To address complex challenges and help advance a systems theory for soils requires soil scientists to be able to engage with knowledges outside the discipline of soil science. However, there is a lack of examples and guidance available to support different ways of producing new knowledge. Drawing on our experience as a transdisciplinary team, we present a roadmap comprising five key steps for undertaking transdisciplinary, soil-centred research. The five steps are: addressing complex challenges, building relationships, weaving knowledges and building connectivity, developing holistic understandings and moving beyond knowledge translation. The central tenet of the roadmap is connectivity, with soil health at the core of the interrelationships of people, soil and food. To illustrate the application of this roadmap, we share learnings from two case studies that focused on understanding connections between people and soil, through food production in an Aotearoa New Zealand context. These case studies weave together m & amacr;tauraka M & amacr;ori (M & amacr;ori Indigenous knowledge) and soil science, guided by social science framings, providing examples of how to undertake Transdisciplinary Research (TDR) and guidance for others looking to extend the boundaries of our field by connecting and applying new approaches to knowledge creation, and in so doing advance the development of a soil systems approach.

Addressing the complex challenges of soil and food security at international and local scales requires moving beyond the boundaries of individual disciplines and knowledge systems. The value of transdisciplinary research approaches is increasingly recognised, including those that value and incorporate Indigenous knowledge systems and holders. Using a case study at P & omacr;hatu, Aotearoa / New Zealand, this paper demonstrates the value of a transdisciplinary approach to explore past M & amacr;ori food landscapes and contribute to contemporary M & amacr;ori soil health and food sovereignty aspirations. Engaging at the interface between soil science and Indigenous knowledge (m & amacr;tauraka M & amacr;ori) in an Aotearoa / New Zealand context, we provide an example and guide for weaving knowledges in a transdisciplinary context. Here, m & amacr;tauraka M & amacr;ori, including waiata (songs) and ingoa w & amacr;hi (place names), provided the map of where to look and why, and soil analysis yielded insight into past cultivation, soil modification, and fertilisation practices. Both knowledges were needed to interpret the findings and support M & amacr;ori in re-establishing traditional horticultural practices. Furthermore, the paper extends the current literature on the numerous conceptual frameworks developed to support and guide transdisciplinary research by providing an example of how to do this type of research in an on-the-ground application.

The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs using ChIP-Seq. We use these data to train BoltzNet, a novel neural network that predicts TF binding energy from DNA sequence. BoltzNet mirrors a quantitative biophysical model and provides directly interpretable predictions genome-wide at nucleotide resolution. We use BoltzNet to quantitatively design novel binding sites, which we validate with biophysical experiments on purified protein. We generate models for 124 TFs that provide insight into global features of TF binding, including clustering of sites, the role of accessory bases, the relevance of weak sites, and the background affinity of the genome. Our paper provides new paradigms for studying TF-DNA binding and for the development of biophysically motivated neural networks.

With increasing urbanisation, there is a growing disconnect between soil, food, and people, centred around those relying on Western food production models. This 'wicked' problem is challenging sustainable soil use and food insecurity. Knowledge of soils through scientific studies alone are unable to address this problem, and we need to extend the boundaries of soil science for real progress to be made. We present a conceptual framework for understanding the reciprocal connections between soil, food, and people in local food production systems in Aotearoa New Zealand, applying principles and practices from a transdisciplinary research methodology. The resultant Food-Landscape Networks framework consists of seven factors that support understanding the inherent connections between soil, food, and people. The factors are: soil health, land suitability, climate, productivity, food quality, well-being, and engagement. These factors have been identified from weaving together m & amacr;tauraka (the K & amacr;i Tahu mita [dialect] is used in this text, where the 'ng' diagraph is replaced with 'k', e.g., m & amacr;tauranga = m & amacr;tauraka) M & amacr;ori (M & amacr;ori knowledge, culture, worldview, and values) and soil science using the He Awa Whiria, Braided Rivers, epistemological framework. M & amacr;tauraka M & amacr;ori guides the traditionally reductionist discipline of soil science into a more holistic space, in an Aotearoa New Zealand context.

Mycobacterium tuberculosis complex (MTBC) infections are treated with combinations of antibiotics; however, these regimens are not as efficacious against multidrug and extensively drug resistant MTBC. Phenotypic (growth-based) drug susceptibility testing on slow growing bacteria like MTBC requires many weeks to months to complete, whereas sequencing-based approaches can predict drug resistance (DR) with reduced turnaround time. We sought to develop a multiplexed, targeted next generation sequencing (tNGS) assay that can predict DR and can be performed directly on clinical respiratory specimens. A multiplex PCR was designed to amplify a group of thirteen full-length genes and promoter regions with mutations known to be involved in resistance to first- and second-line MTBC drugs. Long-read amplicon libraries were sequenced with Oxford Nanopore Technologies platforms and high-confidence resistance mutations were identified in real-time using an in-house developed bioinformatics pipeline. Sensitivity, specificity, reproducibility, and accuracy of the tNGS assay was assessed as part of a clinical validation study. In total, tNGS was performed on 72 primary specimens and 55 MTBC-positive cultures and results were compared to clinical whole genome sequencing (WGS) performed on paired patient cultures. Complete or partial susceptibility profiles were generated from 82% of smear positive primary specimens and the resistance mutations identified by tNGS were 100% concordant with WGS. In addition to performing tNGS on primary clinical samples, this assay can be used to sequence MTBC cultures mixed with other mycobacterial species that would not yield WGS results. The assay can be effectively implemented in a clinical/diagnostic laboratory with a two to three day turnaround time and, even if batched weekly, tNGS results are available on average 15 days earlier than culture-derived WGS results. This study demonstrates that tNGS can reliably predict MTBC drug resistance directly from clinical specimens or cultures and provide critical information in a timely manner for the appropriate treatment of patients with DR tuberculosis.

The creation of more sustainable land use strategies is paramount to designing multifunctional agricultural landscapes that allow grasslands to continually deliver multiple ecosystem services. A mapping modelling approach would provide us with a tool for system diagnosis to better assess the value of a landscape and define place-based practices for designing more context-adjusted systems that are in synergy with the complexity of grasslands. To assess the potential capability of a high-country pastoral livestock production system in New Zealand in delivering ecosystem services, this work uses a geospatial model as a decision support tool to identify management practices that enhance grassland health. The model uses national, climatic, soil, and landcover data to assess the agricultural productivity, flood mitigation, C sequestration, erosion, and sediment delivery capacity of a case study high-country station in New Zealand. Model outcomes suggest that the station has the potential for increased agricultural productivity although varying spatially, a high flood mitigation capacity, a high capacity for C sequestration, a moderate risk of erosion, a capacity to reduce sediment delivery to streams, and overall, a low to moderate nitrogen and phosphorus accumulation. Output maps display a spatial visualisation of ecosystem services associated with the landscape topography, soil, and vegetation patterns that allow the identification of neglected areas and planning of best place-based management practices strategies to enhance the health of grasslands.

Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of, genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert and hence are tolerated as genomic "noise."IMPORTANCE Recent studies have revealed large numbers of transcription factor binding sites within the genes of bacteria. The function, if any, of the vast majority of these binding sites has not been investigated. Here, we map the binding of the transcription factor PhoB across the Escherichia coli genome, revealing that the majority of PhoB binding sites are within genes. We show that PhoB binding sites within genes are not associated with regulation of the overlapping genes. Indeed, our data suggest that bacteria tolerate the presence of large numbers of nonregulatory, intragenic binding sites for transcription factors and that these binding sites are not under selective pressure.

More sustainable pastoral livestock production systems are required to face the challenge of reconciling agricultural production and environmental impact. Although the need for more holistic approaches, such as systems thinking and design theory, is acknowledged, systemic research applying those theories to create healthier systems remains underexplored. A multiple steps holistic approach involving modelling, geographic information systems, and decision-making analysis was used to design, assess, and contrast alternative scenarios that represent distinct grazing management to the current grazing management of a high-country station in New Zealand used as a case study to enhance grassland health. Three alternative scenarios were created, and five main parameters used to assess grassland health were obtained from the evaluation of the designed scenarios. From all the parameters, soil erosion control and increased production were ranked as the most and least important, respectively, to be considered in the design process. A multi-criteria evaluation defined that the best-compromise scenario to enhance grassland health is the scenario with lower soil erosion, as a result of applying adaptive and flexible management at the paddock level, the lower total emission of greenhouse gases (only sheep herd grazing), and greater profitability (due to production costs reduction, as cattle were removed from the station), compared to the ‘status quo’. Our design methodology produced a variety of alternatives that enhanced the health of grasslands in different parameters while still maintaining or increasing profitability. The use of multi-criteria evaluation facilitated the decision of the most contextualised and best-compromise scenario for New Zealand high country grasslands.

Treatment of tuberculosis continues to be challenging due to the widespread latent form of the disease and the emergence of antibiotic-resistant strains of the pathogen, Mycobacterium tuberculosis. Bacterial ribosomes are a common and effective target for antibiotics. Several second line anti-tuberculosis drugs, e.g. kanamycin, amikacin, and capreomycin, target ribosomal RNA to inhibit protein synthesis. However, M. tuberculosis can acquire resistance to these drugs, emphasizing the need to identify new drug targets. Previous cryo-EM structures of the M. tuberculosis and M. smegmatis ribosomes identified two novel ribosomal proteins, bS22 and bL37, in the vicinity of two crucial drug-binding sites: the mRNA-decoding center on the small (30S), and the peptidyl-transferase center on the large (50S) ribosomal subunits, respectively. The functional significance of these two small proteins is unknown. In this study, we observe that an M. smegmatis strain lacking the bs22 gene shows enhanced susceptibility to kanamycin compared to the wild-type strain. Cryo-EM structures of the ribosomes lacking bS22 in the presence and absence of kanamycin suggest a direct role of bS22 in modulating the 16S rRNA kanamycin-binding site. Our structures suggest that amino-acid residue Lys-16 of bS22 interacts directly with the phosphate backbone of helix 44 of 16S rRNA to influence the micro-configuration of the kanamycin-binding pocket. Our analysis shows that similar interactions occur between eukaryotic homologues of bS22, and their corresponding rRNAs, pointing to a common mechanism of aminoglycoside resistance in higher organisms.

Grazing management to reduce soil erosion is paramount for preserving and enhancing grassland health under pastoral livestock production systems. However, as the focus of these production systems is to increase productivity, the inclusion of the soil and its complexity in grazing management has been usually neglected. Detailed consideration of the soil spatio-temporal susceptibility to erosion may be best approached with simulation modelling. To understand and explore the spatio-temporal impact of grazing strategies on soil surface erosion, this work used a geospatial model approach in a high-country pastoral livestock production system in New Zealand as a case study. We modelled 45 scenarios characterized by different stock densities and occupation periods applied for each season of the year and for different livestock types: sheep, beef, and deer, producing a total of 540 scenarios. In addition, we included scenarios to represent ungrazed pastures for each season and the current grazing management of the case study station as the baseline for comparisons (resulting in a total of 545 scenarios). Spatio-temporal variation of natural soil superficial erosion from ungrazed pastures appears to be more relevant than the impact of manipulating grazing intensity and indicates that paddocks in our study area have different capacities to support grazing which also changes during seasons. Increases in occupation period seem more detrimental to soil erosion compared to increases in stock density, and cattle are the most detrimental stock type compared to sheep and deer. Our results suggest that grassland health can be enhanced in LUMGS by applying context-adjusted grazing management strategies according to the station spatio-temporal heterogeneity and susceptibility to erosion.

We report the unusual genotypic characterization of a bacterium isolated from a clinical sample of a patient who grew up in Bangladesh and lives in the United States. Using whole-genome sequencing, we identified the bacterium as a member of the Mycobacterium tuberculosis complex (MTBC). Phylogenetic placement of this strain suggests a new MTBC genotype. Even though it had the same spoligotype as M. caprae strains, single-nucleotide polymorphism–based phylogenetic analysis placed the isolate as a sister lineage distinct from M. caprae, most closely related to 5 previously sequenced genomes isolated from primates and elephants in Asia. We propose a new animal-associated lineage, La4, within MTBC.

Soil acts as the integrator of processes operating within the biological and hydrological landscapes and responds to external disturbances and processes on varying time scales. The impact of any change results in a corresponding response in the system; which is dependent on the resistance of the soil system to the disturbance. Irreversible permanent change results when the soil system shifts over a threshold tipping point; with the soil system experiencing a regime shift with associated structural and functional collapse. Climate change is the most important external disturbance or stressor on these systems due to changes in precipitation, temperature and moisture regimes. Our research at Mt Grand is focused on approaches to increasing land use resiliency in the face of environmental change. Our purpose is to select and apply soil quality indices which can be used to assess soil resilience to external disturbance events for Mt Grand Station in New Zealand. We will identify biophysical variations and landscape drivers in soil resilience; and use these results to match land management practices with variations in soil resilience. For example, soils with low resilience will only have land management practices that have a low impact on the soil resource. We selected soil attributes that represented indicators of resistance, used to quantify the capacity of a soil to recover its functionality. We mapped this soil resilience framework against a national database of soil and landscape attributes for Mt Grand Station. The output from this research is to posit a conceptual framework of soil quality indices which relates to soil resilience, and thus to create a spatial map of soil resilience for Mt Grand Station.

We describe a novel suction plate experiment that uses large, repacked soil cores comprising clasts and a fine-textured matrix to accurately measure the water retention curve of rock fragments (RFs) of high and low porosity. The method incorporates a suction plate-core containment system that can be weighed as a unit, to overcome typical core size restrictions. The method relies on analysing the relationship between total core volumetric water content and RF concentration. Cores are packed with a mix of glass and RFs to maintain a uniform volumetric total clast proportion of 30% while RF concentration varies. A constant total clast volume improves accuracy and precision by ensuring the water-holding characteristics of the matrix varies as little as possible among cores. Highlights We determine the water retention curve of greywacke-pumice clasts in large, repacked soil cores. A suction plate-core containment system that is weighed as a unit allows large cores to be used. WRC is determined with cores of varying rock%, but total clast% stays constant by adding glass. By using the above, the WRC of low and high porosity rocks can be measured precisely.

Nontuberculous mycobacteria (NTM) are environmental bacteria commonly found in soil and water in almost every part of the world. While usually non-pathogenic, they can cause acute respiratory and cutaneous infections under certain circumstances or in patients with underlying medical conditions. Contrary to members of the Mycobacterium tuberculosis complex, documented human-to-human transmissions of NTM have been rarely reported and most cases result from direct environmental exposure. Here we describe the identification of a new NTM species isolated from a hand laceration of a New York State patient after a fall. This new NTM forms rough, orange pigmented colonies and is naturally resistant to doxycycline and tobramycin. Whole genome analysis reveal no close relatives present in public databases, and our findings are in accordance with the recognition of a new taxonomic species of NTM. We propose the name Mycobacterium salfingeri sp. nov. for this new NTM representative. The type strain is 20-157661T (DSM = 113368T, BCCM = ITM 501207T).

Grasslands and ecosystem services are under threat due to common practices adopted by modern livestock farming systems. Design theory has been an alternative to promote changes and develop more sustainable strategies that allow pastoral livestock production systems to evolve continually within grasslands by enhancing their health and enabling the continuous delivery of multiple ecosystem services. To create a design framework to design alternative and more sustainable pastoral livestock production systems, a better comprehension of grassland complexity and dynamism for a diagnostic assessment of its health is needed, from which the systems thinking theory could be an important approach. By using systems thinking theory, the key components of grasslands—soil, plant, ruminant—can be reviewed and better understood from a holistic perspective. The description of soil, plant and ruminant individually is already complex itself, so understanding these components, their interactions, their response to grazing management and herbivory and how they contribute to grassland health under different climatic and topographic conditions is paramount to designing more sustainable pastoral livestock production systems. Therefore, by taking a systems thinking approach, we aim to review the literature to better understand the role of soil, plant, and ruminant on grassland health to build a design framework to diagnose and enhance grassland health under pastoral livestock production systems.

The pH 6 antigen (PsaA) of Yersinia pestis is a virulence factor that is expressed in response to high temperature (37°C) and low pH (6.0). Previous studies have implicated the PsaE and PsaF regulators in the temperature- and pH-dependent regulation of psaA. Here, we show that PsaE levels are themselves controlled by pH and temperature, explaining the regulation of psaA. We identify hundreds of binding sites for PsaE across the Y. pestis genome, with the majority of binding sites located in intergenic regions bound by the nucleoid-associated protein H-NS. However, we detect direct regulation of only two transcripts by PsaE, likely due to displacement of H-NS from the corresponding promoter regions; our data suggest that most PsaE binding sites are nonregulatory or that they require additional environmental cues. We also identify the precise binding sites for PsaE that are required for temperature- and pH-dependent regulation of psaA and psaE. Thus, our data reveal the critical role that PsaE plays in the regulation of psaA and suggest that PsaE may have many additional regulatory targets. IMPORTANCE Y. pestis, the etiologic agent of plague, has been responsible for high mortality in several epidemics throughout human history. The plague bacillus has been used as a biological weapon during human history and is currently one of the most likely biological threats. PsaA and PsaE appear to play important roles during Y. pestis infection. Understanding their regulation by environmental cues would facilitate a solution to impede Y. pestis infection.

ABSTRACTSmall proteins of <51 amino acids are abundant across all domains of life but are often overlooked because their small size makes them difficult to predict computationally, and they are refractory to standard proteomic approaches. Ribosome profiling has been used to infer the existence of small proteins by detecting the translation of the corresponding open reading frames (ORFs). Detection of translated short ORFs by ribosome profiling can be improved by treating cells with drugs that stall ribosomes at specific codons. Here, we combine the analysis of ribosome profiling data for Escherichia coli cells treated with antibiotics that stall ribosomes at either start or stop codons. Thus, we identify ribosome-occupied start and stop codons for ~400 novel putative ORFs with high sensitivity. The newly discovered ORFs are mostly short, with 365 encoding proteins of <51 amino acids. We validate translation of several selected short ORFs, and show that many likely encode unstable proteins. Moreover, we present evidence that most of the newly identified short ORFs are not under purifying selection, suggesting they do not impact cell fitness, although a small subset have the hallmarks of functional ORFs.IMPORTANCESmall proteins of <51 amino acids are abundant across all domains of life but are often overlooked because their small size makes them difficult to predict computationally, and they are refractory to standard proteomic approaches. Recent studies have discovered small proteins by mapping the location of translating ribosomes on RNA using a technique known as ribosome profiling. Discovery of translated sORFs using ribosome profiling can be improved by treating cells with drugs that trap initiating ribosomes. Here, we show that combining these data with equivalent data for cells treated with a drug that stalls terminating ribosomes facilitates the discovery of small proteins. We use this approach to discover 365 putative genes that encode small proteins in Escherichia coli.

Currently, acute postoperative pain during hospitalization is primarily managed by medications, and patients must adhere to restrictive postoperative precautions for 3 months following lumbar spine surgeries. Yoga can be an alternative approach to assist in acute and subacute postoperative pain management, anxiety, and return to function. The purpose of the present work was to develop and test the feasibility and explore the effectiveness of a tailored yoga program, delivered in-person during the hospital stay and electronically after hospital discharge, as a potential new avenue for postoperative care. This pilot study will use a crossover randomized controlled design. Individuals aged between 40 and 80 years who are scheduled for lumbar laminectomy and/or fusion, and who have not practiced regular yoga within the past 6 months at the time of enrollment, will be recruited and randomized to either a tailored yoga program (intervention group) or usual care (control group) during the hospital stay (phase one). Bearing in mind postoperative precautions, all subjects will be instructed to perform a home-based tailored yoga program delivered electronically via YouTube links for 8 weeks post-hospital discharge (phase two). The primary outcome measures assessing feasibility are adherence/compliance. Secondary outcome measures include pain, anxiety, function, sleep, perceived stress, and pain-catastrophizing behavior. Length of hospital stay and pain medication use, gait distance, and overall physical activity during hospitalization will also be collected. Finally, a qualitative interview will be obtained after completion of the hospital and home-based programs. This study will determine the feasibility of a tailored yoga program for acute and subacute postoperative lumbar spine surgery pain, anxiety, and functional outcomes.

Worldwide, rock fragments (RFs) are generally considered inert with respect to bulk soil hydraulic properties, such that all soil water retention properties predicted by national pedotransfer functions (such as S-map) are based on the volumetric fraction of the fine earth (<2 mm fraction) only. Research findings contradict those assumptions, but studies commonly focus on porous RFs, and rely on repacked cores and lab studies, leaving uncertainty as to how low porosity RFs characteristic of common strongly indurated lithologies affect soil in the field. We address this question by examining soil water storage in 52 pits excavated into stony soils on the Canterbury Plains, New Zealand, which are formed in sediment derived from a Mesozoic hard sandstone. The soils at each site were watered to saturation, and then after two days of drainage (a proxy for field capacity), a 30 x 30 cm pit was excavated in 10 cm increments to a depth of 60 cm. From each increment, soil samples were collected and analysed to determine the volumetric size distribution of RFs, the water content of the fine earth and the water content of the RFs themselves. Our results indicated that RFs could influence the fine earth bulk density, porosity, and soil chemistry. RFs could also retain water: 2-20 mm RFs (0.07 m(3) m(-3)) retained twice as much water as >20 mm RFs (0.03 m(3) m(-3)). The water retention of the hard sandstone was low compared to other lithologies, but the volumetric abundance of RFs in the stony soils we sampled meant that they accounted for similar to 10% of the water retained to a depth of 60 cm at field capacity. Our results demonstrate that similar to 13 mm of water retained by RFs at field capacity is not currently considered in water budgets and nutrient leaching predictions, which may be relevant to best practice land management.