Synthesis and Characterization of Organic Impurities in Bortezomib Anhydride Produced by a Convergent Technology

A profile of impurities in bortezomib anhydride, produced by a recently developed convergent technology, has been characterized. HPLC-MS analysis of the drug essence revealed three impurities: an epimer of bortezomib, resulting from partial racemization of l-phenylalanine’s stereogenic center during the chemical synthesis, and two epimeric products of oxidative degradation of bortezomib, in which boron is replaced by the OH group. The impurities were obtained by chemical synthesis and characterized by physical methods

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species

Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions

Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

The chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities

Bacterial and archaeal taxa are reliable indicators of soil restoration across distributed calcareous grasslands

Land use intensification can reduce soil carbon stocks and changes microbial community biodiversity and functionality. However, there is a lack of consensus on whether management consistently affects microbial biodiversity across geographic scales, and how this relates to altered soil function. From a regulatory and monitoring perspective, there is a need to identify functionally relevant indicators of land use in order to evaluate the progress of soil restoration approaches. We performed a landscape scale survey of unimproved calcareous grasslands paired with local arable contrasts, and assessed the consistency of responses in a variety of soil, biotic and functional measures. In addition, adjacent grasslands undergoing restoration were assessed to identify soil microbial indicators of recovery. Organic matter content was consistently larger in grasslands than in arable fields, and increased with time in the restoring sites. Molecular comparisons of grassland versus arable soils revealed numerous bacterial, archaeal and fungal indicators, with more representatives of Ca. Xiphinematobacter, DA101, Bradyrhizobium, Rhodoplanes, Mycobacteria and Mortierella in old grassland soils, while Nitrososphaera, Sporosarcina and Alternaria infectoria were more abundant in arable soils. Extracellular enzymatic responses were more variable with none of the eight investigated enzymes being consistent indicators of grassland or arable soils. Correlation analyses, incorporating the molecular and enzymatic responses across all surveyed soils, revealed that molecular indicators were more strongly correlated with soil organic matter increases with restoration of arable soils. Our results highlight that microbial taxa are among the most sensitive indicators of soil restoration, and we identify consistent responses of specific taxa to management across geographic scales. This discovery will be important for both the instigation and monitoring of the soil restoration

Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration

Acknowledgements The authors would like to thank Mr Kevin Mackenzie and Mrs Gillian Milne (University of Aberdeen) for technical support with scanning electron microscopy, and Dr Robin Walker for access to the Woodlands Field experimental plots at the SRUC,Craibstone Estate, Aberdeen. Funding This work was financially supported by Natural Environmental Research Council (standard grants NE/I027835/1 and NE/L006286/1 and fellowship NE/J019151/1), EC Marie Curie ITN NORA, Grant Agreement No. 316472, the AXA Research Fund and the Centre for Genome Enabled Biology and Medicine, University of Aberdeen.Peer reviewedPublisher PD

Protist diversity on a nature reserve in NW England − with particular reference to their role in soil biogenic silicon pools

Soil protists play fundamental roles in many earth system processes, yet we are only beginning to understand the true diversity of the organisms involved. In this study we used conventional (microscopy-based) methods to characterise the diversity and estimate protist population sizes in soils from a variety of distinct habitats within Mere Sands Wood nature reserve in NW England. We produced population size data for over ninety soil protists belonging to two major eukaryotic functional groups: testate amoebae (TA) and diatoms, adding substantial ‘cryptic diversity’ to the nature reserves recorded biota. From these population size data we estimated relative contributions of TA and diatoms to soil biogenic silicon (BSi) pools and found significant correlations between taxon richness and the TA and diatom Si pool. This could indicate that protist functional diversity can influence terrestrial BSi pools, especially in early successional plant communities where TA and diatoms can potentially increase Si mineralisation and/or create Si ‘hot spots’ and hence, the biological availability of this element for subsequent plant uptake. TA were particularly abundant in mor humus type soils further supporting the idea that they could be important players in nutrient cycling in such soils. Overall, we demonstrate this is a useful approach in order to start to attempt to estimate the role of protists in the Si cycle and other ecological processes

Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific

Natural Environment Research Council (NERC) (NE/E01559X/1)

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits