Bacterial community shifts occur primarily through rhizosphere expansion in response to subsoil amendments

To comprehensively evaluate the impact of agricultural management practices on soil productivity, it is imperative to conduct a thorough analysis of soil bacterial ecology. Deep-banding nutrient-rich amendments is a soil management practice that aims to improve plant growth and soil structure by addressing the plant-growth constraints posed by dense-clay subsoils. However, the response of bacterial communities to deep-banded amendments has not been thoroughly studied. To address this knowledge gap, we conducted a controlled-environment column experiment to examine the effects of different types of soil amendments (poultry litter, wheat straw + chemical fertiliser and chemical fertiliser alone) on bacterial taxonomic composition in simulated dense-clay subsoils. We evaluated the bacterial taxonomic and ecological group composition in soils beside and below the amendment using 16S rRNA amplicon sequencing and robust statistical methods. Our results indicate that deep-banded amendments alter bacterial communities through direct and indirect mechanisms. All amendments directly facilitated a shift in bacterial communities in the absence of growing wheat. However, a combination of amendments with growing wheat led to a more pronounced bacterial community shift which was distinct from and eclipsed the direct impact of the amendments and plants alone. This indirect mechanism was evidenced to be mediated primarily by plant growth and hypothesised to result from an enhancement in wheat root distribution, density and rhizodeposition changes. Therefore, we propose that subsoil amendments regardless of type facilitated an expansion in the rhizosphere which engineered a substantial plant-mediated bacterial community response within the simulated dense-clay subsoils. Overall, our findings highlight the importance of considering the complex and synergistic interactions between soil physicochemical properties, plant growth and bacterial communities when assessing agricultural management strategies for improving soil and plant productivity.

Hyperimmune bovine colostrum containing lipopolysaccharide antibodies (IMM124-E) has a nondetrimental effect on gut microbial communities in unchallenged mice

Enterotoxigenic Escherichia coli (ETEC) is a leading cause of bacterial diarrhea with the potential to cause long-term gastrointestinal (GI) dysfunction. Preventative treatments for ETEC-induced diarrhea exist, yet the effects of these treatments on GI commensals in healthy individuals are unclear. Whether administration of a prophylactic preventative treatment for ETEC-induced diarrhea causes specific shifts in gut microbial populations in controlled environments is also unknown. Here, we studied the effects of a hyperimmune bovine colostrum (IMM-124E) used in the manufacture of Travelan (AUST L 106709) on GI bacteria in healthy C57BL/6 mice. Using next-generation sequencing, we aimed to test the onset and magnitude of potential changes to the mouse gut microbiome in response to the antidiarrheagenic hyperimmune bovine colostrum product, rich in immunoglobulins against select ETEC strains (Travelan, Immuron Ltd). We show that in mice administered colostrum containing lipopolysaccharide (LPS) antibodies, there was an increased abundance of potentially gut-beneficial bacteria, such as Akkermansia and Desulfovibrio, without disrupting the underlying ecology of the GI tract. Compared to controls, there was no difference in overall weight gain, body or cecal weights, or small intestine length following LPS antibody colostrum supplementation. Overall, dietary supplementation with colostrum containing LPS antibodies produced subtle alterations in the gut bacterial composition of mice. Primarily, Travelan LPS antibody treatment decreased the ratio of Firmicutes/Bacteroidetes in gut microbial populations in unchallenged healthy mice. Further studies are required to examine the effect of Travelan LPS antibody treatment to engineer the microbiome in a diseased state and during recovery.

Microsecond Isomer at the N=20 Island of Shape Inversion Observed at FRIB

Excited-state spectroscopy from the first experiment at the Facility for Rare Isotope Beams (FRIB) is reported. A 24(2)-μs isomer was observed with the FRIB Decay Station initiator (FDSi) through a cascade of 224- and 401-keV γ rays in coincidence with ^{32}Na nuclei. This is the only known microsecond isomer (1  μs≤T_{1/2}<1  ms) in the region. This nucleus is at the heart of the N=20 island of shape inversion and is at the crossroads of the spherical shell-model, deformed shell-model, and ab initio theories. It can be represented as the coupling of a proton hole and neutron particle to ^{32}Mg, ^{32}Mg+π^{-1}+ν^{+1}. This odd-odd coupling and isomer formation provides a sensitive measure of the underlying shape degrees of freedom of ^{32}Mg, where the onset of spherical-to-deformed shape inversion begins with a low-lying deformed 2^{+} state at 885 keV and a low-lying shape-coexisting 0_{2}^{+} state at 1058 keV. We suggest two possible explanations for the 625-keV isomer in ^{32}Na: a 6^{-} spherical shape isomer that decays by E2 or a 0^{+} deformed spin isomer that decays by M2. The present results and calculations are most consistent with the latter, indicating that the low-lying states are dominated by deformation.

Interactive mobile application for Parkinson's disease deep brain stimulation (MAP DBS): An open-label, multicenter, randomized, controlled clinical trial

INTRODUCTION

Deep brain stimulation (DBS) is an effective treatment for Parkinson's disease (PD), but its efficacy is tied to DBS programming, which is often time consuming and burdensome for patients, caregivers, and clinicians. Our aim is to test whether the Mobile Application for PD DBS (MAP DBS), a clinical decision support system, can improve programming.

METHODS

We conducted an open-label, 1:1 randomized, controlled, multicenter clinical trial comparing six months of SOC standard of care (SOC) to six months of MAP DBS-aided programming. We enrolled patients between 30 and 80 years old who received DBS to treat idiopathic PD at six expert centers across the United States. The primary outcome was time spent DBS programming and secondary outcomes measured changes in motor symptoms, caregiver strain and medication requirements.

RESULTS

We found a significant reduction in initial visit time (SOC: 43.8 ± 28.9 min n = 37, MAP DBS: 27.4 ± 13.0 min n = 35, p = 0.001). We did not find a significant difference in total programming time between the groups over the 6-month study duration. MAP DBS-aided patients experienced a significantly larger reduction in UPDRS III on-medication scores (-7.0 ± 7.9) compared to SOC (-2.7 ± 6.9, p = 0.01) at six months.

CONCLUSION

MAP DBS was well tolerated and improves key aspects of DBS programming time and clinical efficacy.

Precision Monitoring of Honey Bee (Hymenoptera: Apidae) Activity and Pollen Diversity during Pollination to Evaluate Colony Health

Certain crops depend upon pollination services for fruit set, and, of these, almonds are of high value for Australia. Stressors, such as diseases, parasites, pesticides, and nutrition, can contribute to honey bee Apis mellifera L. colony decline, thereby reducing bee activity and pollination efficiency. In Australia, field studies are required to monitor honey bee health and to ascertain whether factors associated with colony decline are impacting hives. We monitored honey bee colonies during and after pollination services of almond. Video surveillance technology was used to quantify bee activity, and bee-collected pollen was periodically tested for pesticide residues. Plant species diversity was also assessed using DNA metabarcoding of the pollen. Results showed that bee activity increased in almond but not in bushland. Residues detected included four fungicides, although the quantities were of low risk of oral toxicity to bees. Floral diversity was lower in the pollen collected by bees from almonds compared to bushland. However, diversity was higher at the onset and conclusion of the almond bloom, suggesting that bees foraged more widely when availability was low. Our findings suggest that commercial almond orchards may sustain healthier bee colonies compared to bushland in early spring, although the magnitude of the benefit is likely landscape-dependent.

Comparing the Gut Microbiome in Autism and Preclinical Models: A Systematic Review

Many individuals diagnosed with autism spectrum disorder (ASD) experience gastrointestinal (GI) dysfunction and show microbial dysbiosis. Variation in gut microbial populations is associated with increased risk for GI symptoms such as chronic constipation and diarrhoea, which decrease quality of life. Several preclinical models of autism also demonstrate microbial dysbiosis. Given that much pre-clinical research is conducted in mouse models, it is important to understand the similarities and differences between the gut microbiome in humans and these models in the context of autism. We conducted a systematic review of the literature using PubMed, ProQuest and Scopus databases to compare microbiome profiles of patients with autism and transgenic (NL3^R451C, Shank3 KO, 15q dup), phenotype-first (BTBR) and environmental (Poly I:C, Maternal Inflammation Activation (MIA), valproate) mouse models of autism. Overall, we report changes in fecal microbial communities relevant to ASD based on both clinical and preclinical studies. Here, we identify an overlapping cluster of genera that are modified in both fecal samples from individuals with ASD and mouse models of autism. Specifically, we describe an increased abundance of Bilophila, Clostridium, Dorea and Lactobacillus and a decrease in Blautia genera in both humans and rodents relevant to this disorder. Studies in both humans and mice highlighted multidirectional changes in abundance (i.e. in some cases increased abundance whereas other reports showed decreases) for several genera including Akkermansia, Bacteroides, Bifidobacterium, Parabacteroides and Prevotella, suggesting that these genera may be susceptible to modification in autism. Identification of these microbial profiles may assist in characterising underlying biological mechanisms involving host-microbe interactions and provide future therapeutic targets for improving gut health in autism.

From laboratory tests to field trials: a review of cathodic protection and microbially influenced corrosion

Cathodic protection (CP), an electrochemical method for managing corrosion, is widely used in many industries in both marine and buried environments. However, literature surrounding cathodic protection and its ability to prevent microbially influenced corrosion (MIC) is mixed. This review describes the mechanics of CP, how CP may influence MIC, and collates and summarises tests on CP and MIC reported in literature. The aim of the review is to identify any trends and knowledge gaps requiring further study. While the outcomes of CP testing are generally mixed, some trends can be seen and, overall, MIC is detrimental to the protective effects of CP, with CP being less effective when used according to current international standards. Tests conducted in the field or with mix communities of microbes showed that CP could be effective at preventing MIC, while tests with sulfate-reducing bacteria generally proved CP to be highly ineffective. It was commonly seen that the effectiveness of CP can be improved by increasing polarization, to potentials as low as -1000 mV (Ag/AgCl). However, a balance does need to be met via careful monitoring to ensure negative side effects of over protection do not become a major problem.

Biochar reduced extractable dieldrin concentrations and promoted oligotrophic growth including microbial degraders of chlorinated pollutants

The role of organic amendments for natural degradation of aged persistent organic pollutants (POPs) in agricultural soils remains controversial. We hypothesised that organic amendments enhance bacterial activity and function at the community level, facilitating the degradation of aged POPs. An incubation study was conducted in a closed chamber over 12 months to assess the effects of selected organic amendments on extractable residues of aged dieldrin. The role of bacterial diversity and changes in community function was explored through sequenced marker genes. Linear mixed effect models indicated that, independent of amendment type, cumulative CO₂ release was negatively associated with decreases in dieldrin concentration, by up to 7% per µmol CO₂-C respired by microorganisms. The addition of poultry litter led to the highest daily carbon mineralisation, which was associated with low dieldrin dissipation after 9 months. In comparison, biochar resulted in significant decreases in extractable dieldrin residues over time, which coincided with shifts towards aerobic, oligotrophic, gram-negative bacteria, some with dehalogenation metabolism, and with increased potentials for biosynthesis of membrane components such as fatty acids and high redox quinones. The results supported an alternative theory that labile carbon promoted blooms of copiotrophic growth, which suppressed the required community-level traits and oligotrophic diversity to degrade chlorinated pollutants.

Elevated atmospheric CO2 alters the microbial community composition and metabolic potential to mineralize organic phosphorus in the rhizosphere of wheat

BACKGROUND

Understanding how elevated atmospheric CO2 (eCO2) impacts on phosphorus (P) transformation in plant rhizosphere is critical for maintaining ecological sustainability in response to climate change, especially in agricultural systems where soil P availability is low.

METHODS

This study used rhizoboxes to physically separate rhizosphere regions (plant root-soil interface) into 1.5-mm segments. Wheat plants were grown in rhizoboxes under eCO2 (800 ppm) and ambient CO2 (400 ppm) in two farming soils, Chromosol and Vertosol, supplemented with phytate (organic P). Photosynthetic carbon flow in the plant-soil continuum was traced with 13CO2 labeling. Amplicon sequencing was performed on the rhizosphere-associated microbial community in the root-growth zone, and 1.5 mm and 3 mm away from the root.

RESULTS

Elevated CO2 accelerated the mineralization of phytate in the rhizosphere zones, which corresponded with increases in plant-derived 13C enrichment and the relative abundances of discreet phylogenetic clades containing Bacteroidetes and Gemmatimonadetes in the bacterial community, and Funneliformis affiliated to arbuscular mycorrhizas in the fungal community. Although the amplicon sequence variants (ASVs) associated the stimulation of phytate mineralization under eCO2 differed between the two soils, these ASVs belonged to the same phyla associated with phytase and phosphatase production. The symbiotic mycorrhizas in the rhizosphere of wheat under eCO2 benefited from increased plant C supply and increased P access from soil. Further supportive evidence was the eCO2-induced increase in the genetic pool expressing the pentose phosphate pathway, which is the central pathway for biosynthesis of RNA/DNA precursors.

CONCLUSIONS

The results suggested that an increased belowground carbon flow under eCO2 stimulated bacterial growth, changing community composition in favor of phylotypes capable of degrading aromatic P compounds. It is proposed that energy investments by bacteria into anabolic processes increase under eCO2 to level microbial P-use efficiencies and that synergies with symbiotic mycorrhizas further enhance the competition for and mineralization of organic P. Video Abstract.

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem

Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists; genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.

Rewilding with invertebrates and microbes to restore ecosystems: Present trends and future directions

Restoration ecology has historically focused on reconstructing communities of highly visible taxa while less visible taxa, such as invertebrates and microbes, are ignored. This is problematic as invertebrates and microbes make up the vast bulk of biodiversity and drive many key ecosystem processes, yet they are rarely actively reintroduced following restoration, potentially limiting ecosystem function and biodiversity in these areas.In this review, we discuss the current (limited) incorporation of invertebrates and microbes in restoration and rewilding projects. We argue that these groups should be actively rewilded during restoration to improve biodiversity, ecosystem function outcomes, and highlight how they can be used to greater effect in the future. For example, invertebrates and microbes are easily manipulated, meaning whole communities can potentially be rewilded through habitat transplants in a practice that we refer to as "whole-of-community" rewilding.We provide a framework for whole-of-community rewilding and describe empirical case studies as practical applications of this under-researched restoration tool that land managers can use to improve restoration outcomes.We hope this new perspective on whole-of-community restoration will promote applied research into restoration that incorporates all biota, irrespective of size, while also enabling a better understanding of fundamental ecological theory, such as colonization and competition trade-offs. This may be a necessary consideration as invertebrates that are important in providing ecosystem services are declining globally; targeting invertebrate communities during restoration may be crucial in stemming this decline.

Highly decomposed organic carbon mediates the assembly of soil communities with traits for the biodegradation of chlorinated pollutants

To improve biodegradation strategies for chlorinated pollutants, the roles of soil organic matter and microbial function need to be clarified. It was hypothesised that microbial degradation of specific organic fractions in soils enhance community metabolic capability to degrade chlorinated pollutants. This field study used historic records of dieldrin concentrations since 1988 and established relationships between dieldrin dissipation and soil carbon fractions together with bacterial and fungal diversity in surface soils of Kurosol and Chromosol. Sparse partial least squares analysis linked dieldrin dissipation to metabolic activities associated with the highly decomposed carbon fraction. Dieldrin dissipation, after three decades of natural attenuation, was associated with increased bacterial species fitness for the decomposition of recalcitrant carbon substrates including synthetic chlorinated pollutants. These metabolic capabilities were linked to the decomposed carbon fraction, an important driver for the microbial community and function. Common bacterial traits among taxonomic groups enriched in samples with high dieldrin dissipation included their slow growth, large genome and complex metabolism which supported the notion that metabolic strategies for dieldrin degradation evolved in an energy-low soil environment. The findings provide new perspectives for bioremediation strategies and suggest that soil management should aim at stimulating metabolism at the decomposed, fine carbon fraction.

A pioneer calf foetus microbiome

Foetus sterility until parturition is under debate due to reports of microorganisms in the foetal environment and meconium. Sufficient controls to overcome sample contamination and provide direct evidence of microorganism viability in the pre-rectal gastrointestinal tract (GIT) have been lacking. We conducted molecular and culture-based analyses to investigate the presence of a microbiome in the foetal GIT of calves at 5, 6 and 7 months gestation, while controlling for contamination. The 5 components of the GIT (ruminal fluid, ruminal tissue, caecal fluid, caecal tissue and meconium) and amniotic fluid were found to contain a pioneer microbiome of distinct bacterial and archaeal communities. Bacterial and archaeal richness varied between GIT components. The dominant bacterial phyla in amniotic fluid differed to those in ruminal and caecal fluids and meconium. The lowest bacterial and archaeal abundances were associated with ruminal tissues. Viable bacteria unique to the ruminal fluids, which were not found in the controls from 5, 6 and 7 months gestation, were cultured, subcultured, sequenced and identified. We report that the foetal GIT is not sterile but is spatially colonised before birth by a pioneer microbiome.

Physics of Nuclei: Key Role of an Emergent Symmetry

We show through first-principles nuclear structure calculations that the special nature of the strong nuclear force determines highly regular patterns heretofore unrecognized in nuclei that can be tied to an emergent approximate symmetry. This symmetry is ubiquitous and mathematically tracks with a symplectic symmetry group. This, in turn, has important implications for understanding the physics of nuclei: we find that nuclei are made of only a few equilibrium shapes, deformed or not, with associated vibrations and rotations. It also opens the path for ab initio large-scale modeling of open-shell intermediate-mass nuclei without the need for renormalized interactions and effective charges.

Town-scale microbial sewer community and H2S emissions response to common chemical and biological dosing treatments

Controlling hydrogen sulfide (H₂S) odors and emissions using a single, effective treatment across a town-scale sewer network is a challenge faced by many water utilities. Implementation of a sewer diversion provided the opportunity to compare the effectiveness of magnesium hydroxide (Mg(OH)₂) and two biological dosing compounds (Bioproducts A and B), with different modes of action (MOA), in a field-test across a large sewer network. Mg(OH)₂ increases sewer pH allowing suppression of H₂S release into the sewer environment while Bioproduct A acts to disrupt microbial communication through quorum sensing (QS), reducing biofilm integrity. Bioproduct B reduces H₂S odors by scouring the sewer of fats, oils and grease (FOGs), which provide adhesion points for the microbial biofilm. Results revealed that only Mg(OH)₂ altered the microbial community structure and reduced H₂S emissions in a live sewer system, whilst Bioproducts A and B did not reduce H₂S emissions or have an observable effect on the composition of the microbial community at the dosed site. Study results recommend in situ testing of dosing treatments before implementation across an operational system.

Exercise improves metabolic function and alters the microbiome in rats with gestational diabetes

Gestational diabetes mellitus (GDM) is a common pregnancy complication, particularly prevalent in obese women. Importantly, exercise has beneficial impacts on maternal glucose control and may prevent GDM in "at-risk" women. We aimed to determine whether a high-fat diet (HFD) exacerbates metabolic dysfunction and alters gut microbiome in GDM and whether endurance exercise prevents these changes. Uteroplacental insufficiency was induced by bilateral uterine vessel ligation (Restricted) or sham (Control) surgery on E18 in Wistar-Kyoto rats. Female offspring were fed a Chow or HFD (23% fat) from weaning (5 weeks) and at 16 weeks randomly allocated to remain Sedentary or to an exercise protocol of either Exercise prior to and during pregnancy (Exercise); or Exercise during pregnancy only (PregEx). Females were mated (20 weeks) and underwent indirect calorimetry (embryonic day 16; E16), glucose tolerance testing (E18), followed by 24-hr feces collection at E19 (n = 8-10/group). HFD consumption in female rats with GDM exacerbated the adverse metabolic adaptations to pregnancy and altered gut microbial populations. Specifically, the Firmicutes-to-Bacteroidetes ratio was increased, due to an underlying change in abundance of the orders Clostridiales and Bacteroidales. Maternal Exercise, but not PregEx, prevented the development of metabolic dysfunction, increased pancreatic β-cell mass, and prevented the alteration of the gut microbiome in GDM females. Our findings suggest that maternal exercise and diet influence metabolic and microbiome dysfunction in females with GDM, which may impact long-term maternal and offspring health.

Multiple Shape Coexistence in ^{110,112}Cd

From detailed spectroscopy of ^{110}Cd and ^{112}Cd following the β^{+}/electron-capture decay of ^{110,112}In and the β^{-} decay of ^{112}Ag, very weak decay branches from nonyrast states are observed. The transition rates determined from the measured branching ratios and level lifetimes obtained with the Doppler-shift attenuation method following inelastic neutron scattering reveal collective enhancements that are suggestive of a series of rotational bands. In ^{110}Cd, a γ band built on the shape-coexisting intruder configuration is suggested. For ^{112}Cd, the 2^{+} and 3^{+} intruder γ-band members are suggested, the 0_{3}^{+} band is extended to spin 4^{+}, and the 0_{4}^{+} band is identified. The results are interpreted using beyond-mean-field calculations employing the symmetry conserving configuration mixing method with the Gogny D1S energy density functional and with the suggestion that the Cd isotopes exhibit multiple shape coexistence.

Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity

Organic and inorganic amendments with equivalent nutrient content may have comparable fertilizer effects on crop yield, but their effects on the soil microbial community and subsequent plant-soil-microbe interactions in this context are unknown. This experiment aimed to understand the relationship between soil microbial communities, soil physicochemical characteristics and crop performance after addition of amendments to soil. Poultry litter and synthetic fertilizer with balanced total nitrogen (N) content equivalent to 1,200 kg ha⁻¹ were added to the topsoil (0–10 cm) or subsoil layer (20–30 cm) of repacked soil columns. Wheat plants were grown until maturity. Soil samples were taken at Zadoks 87–91 (76 days after sowing) for analysis of bacterial and fungal communities using 16S and ITS amplicon sequencing. The interaction between amendment type and placement depth had significant effects on bacterial and fungal community structure and diversity in the two soil layers. Addition of poultry litter and fertilizer stimulated or suppressed different taxa in the topsoil and subsoil leading to divergence of these layers from the untreated control. Both amendments reduced microbial community richness, diversity and evenness in the topsoil and subsoil compared to the nil-amendment control, with these reductions in diversity being consistently negatively correlated with plant biomass (root and shoot weight, root length, grain weight) and soil fertility (soil NH₄⁺, shoot N). These results indicate that in this experimental system, the soil microbial diversity was correlated negatively with plant productivity.

Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology

Understanding how biotic and abiotic factors govern the assembly of rhizosphere-microbial communities is a long-standing goal in microbial ecology. In phytoremediation research, where plants are used to remediate heavy metal-contaminated soils, a deeper understanding of rhizosphere-microbial ecology is needed to fully exploit the potential of microbial-assisted phytoremediation. This study investigated whether Grime's competitor/stress-tolerator/ruderal (CSR) theory could be used to describe the impact of cadmium (Cd) and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the assembly of soil-bacterial communities using Illumina 16S rRNA profiling and the predictive metagenomic-profiling program, PICRUSt. Using predictions based on CSR theory, we hypothesized that Cd and the presence of a rhizosphere would affect community assembly. We predicted that the additional resource availability in the rhizosphere would enrich for competitive life strategists, while the presence of Cd would select for stress-tolerators. Traits identified as competitive followed CSR predictions, discriminating between rhizosphere and bulk-soil communities whilst stress-tolerance traits increased with Cd dose, but only in bulk-soil communities. These findings suggest that a bacterium's competitive attributes are critical to its ability to occupy and proliferate in a Cd-contaminated rhizosphere. Ruderal traits, which relate to community re-colonization potential, were synergistically decreased by the presence of the rhizosphere and Cd dose. Taken together this microcosm study suggests that the CSR theory is broadly applicable to microbial communities. Further work toward developing a simplified and robust strategy for microbial CSR classification will provide an ecologically meaningful framework to interpret community-level changes across a range of biomes.

Understanding microbiomes through trait-based ecology

Ecology is the study of the interactions amongst organisms and their environment1. In microbial ecology, a major goal is to understand how environmental microbiomes impact ecosystem health and function. This desire to mechanistically link micro and macro processes is increasingly highlighting the importance of functional ecology, which aims to develop an understanding of relationships using functional traits, as opposed to species names. A functional trait may be any morphological or physiological trait that influences the performance or fitness of an individual in a given environment, such as regeneration time, size, antibiotic production or motility2. Although it is not possible to measure a given trait for each individual within an environmental microbiome, community-level functional traits can be derived from the community metagenome either directly via shotgun sequencing or predictively (for bacteria) from 16S rRNA profiles3. In understanding environmental microbiomes, functional traits have unique properties that can be utilised to (1) compare microbiomes using an ecological framework, (2) understand processes governing community assembly, and (3) build predictive ecological models.

Spermidine promotes Bacillus subtilis biofilm formation by activating expression of the matrix regulator slrR

Ubiquitous polyamine spermidine is not required for normal planktonic growth of Bacillus subtilis but is essential for robust biofilm formation. However, the structural features of spermidine required for B. subtilis biofilm formation are unknown and so are the molecular mechanisms of spermidine-stimulated biofilm development. We report here that in a spermidine-deficient B. subtilis mutant, the structural analogue norspermidine, but not homospermidine, restored biofilm formation. Intracellular biosynthesis of another spermidine analogue, aminopropylcadaverine, from exogenously supplied homoagmatine also restored biofilm formation. The differential ability of C-methylated spermidine analogues to functionally replace spermidine in biofilm formation indicated that the aminopropyl moiety of spermidine is more sensitive to C-methylation, which it is essential for biofilm formation, but that the length and symmetry of the molecule is not critical. Transcriptomic analysis of a spermidine-depleted B. subtilis speD mutant uncovered a nitrogen-, methionine-, and S-adenosylmethionine-sufficiency response, resulting in repression of gene expression related to purine catabolism, methionine and S-adenosylmethionine biosynthesis and methionine salvage, and signs of altered membrane status. Consistent with the spermidine requirement in biofilm formation, single-cell analysis of this mutant indicated reduced expression of the operons for production of the exopolysaccharide and TasA protein biofilm matrix components and SinR antagonist slrR. Deletion of sinR or ectopic expression of slrR in the spermidine-deficient ΔspeD background restored biofilm formation, indicating that spermidine is required for expression of the biofilm regulator slrR. Our results indicate that spermidine functions in biofilm development by activating transcription of the biofilm matrix exopolysaccharide and TasA operons through the regulator slrR.

Characteristics of metal-tolerant plant growth-promoting yeast (Cryptococcus sp. NSE1) and its influence on Cd hyperaccumulator Sedum plumbizincicola

Plant growth-promoting yeasts are often over looked as a mechanism to improve phytoremediation of heavy metals. In this study, Cryptococcus sp. NSE1, a Cd-tolerant yeast with plant growth capabilities, was isolated from the rhizosphere of the heavy metal hyperaccumulator Sedum plumbizincicola. The yeast exhibited strong tolerance to a range of heavy metals including Cd, Cu, and Zn on plate assays. The adsorption rate Cd, Cu, Zn by NSE1 was 26.1, 13.2, and 25.2 %, respectively. Irregular spines were formed on the surface of NSE1 when grown in MSM medium supplemented with 200 mg L(-1) Cd. NSE1 was capable of utilizing 1-aminocyclopropane-1-carboxylate (ACC) as a sole nitrogen source and was capable of solubilization of inorganic phosphate at rates of 195.2 mg L(-1). Field experiments demonstrated that NSE1 increased phytoremediation by increasing the biomass of Cd hyperaccumulator S. plumbizincicola (46 %, p < 0.05) during phytoremediation. Overall, Cd accumulation by S. plumbizincicola was increased from 19.6 to 31.1 mg m(-2) though no difference in the concentration of Cd in the shoot biomass was observed between NSE1 and control. A Cd accumulation ratio of 38.0 % for NSE1 and 17.2 % for control was observed. The HCl-extractable Cd and CaCl2-extractable Cd concentration in the soil of the NSE1 treatment were reduced by 39.2 and 29.5 %, respectively. Community-level physiology profiling, assessed using Biolog Eco plates, indicated functional changes to the rhizosphere community inoculated with NSE1 by average well color development (AWCD) and measurement of richness (diversity). Values of Shannon-Weiner index, Simpson index, and McIntosh index showed a slight but no significant increases. These results indicate that inoculation of NSE1 could increase the shoot biomass of S. plumbizincicola, enhance the Cd accumulation in S. plumbizincicola, and decrease the available heavy metal content in soils significantly without overall significant changes to the microbial community.

Superdeformed and Triaxial States in ^{42}Ca

Shape parameters of a weakly deformed ground-state band and highly deformed slightly triaxial sideband in ^{42}Ca were determined from E2 matrix elements measured in the first low-energy Coulomb excitation experiment performed with AGATA. The picture of two coexisting structures is well reproduced by new state-of-the-art large-scale shell model and beyond-mean-field calculations. Experimental evidence for superdeformation of the band built on 0_{2}^{+} has been obtained and the role of triaxiality in the A∼40 mass region is discussed. Furthermore, the potential of Coulomb excitation as a tool to study superdeformation has been demonstrated for the first time.

Shape coexistence in the neutron-deficient even-even (182-188)Hg isotopes studied via coulomb excitation

Coulomb-excitation experiments to study electromagnetic properties of radioactive even-even Hg isotopes were performed with 2.85  MeV/nucleon mercury beams from REX-ISOLDE. Magnitudes and relative signs of the reduced E2 matrix elements that couple the ground state and low-lying excited states in Hg182-188 were extracted. Information on the deformation of the ground and the first excited 0+ states was deduced using the quadrupole sum rules approach. Results show that the ground state is slightly deformed and of oblate nature, while a larger deformation for the excited 0+ state was noted in Hg182,184. The results are compared to beyond mean field and interacting-boson based models and interpreted within a two-state mixing model. Partial agreement with the model calculations was obtained. The presence of two different structures in the light even-mass mercury isotopes that coexist at low excitation energy is firmly established.

Collective structure in 94Zr and subshell effects in shape coexistence

Based on results from a measurement of weak decay branches observed following the β- decay of 94Y and on lifetime data from a study of 94Zr by inelastic neutron scattering, collective structure is deduced in the closed-subshell nucleus 94Zr. These results establish shape coexistence in 94Zr. The role of subshells for nuclear collectivity is suggested to be important.

New features of shape coexistence in ;{152}Sm

Excited states in ;{152}Sm have been investigated with the ;{152}Sm(n,n;{'}gamma) reaction. The lowest four negative-parity band structures have been characterized in detail with respect to their absolute decay properties. Specifically, a new K;{pi} = 0;{-} band has been assigned with its 1;{-} band head at 1681 keV. This newly observed band has a remarkable similarity in its E1 transition rates for decay to the first excited K;{pi} = 0;{+} band at 684 keV to the lowest K;{pi} = 0;{-} band and its decay to the ground-state band. Based on these decay properties, as well as energy considerations, this new band is assigned as a K;{pi} = 0;{-} octupole excitation based on the K;{pi} = 0_{2};{+} state. An emerging pattern of repeating excitations built on the 0_{2};{+} level similar to those built on the ground state may indicate that ;{152}Sm is a complex example of shape coexistence rather than a critical point nucleus.

Implications of deformation and shape coexistence for the nuclear shell model

The successes of the nuclear shell model in explaining the stability properties of magic nuclei are challenged by the observation of rotational bands for which the sequential filling of single-particle energy levels of the spherical shell model are not respected. This Letter proposes criteria for identifying the shell-model configurations appropriate for describing such bands of states.

Low-energy coexisting band in 154Gd

A low-energy coexisting band Jpi (Ex keV) 0(+) (1182), 2(+) (1418), 4(+) (1701) is identified in the deformed nucleus, 154Gd. Detailed gamma-ray spectroscopy following the beta decays of 154Eu (J=3), (g,m(1),m(2))154Tb (J=0,3,7) is used to establish this structure. The structure is explained in terms of the pairing and deformation degrees of freedom, a "pairing isomer," which results from the nu[505] upward arrow Nilsson intruder orbital.

A case-control study of respiratory disease in Thoroughbred racehorses in Sydney, Australia

In order to investigate the role of infectious agents in the aetiology of lower respiratory tract disease in Thoroughbred racehorses, a matched case-control study was conducted. Cases were identified by the presence of coughing, and were compared to a control population matched on time of sample collection and location within the same training establishment. Tracheal wash samples were collected from 100 cases and 148 controls. Case horses were more likely than controls to have endoscopic and cytological evidence of airway inflammation. There was no significant association between serological evidence of infection by commonly implicated respiratory viruses and coughing. Similarly, mycoplasma were rarely isolated and were not associated with disease. In contrast, there was a strong association between isolation of greater than a total of 10(3) colony-forming units/ml of tracheal wash and coughing. Individual bacterial species associated with disease included Streptococcus zooepidemicus, Streptococcus pneumoniae, Streptococcus suis, Streptococcus sanguis, Pasteurella spp and Bordetella bronchiseptica. This study provides evidence of the role of bacterial infection in the aetiology of lower respiratory tract inflammation in racehorses. However, in 58% of cases, few or no bacteria were isolated. Hence, at the time of identification of disease, there was no evidence of viral, bacterial or mycoplasmal infection in the majority of coughing horses. The aetiology of the signs observed in these horses requires further investigation.

Reactive enols in synthesis 2. Synthesis of (+)-latifolic acid and (+)-latifoline

We describe a short, enantioselective synthesis of the naturally occurring pyrrolizidine alkaloid (+)-latifoline (1) employing a tandem [3,3] sigmatropic rearrangement/[1,2] allyl shift as a key step in constructing (+)-latifolic acid (4).

Racehorse injuries, clinical problems and fatalities recorded on British racecourses from flat racing and National Hunt racing during 1996, 1997 and 1998

For improvements to the safety and welfare of racehorses to be possible, it is essential to have access to basic descriptive information about the veterinary incidents encountered during horseracing. A 3 year surveillance study (1996-1998) was conducted by The Jockey Club into racing injuries, other postrace clinical problems and fatalities from all 59 British racecourses (mainland Britain only) to identify risk factors. During the survey there were 222,993 racing starts: 106,897 starts in flat races on turf (47.9%), 26,519 starts in flat races on all-weather surfaces (11.9%), 30,932 starts in chases on turf (13.9%), 51,786 starts in hurdle races on turf (23.2%) and 6,859 starts in National Hunt flat races (3.1%). Information was recorded about age of horses, racing surfaces and clinical events observed or attended by a veterinary team of 2 clinicians and one veterinary surgeon employed by the racing authority. Of the 2358 clinical events reported (1.05% of all starts), 1937 involved the musculoskeletal system and 421 involved other body systems. Six hundred and fifty-seven incidents (0.29% of starts) resulted in death or euthanasia. Eighty-one percent of limb injury reports involved forelimbs and 46% involved flexor tendons/suspensory ligaments. Nonlimb problems included epistaxis (0.83/1000 starts), 'exhausted horse syndrome' (0.47/1000 starts) and paroxysmal atrial fibrillation (0.20/1000 starts). Incidents including fatalities per 1000 starts were 24.7 from chases, 19.45 from hurdle races, 8.46 from National Hunt flat races and 3.97 from flat races. The overall tendon injury was higher in chases than in hurdle races, even though age-specific rates of tendon injury were higher in hurdle races than in chases. The risk of injuries per start increased significantly with age, while softer racing surfaces were associated with fewer fatalities and injuries than firmer surfaces. The survey described in this paper has provided an up-to-date description of the fatal and non-fatal horseracing incidents under conditions on mainland Britain, enabling progress to be made towards improving the safety and welfare of racehorses.

Relationship of the degree of goniodysgenesis and other ocular measurements to glaucoma in Great Danes

OBJECTIVES

To assess the association between goniodysgenesis, ocular measurements, and glaucoma in Great Danes.

ANIMALS

180 Great Danes.

PROCEDURE

Eye examination and measurements were obtained from 180 Great Danes; for 30 of these dogs, depth of the anterior chamber, vitreal body length, and total depth of the globe were also measured. These data were merged with electronic pedigree information on 43,371 kennel club registered Great Danes. Relationships among goniodysgenesis, ocular measurements, and glaucoma and the heritability of goniodysgenesis were estimated.

RESULTS

The degree of goniodysgenesis was significantly and positively associated with the likelihood of glaucoma. There was a significant association between the degree of goniodysgenesis in offspring and parents. The estimated heritability of the degree of goniodysgenesis was 0.52. The depth of the anterior chamber of the eye was also a good predictor of goniodysgenesis (ie, the dog was almost certain to have glaucoma if the depth was < 3.7 mm). If both parents had goniodysgenesis < 70%, then with 95% confidence, the occurrence of glaucoma in the ensuing offspring would be < 4/1000. This strategy translates to ensuring that the depth of the anterior chamber of the eye is > 3.7 mm for both parents.

CONCLUSIONS AND CLINICAL RELEVANCE

The strong and significant correlation among goniodysgenesis, other eye measurements, and glaucoma and the significant heritability of goniodysgenesis suggests that glaucoma may be heritable in Great Danes. If so, glaucoma can be controlled by breeding only from sires and dams with a minimum degree of goniodysgenesis.

An expeditious approach toward the total synthesis of CP-263,114

[reaction: see text] Assembly of the carbocyclic core of CP-263,114 has been accomplished efficiently and in high yield. Key steps include a phenolic oxidation/intramolecular Diels-Alder sequence, tandem radical cyclization, and the late-stage fragmentation of a densely functionalized isotwistane skeleton.

Evolution of a synthetic approach to CP-263,114

[structure: see text] Three different approaches to the carbocyclic core of CP-263,114 are presented that illustrate a strategic evolution from an oxy-Cope rearrangement to variants of the Wharton fragmentation.

Autoregulation of cell-specific MAP kinase control of the tryptophan hydroxylase promoter

The neurotransmitter serotonin controls a wide range of biological systems, including its own synthesis and release. As the rate-limiting enzyme in serotonin biosynthesis, tryptophan hydroxylase (TPH) is a potential target for this autoregulation. Using the serotonergic neuron-like CA77 cell line, we have demonstrated that treatment with a 5-hydroxytryptamine autoreceptor agonist, CGS 12066A, can lower TPH mRNA levels and promoter activity. We reasoned that this repression might involve inhibition of MAP kinases, since 5-HT1 receptors can increase mitogen-activated protein (MAP) kinase phosphatase levels. To test this hypothesis, we first showed that the TPH promoter can be activated 20-fold by mitogen-activated extracellular-signal regulated kinase kinase kinase (MEKK), an activator of MAP kinases. This activation was then blocked by CGS 12066A. The maximal MAP kinase and CGS repression regulatory region was mapped to between -149 and -45 base pairs upstream of the transcription start site. The activation by MEKK appears to be cell-specific, because MEKK did not activate the TPH promoter in nonneuronal cell lines. At least part, but not all, of the MAP kinase responsiveness was mapped to an inverted CCAAT box that binds the transcription factor NF-Y. These data suggest a model for the autoregulation of serotonin biosynthesis by repression of MAP kinase stimulation of the TPH promoter.

Progress toward the total synthesis of kalihinane diterpenoids

[see structure]. Studies toward the total synthesis of marine diterpenoids isolated from Acanthella sp., e.g., kalihinol A, are described. Efficient construction of the functionalized trans-decalin core (11) is achieved through intramolecular Diels-Alder cyclization followed by diastereoselective epoxidation and aziridination.

Efficient syntheses of novel C2'-alkylated (+/-)-K252a analogues

Recent efforts in our laboratories have resulted in a synthetic approach toward C2'-alkylated K252a analogues via extension of a K252a cyclofuranosylation strategy. The bis-indole-N-glycosidic coupling of 6-N-(3,4-dimethoxybenzyl)-staurosporinone (21) with a number of highly functionalized carbohydrates has given access to previously unattainable, biologically relevant analogues.