Seasonal Patterns Contribute More Towards Phyllosphere Bacterial Community Structure than Short-Term Perturbations.

Phyllosphere microorganisms are sensitive to fluctuations in wind, temperature, solar radiation, and rain. However, recent explorations of patterns in phyllosphere communities across time often focus on seasonal shifts and leaf senescence without measuring the contribution of environmental drivers and leaf traits. Here, we focus on the effects of rain on the phyllosphere bacterial community of the wetland macrophyte broadleaf cattail (Typha latifolia) across an entire year, specifically targeting days before and 1, 3, and 5 days after rain events. To isolate the contribution of precipitation from other factors, we covered a subset of plants to shield them from rainfall. We used targeted Illumina sequencing of the V4 region of the bacterial 16S rRNA gene to characterize phyllosphere community composition. Rain events did not have a detectable effect on phyllosphere community richness or evenness regardless of whether the leaves were covered from rain or not, suggesting that foliar microbial communities are robust to such disturbances. While climatic and leaf-based variables effectively modeled seasonal trends in phyllosphere diversity and composition, they provided more limited explanatory value at shorter time scales. These findings underscore the dominance of long-term seasonal patterns related to climatic variation as the main factor influencing the phyllosphere community.

Nutrient foraging strategies are associated with productivity and population growth in forest shrubs.

Background and Aims: Temperate deciduous forest understoreys are experiencing widespread changes in community composition, concurrent with increases in rates of nitrogen supply. These shifts in plant abundance may be driven by interspecific differences in nutrient foraging (i.e. conservative vs. acquisitive strategies) and, thus, adaptation to contemporary nutrient loading conditions. This study sought to determine if interspecific differences in nutrient foraging could help explain patterns of shrub success and decline in eastern North American forests. Methods: Using plants grown in a common garden, fine root traits associated with nutrient foraging were measured for six shrub species. Traits included the mean and skewness of the root diameter distribution, specific root length (SRL), C:N ratio, root tissue density, arbuscular mycorrhizal colonization and foraging precision. Above- and below-ground productivity were also determined for the same plants, and population growth rates were estimated using data from a long-term study of community dynamics. Root traits were compared among species and associations among root traits, measures of productivity and rates of population growth were evaluated. Key Results: Species fell into groups having thick or thin root forms, which correspond to conservative vs. acquisitive nutrient foraging strategies. Interspecific variation in root morphology and tissue construction correlated with measures of productivity and rates of cover expansion. Of the four species with acquisitive traits, three were introduced species that have become invasive in recent decades, and the fourth was a weedy native. In contrast, the two species with conservative traits were historically dominant shrubs that have declined in abundance in eastern North American forests. Conclusions: In forest understoreys of eastern North America, elevated nutrient availability may impose a filter on species success in addition to above-ground processes such as herbivory and overstorey canopy conditions. Shrubs that have root traits associated with rapid uptake of soil nutrients may be more likely to increase in abundance, while species without such traits may be less likely to keep pace with more productive species.

Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest.

The phyllosphere presents a unique system of discrete and easily replicable surfaces colonized primarily by bacteria. However, the biogeography of bacteria in the phyllosphere is little understood, especially at small to intermediate scales. Bacterial communities on the leaves of 91 southern magnolia (Magnolia grandiflora) trees 1-452 m apart in a small forest plot were analyzed and fragments of the 16S ribosomal RNA (rRNA) gene sequenced using the Illumina platform. Assemblages were dominated by members of the Alphaproteobacteria, Bacteroidetes, and Acidobacteria. Patterns in community composition were measured by both relative abundance (theta) and presence-absence (Jaccard) dissimilarity metrics. Distance-based Moran's eigenvector map analyses of the distance-decay relationship found a significant, positive relationship between each dissimilarity metric and significant eigenfunctions derived from geographic distance between trees, indicating trees that were closer together had more similar bacterial phyllosphere communities. Indirect gradient analyses revealed that several environmental parameters (canopy cover, tree elevation, and the slope and aspect of the ground beneath trees) were significantly related to multivariate ordination scores based on relative bacterial sequence abundances; however, these relationships were not significant when looking at the incidence of bacterial taxa. This suggests that bacterial growth and abundance in the phyllosphere is shaped by different assembly mechanisms than bacterial presence or absence. More broadly, this study demonstrates that the distance-decay relationship applies to phyllosphere communities at local scales, and that environmental parameters as well as neutral forces may both influence spatial patterns in the phyllosphere.

Life history strategies among soil bacteria-dichotomy for few, continuum for many.

Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O-H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms' joint 18O-13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.

The Functional Significance of Bacterial Predators.

Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to nonpredatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than nonpredatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolf-pack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than those of nonpredators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from those of nonpredators. This finding supports the ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow and that predatory bacteria influence element flow through microbial food webs.IMPORTANCE The word "predator" may conjure images of leopards killing and eating impala on the African savannah or of great white sharks attacking elephant seals off the coast of California. But microorganisms are also predators, including bacteria that kill and eat other bacteria. While predatory bacteria have been found in many environments, it has been challenging to document their importance in nature. This study quantified the growth of predatory and nonpredatory bacteria in soils (and one stream) by tracking isotopically labeled substrates into newly synthesized DNA. Predatory bacteria were more active than nonpredators, and obligate predators, such as Bdellovibrionales and Vampirovibrionales, increased in growth rate in response to added substrates at the base of the food chain, strong evidence of trophic control. This work provides quantitative measures of predator activity and suggests that predatory bacteria-along with protists, nematodes, and phages-are active and important in microbial food webs.

Canopy position is a stronger determinant of bacterial community composition and diversity than environmental disturbance in the phyllosphere.

The effect of rain on the phyllosphere community has not been extensively explored, especially in the context of spatial variation on the impact of rain throughout the tree canopy. We characterized the response of the phyllosphere bacterial community removed from leaf surfaces of the Southern Magnolia (Magnolia grandiflora) to rain across different spatial locations of the canopy. We hypothesized that: (i) rain would lead to an initial decrease in phyllosphere bacterial diversity, followed by an increase in diversity on subsequent days, but that this effect would be minimized in the lower and interior portion of the canopy, and that (ii) community beta dispersion of phyllosphere microorganisms would be lower following rain, and similarly contingent on canopy position. We used targeted next-generation sequencing of the V4 region of the bacterial 16S rRNA gene to characterize bacterial composition. We found higher bacterial richness in interior canopy and distinct composition across canopy positions. Further, the effect of rain on beta dispersion was contingent on canopy position: rain lowered dispersion in the upper canopy but increased it in the lower and interior canopy. Our results demonstrate that canopy structure should be considered when looking at the impact of rain on the collective phyllosphere community.