Core taxa underpin soil microbial community turnover during secondary succession.

Understanding the processes that underpin the community assembly of bacteria is a key challenge in microbial ecology. We studied soil bacterial communities across a large-scale successional gradient of managed and abandoned grasslands paired with mature forest sites to disentangle drivers of community turnover and assembly. Diversity partitioning and phylogenetic null-modelling showed that bacterial communities in grasslands remain compositionally stable following abandonment and secondary succession but they differ markedly from fully afforested sites. Zeta diversity analyses revealed the persistence of core microbial taxa that both reflected and differed from whole-scale community turnover patterns. Differences in soil pH and C:N were the main drivers of community turnover between paired grassland and forest sites and the variability of pH within successional stages was a key factor related to the relative dominance of deterministic assembly processes. Our results indicate that grassland microbiomes could be compositionally resilient to abandonment and secondary succession and that the major changes in microbial communities between grasslands and forests occur fairly late in the succession when trees have established as the dominant vegetation. We also show that core taxa may show contrasting responses to management and abandonment in grasslands.

Fire severity as a key determinant of aboveground and belowground biological community recovery in managed even-aged boreal forests.

Changes in fire regime of boreal forests in response to climate warming are expected to impact postfire recovery. However, quantitative data on how managed forests sustain and recover from recent fire disturbance are limited.Two years after a large wildfire in managed even-aged boreal forests in Sweden, we investigated how recovery of aboveground and belowground communities, that is, understory vegetation and soil microbial and faunal communities, responded to variation in the severity of soil (i.e., consumption of soil organic matter) and canopy fires (i.e., tree mortality).While fire overall enhanced diversity of understory vegetation through colonization of fire adapted plant species, it reduced the abundance and diversity of soil biota. We observed contrasting effects of tree- and soil-related fire severity on survival and recovery of understory vegetation and soil biological communities. Severe fires that killed overstory Pinus sylvestris promoted a successional stage dominated by the mosses Ceratodon purpureus and Polytrichum juniperinum, but reduced regeneration of tree seedlings and disfavored the ericaceous dwarf-shrub Vaccinium vitis-idaea and the grass Deschampsia flexuosa. Moreover, high tree mortality from fire reduced fungal biomass and changed fungal community composition, in particular that of ectomycorrhizal fungi, and reduced the fungivorous soil Oribatida. In contrast, soil-related fire severity had little impact on vegetation composition, fungal communities, and soil animals. Bacterial communities responded to both tree- and soil-related fire severity. Synthesis: Our results 2 years postfire suggest that a change in fire regime from a historically low-severity ground fire regime, with fires that mainly burns into the soil organic layer, to a stand-replacing fire regime with a high degree of tree mortality, as may be expected with climate change, is likely to impact the short-term recovery of stand structure and above- and belowground species composition of even-aged P. sylvestris boreal forests.

Political deafness may impede transition to biological control.

Biological control has developed into a realistic alternative to replace chemical pesticides. A long-awaited paradigm shift is now adopted by the European Commission through a proposed new Regulation on sustainable use of plant protection products. Unfortunately, the scientific framework underpinning biocontrol is seriously neglected, impeding transition to sustainable plant production.

Can field botany be effectively taught as a distance course? Experiences and reflections from the COVID-19 pandemic.

The COVID-19 pandemic that started in 2020 forced a rapid change in university teaching, with large numbers of courses switching to distance learning with very little time for preparation. Courses involving many practical elements and field excursions required particular care if students were to fulfil planned learning outcomes. Here, we present our experiences in teaching field botany in 2020 and 2021. Using a range of methods and tools to introduce students to the subject, promote self-learning and reflection and give rapid and regular feedback, we were able to produce a course that allowed students to achieve the intended learning outcomes and that obtained similarly positive student evaluations to previous years. The course and its outcomes were further improved in 2021. We describe how we structured field botany as a distance course in order that we could give the best possible learning experience for the students. Finally, we reflect on how digital tools can aid teaching such subjects in the future, in a world where public knowledge of natural history is declining.

Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota.

Addition of organic amendments is a commonly used practice to offset potential loss of soil organic matter from agricultural soils. The aim of the present study was to examine how long-term addition of organic matter affects the abundance of different soil biota across trophic levels and the role that the quality of the organic amendments plays. Here we used a 17-year-old fertilization experiment to investigate soil biota responses to four different organic fertilizers, compared with two mineral nitrogen fertilizers and no fertilization, where the organic fertilizers had similar carbon content but varied in their carbon to nitrogen ratios. We collected soil samples and measured a wide range of organisms belonging to different functional groups and trophic levels of the soil food web. Long-term addition of organic and mineral fertilizers had beneficial effects on the abundances of most soil organisms compared with unfertilized soil, but the responses differed between soil biota. The organic fertilizers generally enhanced bacteria and earthworms. Fungi and nematodes responded positively to certain mineral and organic fertilizers, indicating that multiple factors influenced by the fertilization may affect these heterogeneous groups. Springtails and mites were less affected by fertilization than the other groups, as they were present at relatively high abundances even in the unfertilized treatment. However, soil pH had a great influence on springtail abundance. In summary, the specific fertilizer was more important in determining the numerical and compositional responses of soil biota than whether it was mineral or organic. Overall, biennial organic amendments emerge as insufficient, by themselves, to promote soil organisms in the long run, and would need to be added annually or combined with other practices affecting soil quality, such as no or reduced tillage and other crop rotations, to have a beneficial effect.

Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping.

Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large-scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome-wide association study (GWAS) for in vitro antagonism against the root lesion nematode Pratylenchus penetrans in 53 previously genome re-sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p < .001) between strains, indicating a polygenic inheritance. Twenty-one strains produced culture filtrates with higher (p ≤ .05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p ≤ .05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10-10) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes nps4 and nps5 were generated and showed increased (p ≤ .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p < .001) nematicidal activity and reduced (p ≤ .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.

Below-ground herbivory mitigates biomass loss from above-ground herbivory of nitrogen fertilized plants.

Herbivorous insects can influence grassland ecosystem functions in several ways, notably by altering primary production and nutrient turnover. Interactions between above- and belowground herbivory could affect these functions; an effect that might be modified by nitrogen (N) addition, an important global change driver. To explore this, we added above- (grasshoppers) and belowground (wireworms) insect herbivores and N into enclosed, equally composed, grassland plant communities in a fully factorial field experiment. N addition substantially altered the impact of above- and belowground herbivory on ecosystem functioning. Herbivory and N interacted such that biomass was reduced under above ground herbivory and high N input, while plant biomass remained stable under simultaneous above- and belowground herbivory. Aboveground herbivory lowered nutrient turnover rate in the soil, while belowground herbivory mitigated the effect of aboveground herbivory. Soil decomposition potential and N mineralization rate were faster under belowground herbivory at ambient N, but at elevated N this effect was only observed when aboveground herbivores were also present. We found that N addition does not only influence productivity directly (repeatedly shown by others), but also appears to influence productivity by herbivory mediated effects on nutrient dynamics, which highlights the importance of a better understanding of complex biotic interactions.

Assessing costs and benefits of improved soil quality management in remediation projects: A study of an urban site contaminated with PAH and metals.

Contaminants in the soil may threaten soil functions (SFs) and, in turn, hinder the delivery of ecosystem services (ES). A framework for ecological risk assessments (ERAs) within the APPLICERA - APPLICable site-specific Environmental Risk Assessment research project promotes assessments that consider other soil quality parameters than only contaminant concentrations. The developed framework is: (i) able to differentiate the effects of contamination on SFs from the effects of other soil qualities essential for soil biota; and (ii) provides a robust basis for improved soil quality management in remediation projects. This study evaluates the socio-economic consequences of remediation alternatives stemming from a Tier 1 ERA that focusses on total contaminant concentrations and soil quality standards and a detailed, site-specific Tier 3 Triad approach that is based on the APPLICERA framework. The present study demonstrates how Tier 1 and Tier 3 ERAs differ in terms of the socio-economic consequences of their remediation actions, as well as presents a novel method for the semi-quantitative assessment of on-site ES. Although the presented Tier 3 ERA is more expensive and time-consuming than the more traditional Tier 1 ERA approach, it has the potential to lower the costs of remediation actions, decrease greenhouse gas emissions, reduce other environmental impacts, and minimise socio-economic losses. Furthermore, the remediation actions stemming from the Tier 3 ERA were predicted to exert far less negative ES effects than the actions proposed based on the results of the Tier 1 ERA.

Deletion of the Nonribosomal Peptide Synthetase Gene nps1 in the Fungus Clonostachys rosea Attenuates Antagonism and Biocontrol of Plant Pathogenic Fusarium and Nematodes.

Secondary metabolites produced by biological control agents may influence the outcome of their interactions with plant pathogenic microorganisms and plants. In the present study, we investigated the role of the nonribosomal peptide synthetase gene nps1 expressed by the biocontrol fungus Clonostachys rosea. A gene expression analysis showed that nps1 was induced during confrontations with the plant pathogenic fungus Botrytis cinerea. Gene deletion strains of nps1 displayed increased growth rates and conidiation. However, the nematicidal activity of culture filtrates from C. rosea Δnps1 strains was significantly weaker than that from wild-type filtrates (P ≤ 0.001); after 24 h of incubation with culture filtrates from nps1 deletion strains, only 13 to 33% of a mixed community of nematodes were dead compared with 42% of nematodes incubated with wild-type culture filtrates. The Δnps1 strains also showed reduced biocontrol efficacy during pot experiments, thus failing to protect wheat seedlings from foot rot disease caused by the plant pathogenic fungus Fusarium graminearum. Furthermore, C. rosea Δnps1 strains were not able to reduce populations of plant-parasitic nematodes in soil or in roots of wheat as efficiently as the wild-type strain. Both C. rosea wild-type and Δnps1 strains increased the dry shoot weight and shoot length of wheat by 20 and 13%, respectively. We showed that NPS1, a putative nonribosomal peptide synthetase encoded by nps1, is a biocontrol factor, presumably by producing a hitherto unknown nonribosomal peptide compound with antifungal and nematicidal properties that contributes to the biocontrol properties of C. rosea.

Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea.

BACKGROUND: The ascomycete fungus Clonostachys rosea (order Hypocreales) can control several important plant diseases caused by plant pathogenic fungi and nematodes. Subtilisin-like serine proteases are considered to play an important role in pathogenesis in entomopathogenic, mycoparasitic, and nematophagous fungi used for biological control. In this study, we analysed the evolutionary histories of protease gene families, and investigated sequence divergence and regulation of serine protease genes in C. rosea. RESULTS: Proteases of selected hypocrealean fungal species were classified into families based on the MEROPS peptidase database. The highest number of protease genes (590) was found in Fusarium solani, followed by C. rosea with 576 genes. Analysis of gene family evolution identified non-random changes in gene copy numbers in the five serine protease gene families S1A, S8A, S9X, S12 and S33. Four families, S1A, S8A, S9X, and S33, displayed gene gains in C. rosea. A gene-tree / species-tree reconciliation analysis of the S8A family revealed that the gene copy number increase in C. rosea was primarily associated with the S08.054 (proteinase K) subgroup. In addition, regulatory and predicted structural differences, including twelve sites evolving under positive selection, among eighteen C. rosea S8A serine protease paralog genes were also observed. The C. rosea S8A serine protease gene prs6 was induced during interaction with the plant pathogenic species F. graminearum. CONCLUSIONS: Non-random increases in S8A, S9X and S33 serine protease gene numbers in the mycoparasitic species C. rosea, Trichoderma atroviride and T. virens suggests an involvement in fungal-fungal interactions. Regulatory and predicted structural differences between C. rosea S8A paralogs indicate that functional diversification is driving the observed increase in gene copy numbers. The induction of prs6 expression in C. rosea during confrontation with F. graminearum suggests an involvement of the corresponding protease in fungal-fungal interactions. The results pinpoint the importance of serine proteases for ecological niche adaptation in C. rosea, including a potential role in the mycoparasitic attack on fungal prey.

Evaluation of Clonostachys rosea for Control of Plant-Parasitic Nematodes in Soil and in Roots of Carrot and Wheat.

Biological control is a promising approach to reduce plant diseases caused by nematodes. We tested the effect of the fungus Clonostachys rosea strain IK726 inoculation on nematode community composition in a naturally nematode infested soil in a pot experiment, and the effect of C. rosea on plant health. The numbers of plant-parasitic nematode genera extracted from soil and plant roots decreased by 40 to 73% when C. rosea was applied, while genera of nonparasitic nematodes were not affected. Soil inoculation of C. rosea increased fresh shoot weight and shoot length of wheat plants by 20 and 24%, respectively, while only shoot dry weight increased by 48% in carrots. Light microscopy of in vitro C. rosea-nematode interactions did not reveal evidence of direct parasitism. However, culture filtrates of C. rosea growing in potato dextrose broth, malt extract broth and synthetic nutrient broth exhibited toxicity toward nematodes and immobilized 57, 62, and 100% of the nematodes, respectively, within 48 h. This study demonstrates that C. rosea can control plant-parasitic nematodes and thereby improve plant growth. The most likely mechanism responsible for the antagonism is antibiosis through production of nematicidal compounds, rather than direct parasitism.

A test of the hierarchical model of litter decomposition.

Our basic understanding of plant litter decomposition informs the assumptions underlying widely applied soil biogeochemical models, including those embedded in Earth system models. Confidence in projected carbon cycle-climate feedbacks therefore depends on accurate knowledge about the controls regulating the rate at which plant biomass is decomposed into products such as CO2. Here we test underlying assumptions of the dominant conceptual model of litter decomposition. The model posits that a primary control on the rate of decomposition at regional to global scales is climate (temperature and moisture), with the controlling effects of decomposers negligible at such broad spatial scales. Using a regional-scale litter decomposition experiment at six sites spanning from northern Sweden to southern France-and capturing both within and among site variation in putative controls-we find that contrary to predictions from the hierarchical model, decomposer (microbial) biomass strongly regulates decomposition at regional scales. Furthermore, the size of the microbial biomass dictates the absolute change in decomposition rates with changing climate variables. Our findings suggest the need for revision of the hierarchical model, with decomposers acting as both local- and broad-scale controls on litter decomposition rates, necessitating their explicit consideration in global biogeochemical models.

Above- and belowground insect herbivory modifies the response of a grassland plant community to nitrogen eutrophication.

Understanding the role that species interactions play in determining the rate and direction of ecosystem change due to nitrogen (N) eutrophication is important for predicting the consequences of global change. Insects might play a major role in this context. They consume substantial amounts of plant biomass and can alter competitive interactions among plants, indirectly shaping plant community composition. Nitrogen eutrophication affects plant communities globally, but there is limited experimental evidence of how insect herbivory modifies plant community response to raised N levels. Even less is known about the roles of above- and belowground herbivory in shaping plant communities, and how the interaction between the two might modify a plant community's response to N eutrophication. We conducted a 3-yr field experiment where grassland plant communities were subjected to above- and belowground insect herbivory with and without N addition, in a full-factorial design. We found that herbivory modified plant community responses to N addition. Aboveground herbivory decreased aboveground plant community biomass by 21%, but only at elevated N. When combined, above- and belowground herbivory had a stronger negative effect on plant community biomass at ambient N (11% decrease) than at elevated N (4% decrease). In addition, herbivory shifted the functional composition of the plant community, and the magnitude of the shifts depended on the N level. The N and herbivory treatments synergistically conferred a competitive advantage to forbs, which benefited when both herbivory types were present at elevated N. Evenness among the plant species groups increased when aboveground herbivory was present, but N addition attenuated this increase. Our results demonstrate that a deeper understanding of how plant-herbivore interactions above and below ground shape the composition of a plant community is crucial for making reliable predictions about the ecological consequences of global change.

Aboveground insect herbivory increases plant competitive asymmetry, while belowground herbivory mitigates the effect.

Insect herbivores can shift the composition of a plant community, but the mechanism underlying such shifts remains largely unexplored. A possibility is that insects alter the competitive symmetry between plant species. The effect of herbivory on competition likely depends on whether the plants are subjected to aboveground or belowground herbivory or both, and also depends on soil nitrogen levels. It is unclear how these biotic and abiotic factors interactively affect competition. In a greenhouse experiment, we measured competition between two coexisting grass species that respond differently to nitrogen deposition: Dactylis glomerata L., which is competitively favoured by nitrogen addition, and Festuca rubra L., which is competitively favoured on nitrogen-poor soils. We predicted: (1) that aboveground herbivory would reduce competitive asymmetry at high soil nitrogen by reducing the competitive advantage of D. glomerata; and (2), that belowground herbivory would relax competition at low soil nitrogen, by reducing the competitive advantage of F. rubra. Aboveground herbivory caused a 46% decrease in the competitive ability of F. rubra, and a 23% increase in that of D. glomerata, thus increasing competitive asymmetry, independently of soil nitrogen level. Belowground herbivory did not affect competitive symmetry, but the combined influence of above- and belowground herbivory was weaker than predicted from their individual effects. Belowground herbivory thus mitigated the increased competitive asymmetry caused by aboveground herbivory. D. glomerata remained competitively dominant after the cessation of aboveground herbivory, showing that the influence of herbivory continued beyond the feeding period. We showed that insect herbivory can strongly influence plant competitive interactions. In our experimental plant community, aboveground insect herbivory increased the risk of competitive exclusion of F. rubra. Belowground herbivory appeared to mitigate the influence of aboveground herbivory, and this mechanism may play a role for plant species coexistence.

Long-term effects of plant diversity and composition on soil nematode communities in model grasslands.

An important component of plant-soil feedbacks is how plant species identity anddiversity influence soil organism communities. We examine the effects of grassland plant species growing alone and together up to a richness of 12 species on nematode diversity and feeding group composition, eight years after the establishment of experimental grassland plots at the BIODEPTH site in northern Sweden. This is a substantially longer time than most other experimental studies of plant effects on soil fauna. We address the hypotheses that (la) higher species or functional diversity of plants increases nematode diversity, as well as influences nematode community composition. Alternatively, (1b) individual plant species traits are most important for nematode diversity and community composition. (2) Plant effects on soil organisms will decrease with increasing number of trophic links between plants and soil fauna. Plant species identity was often more important than plant diversity for nematode community composition, supporting hypothesis 1b. There was a weak positive relation between plant and nematode richness;which could be attributed to the presence of the legume Trifolium pratense, but also to some other plant species, suggesting a selection or sampling effect. Several plant species in different functional groups affected nematode community composition. For example, we found that legumes increased bacterial-feeding nematodes, most notably r-selected Rhabditida, while fungal-feeding nematodes were enhanced by forbs. Other bacterial feeders and obligate root feeders were positively related to grasses. Plant effects were usually stronger on plant-, bacterial- and fungal-feeding nematodes than on omnivores/predators, which supports hypothesis 2. Our study suggests that plant identity has stronger effects than plant diversity on nematode community composition, but when comparing our results with similar previous studies the effects of particular plant species appear to vary. We also found that more productive plant species affected bacterial-feeding nematodes more than fungal feeders. Moreover, we observed stronger effects the fewer the number of trophic links there were between a nematode feeding group and plants. Although we found clear effects of plants on soil nematodes, these were probably not large enough to result in strong and persistent plant-soil-organism-plant feedback loops.