Multiscale soil moisture estimates using static and roving cosmic-ray soil moisture sensors

Soil moisture plays a critical role in land surface processes and as such there has been a recent increase in the number and resolution of satellite soil moisture observations and the development of land surface process models with ever increasing resolution. Despite these developments, validation and calibration of these products has been limited because of a lack of observations on corresponding scales. A recently developed mobile soil moisture monitoring platform, known as the "rover", offers opportunities to overcome this scale issue. This paper describes methods, results and testing of soil moisture estimates produced using rover surveys on a range of scales that are commensurate with model and satellite retrievals. Our investigation involved static cosmic-ray neutron sensors and rover surveys across both broad (36 x 36 km at 9 km resolution) and intensive (10 x 10 km at 1 km resolution) scales in a cropping district in the Mallee region of Victoria, Australia. We describe approaches for converting rover survey neutron counts to soil moisture and discuss the factors controlling soil moisture variability. We use independent gravimetric and modelled soil moisture estimates collected across both space and time to validate rover soil moisture products. Measurements revealed that temporal patterns in soil moisture were preserved through time and regression modelling approaches were utilised to produce time series of property-scale soil moisture which may also have applications in calibration and validation studies or local farm management. Intensive-scale rover surveys produced reliable soil moisture estimates at 1 km resolution while broad-scale surveys produced soil moisture estimates at 9 km resolution. We conclude that the multiscale soil moisture products produced in this study are well suited to future analysis of satellite soil moisture retrievals and finer-scale soil moisture models

Gully and Stream Bank Toolbox. A technical guide for gully and stream bank erosion control programs in Great Barrier Reef catchments

This Toolbox is a guide to targeting, designing and implementing gully and stream bank erosion control activities in Great Barrier Reef (GBR) catchments. This third edition builds on 7 years of implementing these activities in multiple programs and it aims to inform the ongoing efforts to reduce the amount of fine sediment and associated nutrients delivered to the GBR lagoon. Sub‑soil erosion, predominantly from gullies and stream banks, contributes the vast bulk of the fine sediment load delivered to the GBR. The large area and extensive erosion in GBR catchments, and the limited resources available, make it important for erosion control to be targeted to cost‑effective sites and implemented using best practice based on best available information. Landholder support and site maintenance increase the likelihood that sediment reductions will persist over the long term

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism

Massively Parallel Sequencing and Analysis of the Necator americanus Transcriptome

The blood-feeding hookworm Necator americanus infects hundreds of millions of people. To elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of adult Necator americanus was studied using next-generation sequencing and in silico analyses. Contigs (n = 19,997) were assembled from the sequence data; 6,771 of them had known orthologues in the free-living nematode Caenorhabditis elegans, and most encoded proteins with WD40 repeats (10.6%), proteinase inhibitors (7.8%) or calcium-binding EF-hand proteins (6.7%). Bioinformatic analyses inferred that C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%), oxidative phosphorylation (63%) and/or proteases (60%). Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. Essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have human homologues. These candidate targets were inferred to be linked to mitochondrial metabolism or amino acid synthesis. This investigation provides detailed insights into the transcriptome of the adult stage of N. americanus

Clear Genetic Distinctiveness between Human- and Pig-Derived Trichuris Based on Analyses of Mitochondrial Datasets

The whipworm, Trichuris trichiura, causes trichuriasis in ∼600 million people worldwide, mainly in developing countries. Whipworms also infect other animal hosts, including pigs (T. suis), dogs (T. vulpis) and non-human primates, and cause disease in these hosts, which is similar to trichuriasis of humans. Although Trichuris species are considered to be host specific, there has been considerable controversy, over the years, as to whether T. trichiura and T. suis are the same or distinct species. Here, we characterised the entire mitochondrial genomes of human-derived Trichuris and pig-derived Trichuris, compared them and then tested the hypothesis that the parasites from these two host species are genetically distinct in a phylogenetic analysis of the sequence data. Taken together, the findings support the proposal that T. trichiura and T. suis are separate species, consistent with previous data for nuclear ribosomal DNA. Using molecular analytical tools, employing genetic markers defined herein, future work should conduct large-scale studies to establish whether T. trichiura is found in pigs and T. suis in humans in endemic regions

Calibration and correction procedures for cosmic-ray neutron\ud soil moisture probes located across Australia

The cosmic-ray probe (CRP) provides continuous estimates of soil moisture over an area of ~30 ha by counting fast neutrons produced from cosmic rays which are predominantly moderated by water molecules in the soil. This paper describes the setup, measurement correction procedures, and field calibration of CRPs at nine locations across Australia with contrasting soil type, climate, and land cover. These probes form the inaugural Australian CRP network, which is known as CosmOz. CRP measurements require neutron count rates to be corrected for effects of atmospheric pressure, water vapor pressure changes, and variations in incoming neutron intensity. We assess the magnitude and importance of these corrections and present standardized approaches for network-wide analysis. In particular, we present a new approach to correct for incoming neutron intensity variations and test its performance against existing procedures used in other studies. Our field calibration results indicate that a generalized calibration function for relating neutron counts to soil moisture is suitable for all soil types, with the possible exception of very sandy soils with low water content. Using multiple calibration data sets, we demonstrate that the generalized calibration function only applies after accounting for persistent sources of hydrogen in the soil profile. Finally, we demonstrate that by following standardized correction procedures and scaling neutron counting rates of all CRPs to a single reference location, differences in calibrations between sites are related to site biomass. This observation provides a means for estimating biomass at a given location or for deriving coefficients for the calibration function in the absence of field calibration data

Response to comment by Daley et al., on “Assessing gully erosion and rehabilitation using multi temporal LiDAR DEMs: Case study from the Great Barrier Reef catchments, Australia”

Daley et al. (2023a) argue that at least 10–15 years apart Digital Elevation Model (DEM) derived DEMs of Difference (DoD) surveys are needed to detect reliable geomorphic change within the gullied landscapes of the Great Barrier Reef, Australia. We acknowledge that the reliability of observed geomorphic change increases as more subtle geomorphic processes are detected with longer monitoring periods. As further good quality long-term legacy datasets become available, we encourage utilising these to improve confidence in targeting erosion rehabilitation. However, our approach to consistently apply 2–3 year DoDs to contrasting gully morphologies enabled capture of more intense geomorphic processes acting over shorter timeframes and provided valuable and timely information on (i) contrasting erosional mechanisms and erosion rates between variable gully morphologies, and (ii) rehabilitation efforts undertaken. In this paper, we take the opportunity to concisely address all the concerns raised by Daley et al. (2023a)

Assessing gully erosion and rehabilitation using multi temporal LiDAR DEMs: Case study from the Great Barrier Reef catchments, Australia

Millions of dollars are being spent on gully rehabilitation to help reduce excess fine sediment delivery to the Great Barrier Reef (GBR). There is an urgent need for (i) prioritisation of active gullies for rehabilitation and (ii) the development of methodologies to inform the effectiveness of remediation. In this study we analyse DEMs of Difference derived from 0.5 m resolution 2–3 year interval multi-temporal LiDAR data collected pre and post rehabilitation at three variable gully morphologies in the Burdekin catchment. Our analysis indicates that the highest annual average fine sediment erosion rates for the untreated control gullies occur at the linear gully (53.38 t ha−1 y−1) followed by linear-alluvial gully (34.24 t ha−1 y−1) and least at the alluvial gully (14.41 t ha−1 y−1). The proportional loss or export of fine sediment from the gullies in their un-treated condition ranges from ∼68 to 90% of what is eroded, and when the gullies are treated the proportion of fine sediment that is retained in the gully proportional to what is eroded increases to ∼60% at all sites. Without pre-treatment baseline erosion rates, and additional post treatment LiDAR captures, it is difficult to quantify the treatment effectiveness. Our results offer insights in the erosion mechanisms within different geomorphic gully morphologies and rehabilitation effects in these erosional landforms. This study provides crucial knowledge of gully dynamics that can be coupled with other lines of evidence for better prioritisation of rehabilitation in the GBR catchments