Soil microbial communities with greater investment in resource acquisition have lower growth yield

Resource acquisition and growth yield are fundamental microbial traits that affect biogeochemical processes and have consequences for ecosystem functioning. However, there is a lack of empirical observations linking these traits. Using a landscape-scale survey of temperate near-neutral pH soils, we show tradeoffs in key community-level parameters linked to these traits. Increased investment into extracellular enzymes estimated using specific potential enzyme activity was associated with reduced growth yield obtained using carbon use efficiency measures from stable isotope tracing. Reduction in growth yield was linked more to carbon than nitrogen acquisition highlighting smaller stoichiometric than energetic constraints on community metabolism in examined soils

Environmental and microbial controls on microbial necromass recycling, an important precursor for soil carbon stabilization

There is an emerging consensus that microbial necromass carbon is the primary constituent of stable soil carbon, yet the controls on the stabilization process are unknown. Prior to stabilization, microbial necromass may be recycled by the microbial community. We propose that the efficiency of this recycling is a critical determinant of soil carbon stabilization rates. Here we explore the controls on necromass recycling efficiency in 27 UK grassland soils using stable isotope tracing and indicator species analysis. We found that recycling efficiency was unaffected by land management. Instead, recycling efficiency increased with microbial growth rate on necromass, and was highest in soils with low historical precipitation. We identified bacterial and fungal indicators of necromass recycling efficiency, which could be used to clarify soil carbon stabilization mechanisms. We conclude that environmental and microbial controls have a strong influence on necromass recycling, and suggest that this, in turn, influences soil carbon stabilization

The effect of root‐associated microbes on plant growth and chemical defence traits across two contrasted elevations

1. Ecotypic differences in plant growth and anti‐herbivore defence phenotypes are determined by the complex interactions between the abiotic and the biotic environment. 2. Root‐associated microbes (RAMs) are pervasive in nature, vary over climatic gradients and have been shown to influence the expression of multiple plant functional traits related to biomass accumulation and biotic interactions. We addressed how variation in climatic conditions between lowland and subalpine habitats in the Alps and RAMs can independently or interactively affect plant growth and anti‐herbivore defence trait expression. 3. To address the contribution of climate and RAMs on growth and chemical defences of high‐ and low‐elevation Plantago major ecotypes, we performed a full‐factorial reciprocal transplant field experiment at two elevations. We coupled it with plant functional trait measurements and metabolomics analyses. 4. We found that local growing climatic conditions mostly influenced how the ecotypes grew, but we also found that the high‐ and low‐elevation ecotypes improved biomass accumulation if in the presence of their own‐elevation RAMs. We also found that while chemical defence expression was affected by climate, they were also more highly expressed when plants were inoculated with low‐elevation RAMs. 5. Synthesis: Our research demonstrated that root‐associated microbes (RAMs) from contrasted elevations impact how plants grow or synthesize toxic secondary metabolites. At low elevation, where biotic interactions are stronger, RAMs enhance plant biomass accumulation and the production of toxic secondary metabolites

Relative contribution of high and low elevation soil microbes and nematodes to ecosystem functioning

1. Ecosystem productivity is largely dependent on soil nutrient cycling which, in turn, is driven by decomposition rates governed by locally adapted below-ground microbial and soil communities. How climate change will impact soil biota and the associated ecosystem functioning, however, remains largely an open question. 2. To address this gap, we first characterized differences in soil microbial and nematode communities as well as functional characteristics from soils collected from the foothills or in sub-alpine elevations of the Alps. We next performed a full-factorial reciprocal transplant common garden experiment at two elevations, and asked whether elevation-related functional and taxonomic differences are maintained or can be altered depending on the local climatic conditions. For this, we separately transplanted soil microbial and nematode communities from low and high elevation in their home or opposite elevation in pots added with a common plant community. 3. We found evidence for taxonomic and functional differentiation of the microbial and nematode communities when collected at high or low elevation. Specifically, we observed a decrease in microbial diversity and activity at high elevation, and additionally, through nematodes' functional characterization, we found increased fungal-dominated energy channels at high elevation. 4. Moreover, according to the reciprocal transplant experiment, while we found little effect of soil biodiversity change based on elevation of origin on plant growth and plant community composition, soils inoculated with microbes originating from low elevation respired more than those originating from high elevation, particularly when at low elevation. This observation correlates well with the observed faster carbon degradation rates by the low elevation microbial communities. 5. Climate change can reshuffle soil communities depending on organism-specific variation in range expansion, ultimately affecting soil fertility and carbon-cycle dynamics

Soil fungal : Bacterial ratios are linked to altered carbon cycling

Acknowledgments We thank Steffen Ruehlow, Agnes Fastnacht, Karl Kuebler, Iris Kuhlmann, Heike Geilmann, and Petra Linke for technical support in establishing the experiment and with stable isotope analyses. We also thank Markus Lange, Daniel Read, and Hyun Gweon for helpful discussions. Funding AM has received funding from Max Planck Society and the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 655240. AM has also received a career orientation grant from the Jena School for Microbial Communication (JSMC) that funded the laboratory visits. DFG SFB Aquadiva funded part of this work.Peer reviewedPublisher PD

Beyond taxonomic identification: integration of ecological responses to a soil bacterial 16S rRNA gene database

High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios

Land use driven change in soil pH affects microbial carbon cycling processes

Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates

Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy. BET bromodomain inhibitors, which have shown efficacy in several models of cancer, have not been evaluated in TNBC. These inhibitors displace BET bromodomain proteins such as BRD4 from chromatin by competing with their acetyl-lysine recognition modules, leading to inhibition of oncogenic transcriptional programs. Here we report the preferential sensitivity of TNBCs to BET bromodomain inhibition in vitro and in vivo, establishing a rationale for clinical investigation and further motivation to understand mechanisms of resistance. In paired cell lines selected for acquired resistance to BET inhibition from previously sensitive TNBCs, we failed to identify gatekeeper mutations, new driver events or drug pump activation. BET-resistant TNBC cells remain dependent on wild-type BRD4, which supports transcription and cell proliferation in a bromodomain-independent manner. Proteomic studies of resistant TNBC identify strong association with MED1 and hyper-phosphorylation of BRD4 attributable to decreased activity of PP2A, identified here as a principal BRD4 serine phosphatase. Together, these studies provide a rationale for BET inhibition in TNBC and present mechanism-based combination strategies to anticipate clinical drug resistance

fungi_wp2_uniq_mcl

Fasta file containing unic sequences. The cluster number corresponds to MOTU numbe