Interactions between plants and soil microbes can strongly influence plant diversity and community dynamics. Soil microbes may promote plant diversity by driving negative frequency‐dependent plant population dynamics, or may favor species exclusion by providing one species an average fitness advantage over others. However, past empirical research has focused overwhelmingly on the consequences of frequency‐dependent feedbacks for plant species coexistence and has generally neglected the consequences of microbially mediated average fitness differences. Here we use theory to develop metrics that quantify microbially mediated plant fitness differences, and show that accounting for these effects can profoundly change our understanding of how microbes influence plant diversity. We show that soil microbes can generate fitness differences that favour plant species exclusion when they disproportionately harm (or favour) one plant species over another, but these fitness differences may also favor coexistence if they trade off with competition for other resources or generate intransitive dominance hierarchies among plants. We also show how the metrics we present can quantify microbially mediated fitness differences in empirical studies, and explore how microbial control over coexistence varies along productivity gradients. In all, our analysis provides a more complete theoretical foundation for understanding how plant–microbe interactions influence plant diversity.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results.

are co-equal second authors.Robert Wayne and Rachel S. Meyer are co-equal senior authors. Abstract 1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable and non-invasive. The longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing and accurate taxonomic assignment. Improvements in bioinformatics tools make addressing each of these demands within a single toolkit a reality.2. The new modular metabarcode sequence toolkit Anacapa (https ://github.com/ limey-bean/Anaca pa/) addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data. A novel aspect of Anacapa is its database building module, "Creating Reference libraries Using eXisting tools" (CRUX), which generates comprehensive reference databases for specific user-defined metabarcoding loci. The Quality Control and ASV Parsing module sorts and processes multiple metabarcoding loci and processes merged, unmerged and unpaired reads maximizing recovered diversity. DADA2 then detects amplicon sequence variants (ASVs) and the Anacapa Classifier module aligns these ASVs to CRUX-generated reference databases using Bowtie2. Lastly, taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. The Anacapa Toolkit also includes an r package, ranacapa, for automated results exploration through standard biodiversity statistical analysis.3. Benchmarking tests verify that the Anacapa Toolkit effectively and efficiently generates comprehensive reference databases that capture taxonomic diversity, and can assign taxonomy to both MiSeq and HiSeq-length sequence data. We demonstrate the value of the Anacapa Toolkit in assigning taxonomy to seawater eDNA samples collected in southern California.

1. Competition-defence trade-offs have long been thought to promote plant coexistence and increase species diversity. However, insights from modern coexistence theory clarify that such trade-offs alone cannot sustain coexistence.Coexistence also requires stabilising niche differences and the ability of competitor populations to persist under consumer pressure. Despite the breadth of potential consequences of competition-defence trade-offs, we have little mechanistic understanding of how they affect diversity in natural communities.2. We investigated the effects of seed harvesting by ants on coexistence in an annual plant community. We parameterised a model of plant competitive population dynamics with data from two field experiments: (a) plant demographic rates and competition coefficients determined by growing plants alone and against intraand interspecific competitor density gradients; (b) plant fitness losses to ant consumers determined by measuring seed removal from experimental depots. We tested for a trade-off between a plant species' demographic potential and its susceptibility to consumption and then determined the bounds of ant effects on pairwise and multispecies coexistence by comparing model projections with and without seed consumption.3. Ants harvested seeds of all plant species, but they strongly preferred the competitively superior large seeded species, inducing a competition-defence trade-off.Unequal seed loss to ants changed competition-based fitness hierarchies, affecting both the number and identities of plant species pairs that were predicted to coexist compared to a scenario without ants. The trade-off most often prevented coexistence by severely disadvantaging the superior competitor or excluding species directly through overconsumption, and a simulated reduction in the overall consumption rate opened few additional opportunities for coexistence. Ant exacerbation of average fitness differences was particularly disruptive to multispecies coexistence, where niche differences were insufficient to stabilise the coexistence of plant triplets and quadruplets. 4. Synthesis. Our results show that the presence of a competition-defence trade-off in a community with stabilising niche differences does not always increase diversity. Instead, the full range of diversity outcomes-positive and negative changes | 1807 Journal of Ecology PETRY ET al. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Petry WK, Kandlikar GS, Kraft NJB, Godoy O, Levine JM. A competition-defence trade-off both promotes and weakens coexistence in an annual plant community.

Significance Understanding the processes that maintain plant diversity is a key goal in ecology. Many previous studies have shown that soil microbes can generate stabilizing or destabilizing feedback loops that drive either plant species coexistence or monodominance. However, theory shows that microbial controls over plant coexistence also arise through microbially mediated competitive imbalances, which have been largely neglected. Using data from 50 studies, we found that soil microbes affect plant dynamics primarily by generating competitive fitness differences rather than stabilizing or destabilizing feedbacks. Consequently, in the absence of other competitive asymmetries among plants, soil microbes are predicted to drive species exclusion more than coexistence. These results underscore the need for measuring competitive fitness differences when evaluating microbial controls over plant coexistence.

Turnover in species composition and the dominant functional strategies in plant communities across environmental gradients is a common pattern across biomes, and is often assumed to reflect shifts in trait optima. However, the extent to which community‐wide trait turnover patterns reflect changes in how plant traits affect the vital rates that ultimately determine fitness remain unclear. We tested whether shifts in the community‐weighted means of four key functional traits across an environmental gradient in a southern California grassland reflect variation in how these traits affect species' germination and fecundity across the landscape. We asked whether models that included trait–environment interactions help explain variation in two key vital rates (germination rates and fecundity), as well as an integrative measure of fitness incorporating both vital rates (the product of germination rate and fecundity). To do so, we planted seeds of 17 annual plant species at 16 sites in cleared patches with no competitors, and quantified the lifetime seed production of 1360 individuals. We also measured community composition and a variety of abiotic variables across the same sites. This allowed us to evaluate whether observed shifts in community‐weighted mean traits matched the direction of any trait–environment interactions detected in the plant performance experiment. We found that commonly measured plant functional traits do help explain variation in species responses to the environment—for example, high‐SLA species had a demographic advantage (higher germination rates and fecundity) in sites with high soil Ca:Mg levels, while low‐SLA species had an advantage in low Ca:Mg soils. We also found that shifts in community‐weighted mean traits often reflect the direction of these trait–environment interactions, though not all trait–environment relationships at the community level reflect changes in optimal trait values across these gradients. Synthesis. Our results show how shifts in trait–fitness relationships can give rise to turnover in plant phenotypes across environmental gradients, a fundamental pattern in ecology. We highlight the value of plant functional traits in predicting species responses to environmental variation, and emphasise the need for more widespread study of trait–performance relationships to improve predictions of community responses to global change.

. 2018. How do we ensure the future of our discipline is vibrant? Student reflections on careers and culture of ecology. Ecosphere 9(2):e02099. 10.1002/ecs2.2099Abstract. Ecology must attract and retain diverse talented people to produce innovative research and relevant solutions to 21st-century environmental problems. Careers and culture form the foundation of scientific advancement, and substantial progress has been made over recent decades in both realms. Yet, important challenges persist in expanding career paths, inclusion of underrepresented groups, and communication with the public. The ESA Student Section organized a horizon scanning exercise to address the following goals: (1) to identify challenges that 21st-century ecologists contend with or expect to contend with in careers and outreach to society, (2) to anticipate opportunities to help ecologists meet challenges, and (3) to identify concrete steps that could be taken by individual laboratories, institutions, and the ESA to foster progress. In spring 2016, the ESA Student Section solicited input from student members and organized a working group to assess the state of the discipline and to envision how we might cultivate a more inclusive and effective community. We identified three major challenges. First, PhDs are produced faster than academic positions become available and disconnects between academia and other sectors may keep early-career ecologists from realizing the breadth of available positions. We propose an online jobs hub to make non-academic sectors more accessible to ecologists. We also suggest students develop skills portfolios to prepare for non-academic positions. Second, the composition of people who are ecologists differs from broader society, partially due to implicit biases and institutional barriers. We propose steps to reduce attrition of diversity in ecology that include countering implicit biases and creating mentorship networks. We offer steps to improve recruitment by increasing awareness of ecology among high school students and undergraduates and providing opportunities to engage in ecological research. Finally, ecology is only relevant if the public perceives it to be. We must improve science communication and begin cultivating trust. We propose that ad hoc communication by all ecologists is insufficient; ❖ www.esajournals.org 1 February 2018 ❖ Volume 9(2) ❖ Article e02099 translational ecologists should be hired in every department and formal training in translational ecology is necessary. We hope this paper catalyzes critical thinking and partnerships among students, professional ecologists, and the ESA to ensure the future of ecology is vibrant.

22Global change is leading to habitat shifts that threaten species persistence throughout 23 California's unique ecosystems. Baseline biodiversity data provide opportunities for 24 ecosystems to be managed for community complexity and connectivity. In 2017, the 25