Plant attributes interact with fungal pathogens and nitrogen addition to drive soil enzymatic activities and their temporal variation

1. Nitrogen enrichment can alter soil communities and their functioning directly, via changes in nutrient availability and stoichiometry, or indirectly, by changing plant communities or the abundance of consumers. However, most studies have only focused on one of these potential drivers and we know little about the relative importance of the different mechanisms (changes in nutrient availability, in plant diversity or functional composition or in consumer abundance) by which nitrogen enrichment affects soil functioning. In addition, soil functions could vary dramatically between seasons; however, they are typically measured only once during the peak growing season. We therefore know little about the drivers of intra-annual stability in soil functioning. 2. In this study, we measured activities of β-glucosidase and acid phosphatase, two extracellular enzymes that indicate soil functioning. We did so in a large grassland experiment which tested the effects, and relative importance, of nitrogen enrichment, plant functional composition and diversity, and foliar pathogen presence (controlled by fungicide) on soil functioning. We measured the activity of the two enzymes across seasons and years to assess the stability and temporal dynamics of soil functioning. 3. Overall β-glucosidase activity was slightly increased by nitrogen enrichment over time but did not respond to the other experimental treatments. Conversely, plant functional diversity and interactions between plant attributes and fungicide application were important drivers of mean acid phosphatase activity. The temporal stability of both soil enzymes was differently affected by two facets of plant diversity: species richness increased temporal stability and functional diversity decreased it; however, these effects were dampened when nitrogen and fungicide were added. 4. The fungicide effects on soil enzyme activities suggest that foliar pathogens can also affect below-ground processes and the interacting effect of fungicide and plant diversity suggests that these plant enemies can modulate the relationship between plant diversity and ecosystem functioning. The contrasting effects of our treatments on the mean versus stability of soil enzyme activities clearly show the need to consider temporal dynamics in below-ground processes, to better understand the responses of soil microbes to environmental changes such as nutrient enrichment.This work is part of the PaNDiv grassland experiment, which was funded by the Swiss National Science Foundation (Project Number: 310030_185260). We thank the Ramon y Cajal programme (RyC-2016-20604) founded by Spanish Ministry of Science, the Swedish Research Council for Sustainable Development for funding NIM (FORMAS 2018-00748), the Swiss National Science Foundation for funding AK (P3P3PA_160992) and the Federal Commission for Scholarships for foreign students (FCS) for funding TZN

Northward range expansion of rooting ungulates decreases detritivore and predatory mite abundances in boreal forests.

In the last few decades wild boar populations have expanded northwards, colonizing boreal forests. The soil disturbances caused by wild boar rooting may have an impact on soil organisms that play a key role in organic matter turnover. However, the impact of wild boar colonization on boreal forest ecosystems and soil organisms remains largely unknown. We investigated the effect of natural and simulated rooting on decomposer and predatory soil mites (total, adult and juvenile abundances; and adult-juvenile proportion). Our simulated rooting experiment aimed to disentangle the effects of (i) bioturbation due to soil mixing and (ii) removing organic material (wild boar food resources) on soil mites. Our results showed a decline in the abundance of adult soil mites in response to both natural and artificial rooting, while juvenile abundance and the relative proportion of adults and juveniles were not affected. The expansion of wild boar northwards and into new habitats has negative effects on soil decomposer abundances in boreal forests which may cascade through the soil food web ultimately affecting ecosystem processes. Our study also suggests that a combined use of natural and controlled experimental approaches is the way forward to reveal any subtle interaction between aboveground and belowground organisms and the ecosystem functions they drive

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Tiny Fungi in the Soil Are Like Medicine for Nature

Like humans, plant and animal species have a specific type of place, called an ecosystem, where they prefer to live. If the ecosystem changes too much, some species will disappear, much the same way people avoid living in the desert because it is too hot and dry. Humans modify many ecosystems, sometimes so severely that almost no plants or animals can live there anymore. To help damaged ecosystems recover, we often start by planting trees or other plants. Biologists found that mycorrhizal fungi, tiny fungi living in the soil and inside plant roots, could speed up ecosystem recovery by making plants grow back faster and stronger. In this article, we describe how the recovery of ecosystems can be enhanced by mycorrhizal fungi, and when mycorrhizal fungi are especially helpful

Low and High Nitrogen Deposition Rates in Northern Coniferous Forests Have Different Impacts on Aboveground Litter Production, Soil Respiration, and Soil Carbon Stocks

Nitrogen (N) deposition can change the carbon (C) sink of northern coniferous forests by changing the balance between net primary production and soil respiration. We used a field experiment in an N poor Pinus sylvestris forest where five levels of N (0, 3, 6, 12, and 50 kg N ha−1 yr−1, n = 6) had been added annually for 12–13 years to investigate how litter C inputs and soil respiration, divided into its autotrophic and heterotrophic sources, respond to different rates of N input, and its subsequent effect on soil C storage. The highest N addition rate (50 kg N ha−1 yr−1) stimulated soil C accumulation in the organic layer by 22.3 kg C kg−1 N added, increased litter inputs by 46%, and decreased soil respiration per mass unit of soil C by 31.2%, mainly by decreasing autotrophic respiration. Lower N addition rates (≤ 12 kg N ha−1 yr−1) had no effect on litter inputs or soil respiration. These results support previous studies reporting on increased litter inputs coupled to impeded soil C mineralization, contributing to enhancing the soil C sink when N is supplied at high rates, but add observations for lower N addition rates more realistic for N deposition. In doing so, we show that litter production in N poor northern coniferous forests can be relatively unresponsive to low N deposition levels, that stimulation of microbial activity at low N additions is unlikely to reduce the soil C sink, and that high levels of N deposition enhance the soil C sink by increasing litter inputs and decreasing soil respiration

Chronic Nitrogen Deposition Has a Minor Effect on the Quantity and Quality of Aboveground Litter in a Boreal Forest.

There is evidence that anthropogenic nitrogen (N) deposition enhances carbon (C) sequestration in boreal soils. However, key underlying mechanisms explaining this increase have not been resolved. Two potentially important mechanisms are that aboveground litter production increases, or that litter quality changes in response to N enrichment. As such, our aim was to quantify whether simulated chronic N deposition caused changes in aboveground litter production or quality in a boreal forest. We conducted a long-term (17 years) stand-scale (0.1 ha) forest experiment, consisting of three N addition levels (0, 12.5, and 50 kg N ha-1 yr-1) in northern Sweden, where background N deposition rates are very low. We measured the annual quantity of litter produced for 8 different litter categories, as well as their concentrations of C, N, phosphorus (P), lignin, cellulose and hemi-cellulose. Our results indicate that mosses were the only major litter component showing significant quantitative and qualitative alterations in response to the N additions, indicative of their ability to intercept a substantial portion of the N added. These effects were, however, offset by the other litter fractions where we found no changes in the total litter fluxes, or individual chemical constituents when all litter categories were summed. This study indicates that the current annual litter fluxes cannot explain the increase in soil C that has occurred in our study system in response to simulated chronic N application. These results suggest that other mechanisms are likely to explain the increased soil C accumulation rate we have observed, such as changes in soil microbial activity, or potentially transient changes in aboveground litter inputs that were no longer present at the time of our study

Nitrogen enrichment impacts on boreal litter decomposition are driven by changes in soil microbiota rather than litter quality

In nitrogen (N) limited boreal forests, N enrichment can impact litter decomposition by affecting litter quality and by changing the soil environment where litter decomposes. We investigated the importance of litter quality and soil factors on litter decomposition using a 2-year reciprocal transplant experiment for Picea abies needle litter, derived from plots subjected to 17 years of N addition, including control, low and high N treatments (ambient, 12.5 and 50 kg N ha(-1) yr(-1), respectively). Our data show that changes in soil factors were the main pathway through which N impacted litter decomposition, with rates reduced by approximate to 15% when placed in high N relative to control plots, regardless of litter origin. Litter decomposition was correlated to soil microbiota, with Picea abies litter decomposition positively correlated with gram negative and fungal functional groups. Our results suggest that previous findings of increase soil C accumulation in response to N deposition is likely to occur as a result of changes in soil microbiota rather than altered litter quality

Host plant height explains the effect of nitrogen enrichment on arbuscular mycorrhizal fungal communities.

Nitrogen (N) enrichment is widely known to affect the root-associated arbuscular mycorrhizal fungal (AMF) community in different ways, for example, via altering soil properties and/or shifting host plant functional structure. However, empirical knowledge of their relative importance is still lacking. Using a long-term N addition experiment, we measured the AMF community taxonomic and phylogenetic diversity at the single plant species (roots of 15 plant species) and plant community (mixed roots) levels. We also measured four functional traits of 35 common plant species along the N addition gradient. We found divergent responses of AMF diversity to N addition for host plants with different innate heights (i.e. plant natural height under unfertilized treatment). Furthermore, our data showed that species-specific responses of AMF diversity to N addition were negatively related to the change in maximum plant height. When scaling up to the community level, N addition affected AMF diversity mainly through increasing the maximum plant height, rather than altering soil properties. Our results highlight the importance of plant height in driving AMF community dynamics under N enrichment at both species and community levels, thus providing important implications for understanding the response of AMF diversity to anthropogenic N deposition

Mean annual litter biomass in response to nitrogen addition.

<p>Mean (Mg ha^-1 yr^-1) biomass of 8 litter categories (moss tissue, <i>V</i>. <i>myrtillus</i> leaf, reproductive organ, tree twig, tree branch litter, <i>P</i>. <i>abies</i> needle, <i>P</i>. <i>sylvestris</i> needle and deciduous tree leaf litter) in response to long-term N addition (0, 12.5 or 50 kg N ha-1 yr-1; n = 5). The total bar height represents the total (+SE) litter biomass (Mg ha^-1 yr^-1). Different letters (a or b) across bar segments with the same shade indicate significant differences pair-wise difference using Student-Newman-Keuls <i>post-hoc</i> tests.</p

Litter element and carbon chemistry fluxes.

<p>Total mean (+SE) litter carbon (a), nitrogen (b), phosphorus (c), lignin (d), cellulose (e) or hemi-cellulose (f) fluxes in response to long-term N addition (0, 12.5 or 50 kg N ha^-1 yr^-1; n = 5) for each litter category: moss, <i>V</i>. <i>myrtillus</i> leaves (V. m.), reproductive organs (Rep. org.), deciduous tree leaves (Dec. L.), <i>P</i>. <i>abies</i> needles (Spruce), <i>P</i>. <i>sylvestris</i> (Pine), twigs and branches. V. m and Dec. L. litter categories are missing from panels (d), (e) and (f) because insufficient litter material was available for these analyses. Different letters (a or b) next to each group of bars indicate significant differences between treatments (α = 0.05) determined using Student-Newman-Keuls <i>post-hoc</i> tests. Nearly significant difference at (0.05 < P < 0.10) are indicated by a star (*). Non-significant differences are indicated by n.s.</p