In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge.

Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.

Arctic rooting depth distribution influences modelled carbon emissions but cannot be inferred from aboveground vegetation type.

The distribution of roots throughout the soil drives depth-dependent plant-soil interactions and ecosystem processes, particularly in arctic tundra where plant biomass, is predominantly belowground. Vegetation is usually classified from aboveground, but it is unclear whether such classifications are suitable to estimate belowground attributes and their consequences, such as rooting depth distribution and its influence on carbon cycling. We performed a meta-analysis of 55 published arctic rooting depth profiles, testing for differences both between distributions based on aboveground vegetation types (Graminoid, Wetland, Erect-shrub, and Prostrate-shrub tundra) and between 'Root Profile Types' for which we defined three representative and contrasting clusters. We further analyzed potential impacts of these different rooting depth distributions on rhizosphere priming-induced carbon losses from tundra soils. Rooting depth distribution hardly differed between aboveground vegetation types but varied between Root Profile Types. Accordingly, modelled priming-induced carbon emissions were similar between aboveground vegetation types when they were applied to the entire tundra, but ranged from 7.2 to 17.6 Pg C cumulative emissions until 2100 between individual Root Profile Types. Variations in rooting depth distribution are important for the circumpolar tundra carbon-climate feedback but can currently not be inferred adequately from aboveground vegetation type classifications.

Controlling biases in targeted plant removal experiments.

Targeted removal experiments are a powerful tool to assess the effects of plant species or (functional) groups on ecosystem functions. However, removing plant biomass in itself can bias the observed responses. This bias is commonly addressed by waiting until ecosystem recovery, but this is inherently based on unverified proxies or anecdotal evidence. Statistical control methods are efficient, but restricted in scope by underlying assumptions. We propose accounting for such biases within the experimental design, using a gradient of biomass removal controls. We demonstrate the relevance of this design by presenting (1) conceptual examples of suspected biases and (2) how to observe and control for these biases. Using data from a mycorrhizal association-based removal experiment, we show that ignoring biomass removal biases (including by assuming ecosystem recovery) can lead to incorrect, or even contrary conclusions (e.g. false positive and false negative). Our gradient design can prevent such incorrect interpretations, regardless of whether aboveground biomass has fully recovered. Our approach provides more objective and quantitative insights, independently assessed for each variable, than using a proxy to assume ecosystem recovery. Our approach circumvents the strict statistical assumptions of, for example, ANCOVA and thus offers greater flexibility in data analysis.

Warming nondormant tree roots advances aboveground spring phenology in temperate trees.

Climate warming advances the onset of tree growth in spring, but above- and belowground phenology are not always synchronized. These differences in growth responses may result from differences in root and bud dormancy dynamics, but root dormancy is largely unexplored. We measured dormancy in roots and leaf buds of Fagus sylvatica and Populus nigra by quantifying the warming sum required to initiate above- and belowground growth in October, January and February. We furthermore carried out seven experiments, manipulating only the soil and not air temperature before or during tree leaf-out to evaluate the potential of warmer roots to influence budburst timing using seedlings and adult trees of F. sylvatica and seedlings of Betula pendula. Root dormancy was virtually absent in comparison with the much deeper winter bud dormancy. Roots were able to start growing immediately as soils were warmed during the winter. Interestingly, higher soil temperature advanced budburst across all experiments, with soil temperature possibly accounting for c. 44% of the effect of air temperature in advancing aboveground spring phenology per growing degree hour. Therefore, differences in root and bud dormancy dynamics, together with their interaction, likely explain the nonsynchronized above- and belowground plant growth responses to climate warming.

Root biomass and root traits of Alnus glutinosa show size-dependent and opposite patterns in a drained and a rewetted forest peatland.

BACKGROUND AND AIMS: Forest peatlands represent 25 % of global peatlands and store large amounts of carbon (C) as peat. Traditionally they have been drained in order to increase forestry yield, which may cause large losses of C from the peat. Rewetting aims to stop these losses and to restore the initial storage function of the peatlands. As roots represent major peat-forming elements in these systems, we sampled roots with diameter <5 mm in a drained and a rewetted forest peatland in north-east Germany to evaluate differences in tree biomass investments below ground, root functional characteristics and root age. METHODS: We cored soil next to Alnus glutinosa stems and sorted root biomass into <1, 1-2 and 2-5 mm diameter classes. We measured biomass distribution and specific root area (SRA) in 10-cm depth increments down to 50 cm, and estimated root age from annual growth rings. KEY RESULTS: Root biomass in the rewetted site was more than double that in the drained site. This difference was mostly driven by very fine roots <1 mm, which accounted for 51 % of the total root biomass and were mostly (75 %) located in the upper 20 cm. For roots <1 mm, SRA did not differ between the sites. However, SRA of the 1-2 mm and 2-5 mm diameter roots was higher in the drained than in the rewetted site. Root age did not differ between sites. CONCLUSIONS: The size-dependent opposite patterns between root biomass and their functional characteristics under contrasting water regimes indicate differences between fine and coarse roots in their response to environmental changes. Root age distribution points to similar root turnover rates between the sites, while higher root biomass in the rewetted site clearly indicates larger tree C stocks below ground under rewetting, supporting the C sink function of the ecosystem.

Dwelling in the deep - strongly increased root growth and rooting depth enhance plant interactions with thawing permafrost soil.

Climate-warming-induced permafrost thaw exposes large amounts of carbon and nitrogen in soil at considerable depths, below the seasonally thawing active layer. The extent to which plant roots can reach and interact with these hitherto detached, deep carbon and nitrogen stores remains unknown. We aimed to quantify how permafrost thaw affects root dynamics across soil depths and plant functional types compared with above-ground abundance, and potential consequences for plant-soil interactions. A decade of experimental permafrost thaw strongly increased total root length and growth in the active layer, and deep roots invaded the newly thawed permafrost underneath. Root litter input to soil across all depths was 10 times greater with permafrost thaw. Root growth timing was unaffected by experimental permafrost thaw but peaked later in deeper soil, reflecting the seasonally receding thaw front. Deep-rooting species could sequester 15 N added at the base of the ambient active layer in October, which was after root growth had ceased. Deep soil organic matter that has long been locked up in permafrost is thus no longer detached from plant processes upon thaw. Whether via nutrient uptake, carbon storage, or rhizosphere priming, plant root interactions with thawing permafrost soils may feed back on our climate both positively and negatively.

Exploring drivers of litter decomposition in a greening Arctic: results from a transplant experiment across a treeline.

Decomposition of plant litter is a key control over carbon (C) storage in the soil. The biochemistry of the litter being produced, the environment in which the decomposition is taking place, and the community composition and metabolism of the decomposer organisms exert a combined influence over decomposition rates. As deciduous shrubs and trees are expanding into tundra ecosystems as a result of regional climate warming, this change in vegetation represents a change in litter input to tundra soils and a change in the environment in which litter decomposes. To test the importance of litter biochemistry and environment in determining litter mass loss, we reciprocally transplanted litter between heath (Empetrum nigrum), shrub (Betula nana), and forest (Betula pubescens) at a sub-Arctic treeline in Sweden. As expansion of shrubs and trees promotes deeper snow, we also used a snow fence experiment in a tundra heath environment to understand the importance of snow depth, relative to other factors, in the decomposition of litter. Our results show that B. pubescens and B. nana leaf litter decomposed at faster rates than E. nigrum litter across all environments, while all litter species decomposed at faster rates in the forest and shrub environments than in the tundra heath. The effect of increased snow on decomposition was minimal, leading us to conclude that microbial activity over summer in the productive forest and shrub vegetation is driving increased mass loss compared to the heath. Using B. pubescens and E. nigrum litter, we demonstrate that degradation of carbohydrate-C is a significant driver of mass loss in the forest. This pathway was less prominent in the heath, which is consistent with observations that tundra soils typically have high concentrations of "labile" C. This experiment suggests that further expansion of shrubs and trees may stimulate the loss of undecomposed carbohydrate C in the tundra.

The hidden season: growing season is 50% longer below than above ground along an arctic elevation gradient.

There is compelling evidence from experiments and observations that climate warming prolongs the growing season in arctic regions. Until now, the start, peak, and end of the growing season, which are used to model influences of vegetation on biogeochemical cycles, were commonly quantified using above-ground phenological data. Yet, over 80% of the plant biomass in arctic regions can be below ground, and the timing of root growth affects biogeochemical processes by influencing plant water and nutrient uptake, soil carbon input and microbial activity. We measured timing of above- and below-ground production in three plant communities along an arctic elevation gradient over two growing seasons. Below-ground production peaked later in the season and was more temporally uniform than above-ground production. Most importantly, the growing season continued c. 50% longer below than above ground. Our results strongly suggest that traditional above-ground estimates of phenology in arctic regions, including remotely sensed information, are not as complete a representation of whole-plant production intensity or duration, as studies that include root phenology. We therefore argue for explicit consideration of root phenology in studies of carbon and nutrient cycling, in terrestrial biosphere models, and scenarios of how arctic ecosystems will respond to climate warming.

Cascading effects of earthworm invasion increase graminoid density and rodent grazing intensities.

Human-mediated dispersal of non-native earthworms can cause substantial changes to the functioning and composition of ecosystems previously earthworm-free. Some of these earthworm species have the potential to "geoengineer" soils and increase plant nitrogen (N) uptake. Yet the possible consequences of increased plant N concentrations on rodent grazing remains poorly understood. In this study, we present findings from a common garden experiment with two tundra communities, meadow (forb dominated) and heath (shrub dominated), half of them subjected to 4 years of earthworm presence (Lumbricus spp. and Aporrectodea spp.). Within four summers, our earthworm treatment changed plant community composition by increasing graminoid density by, on average, 94% in the heath vegetation and by 49% in the meadow. Rodent winter grazing was more intense on plants growing in soils with earthworms, an effect that coincided with higher N concentrations in plants, indicating a higher palatability. Even though earthworms reduced soil moisture, plant community productivity, as indicated by vegetation greenness (normalized difference vegetation index), was not negatively impacted. We conclude that earthworm-induced changes in plant composition and trophic interactions may fundamentally alter the functioning of tundra ecosystems.

Plant roots but not hydrology control microbiome composition and methane flux in temperate fen mesocosms.

The rewetting of formerly drained peatlands can help to counteract climate change through the reduction of CO2 emissions. However, this can lead to resuming CH4 emissions due to changes in the microbiome, favoring CH4-producing archaea. How plants, hydrology and microbiomes interact as ultimate determinants of CH4 dynamics is still poorly understood. Using a mesocosm approach, we studied peat microbiomes, below-ground root biomass and CH4 fluxes with three different water level regimes (stable high, stable low and fluctuating) and four different plant communities (bare peat, Carex rostrata, Juncus inflexus and their mixture) over the course of one growing season. A significant difference in microbiome composition was found between mesocosms with and without plants, while the difference between plant species identity or water regimes was rather weak. A significant difference was also found between the upper and lower peat, with the difference increasing as plants grew. By the end of the growing season, the methanogen relative abundance was higher in the sub-soil layer, as well as in the bare peat and C. rostrata pots, as compared to J. inflexus or mixture pots. This was inversely linked to the larger root area of J. inflexus. The root area also negatively correlated with CH4 fluxes which positively correlated with the relative abundance of methanogens. Despite the absence or low abundance of methanotrophs in many samples, the integration of methanotroph abundance improved the quality of the correlation with CH4 fluxes, and methanogens and methanotrophs together determined CH4 fluxes in a structural equation model. However, water regime showed no significant impact on plant roots and methanogens, and consequently, on CH4 fluxes. This study showed that plant roots determined the microbiome composition and, in particular, the relative abundance of methanogens and methanotrophs, which, in interaction, drove the CH4 fluxes.

As good as human experts in detecting plant roots in minirhizotron images but efficient and reproducible: the convolutional neural network "RootDetector".

Plant roots influence many ecological and biogeochemical processes, such as carbon, water and nutrient cycling. Because of difficult accessibility, knowledge on plant root growth dynamics in field conditions, however, is fragmentary at best. Minirhizotrons, i.e. transparent tubes placed in the substrate into which specialized cameras or circular scanners are inserted, facilitate the capture of high-resolution images of root dynamics at the soil-tube interface with little to no disturbance after the initial installation. Their use, especially in field studies with multiple species and heterogeneous substrates, though, is limited by the amount of work that subsequent manual tracing of roots in the images requires. Furthermore, the reproducibility and objectivity of manual root detection is questionable. Here, we use a Convolutional Neural Network (CNN) for the automatic detection of roots in minirhizotron images and compare the performance of our RootDetector with human analysts with different levels of expertise. Our minirhizotron data come from various wetlands on organic soils, i.e. highly heterogeneous substrates consisting of dead plant material, often times mainly roots, in various degrees of decomposition. This may be seen as one of the most challenging soil types for root segmentation in minirhizotron images. RootDetector showed a high capability to correctly segment root pixels in minirhizotron images from field observations (F1 = 0.6044; r2 compared to a human expert = 0.99). Reproducibility among humans, however, depended strongly on expertise level, with novices showing drastic variation among individual analysts and annotating on average more than 13-times higher root length/cm2 per image compared to expert analysts. CNNs such as RootDetector provide a reliable and efficient method for the detection of roots and root length in minirhizotron images even from challenging field conditions. Analyses with RootDetector thus save resources, are reproducible and objective, and are as accurate as manual analyses performed by human experts.

Reasons to not correct for leaching in TBI; Reply to Lind et al. (2022).

We believe that correcting for leaching in (terrestrial) litterbags studies such as the Tea Bag Index will result in more uncertainties than it resolves. This is mainly because leaching occurs in pulses upon changes in the environment and because leached material can still be mineralized after leaching. Furthermore, amount of material that potentially leaches from tea is comparable to other litter types. When correcting for leaching, it is key to be specific about the employed method, just like being specific about the study specific definition of decomposition.

Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands.

In the last decades, rewetting of drained peatlands is on the rise worldwide, to restore their significant carbon sink function. Despite the increasing understanding of peat microbiomes, little is known about the seasonal dynamics and network interactions of the microbial communities in these ecosystems, especially in rewetted fens (groundwater-fed peatlands). Here, we investigated the seasonal dynamics in both prokaryotic and eukaryotic microbiomes in three common fen types in Northern Germany. The eukaryotic microbiomes, including fungi, protists and microbial metazoa, showed significant changes in their community structures across the seasons in contrast to largely unaffected prokaryotic microbiomes. Furthermore, our results proved that the dynamics in eukaryotic microbiomes in the rewetted sites differed between fen types, specifically in terms of saprotrophs, arbuscular mycorrhiza and grazers of bacteria. The co-occurrence networks also exhibited strong seasonal dynamics that differed between rewetted and drained sites, and the correlations involving protists and prokaryotes were the major contributors to these dynamics. Our study provides the insight that microbial eukaryotes mainly define the seasonal dynamics of microbiomes in rewetted fen peatlands. Accordingly, future research should unravel the importance of eukaryotes for biogeochemical processes, especially the under-characterized protists and metazoa, in these poorly understood ecosystems.

Invasive earthworms unlock arctic plant nitrogen limitation.

Arctic plant growth is predominantly nitrogen (N) limited. This limitation is generally attributed to slow soil microbial processes due to low temperatures. Here, we show that arctic plant-soil N cycling is also substantially constrained by the lack of larger detritivores (earthworms) able to mineralize and physically translocate litter and soil organic matter. These new functions provided by earthworms increased shrub and grass N concentration in our common garden experiment. Earthworm activity also increased either the height or number of floral shoots, while enhancing fine root production and vegetation greenness in heath and meadow communities to a level that exceeded the inherent differences between these two common arctic plant communities. Moreover, these worming effects on plant N and greening exceeded reported effects of warming, herbivory and nutrient addition, suggesting that human spreading of earthworms may lead to substantial changes in the structure and function of arctic ecosystems.

Correction: Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration.

Since the publication of the original article, the authors noticed some errors in reference citation had been introduced throughout the paper. The following text contains excerpts from the original article and how they should appear with correct referencing. The publisher apologises for any inconvenience this has caused readers.

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration.

The decomposition of large stocks of soil organic carbon in thawing permafrost might depend on more than climate change-induced temperature increases: indirect effects of thawing via altered bacterial community structure (BCS) or rooting patterns are largely unexplored. We used a 10-year in situ permafrost thaw experiment and aerobic incubations to investigate alterations in BCS and potential respiration at different depths, and the extent to which they are related with each other and with root density. Active layer and permafrost BCS strongly differed, and the BCS in formerly frozen soils (below the natural thawfront) converged under induced deep thaw to strongly resemble the active layer BCS, possibly as a result of colonization by overlying microorganisms. Overall, respiration rates decreased with depth and soils showed lower potential respiration when subjected to deeper thaw, which we attributed to gradual labile carbon pool depletion. Despite deeper rooting under induced deep thaw, root density measurements did not improve soil chemistry-based models of potential respiration. However, BCS explained an additional unique portion of variation in respiration, particularly when accounting for differences in organic matter content. Our results suggest that by measuring bacterial community composition, we can improve both our understanding and the modeling of the permafrost carbon feedback.