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The expansion of woody species from their historical ranges into grasslands is a global problem. Understanding the mechanisms that enable species to successfully establish and then re‐encroach following their removal is critical to effectively managing problem species. Legacy effects are a mechanism that could be critical to the reestablishment of woody encroachers following their removal. Legacy effects occur when a species alters the biotic and abiotic environment in a way that affects communities that establish subsequently. In this study, we assess whether the eastern redcedar (Juniperus virginiana), a North American woody encroacher, generates legacy effects that affect communities that establish following removal of this species from an experimental grass community. We conducted a series of experiments to evaluate the effects ofJ. virginiana, roots on the germination and growth of grasses and to determine if the effects of root‐addition treatments were derived from a microbial or allelopathic origin. Aqueous extracts ofJ. virginianaroots were found to inhibit the germination of grasses. We found escalating suppression of overall community biomass and the biomass of each individual species with increasing root treatments. Finally, we determined the origin of the observed suppressive effect is unlikely to be of microbial origin.Synthesis: Our results suggest thatJ. virginianaexudes an allelochemical into soils that inhibits the growth of certain grasses and thus has the potential to have legacy effects on future occupants. We suggest that the inhibition of the development of grasses in areas whereJ. virginianahas been removed is a mechanism that may favor the reestablishment ofJ. virginiana. Our results indicate the legacy effects ofJ. virginianamust be considered when conducting removal and restoration ofJ. virginianainfested lands.

 

Eastern redcedar Juniperus virginiana is encroaching into new habitats, which will affect native ecosystems as this species competes with other plants for available resources, including water. We designed a greenhouse experiment to investigate changes in soil moisture content and rooting depths of two-year-old J . virginiana saplings growing with or without competition. We had four competition treatments: 1) none, 2) with a native tree ( Quercus stellata ), 3) with an invasive grass ( Bromus inermis ), and 4) with both Q . stellata and B . inermis . We measured soil moisture content over two years as well as root length, total biomass, relative water content, midday water potential, and mortality at the end of the experiment. When J . virginiana and B . inermis grew together, water depletion occurred at both 30–40 cm and 10–20 cm. Combined with root length results, we can infer that J . virginiana most likely took up water from the deeper layers whereas B . inermis used water from the top layers. We found a similar pattern of water depletion and uptake when J . virginiana grew with Q . stellata , indicating that J . virginiana took up water from the deeper layers and Q . stellata used water mostly from the top soil layers. When the three species grew together, we found root overlap between J . virginiana and Q . stellata . Despite the root overlap, our relative water content and water potential indicate that J . virginiana was not water stressed in any of the plant combinations. Regardless, J . virginiana saplings had less total biomass in treatments with B . inermis and we recorded a significantly higher mortality when J . virginiana grew with both competitors. Root overlap and partitioning can affect how J . virginiana perform and adapt to new competitors and can allow their co-existence with grasses and other woody species, which can facilitate J . virginiana encroachment into grasslands and woodlands. Our data also show that competition with both Q . stellata and B . inermis could limit establishment, regardless of water availability. 

Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marinaL.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival ofZ. marinain the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

 

Ecological theory posits that temporal stability patterns in plant populations are associated with differences in species' ecological strategies. However, empirical evidence is lacking about which traits, or trade-offs, underlie species stability, especially across different biomes. We compiled a worldwide collection of long-term permanent vegetation records (greater than 7000 plots from 78 datasets) from a large range of habitats which we combined with existing trait databases. We tested whether the observed inter-annual variability in species abundance (coefficient of variation) was related to multiple individual traits. We found that populations with greater leaf dry matter content and seed mass were more stable over time. Despite the variability explained by these traits being low, their effect was consistent across different datasets. Other traits played a significant, albeit weaker, role in species stability, and the inclusion of multi-variate axes or phylogeny did not substantially modify nor improve predictions. These results provide empirical evidence and highlight the relevance of specific ecological trade-offs, i.e. in different resource-use and dispersal strategies, for plant populations stability across multiple biomes. Further research is, however, necessary to integrate and evaluate the role of other specific traits, often not available in databases, and intraspecific trait variability in modulating species stability. 

The expansion of woody plants into grasslands and old fields is often ascribed to fire suppression and heavy grazing, especially by domestic livestock. However, it is also recognized that nutrient availability and interspecific competition with grasses and other woody plants play a role in certain habitats. I examined potential factors causing range- and niche expansion by the eastern redcedar Juniperus virginiana , the most widespread conifer in the eastern United States, in multifactorial experiments in a greenhouse. Historical records suggest that the eastern redcedar is a pioneer forest species, and may be replaced as the forest increases in tree density due to shading. Another possible factor that affects its distribution may be nutrient availability, which is higher in old fields and other disturbed lands than in undisturbed habitats. In its historic range, eastern redcedars are particularly abundant on limestone outcrops, often termed ‘cedar barrens’. However, the higher abundance on limestone could be due to reduced interspecific competition rather than a preference for high pH substrates. I manipulated shade, fertilization, lime, and interspecific competition with a common dominant tree, the post oak Quercus stellata . In a separate experiment, I manipulated fire and grass competition. I measured growth rates (height and diameter) and above- and belowground biomass at the end of both experiments. I also measured total non-structural carbohydrates and nitrogen in these plants. Shade was the most important factor limiting the growth rates and biomass of eastern redcedars. I also found that there were significant declines in nitrogen and non-structural carbohydrates when shaded. These results are consistent with the notion that the eastern redcedar is a pioneer forest species, and that shade is the reason that these redcedars are replaced by other tree species. In the second experiment, I found that a single fire had a negative effect on young trees. There was no significant effect of competition with grass, perhaps because the competitive effect was shading by grasses and not nutrient depletion. Overall, the effects of shade were far more apparent than the effects of fire. 

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyze 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical, and gene neighborhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.