Native and invasive inoculation sources modify fungal community assembly and biomass production of a chaparral shrub

Feedbacks between plants and surrounding soil microbes can contribute to the establishment and persistence of invasive annual grasses as well as limit the success of restoration efforts. In this study, we aim to understand how three sources of soil inocula – native, invasive (from under Bromus diandrus) and sterile – affect the growth response and fungal community composition in the roots of a chaparral shrub, Adenostoma fasciculatum. We grew A. fasciculatum from seed in a greenhouse with each inoculum source and harvested at six months. We measured above- and below-ground biomass, arbuscular mycorrhizal fungal (AMF) colonization and conducted targeted-amplicon sequencing of the 18S and ITS2 loci to characterize AMF and general fungal community composition, respectively. Native inoculum resulted in roots with richer communities of some groups of AMF and non-AMF symbionts, when compared to roots grown with invasive or sterile inoculum. Seedlings grown with invasive and native inoculum did not have different growth responses, but both produced more biomass than a sterile control. These findings suggest that inoculation with soil from native species can increase the diversity of multiple groups of fungal symbionts and inoculation with live soil (invasive or native) can increase seedling biomass. Moreover, future work would benefit from assessing if a more diverse community of fungal symbionts increases seedling survival when planted in field restoration sites

Meta-analysis reveals ammonia-oxidizing bacteria respond more strongly to nitrogen addition than ammonia-oxidizing archaea

Shifts in microbial communities driven by anthropogenic nitrogen (N) addition have broad-scale ecological consequences. However, responses of microbial groups to exogenous N supply vary considerably across studies, hindering efforts to predict community changes. We used meta-analytical techniques to explore how amoA gene abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) respond to N addition, and found that N addition increased AOA and AOB abundances by an average of 27% and 326%, respectively. Responses of AOB varied by study type, ecosystem, fertilizer type, and soil pH, and were strongest in unmanaged wildland soils and soils fertilized with inorganic N sources. Increases in nitrification potential with N addition significantly correlated with only AOB. Our analyses suggest that elevated N supply enhances soil nitrification potential by increasing AOB populations, and that this effect may be most pronounced in unmanaged wildland soils

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

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions

Predicting death from surgery for lung cancer: a comparison of two scoring systems in two European countries

Objectives: Current British guidelines advocate the use of risk prediction scores such as Thoracoscore to estimate mortality prior to radical surgery for non-small cell lung cancer (NSCLC). A recent publication used the National Lung Cancer Audit (NLCA) to produce a score to predict 90 day mortality (NLCA score). The aim of this study is to validate the NLCA score, and compare its performance with Thoracoscore. Materials and methods: We performed an internal validation using 2858 surgical patients from NLCA and an external validation using 3191 surgical patients from the Danish Lung Cancer Registry (DLCR). We calculated the proportion that died within 90 days of surgery. The discriminatory power of both scores was assessed by a receiver operating characteristic (ROC) and an area under the curve (AUC) calculation. Results: Ninety day mortality was 5% in both groups. AUC values for internal and external validation of NLCA score and validation of Thoracoscore were 0.68 (95% CI 0.63–0.72), 0.60 (95% CI 0.56–0.65) and 0.60 (95% CI 0.54–0.66) respectively. Post-hoc analysis was performed using NLCA records on 15554 surgical patients to derive summary tables for 30 and 90 day mortality, stratified by procedure type, age and performance status. Conclusions: Neither score performs well enough to be advocated for individual risk stratification prior to lung cancer surgery. It may be that additional physiological parameters are required; however this is a further project. In the interim we propose the use of our summary tables that provide the real-life range of mortality for lobectomy and pneumonectomy