Restoration age and reintroduced bison may shape soil bacterial communities in restored tallgrass prairies

Knowledge of how habitat restoration shapes soil microbial communities often is limited despite their critical roles in ecosystem function. Soil community diversity and composition change after restoration, but the trajectory of these successional changes may be influenced by disturbances imposed for habitat management. We studied soil bacterial communities in a restored tallgrass prairie chronosequence for >6 years to document how diversity and composition changed with age, management through fire, and grazing by reintroduced bison, and in comparison to pre-restoration agricultural fields and remnant prairies. Soil C:N increased with restoration age and bison, and soil pH first increased and then declined with age, although bison weakened this pattern. Bacterial richness and diversity followed a similar hump-shaped pattern as soil pH, such that the oldest restorations approached the low diversity of remnant prairies. β-diversity patterns indicated that composition in older restorations with bison resembled bison-free sites, but over time they became more distinct. In contrast, younger restorations with bison maintained unique compositions throughout the study, suggesting bison disturbances may cause a different successional trajectory. We used a novel random forest approach to identify taxa that indicate these differences, finding that they were frequently associated with bacteria that respond to grazing in other grasslands.

Agroecosystem edge effects on vegetation, soil properties, and the soil microbial community in the Canadian prairie

Edge effects resulting from adjacent land uses are poorly understood in agroecosystems yet understanding above and belowground edge effects is crucial for maintaining ecosystem function. The aim of our study was to examine impacts of land management on aboveground and belowground edge effects, measured by changes in plant community, soil properties, and soil microbial communities across agroecosystem edges. We measured plant composition and biomass, soil properties (total carbon, total nitrogen, pH, nitrate, and ammonium), and soil fungal and bacterial community composition across perennial grassland-annual cropland edges. Edge effects due to land management were detected both aboveground and belowground. The plant community at the edge was distinct from the adjacent land uses, where annual, non-native, plant species were abundant. Soil total nitrogen and carbon significantly decreased across the edge (P < 0.001), with the highest values in the perennial grasslands. Both bacterial and fungal communities were different across the edge with clear changes in fungal communities driven directly and indirectly by land management. A higher abundance of pathogens in the more heavily managed land uses (i.e. crop and edge) was detected. Changes in plant community composition, along with soil carbon and nitrogen also influenced the soil fungal community across these agroecosystems edges. Characterizing edge effects in agroecosystem, especially those associated with soil microbial communities, is an important first step in ensuring soil health and resilience in these managed landscapes.

Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines

Holobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part. The root was primarily dominated by stochastic community assembly processes, which is inconsistent with previous studies that suggest of a highly selective root environment. Leaf assembly processes were primarily stochastic as well. In contrast, the rhizosphere was a highly selective environment. The dominant rhizosphere selection process leads to more similar communities. Assembly processes in all plant compartments were dependent on plant growth stage with little line effect on community assembly. The foundations of assembly in the leaf were due to the harsh environment, leading to dominance of stochastic effects, whereas the stochastic effects in the root interior likely arise due to competitive exclusion or priority effects. Engineering canola microbiomes should occur during periods of strong selection assuming strong selection could promote beneficial bacteria. For example, engineering the microbiome to resist pathogens, which are typically aerially born, should focus on the flowering period, whereas microbiomes to enhance yield should likely be engineered postflowering as the rhizosphere is undergoing strong selection. IMPORTANCE In order to harness the microbiome for more sustainable crop production, we must first have a better understanding of microbial community assembly processes that occurring during plant development. This study examines the bacterial community assembly processes of the leaf, root, and rhizosphere of eight different lines of Brassica napus over the growing season. The influence of growth stage and B. napus line were examined in conjunction with the assembly processes. Understanding what influences the assembly processes of crops might allow for more targeted breeding efforts by working with the plant to manipulate the microbiome when it is undergoing the strongest selection pressure.

An intensive multilocation temporal dataset of fungal and bacterial communities in the root and rhizosphere of Brassica napus

The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of bacterial and fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. We sequenced the bacterial 16S ribosomal RNA gene generating a total of 127.7 million reads and the fungal internal transcribed spacer (ITS) region generating 113.4 million reads. 14,944 unique fungal amplicon sequence variants (ASV) were detected, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. We detected 10,882 unique bacterial ASVs with an average of 249 ASVs per sample. Temporal, site-to-site, and line-driven variability were key determinants of microbial community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.

An intensive multilocation temporal dataset of fungal communities in the root and rhizosphere of Brassica napus

The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. 14,944 unique amplicon sequence variants (ASV) were detected based on the internal transcribed spacer region, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. Temporal, site-to-site, and line-driven variability were key determinants of fungal community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.

A survey of invasive plants on grassland soil microbial communities and ecosystem services

Invasive plants can cause changes in the structure and function of the ecosystem being invaded. Any changes in ecosystem diversity and community composition will likely alter ecosystem services provided by that ecosystem. However, how these ecosystem services may change is poorly understood. To elucidate how these ecosystem services will change with invasion, we sampled 561 plots undergoing invasion by smooth brome (Bromus inermis) and four other invasive species at a native Rough Fescue prairie located near Saskatoon, Saskatchewan, Canada. Soil and plant surveys were undertaken weekly for 26 weeks between May of 2014 and November of 2014, or the growing season. We measured a suite of ecosystem services, including greenhouse gasses, extracellular enzyme function, forage production, glyphosate degradation and decomposition. Furthermore, soil physical and chemical properties were measured, and soil bacterial and fungal communities were sequenced. This is a large and multifaceted dataset with complex temporal and spatial attributes which can be used to answer numerous questions regarding the functioning of prairie ecosystems and how invasive species will impact that functioning.

Measurement(s)	invasive species • native species • ecosystem decay • greenhouse gas • DNA
Technology Type(s)	Survey • monitoring device • DNA sequencing
Factor Type(s)	geographic location • sampling date
Sample Characteristic - Environment	prairie • soil
Sample Characteristic - Location	Saskatoon

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11898213

Core and Differentially Abundant Bacterial Taxa in the Rhizosphere of Field Grown Brassica napus Genotypes: Implications for Canola Breeding

Modifying the rhizosphere microbiome through targeted plant breeding is key to harnessing positive plant-microbial interrelationships in cropping agroecosystems. Here, we examine the composition of rhizosphere bacterial communities of diverse Brassica napus genotypes to identify: (1) taxa that preferentially associate with genotypes, (2) core bacterial microbiota associated with B. napus, (3) heritable alpha diversity measures at flowering and whole growing season, and (4) correlation between microbial and plant genetic distance among canola genotypes at different growth stages. Our aim is to identify and describe signature microbiota with potential positive benefits that could be integrated in B. napus breeding and management strategies. Rhizosphere soils of 16 diverse genotypes sampled weekly over a 10-week period at single location as well as at three time points at two additional locations were analyzed using 16S rRNA gene amplicon sequencing. The B. napus rhizosphere microbiome was characterized by diverse bacterial communities with 32 named bacterial phyla. The most abundant phyla were Proteobacteria, Actinobacteria, and Acidobacteria. Overall microbial and plant genetic distances were highly correlated (R = 0.65). Alpha diversity heritability estimates were between 0.16 and 0.41 when evaluated across growth stage and between 0.24 and 0.59 at flowering. Compared with a reference B. napus genotype, a total of 81 genera were significantly more abundant and 71 were significantly less abundant in at least one B. napus genotype out of the total 558 bacterial genera. Most differentially abundant genera were Proteobacteria and Actinobacteria followed by Bacteroidetes and Firmicutes. Here, we also show that B. napus genotypes select an overall core bacterial microbiome with growth-stage-related patterns as to how taxa joined the core membership. In addition, we report that sets of B. napus core taxa were consistent across our three sites and 2 years. Both differential abundance and core analysis implicate numerous bacteria that have been reported to have beneficial effects on plant growth including disease suppression, antifungal properties, and plant growth promotion. Using a multi-site year, temporally intensive field sampling approach, we showed that small plant genetic differences cause predictable changes in canola microbiome and are potential target for direct and indirect selection within breeding programs.

An Initial Study of Reading and Comprehension Rates for Students who Received Optical Devices

Initial reading speeds across grades show points at which children with low vision are at risk of developing low literacy skills. Outcome group measures showed that children who received optical devices increased their silent reading speeds and comprehension rates. Findings indicate the provision of optical devices offer a benefit for deciphering text but not for the mechanics of reading.

Providing Access to the Visual Environment: A Model of Low Vision Services for Children

Providing Access to the Visual Environment (Project PAVE) is a statewide multidisciplinary project that provides low vision services to children aged 3–21 in Tennessee. This article describes the project's administrative, direct service, and research components and the philosophy on which it is based.

Analysis of a National Programme for Selective Internal Radiation Therapy for Colorectal Cancer Liver Metastases

AIMS

Patients with chemotherapy-refractory colorectal cancer liver metastases have limited therapeutic options. Selective internal radiation therapy (SIRT) delivers yttrium 90 microspheres as a minimally invasive procedure. This prospective, single-arm, observational, service-evaluation study was part of National Health Service England Commissioning through Evaluation.

METHODS

Patients eligible for treatment had histologically confirmed carcinoma with liver-only/liver-dominant metastases with clinical progression during or following oxaliplatin-based and irinotecan-based chemotherapy. All patients received SIRT plus standard of care. The primary outcome was overall survival; secondary outcomes included safety, progression-free survival (PFS) and liver-specific PFS (LPFS).

RESULTS

Between December 2013 and March 2017, 399 patients were treated in 10 centres with a median follow-up of 14.3 months (95% confidence interval 9.2-19.4). The median overall survival was 7.6 months (95% confidence interval 6.9-8.3). The median PFS and LPFS were 3.0 months (95% confidence interval 2.8-3.1) and 3.7 months (95% confidence interval 3.2-4.3), respectively. During the follow-up period, 143 patients experienced an adverse event and 8% of the events were grade 3.

CONCLUSION

Survival estimates from this pragmatic study show clinical outcomes attainable in the National Health Service comparable with previously published data. This study shows the value of a registry-based commissioning model to aid national commissioning decisions for highly specialist cancer treatments.

Analysis of the complement sensitivity of oral treponemes and the potential influence of FH binding, FH cleavage and dentilisin activity on the pathogenesis of periodontal disease

Treponema denticola, a periopathogen, evades complement-mediated killing by binding the negative complement regulatory protein factor H (FH) to its surface via the FhbB protein. Paradoxically, bound FH is cleaved by T. denticola's dentilisin protease, a process hypothesized to trigger localized dysregulation of complement activation in periodontal pockets. The ability of other oral treponemes to evade complement-mediated killing and bind and cleave FH has not been assessed. In this report, we demonstrate that representative isolates of Treponema socranskii, Treponema medium, Treponema pectinovorum and Treponema maltophilum are also serum resistant, whereas Treponema vincentii and Treponema amylovorum are serum sensitive. Although T. denticola's ability to evade complement-mediated killing is strictly dependent on FH binding, other serum-resistant treponemal species lack FhbB and do not bind FH, indicating an FH-independent mechanism of complement evasion. To assess the influence of FhbB sequence variation on FH binding and cleavage by T. denticola, fhbB sequences were determined for 30 isolates. Three distinct phyletic types were identified. All T. denticola strains bound FH and were serum resistant, but differences in binding kinetics, dentilisin activity and FH cleavage ability were observed. Based on these analyses, we hypothesize that the composition of the T. denticola population is a determining factor that influences the progression and severity of periodontal disease.

A repetitive movement detector used for automatic monitoring and quantification of scratching in mice

We have designed an economical non-invasive movement detector for small animal studies and used it for monitoring and quantifying itch in mice. The system is based on a sensitive force transducer positioned below a recording platform holding a lightweight polystyrene recording box in which an animal is placed. A programmed micro-controller is used to discriminate between non-specific movement, grooming behaviour, and scratching movements made by the animal's hind limb. Following sub-dermal injection of histamine receptor agonists into the neck of a mouse, dose-related scratching occurred which was detected and quantified. There was 91% correlation between bouts of scratching as counted manually from playback of the video recording and recorded by the detector. The detector was also able rapidly to count the individual scratch movements of the hind limb that comprise a bout, with 95% accuracy in comparison with manual counting during slow motion playback of video tape, something that is impossible for an unaided observer to achieve because individual scratch movements are too fast to discriminate by eye. Separate detectors were used for the efficient non-invasive study of four animals simultaneously, and this number could easily be increased by adding more platforms. The system could also be modified to record the animal's position within the box, which would be of value in studies involving exploratory behaviour. In summary, the non-invasive multichannel repetitive movement detector will be very useful for accurate measurement of scratching during pruritus studies in small animals, with considerable savings in staff time and effort. It should therefore be a valuable tool for helping to investigate pruritus and in the evaluation of anti-pruritic drugs.

Bispectral index monitoring for conscious sedation in intervention: better, safer, faster

AIM

The aim of this study was to compare subjective (Ramsay sedation score, RSS) with objective electroencephalogram-based bispectral index (BIS) assessment, and to validate the appropriate BIS range for measurement of conscious sedation in interventional procedures.

MATERIALS AND METHODS

One hundred patients undergoing sedo-analgesia (midazolam and fentanyl) for interventional gastrointestinal procedures were divided into two groups. In group A (n=30) sedation was guided by the RSS with the operator blinded to the BIS recording. In group B (n=70) the operator titrated intravenous sedation to maintain an optimal BIS, predetermined from the results in group A. Recovery time, procedure duration, physiological parameters and unplanned events were recorded in both groups.

RESULTS

There was a significant correlation between the BIS and RSS (p<0.001). BIS values of 87.2 and 80.9 corresponded to an RSS of 3 and 4, respectively. The optimal BIS level was defined as 80-85. Fifty-seven point five percent of readings were within this range in group B compared with 26.5% in group A (p<0.001). Sedation approaching general anaesthesia (BIS<60) occurred in 5.5% of patients in group A but not in group B. Mean recovery time, duration of procedure, midazolam and fentanyl doses were significantly reduced in group B. Unplanned events were reduced from 27 to 17%, but this was not statistically significant (p=0.29).

CONCLUSION

BIS monitoring enables more effective titration of sedatives to maintain a suitable level of consciousness, whilst reducing procedure time. The BIS offers an objective, safe and reliable measure of sedation, without disturbing either patient or operator. BIS monitoring raises the standard of patient care, and in our view, should be used to augment standard assessment.

Involvement of histamine H4 and H1 receptors in scratching induced by histamine receptor agonists in Balb C mice

The role of histamine H(1), H(2), H(3) and H(4) receptors in acute itch induced by histamine was investigated in female BalbC mice. Scratching was induced by intradermal injections of pruritogen into the back of the neck and "itch" assessed by quantifying the scratching evoked. Histamine (0.03-80 micromol), histamine-trifluoromethyl-toluidine (HTMT, H(1) agonist, 0.002-2 micromol), clobenpropit (H(4) agonist, H(3) antagonist, 0.002-0.6 micromol) and to a lesser extent imetit (H(3)/H(4) agonist, 0.03-3 micromol) all induced dose-dependent scratching. Dimaprit (H(2) agonist, 0.04-40 micromol) did not cause scratching. Mepyramine (H(1) antagonist, 20 mg kg(-1), i.p.) reduced scratching evoked by histamine and HTMT, but not that caused by H(3) or H(4) agonists. Thioperamide (H(3)/H(4) antagonist, 20 mg kg(-1), i.p.) reduced scratching induced by histamine, H(3) and H(4) agonists, but not that caused by HTMT. The non-sedating H(1) antagonist, terfenadine, also significantly reduced the scratching induced by the H(1) agonist, HTMT. Cimetidine (H(2) antagonist, 20 mg kg(-1), i.p.) did not affect histamine-induced scratching. These results indicate that activation of histamine H(4) receptors causes itch in mice, in addition to the previously recognised role for H(1) receptors in evoking itch. Histamine H(4) receptor antagonists therefore merit investigation as antipruritic agents.

Structural analyses of a malate dehydrogenase with a variable active site

Malate dehydrogenase specifically oxidizes malate to oxaloacetate. The specificity arises from three arginines in the active site pocket that coordinate the carboxyl groups of the substrate and stabilize the newly forming hydroxyl/keto group during catalysis. Here, the role of Arg-153 in distinguishing substrate specificity is examined by the mutant R153C. The x-ray structure of the NAD binary complex at 2.1 A reveals two sulfate ions bound in the closed form of the active site. The sulfate that occupies the substrate binding site has been translated approximately 2 A toward the opening of the active site cavity. Its new location suggests that the low catalytic turnover observed in the R153C mutant may be due to misalignment of the hydroxyl or ketone group of the substrate with the appropriate catalytic residues. In the NAD.pyruvate ternary complex, the monocarboxylic inhibitor is bound in the open conformation of the active site. The pyruvate is coordinated not by the active site arginines, but through weak hydrogen bonds to the amide backbone. Energy minimized molecular models of unnatural analogues of R153C (Wright, S. K., and Viola, R. E. (2001) J. Biol. Chem. 276, 31151-31155) reveal that the regenerated amino and amido side chains can form favorable hydrogen-bonding interactions with the substrate, although a return to native enzymatic activity is not observed. The low activity of the modified R153C enzymes suggests that precise positioning of the guanidino side chain is essential for optimal orientation of the substrate.