm depth. Principal coordinate analysis (PCoA) and two-way analysis of variance (ANOVA) indicated that microbial community composition was more significantly influenced by forest type than soil depth. Redundancy analysis (RDA) showed that microbial community structure was strongly affected by soil physicochemical properties such as nitrate nitrogen (NO3−-N), pH, and total organic carbon (TOC). These results offer insights into the potential relationship between soil microbial community and forest conversion in high latitude permafrost ecosystems.

Effects of Tree Composition and Soil Depth on Structure and Functionality of Belowground Microbial Communities in Temperate European Forests

Depending on their tree species composition, forests recruit different soil microbial communities. Likewise, the vertical nutrient gradient along soil profiles impacts these communities and their activities. In forest soils, bacteria and fungi commonly compete, coexist, and interact, which is challenging for understanding the complex mechanisms behind microbial structuring. Using amplicon sequencing, we analyzed bacterial and fungal diversity in relation to forest composition and soil depth. Moreover, employing random forest models, we identified microbial indicator taxa of forest plots composed of either deciduous or evergreen trees, or their mixtures, as well as of three soil depths. We expected that forest composition and soil depth affect bacterial and fungal diversity and community structure differently. Indeed, relative abundances of microbial communities changed more across soil depths than in relation to forest composition. The microbial Shannon diversity was particularly affected by soil depth and by the proportion of evergreen trees. Our results also reflected that bacterial communities are primarily shaped by soil depth, while fungi were influenced by forest tree species composition. An increasing proportion of evergreen trees did not provoke differences in main bacterial metabolic functions, e.g., carbon fixation, degradation, or photosynthesis. However, significant responses related to specialized bacterial metabolisms were detected. Saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi were related to the proportion of evergreen trees, particularly in topsoil. Prominent microbial indicator taxa in the deciduous forests were characterized to be r-strategists, whereas K-strategists dominated evergreen plots. Considering simultaneously forest composition and soil depth to unravel differences in microbial communities, metabolic pathways and functional guilds have the potential to enlighten mechanisms that maintain forest soil functionality and provide resistance against disturbances.

Microbial Community Changes in 26,500-Year-Old Thawing Permafrost

Northern permafrost soils store more than half of the global soil carbon. Frozen for at least two consecutive years, but often for millennia, permafrost temperatures have increased drastically in the last decades. The resulting thermal erosion leads not only to gradual thaw, resulting in an increase of seasonally thawing soil thickness, but also to abrupt thaw events, such as sudden collapses of the soil surface. These could affect 20% of the permafrost zone and half of its organic carbon, increasing accessibility for deeper rooting vegetation and microbial decomposition into greenhouse gases. Knowledge gaps include the impact of permafrost thaw on the soil microfauna as well as key taxa to change the microbial mineralization of ancient permafrost carbon stocks during erosion. Here, we present the first sequencing study of an abrupt permafrost erosion microbiome in Northeast Greenland, where a thermal erosion gully collapsed in the summer of 2018, leading to the thawing of 26,500-year-old permafrost material. We investigated which soil parameters (pH, soil carbon content, age and moisture, organic and mineral horizons, and permafrost layers) most significantly drove changes of taxonomic diversity and the abundance of soil microorganisms in two consecutive years of intense erosion. Sequencing of the prokaryotic 16S rRNA and fungal ITS2 gene regions at finely scaled depth increments revealed decreasing alpha diversity with depth, soil age, and pH. The most significant drivers of variation were found in the soil age, horizons, and permafrost layer for prokaryotic and fungal beta diversity. Permafrost was mainly dominated by Proteobacteria and Firmicutes, with Polaromonas identified as the most abundant taxon. Thawed permafrost samples indicated increased abundance of several copiotrophic phyla, such as Bacteroidia, suggesting alterations of carbon utilization pathways within eroding permafrost.

Trends in Microbial Community Composition and Function by Soil Depth

Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.

Characterization of antimicrobial resistance genes and virulence factor genes in an Arctic permafrost region revealed by metagenomics

Antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) constitute a serious threat to public health, and climate change has been predicted to affect the increase in bacterial pathogens harboring ARGs and VFGs. However, studies on bacterial pathogens and their ARGs and VFGs in permafrost region have received limited attention. In this study, a metagenomic approach was applied to a comprehensive survey to detect potential ARGs, VFGs, and pathogenic antibiotic resistant bacteria (PARB) carrying both ARGs and VFGs in the active layer and permafrost. Overall, 70 unique ARGs against 18 antimicrobial drug classes and 599 VFGs classified as 38 virulence factors were detected in the Arctic permafrost region. Eight genes with mobile genetic elements (MGEs) carrying ARGs were identified; most MGEs were classified as phages. In the metagenome-assembled genomes, the presence of 15 PARB was confirmed. The soil profile showed that the transcripts per million (TPM) values of ARGs and VFGs in the sub-soil horizon were significantly lower than those in the top soil horizon. Based on the TPM value of each gene, major ARGs, VFGs, and these genes in PARB from the Arctic permafrost region were identified and their distribution was confirmed. The major host bacteria for ARGs and VFGs and PARB were identified. A comparison of the percentage identity distribution of ARGs and VFGs to reference databases indicated that ARGs and VFGs in the Arctic soils differ from previously identified genes. Our results may help understand the characteristics and distribution of ARGs, VFGs, and these genes in PARB in the Arctic permafrost region. This findings suggest that the Arctic permafrost region may serve as potential reservoirs for ARGs, VFGs, and PARB. These genes could pose a new threat to human health if they are released by permafrost thawing owing to global warming and propagate to other regions.

Bioavailable metal(loid)s and physicochemical features co-mediating microbial communities at combined metal(loid) pollution sites

Heavy metal contamination poses considerable threats to various ecosystems, yet little is known about the assembly and adaptation of microbial communities at sites with combined heavy metal(loid) pollution. Here, we examined metal(loid) pollutants and bacterial communities in three zones (Zones Ⅰ, Ⅱ, and Ⅲ) of an abandoned sewage reservoir with different usage years. The contamination level of multiple metal(loid)s was higher in Zone Ⅰ than in the other zones, and arsenic (As), zinc (Zn), selenium (Se), copper (Cu), tin (Sn), molybdenum (Mo), antimony (Sb), cadmium (Cd), lead (Pb), thallium (Tl), and nickel (Ni) were the major contaminants (pollution load index > 1). Bioavailable forms of titanium (Ti), chromium (Cr), Sn, and cobalt (Co) played essential roles in shaping the microbial structure, and physicochemical properties, especially organic matter (OM) and pH, also mediated the microbial diversity and composition in the metal(loid) contaminated zones. Metal-microbe interactions and heatmap analysis revealed that the bioavailability of metal(loid)s promoted the niche partitioning of microbial species. Metal-resistant species were abundant in Zone Ⅰ that had the highest metal-contaminated level, whereas metal-sensitive species prevailed in Zone Ⅲ that had the lowest pollution level. The bioavailable metal(loid)s rather than physicochemical and spatial variables explained a larger portion of the variance in the microbial community, and the homogeneous selection was the dominant ecological process driving the assembly of the microbial community. Overall, our study highlighted the importance of metal(loid) bioavailability in shaping microbial structure, future bioremediation, and environmental management of metal(loid) contaminated sites.

The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession

The Northern high latitudes are warming twice as fast as the global average, and permafrost has become vulnerable to thaw. Changes to the environment during thaw leads to shifts in microbial communities and their associated functions, such as greenhouse gas emissions. Understanding the ecological processes that structure the identity and abundance (i.e., assembly) of pre- and post-thaw communities may improve predictions of the functional outcomes of permafrost thaw. We characterized microbial community assembly during permafrost thaw using in situ observations and a laboratory incubation of soils from the Storflaket Mire in Abisko, Sweden, where permafrost thaw has occurred over the past decade. In situ observations indicated that bacterial community assembly was driven by randomness (i.e., stochastic processes) immediately after thaw with drift and dispersal limitation being the dominant processes. As post-thaw succession progressed, environmentally driven (i.e., deterministic) processes became increasingly important in structuring microbial communities where homogenizing selection was the only process structuring upper active layer soils. Furthermore, laboratory-induced thaw reflected assembly dynamics immediately after thaw indicated by an increase in drift, but did not capture the long-term effects of permafrost thaw on microbial community dynamics. Our results did not reflect a link between assembly dynamics and carbon emissions, likely because respiration is the product of many processes in microbial communities. Identification of dominant microbial community assembly processes has the potential to improve our understanding of the ecological impact of permafrost thaw and the permafrost-climate feedback.