Restoration ecology through the lens of coexistence theory.

Advances in restoration ecology are needed to guide ecological restoration in a variable and changing world. Coexistence theory provides a framework for how variability in environmental conditions and species interactions affects species success. Here, we conceptually link coexistence theory and restoration ecology. First, including low-density growth rates (LDGRs), a classic metric of coexistence, can improve abundance-based restoration goals, because abundances are sensitive to initial treatments and ongoing variability. Second, growth-rate partitioning, developed to identify coexistence mechanisms, can improve restoration practice by informing site selection and indicating necessary interventions (e.g., site amelioration or competitor removal). Finally, coexistence methods can improve restoration assessment, because initial growth rates indicate trajectories, average growth rates measure success, and growth partitioning highlights interventions needed in future.

Soil surface treatments and precipitation timing determine seedling development across southwestern US restoration sites.

Restoration in dryland ecosystems often has poor success due to low and variable water availability, degraded soil conditions, and slow plant community recovery rates. Restoration treatments can mitigate these constraints but, because treatments and subsequent monitoring are typically limited in space and time, our understanding of their applicability across broader environmental gradients remains limited. To address this limitation, we implemented and monitored a standardized set of seeding and soil surface treatments (pits, mulch, and ConMod artificial nurse plants) designed to enhance soil moisture and seedling establishment across RestoreNet, a growing network of 21 diverse dryland restoration sites in the southwestern USA over 3 years. Generally, we found that the timing of precipitation relative to seeding and the use of soil surface treatments were more important in determining seeded species emergence, survival, and growth than site-specific characteristics. Using soil surface treatments in tandem with seeding promoted up to 3× greater seedling emergence densities compared with seeding alone. The positive effect of soil surface treatments became more prominent with increased cumulative precipitation since seeding. The seed mix type with species currently found within or near a site and adapted to the historical climate promoted greater seedling emergence densities compared with the seed mix type with species from warmer, drier conditions expected to perform well under climate change. Seed mix and soil surface treatments had a diminishing effect as plants developed beyond the first season of establishment. However, we found strong effects of the initial period seeded and of the precipitation leading up to each monitoring date on seedling survival over time, especially for annual and perennial forbs. The presence of exotic species exerted a negative influence on seedling survival and growth, but not initial emergence. Our findings suggest that seeded species recruitment across drylands can generally be promoted, regardless of location, by (1) incorporation of soil surface treatments, (2) employment of near-term seasonal climate forecasts, (3) suppression of exotic species, and (4) seeding at multiple times. Taken together, these results point to a multifaceted approach to ameliorate harsh environmental conditions for improved seeding success in drylands, both now and under expected aridification.

Rapid bacterial and fungal successional dynamics in first year after chaparral wildfire.

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of 16S and ITS2 amplicons. Fire severely reduced bacterial biomass by 47%, bacterial richness by 46%, fungal biomass by 86%, and fungal richness by 68%. The burned bacterial and fungal communities experienced rapid succession, with 5-6 compositional turnover periods. Analogous to plants, turnover was driven by "fire-loving" pyrophilous microbes, many of which have been previously found in forests worldwide and changed markedly in abundance over time. Fungal secondary succession was initiated by the Basidiomycete yeast Geminibasidium, which traded off against the filamentous Ascomycetes Pyronema, Aspergillus, and Penicillium. For bacteria, the Proteobacteria Massilia dominated all year, but the Firmicute Bacillus and Proteobacteria Noviherbaspirillum increased in abundance over time. Our high-resolution temporal sampling allowed us to capture post-fire microbial secondary successional dynamics and suggest that putative tradeoffs in thermotolerance, colonization, and competition among dominant pyrophilous microbes control microbial succession with possible implications for ecosystem function.

Application of modern coexistence theory to rare plant restoration provides early indication of restoration trajectories.

Restoration ecology commonly seeks to re-establish species of interest in degraded habitats. Despite a rich understanding of how succession influences re-establishment, there are several outstanding questions that remain unaddressed: are short-term abundances sufficient to determine long-term re-establishment success, and what factors contribute to unpredictable restorations outcomes? In other words, when restoration fails, is it because the restored habitat is substandard, because of strong competition with invasive species, or alternatively due to changing environmental conditions that would equally impact established populations? Here, we re-purpose tools developed from modern coexistence theory to address these questions, and apply them to an effort to restore the endangered Contra Costa goldfields (Lasthenia conjugens) in constructed ("restored") California vernal pools. Using 16 years of data, we construct a population model of L. conjugens, a species of conservation concern due primarily to habitat loss and invasion of exotic grasses. We show that initial, short-term appearances of restoration success from population abundances is misleading, as year-to-year fluctuations cause long-term population growth rates to fall below zero. The failure of constructed pools is driven by lower maximum growth rates compared with reference ("natural") pools, coupled with a stronger negative sensitivity to annual fluctuations in abiotic conditions that yield decreased maximum growth rates. Nonetheless, our modeling shows that fluctuations in competition (mainly with exotic grasses) benefit L. conjugens through periods of competitive release, especially in constructed pools of intermediate pool depth. We therefore show how reductions in invasives and seed addition in pools of particular depths could change the outcome of restoration for L. conjugens. By applying a largely theoretical framework to the urgent goal of ecological restoration, our study provides a blueprint for predicting restoration success, and identifies future actions to reverse species loss.

Disentangling key species interactions in diverse and heterogeneous communities: A Bayesian sparse modelling approach.

Modelling species interactions in diverse communities traditionally requires a prohibitively large number of species-interaction coefficients, especially when considering environmental dependence of parameters. We implemented Bayesian variable selection via sparsity-inducing priors on non-linear species abundance models to determine which species interactions should be retained and which can be represented as an average heterospecific interaction term, reducing the number of model parameters. We evaluated model performance using simulated communities, computing out-of-sample predictive accuracy and parameter recovery across different input sample sizes. We applied our method to a diverse empirical community, allowing us to disentangle the direct role of environmental gradients on species' intrinsic growth rates from indirect effects via competitive interactions. We also identified a few neighbouring species from the diverse community that had non-generic interactions with our focal species. This sparse modelling approach facilitates exploration of species interactions in diverse communities while maintaining a manageable number of parameters.

Competition and soil resource environment alter plant-soil feedbacks for native and exotic grasses.

Feedbacks between plants and soil biota are increasingly identified as key determinants of species abundance patterns within plant communities. However, our understanding of how plant-soil feedbacks (PSFs) may contribute to invasions is limited by our understanding of how feedbacks may shift in the light of other ecological processes. Here we assess how the strength of PSFs may shift as soil microbial communities change along a gradient of soil nitrogen (N) availability and how these dynamics may be further altered by the presence of a competitor. We conducted a greenhouse experiment where we grew native Stipa pulchra and exotic Avena fatua, alone and in competition, in soils inoculated with conspecific and heterospecific soil microbial communities conditioned in low, ambient and high N environments. Stipa pulchra decreased in heterospecific soil and in the presence of a competitor, while the performance of the exotic A. fatua shifted with soil microbial communities from altered N environments. Moreover, competition and soil microbial communities from the high N environment eliminated the positive PSFs of Stipa. Our results highlight the importance of examining how individual PSFs may interact in a broader community context and contribute to the establishment, spread and dominance of invaders.

Seed supply, recruitment, and assembly: quantifying relative seed and establishment limitation in a plant community context.

There is a growing consensus that the relative constraints of seed limitation and establishment limitation in recruitment strongly influence abundance patterns in plant communities. Although these constraints have direct relevance to coexistence, most investigations utilize a seed addition approach that offers limited insight into these dynamics. Here we report the results of an assembly experiment with annual plant species from California grasslands to examine how propagule pool characteristics (dominant species abundance, functional diversity) influence establishment and seed limitation (density independence and density dependence across a gradient of seed supply) for each species, as well as how these constraints affect community diversity. Species were predominantly colimited by seed and establishment constraints, exhibiting saturating recruitment functions with increased seed supply. Consistent with competition-colonization trade-off predictions, recruitment constraints often depended on the degree of seed limitation of the competitive dominant, Brassica nigra; diversity was greatest in communities where Brassica was seed limited. Functional similarity within the propagule pool did not affect recruitment across a range of seed supply; likewise, functional diversity of the propagule pool was not related to community diversity. We conclude that seed limitation of the dominant species rather than niche similarity influences interspecific competition for safe sites and scales up to affect community-level diversity.