General Information

This is a master course on the causes and consequences of plant biodiversity. The course covers all aspects of biodiversity, including genetic, species, phylogenetic and functional diversity. Short lectures will give introductions to the different topics. For the major part, students will have to read, present and discuss the literature, which includes book chapters, classical papers as well as examples from the recent literature. These papers cover conceptual or theoretical approaches to the study of biodiversity, reviews of existing knowledge, famous experiments, or novel and innovative methodologies. Referring to Sustainability we read and discuss at least two papers related to ecosystem services / global change per semester.

Time Table

Date Paper Presenter Key1 Key2 Approach Additional.reading
22-Feb (Averill et al., 2022) 1 microbiome conservation comment NA
01-Mar (Li et al., 2022) 2 climate change trophic interactions Review NA
08-Mar (Delory et al., 2021) 3 metabolome functional traits Experimental NA
15-Mar (Schmid et al., 2022) 4 BEF Experiment NA
22-Mar (Hülsmann et al., 2021) 5 coexistence upscaling JC effects Model NA
29-Mar (Hurlbert, 1984) 6 experimental design pseudoreplication Classic NA
05-Apr (Liu et al., 2022) 7 BEFdisease climate change N addition Experiment NA
12-Apr holidays NA NA
19-Apr (Lundell et al., 2022) 8 precipitation PSF & BEF Experiment NA
26-Apr (in ’t Zandt et al., 2021) 9 plant abundance PSF Experiment NA
03-May (Armstrong et al., 2022) 10 reintroduction fragmentation Observational NA
10-May (Jandt et al., 2022) 11 climate change plant diversity Experiment NA
17-May (Naidu et al., 2022) 12 soil C herbivores Experiment NA
24-May (Steidinger et al., 2022) 13 climate change niche Observational NA
31-May (Mahecha et al., 2022) 14 climate change forest diversity Comment NA

Student information

Aims

In the journal club in plant diversity we read and discuss papers on a range of topics in ecology. The course is attended by PhDs and postdocs in the groups of Eric Allan and Markus Fischer, together with students following the course. The aim of the course is to introduce students to the scientific literature, so that they learn how to read and critique a paper. The course aims to teach critical thinking and engagement with the papers. Remember all papers have their flaws and (usually) their strengths. As a scientist it is essential that you are able to review papers and to decide whether they make an important contribution to the field and to see what problems they might have.

Structure

Each week one participant in the journal club presents the paper: to do this they need to explain a bit of background about the papers and describe the methods and results, so that everyone can understand what has been done. Following this everyone discusses the pros and cons of the paper, i.e. whether we think the methods are appropriate, whether the conclusions are supported by the data, whether the writing and figures are clear, how the paper relates to others in the field, what the next major steps might be, what we think of the broader issues raised by the paper.

Participation

As students taking the course you have to attend all of the journal clubs (exceptions are made for illness or military service) and participate in the discussion. To help you participate you should think of one thing you liked and one thing you did not like about the paper under discussion. We will hear these immediately after the presentation. You are also strongly encouraged to participate in the discussion throughout, which can involve asking questions about things you did not understand in the paper and, of course, giving your own opinion on the topics under discussion.

Presentation

In addition, you will have to present one of the papers. Take a look at the list of papers and select one that interests you. Send your choice to Gemma within one week (i.e. before the second journal club). For the presentation you should spend 10-15 minutes introducing the paper and explaining the methods that it used. If there is something that you didn’t understand in the paper you can also ask for help in explaining this part. The presentations are without power point but there is a white board that can be used to draw diagrams if you like.

Review

To be submitted no later than 3wks after the last meeting

Finally, you should write a short review of the paper. This should be in the style of a review for a journal. It should be 800-1000 words long and should have a brief introduction where you shortly explain what was done in the paper and what were the main results. You should then mention what the good points of the paper were: i.e. were the results novel, did it use an interesting new approach? Were the results surprising? Was it very clearly written? Does it use a large dataset? Then mention what was (were) the main problem(s): are there major flaws in the methods? Do the conclusions go beyond the data? Is the writing poor? You can then mention more minor concerns that you have with the paper. Remember to be constructive in your review: don’t just point out flaws but try to explain how the authors could deal with the problems. To write your review you should listen to the discussion in the journal club and of course think about the issues yourself.

Mark

The final mark is an average of the mark for the presentation, your participation during the course and the review. Each part counts the same.

References & Abstracts

Armstrong, D. P., Boulton, R. L., McArthur, N., Govella, S., Gorman, N., Pike, R., & Richard, Y. (2022). Using experimental reintroductions to resolve the roles of habitat quality and metapopulation dynamics on patch occupancy in fragmented landscapes. Conservation Biology, 36(3), 1–9. https://doi.org/10.1111/cobi.13843
Declines of species in fragmented landscapes can potentially be reversed either by restoring connectivity or restoring local habitat quality. Models fitted to snapshot occupancy data can be used to predict the effectiveness of these actions. However, such inferences can be misleading if the reliability of the habitat and landscape metrics used is unknown. The only way to unambiguously resolve the roles of habitat quality and metapopulation dynamics is to conduct experimental reintroductions to unoccupied patches so that habitat quality can be measured directly from data on vital rates. We, therefore, conducted a 15-year study that involved reintroducing a threatened New Zealand bird to unoccupied forest fragments to obtain reliable data on their habitat quality and reassess initial inferences made by modeling occupancy against habitat and landscape metrics. Although reproductive rates were similar among fragments, subtle differences in adult survival rates resulted in \(\lambda\) (finite rate of increase) estimations of <0.9 for 9 of the 12 fragments that were previously unoccupied. This was the case for only 1 of 14 naturally occupied fragments. This variation in \(\lambda\) largely explained the original occupancy pattern, reversing our original conclusion from occupancy modeling that this occupancy pattern was isolation driven and suggesting that it would be detrimental to increase connectivity without improving local habitat quality. These results illustrate that inferences from snapshot occupancy should be treated with caution and subjected to testing through experimental reintroductions in selected model systems.
Averill, C., Anthony, M. A., Baldrian, P., Finkbeiner, F., Hoogen, J. van den, Kiers, T., Kohout, P., Hirt, E., Smith, G. R., & Crowther, T. W. (2022). Defending Earth’s terrestrial microbiome. Nature Microbiology, 7(11), 1717–1725. https://doi.org/10.1038/s41564-022-01228-3
Microbial life represents the majority of Earth’s biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth’s microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet’s breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth’s microbiome.
Delory, B. M., Schempp, H., Spachmann, S. M., Störzer, L., Dam, N. M. van, Temperton, V. M., & Weinhold, A. (2021). Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants. Plant Cell and Environment, 44(4), 1215–1230. https://doi.org/10.1111/pce.13999
Soil legacies play an important role for the creation of priority effects. However, we still poorly understand to what extent the metabolome found in the soil solution of a plant community is conditioned by its species composition and whether soil chemical legacies affect subsequent species during assembly. To test these hypotheses, we collected soil solutions from forb or grass communities and evaluated how the metabolome of these soil solutions affected the growth, biomass allocation and functional traits of a forb (Dianthus deltoides) and a grass species (Festuca rubra). Results showed that the metabolomes found in the soil solutions of forb and grass communities differed in composition and chemical diversity. While soil chemical legacies did not have any effect on F. rubra, root foraging by D. deltoides decreased when plants received the soil solution from a grass or a forb community. Structural equation modelling showed that reduced soil exploration by D. deltoides arose via either a root growth-dependent pathway (forb metabolome) or a root trait-dependent pathway (grass metabolome). Reduced root foraging was not connected to a decrease in total N uptake. Our findings reveal that soil chemical legacies can create belowground priority effects by affecting root foraging in later arriving plants.
Hülsmann, L., Chisholm, R. A., & Hartig, F. (2021). Is Variation in Conspecific Negative Density Dependence Driving Tree Diversity Patterns at Large Scales? Trends in Ecology and Evolution, 36(2), 151–163. https://doi.org/10.1016/j.tree.2020.10.003
Half a century ago, Janzen and Connell hypothesized that the high tree species diversity in tropical forests is maintained by specialized natural enemies. Along with other mechanisms, these can cause conspecific negative density dependence (CNDD) and thus maintain species diversity. Numerous studies have measured proxies of CNDD worldwide, but doubt about its relative importance remains. We find ample evidence for CNDD in local populations, but methodological limitations make it difficult to assess if CNDD scales up to control community diversity and thereby local and global biodiversity patterns. A combination of more robust statistical methods, new study designs, and eco-evolutionary models are needed to provide a more definite evaluation of the importance of CNDD for geographic variation in plant species diversity.
Hurlbert, S. H. (1984). Pseudoreplication and the design of ecological field experiments. Ecological Monographs, 54(2), 187–211.
Pseudoreplication is defined as the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates are not statistically independent. In ANOVA terminology, it is the testing for treatment effects with an error term inappropriate to the hypothesis being considered. Scrutiny of 176 experi- mental studies published between 1960 and the present revealed that pseudoreplication occurred in 27% of them, or 48% of all such studies that applied inferential statistics. The incidence of pseudo- replication is especially high in studies of marine benthos and small mammals. The critical features of controlled experimentation are reviewed. Nondemonic intrusion is defined as the impingement of chance events on an experiment in progress. As a safeguard against both it and preexisting gradients, interspersion of treatments is argued to be an obligatory feature of good design. Especially in small experiments, adequate interspersion can sometimes be assured only by dispensing with strict random- ization procedures. Comprehension of this conflict between interspersion and randomization is aided by distinguishing pre-layout (or conventional) and layout-specific alpha (probability of type I error). Suggestions are offered to statisticians and editors of ecological journals as to how ecologists’ under- standing of experimental design and statistics might be improved.
in ’t Zandt, D., Herben, T., Brink, A. van den, Visser, E. J. W., & Kroon, H. de. (2021). Species abundance fluctuations over 31 years are associated with plant–soil feedback in a species-rich mountain meadow. Journal of Ecology, 109(3), 1511–1523. https://doi.org/10.1111/1365-2745.13574
Increasing evidence suggest that plant–soil interactions play an essential role in plant community assembly processes. Empirical investigations show that plant species abundance in the field is often related to plant–soil biota interactions; however, the direction of these relations have yielded inconsistent results. We combined unique 31-year long field data on species abundances from a species-rich mountain meadow with single time point plant–soil feedback greenhouse experiments of 24 co-occurring plant species. We tested whether these relations were dynamic in time, whether coupled increases and decreases in abundance between years were related to plant–soil feedback and whether these changes were underlain by years in which manuring was applied. The prevailingly negative relationship between plant–soil feedback and plant relative abundance in the field was significantly time-dependent, which may reconcile the contrasting results in literature. Furthermore, significantly coupled oscillations appeared between species relative abundance changes and plant–soil feedback, which were likely moderated by years in which manuring was applied. Our results are consistent with the notion that the more abundant species are stabilised by negative plant–soil feedback, and the less abundant species co-vary with the fluctuations of these more competitive species. Synthesis. Our results project plant–soil feedback as an important regulatory mechanism in plant communities, operating in conjunction with species’ competitive ability and soil nutrient availability. We suggest that negative feedback is particularly prominent in more abundant plant species that profit from more readily available soil nutrients than less abundant species with positive feedback. Negative plant–soil feedback may thus prevent more abundant plant species from out-competing less abundant plant species, facilitating stable species co-existence.
Jandt, U., Bruelheide, H., Jansen, F., Bonn, A., Grescho, V., Klenke, R. A., Sabatini, F. M., Bernhardt-Römermann, M., Blüml, V., Dengler, J., Diekmann, M., Doerfler, I., Döring, U., Dullinger, S., Haider, S., Heinken, T., Horchler, P., Kuhn, G., Lindner, M., … Wulf, M. (2022). More losses than gains during one century of plant biodiversity change in Germany. Nature, 611(November). https://doi.org/10.1038/s41586-022-05320-w
Long-term analyses of biodiversity data highlight a ‘biodiversity conservation paradox’: biological communities show substantial species turnover over the past century1,2, but changes in species richness are marginal1,3–5. Most studies, however, have focused only on the incidence of species, and have not considered changes in local abundance. Here we asked whether analysing changes in the cover of plant species could reveal previously unrecognized patterns of biodiversity change and provide insights into the underlying mechanisms. We compiled and analysed a dataset of 7,738 permanent and semi-permanent vegetation plots from Germany that were surveyed between 2 and 54 times from 1927 to 2020, in total comprising 1,794 species of vascular plants. We found that decrements in cover, averaged across all species and plots, occurred more often than increments; that the number of species that decreased in cover was higher than the number of species that increased; and that decrements were more equally distributed among losers than were gains among winners. Null model simulations confirmed that these trends do not emerge by chance, but are the consequence of species-specific negative effects of environmental changes. In the long run, these trends might result in substantial losses of species at both local and regional scales. Summarizing the changes by decade shows that the inequality in the mean change in species cover of losers and winners diverged as early as the 1960s. We conclude that changes in species cover in communities represent an important but understudied dimension of biodiversity change that should more routinely be considered in time-series analyses.
Li, K., Veen, G. F., Hooven, F. C. ten, Harvey, J. A., & Putten, W. H. van der. (2022). Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities. Ecology Letters, July, 1–16. https://doi.org/10.1111/ele.14129
Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant–insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought and their interactions on plants, aphids and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by the previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that legacies can be contained as soil ‘memories’ that influence aboveground plant community interactions in the next growing season. These soil-borne ‘memories’ can be altered by climate warming-induced plant range shifts and extreme drought.
Liu, X., Xiao, Y., Lin, Z., Wang, X., Hu, K., Liu, M., Zhao, Y., Qi, Y., & Zhou, S. (2022). Spatial scale-dependent dilution effects of biodiversity on plant diseases in grasslands (pp. 0–3). https://doi.org/10.1002/ecy.3944
The rapid biodiversity losses of the Anthropocene have motivated ecologists to understand how biodiversity affects infectious diseases. Spatial scale is thought to moderate negative biodiversity–disease relationships (i.e., dilution effects) in zoonotic diseases, whereas evidence from plant communities for an effect of scale remains limited, especially at local scales where the mechanisms (e.g., encounter reduction) underlying dilution effects actually work. Here, we tested how spatial scale affects the direction and magnitude of biodiversity–disease relationships. We utilized a 10-year-old nitrogen addition experiment in a Tibetan alpine meadow, with 0, 5, 10, and 15 g/m2 nitrogen addition treatments. Within the treatment plots, we arranged a total of 216 quadrats (of either 0.125 × 0.125 m, 0.25 × 0.25 m or 0.5 × 0.5 m size) to test how the sample area affects the relationship between plant species richness and foliar fungal disease severity. We found that the dilution effects were stronger in the 0.125 × 0.125 m and 0.25 × 0.25 m quadrats, compared with 0.5 × 0.5 m quadrats. There was a significant interaction between species richness and nitrogen addition in the 0.125 × 0.125 m and 0.25 × 0.25 m quadrats, indicating that a dilution effect was more easily observed under higher levels of nitrogen addition. Based on multigroup structural equation models, we found that even accounting for the direct impact of nitrogen addition (i.e., “nitrogen-disease hypothesis”), the dilution effect still worked at the 0.125 × 0.125 m scale. Overall, these findings suggest that spatial scale directly determines the occurrence of dilution effects, and can partly explain the observed variation in biodiversity–disease relationships in grasslands. Next-generation frameworks for predicting infectious diseases under rapid biodiversity loss scenarios need to incorporate spatial information.
Lundell, S., Batbaatar, A., Carlyle, C. N., Lamb, E. G., Otfinowski, R., Schellenberg, M. P., & Bennett, J. A. (2022). Plant responses to soil biota depend on precipitation history, plant diversity, and productivity. Ecology, 103(10), 1–11. https://doi.org/10.1002/ecy.3784
Soil biota are critical drivers of plant growth, population dynamics, and community structure and thus have wide-ranging effects on ecosystem function. Interactions between plants and soil biota are complex, however, and can depend on the diversity and productivity of the plant community and environmental conditions. Plant–soil biota interactions may be especially important during stressful periods, such as drought, when plants can gain great benefits from beneficial biota but may be susceptible to antagonists. How soil biota respond to drought is also important and can influence plant growth following drought and leave legacies that affect future plant responses to soil biota and further drought. To explore how drought legacies and plant community context influence plant growth responses to soil biota and further drought, we collected soils from 12 grasslands varying in plant diversity and productivity where precipitation was experimentally reduced. We used these soils as inoculum in a growth chamber experiment testing how precipitation history (ambient or reduced) and soil biota (live or sterile soil inoculum) mediate plant growth and drought responses within an experimental plant community. We also tested whether these responses differed with the diversity and productivity of the community where the soil was collected. Plant growth responses to soil biota were positive when inoculated with soils from less diverse and productive plant communities and became negative as the diversity and productivity of the conditioning community increased. At low diversity, however, positive soil biota effects on plant growth were eliminated if precipitation had been reduced in the field, suggesting that diversity loss may heighten climate change sensitivity. Differences among species within the experimental community in their responses to soil biota and drought suggest that species benefitting from less drought sensitive soil biota may be able to compensate for some of this loss of productivity. Regardless of the plant species and soil origin, further drought eliminated any effects of soil biota on plant growth. Consequently, soil biota may be unable to buffer the effects of drought on primary productivity or other ecosystem functions as extreme events increase in frequency.
Mahecha, M. D., Bastos, A., Bohn, F. J., Eisenhauer, N., Hartmann, H., Hickler, T., Kalesse-los, H., Otto, F. E. L., Peng, J., Quaas, J., Tegen, I., Weigelt, A., Wendisch, M., & Wirth, C. (2022). Biodiversity loss and climate extremes — study the feedbacks. Nature, 612, 30–32.
Enough of silos: develop a joint scientific agenda to understand the intertwined global crises of the Earth system
Naidu, D. G. T., Roy, S., & Bagchi, S. (2022). Loss of grazing by large mammalian herbivores can destabilize the soil carbon pool. Proceedings of the National Academy of Sciences of the United States of America, 119(43), 1–7. https://doi.org/10.1073/pnas.2211317119
Grazing by mammalian herbivores can be a climate mitigation strategy as it influences the size and stability of a large soil carbon (soil-C) pool (more than 500 Pg C in the world’s grasslands, steppes, and savannas). With continuing declines in the numbers of large mammalian herbivores, the resultant loss in grazer functions can be consequential for this soil-C pool and ultimately for the global carbon cycle. While herbivore effects on the size of the soil-C pool and the conditions under which they lead to gain or loss in soil-C are becoming increasingly clear, their effect on the equally important aspect of stability of soil-C remains unknown. We used a replicated long-term field experiment in the Trans-Himalayan grazing ecosystem to evaluate the consequences of herbivore exclusion on interannual fluctuations in soil-C (2006 to 2021). Interannual fluctuations in soil-C and soil-N were 30 to 40% higher after herbivore exclusion than under grazing. Structural equation modeling suggested that grazing appears to mediate the stabilizing versus destabilizing influences of nitrogen (N) on soil-C. This may explain why N addition stimulates soil-C loss in the absence of herbivores around the world. Herbivore loss, and the consequent decline in grazer functions, can therefore undermine the stability of soil-C. Soil-C is not inert but a very dynamic pool. It can provide nature-based climate solutions by conserving and restoring a functional role of large mammalian herbivores that extends to the stoichiometric coupling between soil-C and soil-N.
Schmid, B., Schmitz, M., Rzanny, M., Scherer‐Lorenzen, M., Mwangi, P. N., Weisser, W. W., Hector, A., Schmid, R., & Flynn, D. F. B. (2022). Removing subordinate species in a biodiversity experiment to mimic observational field studies. Grassland Research, 1(1), 53–62. https://doi.org/10.1002/glr2.12009
Background: Positive effects of plant species richness on community biomass in biodiversity experiments are often stronger than those from observational field studies. This may be because experiments are initiated with randomly assembled species compositions whereas field communities have experienced filtering. Methods: We compared aboveground biomass production of randomly assembled communities of 2–16 species (controls) with experimentally filtered communities from which subordinate species were removed, resulting in removal communities of 1–8 species. Results: Removal communities had (1) 12.6% higher biomass than control communities from which they were derived, that is, with double species richness and (2) 32.0% higher biomass than control communities of equal richness. These differences were maintained along the richness gradient. The increased productivity of removal communities was paralleled by increased species evenness and complementarity. Conclusions: Result (1) indicates that subordinate species can reduce community biomass production, suggesting a possible explanation for why the most diverse field communities sometimes do not have the highest productivity. Result (2) suggests that if a community of S species has been derived by filtering from a pool of 2S randomly chosen species it is more productive than a community derived from a pool of S randomly chosen species without filtering
Steidinger, B. S., Büntgen, U., Stobbe, U., Tegel, W., Sproll, L., Haeni, M., Moser, B., Bagi, I., Bonet, J. A., Buée, M., Dauphin, B., Martínez-Peña, F., Molinier, V., Zweifel, R., Egli, S., & Peter, M. (2022). The fall of the summer truffle: Recurring hot, dry summers result in declining fruitbody production of Tuber aestivum in Central Europe. Global Change Biology, November 2021, 1–15. https://doi.org/10.1111/gcb.16424
Global warming is pushing populations outside their range of physiological tolerance. According to the environmental envelope framework, the most vulnerable populations occur near the climatic edge of their species’ distributions. In contrast, populations from the climatic center of the species range should be relatively buffered against climate warming. We tested this latter prediction using a combination of linear mixed effects and machine learning algorithms on an extensive, citizen-scientist generated dataset on the fruitbody productivity of the Burgundy (aka summer) truffle (Tuber aestivum Vittad.), a keystone, ectomycorrhizal tree-symbiont occurring on a wide range of temperate climates. T. aestivum’s fruitbody productivity was monitored at 3-week resolution over up to 8 continuous years at 20 sites distributed in the climatic center of its European distribution in southwest Germany and Switzerland. We found that T. aestivum fruitbody production is more sensitive to summer drought than would be expected from the breadth of its species’ climatic niche. The monitored populations occurring nearly 5°C colder than the edge of their species’ climatic distribution. However, interannual fruitbody productivity (truffle mass year−1) fell by a median loss of 22% for every 1°C increase in summer temperature over a site’s 30-year mean. Among the most productive monitored populations, the temperature sensitivity was even higher, with single summer temperature anomalies of 3°C sufficient to stop fruitbody production altogether. Interannual truffle productivity was also related to the phenology of host trees, with ~22 g less truffle mass for each 1-day reduction in the length of the tree growing season. Increasing summer drought extremes are therefore likely to reduce fruiting among summer truffle populations throughout Central Europe. Our results suggest that European T. aestivum may be a mosaic of vulnerable populations, sensitive to climate-driven declines at lower thresholds than implied by its species distribution model.