The Biogeography of Ammonia-Oxidizing Bacterial Communities in Soil

Although ammonia-oxidizing bacteria (AOB) are likely to play a key role in the soil nitrogen cycle, we have only a limited understanding of how the diversity and composition of soil AOB communities change across ecosystem types. We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suite of environmental variables measured, we found the strongest correlation between temperature and AOB community composition; soils exposed to similar mean annual temperatures tended to have similar AOB communities. This finding is consistent with previous studies and suggests that temperature selects for specific AOB lineages. Given that distinct AOB taxa are likely to have unique functional attributes, the biogeographical patterns exhibited by soil AOB may be directly relevant to understanding soil nitrogen dynamics under changing environmental conditions.     

Bacterial Succession on the Leaf Surface: A Novel System for Studying Successional Dynamics

Succession is a widely studied process in plant and animal systems, but succession in microbial communities has received relatively little attention despite the ubiquity of microorganisms in natural habitats. One important microbial habitat is the phyllosphere, or leaf surface, which harbors large, diverse populations of bacteria and offers unique opportunities for the study of succession and temporal community assembly patterns. To explore bacterial community successional patterns, we sampled phyllosphere communities on cottonwood (Populus deltoides) trees multiple times across the growing season, from leaf emergence to leaf fall. Bacterial community composition was highly variable throughout the growing season; leaves sampled as little as a week apart were found to harbor significantly different communities, and the temporal variability on a given tree exceeded the variability in community composition between individual trees sampled on a given day. The bacterial communities clearly clustered into early-, mid-, and late-season clusters, with early- and late-season communities being more similar to each other than to the mid-season communities, and these patterns appeared consistent from year to year. Although we observed clear and predictable changes in bacterial community composition during the course of the growing season, changes in phyllosphere bacterial diversity were less predictable. We examined the species–time relationship, a measure of species turnover rate, and found that the relationship was fundamentally similar to that observed in plant and invertebrate communities, just on a shorter time scale. The temporal dynamics we observed suggest that although phyllosphere bacterial communities have high levels of phylogenetic diversity and rapid turnover rates, these communities follow predictable successional patterns from season to season.     

tRNAs: Cellular barcodes for amino acids

The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl-tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of tRNA is to deliver amino acids for a variety of processes that includes, but is not limited to, protein synthesis.     

Relating belowground microbial composition to the taxonomic,phylogenetic, and functional trait distributions of trees in a tropical forest

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot‐level variability in belowground microbial communities.     

Reduction of the temperature sensitivity of soil organic matter decomposition with sustained temperature increase

The degree to which microbial communities adjust their decomposition of soil carbon over time in response to long-term increases in temperature is one of the key uncertainties in our modeling of the responses of terrestrial ecosystems to warming. To better understand changes in temperature sensitivity of soil microbial communities to long-term increases in soil temperature, we incubated 27 soils for one year with both short-term and long-term manipulations of temperature. In response to increasing temperature short-term from 20 to 30 °C, respiration rates increased more than threefold on average across soils. Yet, in response to long-term increases in temperature, respiration rates increased approximately half as much as they did to short-term increases in temperature. Short-term Q₁₀ of recalcitrant C correlated positively with long-term Q₁₀ measured between 10 and 20 °C, yet there was no relationship between short-term Q₁₀ and long-term Q₁₀ between 20 and 30 °C. In all, under laboratory conditions, it is clear that there is reduction in the temperature sensitivity of decomposition to long-term increases in temperature that disassociate short- and long-term responses of microbial decomposition to temperature. Determining the fate of soil organic matter to increased temperature will not only require further research on the controls and mechanisms of these patterns, but also require models to incorporate responses to both short-term and long-term increases in temperature.     

Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation

Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20?cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6?months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.     

Combined Surgical Approach to Young Adults with Hip Dysplasia and Concomitant Intra-Articular Pathology Using Intra-Abdominal Monitoring

BackgroundCombined hip arthroscopy and periacetabular osteotomy (PAO) allows for treatment of intra-articular hip pathology with simultaneous correction of acetabular version and femoral head coverage in patients with symptomatic hip dysplasia. Currently, scant data is available to surgeons regarding optimal technique, sequence of repair, perioperative management, and the use of intra-abdominal monitoring in patients undergoing these combined procedures. The purpose of this study is to describe a two-surgeon, muscle-sparing, approach for sequential hip arthroscopy and PAO for the treatment of adults with acetabular dysplasia and concomitant intra-articular hip pathology.MethodsIn this article, we present the indications for combined hip arthroscopy and PAO, in addition to patient set-up and positioning. A detailed discussion of hip arthroscopy and a muscle sparing PAO techniques are then presented, with overview of a novel intra-abdominal pressure monitoring technique and post-operative rehabilitation protocol.ResultsThrough technical refinement and experience, our indications and protocol for the treatment of patients with symptomatic acetabular dysplasia with concomitant intra-articular hip pathology involves a refined and reproducible, two surgeon procedure utilizing hip arthroscopy followed by PAO. The use of intra-abdominal monitoring allows for assessment of intra-peritoneal pressures to monitor for the development of abdominal compartment syndrome secondary to fluid extravasation.ConclusionThe performance of concomitant hip arthroscopy and PAO for concurrent hip dysplasia and intra-articular hip pathology represents an increasingly common approach in hip preservation surgery. The hip arthroscopy and muscle-sparing PAO protocol using intra-abdominal monitoring described here serves to further refine and advance the indications and technical aspects of this challenging procedure.Level of Evidence: V     

Applying structure-from-motion habitat reconstruction and GIS terrain analysis to test hypotheses about nest-site selection by shorebirds

Habitat variables related to vegetation type and structure are routinely identified as important components of nest-site selection for birds. For ground-nesting birds, small-scale (< 0.5 m) microtopography may also play a role in nest-site selection through its effects on nest concealment and microclimate. Manual measurements of microtopography are challenging, time-consuming, and subject to user error. Ultrahigh-density point clouds generated using structure-from-motion (SfM) algorithms and photomosaics captured during Unmanned Aerial Vehicle (UAV) surveys can potentially provide detailed topographical measurements with less error. We used multiple indices of surface roughness to examine the effect of microtopography on nest site selection by White-rumped Sandpipers (Calidris fuscicollis) at East Bay Migratory Bird Sanctuary, Nunavut, Canada. We measured microtopography manually using the relative height index within a 1-m radius of used and unused sites. We generated three digital indices of surface roughness for 1-m and 5-m scales around nests and unused sites, including standard deviation of slope, slope variability, and 2D:3D area ratio. We compared the digital indices of used and unused sites at both spatial scales. Relative height of nearby hummocks was significantly lower at nests than at unused sites, indicating selection for flatter sites. Similarly, two of three digitally calculated terrain roughness indices were significantly lower at nests than unused sites at both the 1-m and 5-m scales. The 2D:3D ratio did not differ between nests and unused sites. Manual and UAV-derived measures were significantly correlated, but with substantial unexplained variation (Pearson’s r = 0.35–0.46). Our results suggest that White-rumped Sandpipers select nest sites in areas with low terrain roughness, potentially to increase their field of view to monitor approaching predators. We also demonstrate the applicability of SfM habitat reconstruction for testing hypotheses of small-scale habitat variables that may be impossible to study using traditional methods.