Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat.

The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification have been limited. This study investigated how endogenous (genome polyploidization), and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture -independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root-soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria (PGPR) in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.

Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency.

Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.

Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria.

The profound negative effect of inorganic chemical fertilizer application on rhizobacterial diversity has been well documented using 16S rRNA gene amplicon sequencing and predictive metagenomics. We aimed to measure the function and relative abundance of readily culturable putative plant growth-promoting rhizobacterial (PGPR) isolates from wheat root soil samples under contrasting inorganic fertilization regimes. We hypothesized that putative PGPR abundance will be reduced in fertilized relative to unfertilized samples. Triticum aestivum cv. Cadenza seeds were sown in a nutrient depleted agricultural soil in pots treated with and without Osmocote® fertilizer containing nitrogen-phosphorous-potassium (NPK). Rhizosphere and rhizoplane samples were collected at flowering stage (10 weeks) and analyzed by culture-independent (CI) amplicon sequence variant (ASV) analysis of rhizobacterial DNA as well as culture-dependent (CD) techniques. Rhizosphere and rhizoplane derived microbiota culture collections were tested for plant growth-promoting traits using functional bioassays. In general, fertilizer addition decreased the proportion of nutrient-solubilizing bacteria (nitrate, phosphate, potassium, iron, and zinc) isolated from rhizocompartments in wheat whereas salt tolerant bacteria were not affected. A "PGPR" database was created from isolate 16S rRNA gene sequences against which total amplified 16S rRNA soil DNA was searched, identifying 1.52% of total community ASVs as culturable PGPR isolates. Bioassays identified a higher proportion of PGPR in non-fertilized samples [rhizosphere (49%) and rhizoplane (91%)] compared to fertilized samples [rhizosphere (21%) and rhizoplane (19%)] which constituted approximately 1.95 and 1.25% in non-fertilized and fertilized total community DNA, respectively. The analyses of 16S rRNA genes and deduced functional profiles provide an in-depth understanding of the responses of bacterial communities to fertilizer; our study suggests that rhizobacteria that potentially benefit plants by mobilizing insoluble nutrients in soil are reduced by chemical fertilizer addition. This knowledge will benefit the development of more targeted biofertilization strategies.

Estimating food production in an urban landscape.

There is increasing interest in urban food production for reasons of food security, environmental sustainability, social and health benefits. In developed nations urban food growing is largely informal and localised, in gardens, allotments and public spaces, but we know little about the magnitude of this production. Here we couple own-grown crop yield data with garden and allotment areal surveys and urban fruit tree occurrence to provide one of the first estimates for current and potential food production in a UK urban setting. Current production is estimated to be sufficient to supply the urban population with fruit and vegetables for about 30 days per year, while the most optimistic model results suggest that existing land cultivated for food could supply over half of the annual demand. Our findings provide a baseline for current production whilst highlighting the potential for change under the scaling up of cultivation on existing land.

Lysis Performance of Bacteriophages with Different Plaque Sizes and Comparison of Lysis Kinetics After Simultaneous and Sequential Phage Addition.

Background: Although bacteriophages see a revival for specifically removing undesired bacteria, there is still much uncertainty about how to achieve the most rapid and long-lasting clearance. Materials and Methods: This study investigated the lysis kinetics of three distinct environmental coliphages, reproducibly forming different plaque sizes (big, medium, and small). Lysis performance by individual phages was compared with the one obtained after simultaneous or sequential addition of all three phages. Kinetics was monitored by density absorbance or by flow cytometry, with the latter having the advantage of providing higher sensitivity. Results: Plaque size happened to correlate with lysis kinetics in liquid suspensions, with phages producing big (phage B), medium (phage M), and small (phage S) plaques showing maximal bacterial clearance under the chosen conditions within ∼6, 12, and 18 h, respectively. Use of a phage cocktail (all three phages added simultaneously) resulted in slower initial lysis compared with the fastest lysing phage with the greatest plaque size alone, but it showed longer efficacy in suppression. When adding phages sequentially, overall lysis kinetics could be influenced by administering phages at different time points. The lowest bacterial concentration after 36 h was obtained when administering phages in the sequence S, M, and B although this combination initially took the longest to achieve bacterial clearance. Conclusions: Results support that timing and order of phage addition can modulate strength and duration of bacterial suppression and, thus, influence the overall success of phage treatment.

Characterising the biophysical, economic and social impacts of soil carbon sequestration as a greenhouse gas removal technology.

To limit warming to well below 2°C, most scenario projections rely on greenhouse gas removal technologies (GGRTs); one such GGRT uses soil carbon sequestration (SCS) in agricultural land. In addition to their role in mitigating climate change, SCS practices play a role in delivering agroecosystem resilience, climate change adaptability and food security. Environmental heterogeneity and differences in agricultural practices challenge the practical implementation of SCS, and our analysis addresses the associated knowledge gap. Previous assessments have focused on global potentials, but there is a need among policymakers to operationalise SCS. Here, we assess a range of practices already proposed to deliver SCS, and distil these into a subset of specific measures. We provide a multidisciplinary summary of the barriers and potential incentives towards practical implementation of these measures. First, we identify specific practices with potential for both a positive impact on SCS at farm level and an uptake rate compatible with global impact. These focus on: (a) optimising crop primary productivity (e.g. nutrient optimisation, pH management, irrigation); (b) reducing soil disturbance and managing soil physical properties (e.g. improved rotations, minimum till); (c) minimising deliberate removal of C or lateral transport via erosion processes (e.g. support measures, bare fallow reduction); (d) addition of C produced outside the system (e.g. organic manure amendments, biochar addition); (e) provision of additional C inputs within the cropping system (e.g. agroforestry, cover cropping). We then consider economic and non-cost barriers and incentives for land managers implementing these measures, along with the potential externalised impacts of implementation. This offers a framework and reference point for holistic assessment of the impacts of SCS. Finally, we summarise and discuss the ability of extant scientific approaches to quantify the technical potential and externalities of SCS measures, and the barriers and incentives to their implementation in global agricultural systems.

Initial soil community drives heathland fungal community trajectory over multiple years through altered plant-soil interactions.

Dispersal limitation, biotic interactions, and environmental filters interact to drive plant and fungal community assembly, but their combined effects are rarely investigated. This study examines how different heathland plant and fungal colonization scenarios realized via three biotic treatments - addition of mature heathland-derived sod, addition of hay, and no additions - affect soil fungal community development over 6 yr along a manipulated pH gradient in a large-scale experiment starting from an agricultural, topsoil removed state. Our results show that both biotic and abiotic (pH) treatments had a persistent influence on the development of fungal communities, but that sod additions diminished the effect of abiotic treatments through time. Analysis of correlation networks between soil fungi and plants suggests that the reduced effect of pH in the sod treatment, where both soil and plant propagules were added, might be due to plant-fungal interactions since the sod additions caused stronger, more specific, and more consistent connections compared with the no addition treatment. Based on these results, we suggest that the initial availability of heathland fungal and plant taxa, which reinforce each other, can significantly steer further fungal community development to an alternative configuration, overriding the otherwise prominent effect of abiotic (pH) conditions.

Urban meadows as an alternative to short mown grassland: effects of composition and height on biodiversity.

There are increasing calls to provide greenspace in urban areas, yet the ecological quality, as well as quantity, of greenspace is important. Short mown grassland designed for recreational use is the dominant form of urban greenspace in temperate regions but requires considerable maintenance and typically provides limited habitat value for most taxa. Alternatives are increasingly proposed, but the biodiversity potential of these is not well understood. In a replicated experiment across six public urban greenspaces, we used nine different perennial meadow plantings to quantify the relative roles of floristic diversity and height of sown meadows on the richness and composition of three taxonomic groups: plants, invertebrates, and soil microbes. We found that all meadow treatments were colonized by plant species not sown in the plots, suggesting that establishing sown meadows does not preclude further locally determined grassland development if management is appropriate. Colonizing species were rarer in taller and more diverse plots, indicating competition may limit invasion rates. Urban meadow treatments contained invertebrate and microbial communities that differed from mown grassland. Invertebrate taxa responded to changes in both height and richness of meadow vegetation, but most orders were more abundant where vegetation height was longer than mown grassland. Order richness also increased in longer vegetation and Coleoptera family richness increased with plant diversity in summer. Microbial community composition seems sensitive to plant species composition at the soil surface (0-10 cm), but in deeper soils (11-20 cm) community variation was most responsive to plant height, with bacteria and fungi responding differently. In addition to improving local residents' site satisfaction, native perennial meadow plantings can produce biologically diverse grasslands that support richer and more abundant invertebrate communities, and restructured plant, invertebrate, and soil microbial communities compared with short mown grassland. Our results suggest that diversification of urban greenspace by planting urban meadows in place of some mown amenity grassland is likely to generate substantial biodiversity benefits, with a mosaic of meadow types likely to maximize such benefits.

Patient involvement in qualitative data analysis in a trial of a patient-centred intervention: Reconciling lay knowledge and scientific method.

BACKGROUND: We conducted a pilot study of an intervention to facilitate patients' agenda setting in clinical consultations. The primary aim of the study was to test the feasibility of running the randomized controlled trial. A secondary objective was to assess the extent to which patient and public involvement (PPI) could contribute to the process of qualitative data analysis (QDA). AIMS: To describe a novel approach to including patient partners in QDA; to illustrate the kinds of contribution that patient partners made to QDA in this context; and to propose a characterization of a process by which patient involvement can contribute to knowledge production. METHODS: Six patient and public representatives were supported to contribute to data analysis via a range of modalities. During a series of QDA workshops, experienced research staff role-played consultations and interviews, and provided vignettes. Workshop data and PPI diaries were analysed using thematic discourse analysis. RESULTS: We characterized a process of thesis, antithesis and synthesis. This PPI group contributed to the rigour and validity of the study findings by challenging their own and the researchers' assumptions, and by testing the emerging hypotheses. By training PPI representatives to undertake qualitative data analysis, we transformed our understanding of doctor-patient consultations. CONCLUSIONS: This research required changes to our usual research practices but was in keeping with the objective of establishing meaningful patient involvement for a future definitive trial. This work was informed by concepts of critical humility, and a process of knowledge production enabled via the construction of a knowledge space.

The absence or presence of a lytic coliphage affects the response of Escherichia coli to heat, chlorine, or UV exposure.

Disinfection aims at maximal inactivation of target organisms and the sustainable suppression of their regrowth. Whereas many disinfection efforts achieve efficient inactivation when the effect is measured directly after treatment, there are questions about the sustainability of this effect. One aspect is that the treated bacteria might recover and regain the ability to grow. In an environmental context, another question is how amenable surviving bacteria are to predation by omnipresent bacteriophages. Provisional data suggested that bacteria when subjected to sublethal heat stress might develop a phage-resistant phenotype. The result made us wonder about the susceptibility to phage-mediated lysis for bacteria exposed to a gradient of chlorine and UV-LED disinfection strengths. Whereas bacteria exposed to low sublethal chlorine doses still underwent phage-mediated lysis, the critical chlorine Ct of 0.5 mg min/L eliminated this susceptibility and induced phage resistance in the cells that survived treatment. In the case of UV, even the smallest tested dose of 2.8 mJ/cm2 abolished phage lysis leading to direct regrowth. Results suggest that bacteria surviving disinfection might have higher environmental survival chances directly after treatment compared to non-treated cells. A reason could possibly lie in their compromised metabolism that is essential for phage replication.

A Comparison of Change Blindness in Real-World and On-Screen Viewing of Museum Artefacts.

Change blindness is a phenomenon of visual perception that occurs when a stimulus undergoes a change without this being noticed by its observer. To date, the effect has been produced by changing images displayed on screen as well as changing people and objects in an individual's environment. In this experiment, we combine these two approaches to directly compare the levels of change blindness produced in real-world vs. on-screen viewing of museum artefacts. In the real-world viewing condition, one group of participants viewed a series of pairs of similar but slightly different artefacts across eye saccades, while in the on-screen viewing condition, a second group of participants viewed the same artefacts across camera pans on video captured from a head-mounted camera worn by the first set of participants. We present three main findings. First, that change blindness does occur in a museum setting when similar ancient artefacts are viewed briefly one after another in both real-world and on-screen viewing conditions. We discuss this finding in relation to the notion that visual perceptual performance may be enhanced within museums. Second, we found that there was no statistically significant difference between the mean levels of change blindness produced in real-world and on-screen viewing conditions (real-world 42.62%, on-screen 47.35%, X2 = 1.626, p > 0.05 1 d.f.). We discuss possible implications of these results for understanding change blindness, such as the role of binocular vs. monocular vision and that of head and eye movements, as well as reflecting on the evolution of change detection systems, and the impact of the experimental design itself on our results. Third, we combined the data from both viewing conditions to identify groups of artefacts that were independently associated with high and low levels of change blindness, and show that change detection rates were influenced mainly by bottom-up factors, including the visible area and contrast of changes. Finally, we discuss the limitations of this experiment and look to future directions for research into museum perception, change blindness, real-world and on-screen comparisons, and the role of bottom-up and top-down factors in the perception of change.

Linking ecosystem services, urban form and green space configuration using multivariate landscape metric analysis.

CONTEXT: Landscape metrics represent powerful tools for quantifying landscape structure, but uncertainties persist around their interpretation. Urban settings add unique considerations, containing habitat structures driven by the surrounding built-up environment. Understanding urban ecosystems, however, should focus on the habitats rather than the matrix. OBJECTIVES: We coupled a multivariate approach with landscape metric analysis to overcome existing shortcomings in interpretation. We then explored relationships between landscape characteristics and modelled ecosystem service provision. METHODS: We used principal component analysis and cluster analysis to isolate the most effective measures of landscape variability and then grouped habitat patches according to their attributes, independent of the surrounding urban form. We compared results to the modelled provision of three ecosystem services. Seven classes resulting from cluster analysis were separated primarily on patch area, and secondarily by measures of shape complexity and inter-patch distance. RESULTS: When compared to modelled ecosystem services, larger patches up to 10 ha in size consistently stored more carbon per area and supported more pollinators, while exhibiting a greater risk of soil erosion. Smaller, isolated patches showed the opposite, and patches larger than 10 ha exhibited no additional areal benefit. CONCLUSIONS: Multivariate landscape metric analysis offers greater confidence and consistency than analysing landscape metrics individually. Independent classification avoids the influence of the urban matrix surrounding habitats of interest, and allows patches to be grouped according to their own attributes. Such a grouping is useful as it may correlate more strongly with the characteristics of landscape structure that directly affect ecosystem function.

Ecological connectivity networks in rapidly expanding cities.

Urban expansion increases fragmentation of the landscape. In effect, fragmentation decreases connectivity, causes green space loss and impacts upon the ecology and function of green space. Restoration of the functionality of green space often requires restoring the ecological connectivity of this green space within the city matrix. However, identifying ecological corridors that integrate different structural and functional connectivity of green space remains vague. Assessing connectivity for developing an ecological network by using efficient models is essential to improve these networks under rapid urban expansion. This paper presents a novel methodological approach to assess and model connectivity for the Eurasian tree sparrow (Passer montanus) and Yellow-vented bulbul (Pycnonotus goiavier) in three cities (Kuala Lumpur, Malaysia; Jakarta, Indonesia and Metro Manila, Philippines). The approach identifies potential priority corridors for ecological connectivity networks. The study combined circuit models, connectivity analysis and least-cost models to identify potential corridors by integrating structure and function of green space patches to provide reliable ecological connectivity network models in the cities. Relevant parameters such as landscape resistance and green space structure (vegetation density, patch size and patch distance) were derived from an expert and literature-based approach based on the preference of bird behaviour. The integrated models allowed the assessment of connectivity for both species using different measures of green space structure revealing the potential corridors and least-cost pathways for both bird species at the patch sites. The implementation of improvements to the identified corridors could increase the connectivity of green space. This study provides examples of how combining models can contribute to the improvement of ecological networks in rapidly expanding cities and demonstrates the usefulness of such models for biodiversity conservation and urban planning.

A preconsultation web-based tool to generate an agenda for discussion in diabetes outpatient clinics to improve patient outcomes (DIAT): a feasibility study.

OBJECTIVE: To test the feasibility of running a randomised controlled trial of a preconsultation web-based intervention (Presenting Asking Checking Expressing (PACE-D)) to improve the quality of care and clinical outcomes in patients with diabetes. DESIGN AND SETTING: A feasibility study (with randomisation) conducted at outpatient diabetes clinics at two secondary care hospitals in Devon, UK. PARTICIPANTS: People with diabetes (type 1 and type 2) attending secondary care general diabetes outpatient clinics. INTERVENTION: The PACE-D, a web-based tool adapted for patients with diabetes to use before their consultation to generate an agenda of topics to discuss with their diabetologist. OUTCOMES: The percentage of eligible patients who were recruited and the percentage of participants for whom routine glycosylated haemoglobin (HbA1c) data (the putative primary outcome) could be extracted from medical notes and who completed secondary outcome assessments via questionnaire at follow-up were reported. RESULTS: In contrast with the planned recruitment of 120 participants, only 71 participants were randomised during the 7-month recruitment period. This comprised 18.7% (95% CI 14.9% to 23.0%) of those who were eligible. Mean (SD) age of the participants was 56.5 (12.4) years and 66.2% had type 1 diabetes. Thirty-eight patients were randomised to the intervention arm and 33 to the control arm. HbA1c data were available for only 73% (95% CI 61% to 83%) of participants at the 6 months follow-up. The questionnaire-based data were collected for 66% (95% CI 54% to 77%) of the participants at 6 months follow-up. Participants reported that the PACE-D tool was easy to use. CONCLUSIONS: A randomised controlled trial of the preconsultation web-based intervention as set out in our current protocol is not feasible without significant modification to improve recruitment and follow-up of participants. The study also provides insights into the feasibility and challenges of conducting complex intervention trials in everyday clinical practice. TRIAL REGISTRATION: ISRCTN75070242.

A bird's eye view: using circuit theory to study urban landscape connectivity for birds.

CONTEXT: Connectivity is fundamental to understanding how landscape form influences ecological function. However, uncertainties persist due to the difficulty and expense of gathering empirical data to drive or to validate connectivity models, especially in urban areas, where relationships are multifaceted and the habitat matrix cannot be considered to be binary. OBJECTIVES: This research used circuit theory to model urban bird flows (i.e. 'current'), and compared results to observed abundance. The aims were to explore the ability of this approach to predict wildlife flows and to test relationships between modelled connectivity and variation in abundance. METHODS: Circuitscape was used to model functional connectivity in Bedford, Luton/Dunstable, and Milton Keynes, UK, for great tits (Parus major) and blue tits (Cyanistes caeruleus), drawing parameters from published studies of woodland bird flows in urban environments. Model performance was then tested against observed abundance data. RESULTS: Modelled current showed a weak yet positive agreement with combined abundance for P. major and C. caeruleus. Weaker correlations were found for other woodland species, suggesting the approach may be expandable if re-parameterised. CONCLUSIONS: Trees provide suitable habitat for urban woodland bird species, but their location in large, contiguous patches and corridors along barriers also facilitates connectivity networks throughout the urban matrix. Urban connectivity studies are well-served by the advantages of circuit theory approaches, and benefit from the empirical study of wildlife flows in these landscapes to parameterise this type of modelling more explicitly. Such results can prove informative and beneficial in designing urban green space and new developments.