Variation in bacterial, archaeal and fungal community structure and abundance in High Arctic tundra soil

Arctic ecosystems are under pressure from climate change and atmospheric nitrogen (N) deposition. However, knowledge of the ecology of microbial communities and their responses to such challenges in Arctic tundra soil remain limited, despite the central role these organisms play for ecosystem functioning. We utilised a plot-scale experiment in High Arctic tundra on Svalbard to investigate short-term variation (9 days), following simulation of a N deposition event (4 kg N ha?1 yr?1), in the structure and abundance of bacterial, archaeal and fungal communities between organic and mineral soil horizons. T-RFLP analysis showed significant differences between horizons in bacterial and archaeal community structure. Q-PCR analysis showed that fungal abundance did not differ significantly between soil horizons, whilst bacterial and archaeal abundance was significantly higher in mineral than in organic horizons, despite soil water and total C and N contents being significantly greater in the organic horizon. In the organic horizon, bacterial community structure and fungal abundance varied significantly over time. In the mineral horizon, there was significant variation over time in bacterial abundance, in archaeal community structure and in both fungal community structure and abundance. In contrast, N deposition did not lead to significant variation in either the structure or the abundance of microbial communities. This research demonstrates that microbial community structure and abundance can change rapidly (over only a few days) in Arctic tundra soils and also differently between soil horizons in response to different environmental drivers. Moreover, this variability in microbial community structure and abundance is soil horizon- and taxonomic domain-specific, highlighting the importance of investigating microbial communities across all soil horizons and over short periods of time

Analysing the effect of soil organic matter on bacterial communities using T-RFLP fingerprinting: different methods, different stories?

Soil microbial ecology needs robust tools to elucidate ecological questions, such as the impact of fertilisation on soil microbial communities. However, the methods and data analysis used can directly affect the biological conclusions. In this study, the sensitivity of terminal-restriction fragment length polyphorism (T-RFLP) to four restriction enzymes (RE), six peak area thresholds (PAT) from 0 to 10 % and two matrices (presence/absence and relative abundance) was assessed on soils subjected to eight different long-term amendments. The T-RFLP profiles were analysed using a three-step multivariate analysis approach: (i) cluster analysis and non-metric multi-dimensional scaling, (ii) ANOSIM and PERMANOVA and (iii) correlations. The application of organic and mineral fertilisers over 53 years changed the bacterial community composition regardless if the RE, PAT and matrix were used. However, the clustering of the community, the strength of these differences, the correlations with environmental variables and, subsequently, the biological conclusions varied with the use of RE, PAT and matrix. Hence, the bacterial community composition was found to be either highly sensitive to any changes in soil organic matter strongly correlated to C and N concentration, or only affected by large inputs of C or soil management. Different REs can reveal different bacterial populations affected by different drivers, but PATs 0.5 and 1 % should be used especially when using presence/absence matrix. This study also shows the complexity of the effect of organic and mineral amendment on bacterial community composition and stresses the importance to inform on methodological and data analysis parameters

Dynamics of bacterial communities in relation to soil aggregate formation during the decomposition of 13C-labelled rice straw

The addition of fresh organic matter is known to modify both microbial community structure and soil aggregation. The objective of this study was to understand the relationship between the dynamics of the soil microbial community structure in relation to that of their habitats during the decomposition of straw. Soil samples, ground (2000 μm) were measured. Fatty acid methyl ester (FAME) profiling was used to determine total bacterial community structure and FAME based stable isotope probing (FAME-SIP) was used to characterise the straw degrader communities. The mineralisation rate of the native C and the CStraw was high. The formation of macroaggregates (>2000 μm) occurred within 2 days in amended and unamended samples but did so to a greater extent in the amended samples. The CStraw was mainly located in fractions >200 μm, where degraders were the most abundant. The ¹³C-FAME profiles followed the same trends as total FAME profiles through time and within soil fractions, suggesting common dynamics between straw degraders and total bacterial communities: Gram-negative were more important in fraction >200 μm and during the early stages of the incubation while Gram-positive and actinobacteria dominated in fine fractions and at the end of the incubation. Bacterial community structure changed rapidly (within 2 days) in conjunction with the formation of new microbial habitats, suggesting that the relationship between the two is very close

Arctic soil microbial diversity in a changing world

The Arctic region is a unique environment, subject to extreme environmental conditions, shaping life therein and contributing to its sensitivity to environmental change. The Arctic is under increasing environmental pressure from anthropogenic activity and global warming. The unique microbial diversity of Arctic regions, that has a critical role in biogeochemical cycling and in the production of greenhouse gases, will be directly affected by and affect, global changes. This article reviews current knowledge and understanding of microbial taxonomic and functional diversity in Arctic soils, the contributions of microbial diversity to ecosystem processes and their responses to environmental change

Analysing the impact of compaction of soil aggregates using X-ray microtomography and water flow simulations

Soil aggregates are structural units of soil, which create complex pore systems controlling gas and water storage and fluxes in soil. Aggregates can be destroyed during swelling and shrinking or by external forces like mechanical compaction and yet, the knowledge of how physical impact alters aggregate structure remains limited. The aim of the study was to quantify the impact of compaction on macroaggregates, mainly on the pore size distribution and water flow. In this study, aggregates (2–5 mm) were collected by dry sieving in grassland of the Fuchsenbigl–Marchfeld Critical Zone Observatory (Austria). The structural alterations of these soil aggregates under controlled compaction were investigated with a non-invasive 3D X-ray microtomography (XMT). The detailed changes in pore size distribution between aggregates (interpores, diameter >90 μm) and within the aggregates (intrapores, diameter ≤90 μm) in pre- and post-compacted soils were revealed at two soil moisture (9.3% and 18.3% w/w) and two bulk density increments (0.28 and 0.71 g cm−3 from the initial values). The soil permeability was simulated using lattice Boltzmann method (LBM) based on 3D images. Soil compaction significantly reduced total pores volume and the proportion of interpores volume and surface area, while total pore surface area and the proportion of intrapores volume and surface area increased. The increases in soil moisture tended to reduce the effects of compaction on interpores and intrapores, while the high compaction increment drastically changed the pore size distribution. The aggregate compaction decreased water penetration potential due to the increase of small intra-aggregate pores and cavities as demonstrated by LBM. Notably, the LBM results showed a significant linear correlation between the water flow rate and bulk density of soil aggregates and predicted that the water flow could be reduced by up to 97–99% at bulk density of ≥1.6 g cm−3 with soil water content of 18.3% w/w. Thus, a combination of imaging and modelling provided new insights on the compaction effects on aggregates, underpinning the importance of protecting soil structure from mechanical compaction to minimise environmental impacts of soil compaction and maintain water infiltration and percolation in arable soils

Nitrogen accumulation and partitioning in a High Arctic tundra ecosystem from extreme atmospheric N deposition events

Arctic ecosystems are threatened by pollution from recently detected extreme atmospheric nitrogen (N) deposition events in which up to 90% of the annual N deposition can occur in just a few days. We undertook the first assessment of the fate of N from extreme deposition in High Arctic tundra and are presenting the results from the whole ecosystem 15N labelling experiment. In 2010, we simulated N depositions at rates of 0, 0.04, 0.4 and 1.2 g N m− 2 yr− 1, applied as 15NH415NO3 in Svalbard (79°N), during the summer. Separate applications of 15NO3− and 15NH4+ were also made to determine the importance of N form in their retention.More than 95% of the total 15N applied was recovered after one growing season (~ 90% after two), demonstrating a considerable capacity of Arctic tundra to retain N from these deposition events. Important sinks for the deposited N, regardless of its application rate or form, were non-vascular plants > vascular plants > organic soil > litter > mineral soil, suggesting that non-vascular plants could be the primary component of this ecosystem to undergo measurable changes due to N enrichment from extreme deposition events. Substantial retention of N by soil microbial biomass (70% and 39% of 15N in organic and mineral horizon, respectively) during the initial partitioning demonstrated their capacity to act as effective buffers for N leaching. Between the two N forms, vascular plants (Salix polaris) in particular showed difference in their N recovery, incorporating four times greater 15NO3− than 15NH4+, suggesting deposition rich in nitrate will impact them more. Overall, these findings show that despite the deposition rates being extreme in statistical terms, biologically they do not exceed the capacity of tundra to sequester pollutant N during the growing season. Therefore, current and future extreme events may represent a major source of eutrophication

Bacterial community structure in soil microaggregates and on particulate organic matter fractions located outside or inside soil macroaggregates

Soil aggregates and particulate organic matter (POM) are thought to represent distinct soil microhabitats for microbial communities. This study investigated whether organo-mineral (0–20, 20–50 and 50–200 μm) and POM (two sizes: >200 and 200 μm). The denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial communities structure of organo-mineral soil fractions were significantly different in comparison to the unfractionated soil. Conversely, there were little differences in C concentrations, C:N ratios and no differences in DGGE profiles between organo-mineral fractions. Bacterial communities between soil fractions located inside or outside macroaggregates were not significantly different. However, the bacterial communities on POM fractions were significantly different in comparison to organo-mineral soil fractions and unfractionated soil, and also between the 2 sizes of POM. Thus in the studied soil, only POM fractions represented distinct microhabitats for bacterial community, which likely vary with the state of decomposition of the POM

Spatial zoning of microbial functions and plant-soil nitrogen dynamics across a riparian area in an extensively grazed livestock system

Anthropogenic activities have significantly altered global biogeochemical nitrogen (N) cycling leading to major environmental problems such as freshwater eutrophication, biodiversity loss and enhanced greenhouse gas emissions. The soils in the riparian interface between terrestrial and aquatic ecosystems may prevent excess N from entering freshwaters (e.g. via plant uptake, microbial transformations and denitrification). Although these processes are well documented in intensively managed agroecosystems, our understanding of riparian N removal in semi-natural systems remains poor. Our aim was to assess the spatial zoning of soil microbial communities (PLFA), N cycling gene abundance (archaeal and bacterial amoA, nifH, nirK, nirS, nosZ), N processing rates and plant N uptake across an extensively sheep grazed riparian area. As expected, soil properties differed greatly across the riparian transect, with significant decreases in organic matter, NH4+, carbon (C) and N content closest to the river (10 m), while ammonia oxidising archaea (AOA) increased in abundance towards the river. N2O emissions rates were limited by C and to a lesser extent by N with greater emissions close to the river. Plant uptake of urea-derived 15N was high (ca. 55–70% of that added to the soil) but 30–65% of the N was potentially lost by denitrification or leaching. Percentage recovered also suggests that the spatial patterning of plant and microbial N removal processes are different across the riparian zone. Our study provides novel insights into the underlying mechanisms controlling the spatial variability of N cycling in semi-natural riparian ecosystems

Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon.

The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions

Land use driven change in soil pH affects microbial carbon cycling processes

Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates