From Surface to Subsurface: Diversity, Composition, and Abundance of Sessile and Endolithic Bacterial, Archaeal, and Eukaryotic Communities in Sand, Clay and Rock Substrates in the Laurentians (Quebec, Canada)

Microbial communities play an important role in shallow terrestrial subsurface ecosystems. Most studies of this habitat have focused on planktonic communities that are found in the groundwater of aquifer systems and only target specific microbial groups. Therefore, a systematic understanding of the processes that govern the assembly of endolithic and sessile communities is still missing. This study aims to understand the effect of depth and biotic factors on these communities, to better unravel their origins and to compare their composition with the communities detected in groundwater. To do so, we collected samples from two profiles (~0–50 m) in aquifer sites in the Laurentians (Quebec, Canada), performed DNA extractions and Illumina sequencing. The results suggest that changes in geological material characteristics with depth represent a strong ecological and phylogenetical filter for most archaeal and bacterial communities. Additionally, the vertical movement of water from the surface plays a major role in shallow subsurface microbial assembly processes. Furthermore, biotic interactions between bacteria and eukaryotes were mostly positive which may indicate cooperative or mutualistic potential associations, such as cross-feeding and/or syntrophic relationships in the terrestrial subsurface. Our results also point toward the importance of sampling both the geological formation and groundwater when it comes to studying its overall microbiology.

Global change re-structures alpine plant communities under 15 years of warming, nitrogen, and snow addition: disentangling density independent and dependent effects

Global change is altering patterns of community assembly, with net outcomes dependent on species’ responses to the environment, both directly and mediated through biotic interactions. Here, we assess alpine plant community responses in a 15-year factorial nitrogen addition, warming and snow manipulation experiment. We used a dynamic competition model to estimate the density-dependent and independent processes underlying changes in species-group abundances over time. Density-dependent shifts in competitive interactions drove long-term changes in abundance of species-groups under global change. Density-independent processes were important when counteracting environmental drivers limited the growth response of the dominant species. Furthermore, competitive interactions shifted with environmental change, primarily with nitrogen, and drove non-linear abundance responses across environmental gradients. Our results highlight that global change can either reshuffle species hierarchies or further favor already dominant species; predicting which outcome will occur requires incorporating both density-dependent and independent mechanisms and how they interact across multiple global change factors.

Of mutualism and migration: will interactions with novel ericoid mycorrhizal communities help or hinder northward Rhododendron range shifts?

Rapid climate change imperils many small-ranged endemic species as the climate envelopes of their native ranges shift poleward. In addition to abiotic changes, biotic interactions are expected to play a critical role in plant species’ responses. Below-ground interactions are of particular interest given increasing evidence of microbial effects on plant performance and the prevalence of mycorrhizal mutualisms. We used greenhouse mesocosm experiments to investigate how natural northward migration/assisted colonization of Rhododendron catawbiense, a small-ranged endemic eastern U.S. shrub, might be influenced by novel below-ground biotic interactions from soils north of its native range, particularly with ericoid mycorrhizal fungi (ERM). We compared germination, leaf size, survival, and ERM colonization rates of endemic R. catawbiense and widespread R. maximum when sown on different soil inoculum treatments: a sterilized control; a non-ERM biotic control; ERM communities from northern R. maximum populations; and ERM communities collected from the native range of R. catawbiense. Germination rates for both species when inoculated with congeners' novel soils were significantly higher than when inoculated with conspecific soils, or non-mycorrhizal controls. Mortality rates were unaffected by treatment, suggesting that the unexpected reciprocal effect of each species’ increased establishment in association with heterospecific ERM could have lasting demographic effects. Our results suggest that seedling establishment of R. catawbiense in northern regions outside its native range could be facilitated by the presence of extant congeners like R. maximum and their associated soil microbiota. These findings have direct relevance to the potential for successful poleward migration or future assisted colonization efforts.

Predicting potential distribution and evaluating biotic interactions of threatened species: a case study of Discocactus ferricola (Cactaceae)

Information on distribution, number of populations, and biotic interactions are essential for assessing the threat status of species and to establish more effective conservation initiatives. Ecological niche modeling have been successfully applied to identify the potential distribution, even for rare species that have few recorded occurrence points. In this study, we evaluated the potential distribution and additionally generated the first data on the reproductive biology of Discocactus ferricola, due to its degree of threat and the absence of ecological data for that species. The potential distribution map highlighted areas with higher probability of occurrence of D. ferricola on the Residual Plateau of Maciço do Urucum located in Mato Grosso do Sul, Brazil. The occurrence of D. ferricola populations was limited to outcrops of flat ironstone (cangas) distributed in patches across the landscape, increasing the chances of serious threats, such as habitat loss due to mining and species extraction. We also found that D. ferricola is xenogamous. Therefore, in situ conservation actions must prioritize the maintenance of interactions with pollinators by preserving the flora and fauna of rocky outcrops and adjacent forests in areas of greater environmental suitability for D. ferricola. Our study highlights the use of ecological niche modeling and data on biotic interactions to evaluate species potential distribution, to guide new sampling efforts, and to assist conservation and management initiatives.

The Influence of the Interaction between Climate and Competition on the Distributional Limits of European Shrews

It is known that species’ distributions are influenced by several ecological factors. Nonetheless, the geographical scale upon which the influence of these factors is perceived is largely undefined. We assessed the importance of competition in regulating the distributional limits of species at large geographical scales. We focus on species with similar diets, the European Soricidae shrews, and how interspecific competition changes along climatic gradients. We used presence data for the seven most widespread terrestrial species of Soricidae in Europe, gathered from GBIF, European museums, and climate data from WorldClim. We made use of two Joint Species Distribution Models to analyse the correlations between species’ presences, aiming to understand the distinct roles of climate and competition in shaping species’ distributions. Our results support three key conclusions: (i) climate alone does not explain all species’ distributions at large scales; (ii) negative interactions, such as competition, seem to play a strong role in defining species’ range limits, even at large scales; and (iii) the impact of competition on a species’ distribution varies along a climatic gradient, becoming stronger at the climatic extremes. Our conclusions support previous research, highlighting the importance of considering biotic interactions when studying species’ distributions, regardless of geographical scale.

Enriched root bacterial microbiome in invaded vs native ranges of the model grass allotetraploid Brachypodium hybridum

Invasive species can shift the composition of key soil microbial groups, thus creating novel soil microbial communities. To better understand the biological drivers of invasion, we studied plant-microbial interactions in species of the Brachypodium distachyon complex, a model system for functional genomic studies of temperate grasses and bioenergy crops. While Brachypodium hybridum invasion in California is in an incipient stage, threatening natural and agricultural systems, its diploid progenitor species B. distachyon is not invasive in California. We investigated the root, soil, and rhizosphere bacterial composition of Brachypodium hybridum in both its native and invaded range, and of B. distachyon in the native range. We used high-throughput, amplicon sequencing to evaluate if the bacteria associated with these plants differ, and whether biotic controls may be driving B. hybridum invasion. Bacterial community composition of B. hybridum differed based on provenance (native or invaded range) for root, rhizosphere, and bulk soils, as did the abundance of dominant bacterial taxa. Bacteroidetes, Cyanobacteria and Bacillus spp. (species) were significantly more abundant in B. hybridum roots from the invaded range, whereas Proteobacteria, Firmicutes, Erwinia and Pseudomonas were more abundant in the native range roots. Brachypodium hybridum forms novel biotic interactions with a diverse suite of rhizosphere microbes from the invaded range, which may not exert a similar influence within its native range, ostensibly contributing to B. hybridum’s invasiveness. These associated plant microbiomes could inform future management approaches for B. hybridum in its invaded range and could be key to understanding, predicting, and preventing future plant invasions.

Inferring community assembly processes from functional seed trait variation along temperature gradient

Assembly of plant communities has long been scrutinized through the lens of trait-based ecology. Studies generally analyze functional traits related to the vegetative growth, survival and resource acquisition and thus ignore how ecological processes may affect plants at other stages of their lifecycle, particularly when seeds disperse, persist in soil and germinate. Here, we analyzed an extensive data set of 16 traits for 167 species measured in-situ in 36 grasslands located along an elevational gradient and compared the impact of abiotic filtering, biotic interactions and dispersal on traits reflecting different trait categories: plant vegetative growth, germination, dispersal, and seed morphology. For each community, we quantified community weighted mean (CWM) and functional diversity (FD) for all traits and established their relationships to mean annual temperature. The seed traits were weakly correlated to vegetative traits and thus constituted independent axes of plant phenotypical variation that were affected differently by the ecological processes considered. Abiotic filtering impacted mostly the vegetative traits and to a lesser extent on seed germination and morphological traits. Increasing low-temperature stress towards colder sites selected for short-stature, slow-growing and frost-tolerant species that produce small quantity of smaller seeds with higher degree of dormancy, high temperature requirements for germination and comparatively low germination speed. Biotic interactions, specifically competition in the lowlands and facilitation in uplands, also filtered certain functional traits in the study communities. The benign climate in lowlands promoted plant with competitive strategies including fast growth and resource acquisition (vegetative growth traits) and early and fast germination (germination traits), whereas the effects of facilitation on the vegetative and germination traits were cancelled out by the strong abiotic filtering. The changes in the main dispersal vector from zoochory to anemochory along the gradient strongly affected the dispersal and the seed morphological trait structure of the communities. Specifically, stronger vertical turbulence and moderate warm-upwinds combined with low grazing intensity selected for light and non-round shaped seeds with lower terminal velocity and endozoochorous potential. Synthesis: We clearly demonstrate that, in addition to vegetation traits, seed traits can substantially contribute to functional structuring of plant communities along environmental gradients. Thus, the hard seed traits related to germination and dispersal are critical to detect multiple, complex community assembly rules. Consequently, such traits should be included in core lists of plant traits and, when applicable, be incorporated into analysis of community assembly.