Microsatellite primers for the rare sedge Lepidosperma bungalbin (Cyperaceae)

Premise of the study: Microsatellite markers were developed for the rare sedge Lepidosperma bungalbin (Cyperaceae) to assess genetic variation and its spatial structuring. Methods and Results: We conducted shotgun sequencing on an Illumina MiSeq and produced 6,215,872 sequence reads. The QDD pipeline was used to design 60 primer pairs that were screened using PCR. We developed 17 loci, of which 12 loci were identified that were polymorphic, amplified reliably, and could be consistently scored. We then screened these loci for variation in individuals from three populations. The number of alleles observed for these 12 loci across the three populations ranged from nine to 19 and expected heterozygosity ranged from 0.41 to 0.89. Conclusions: These markers will enable the quantification of the potential impact of mining on genetic variation within L. bungalbin and establish a baseline for future management of genetic variation of the rare sedge

Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia

Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000 bp with one of 189,000 bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences

Preparing for the worst: Utilizing stress-tolerant soil microbial communities to aid ecological restoration in the Anthropocene

1. Multiple drivers of environmental change pose a significant challenge for ecological restoration, including climate change, soil salinization and environmental pollution. Due to the important role that soil biota play in enabling plants to cope with a variety of abiotic stressors, there is growing interest in the use of microbial inoculations to facilitate native plant restoration in the face of such change. 2. Recently, novel methods have begun being explored in agriculture to harness stress-conditioned soil biota for improving abiotic stress tolerance in crop species. Similar applications in ecological restoration – where plants are inoculated with indigenous soil microbial communities that are preconditioned to various abiotic stressors – could potentially increase our capacity to restore degraded ecosystems under global change. 3. In this paper, we aim to (1) outline the ways in which soil microbial communities might be conditioned in order to confer greater stress tolerance to plants that are targets for restoration; (2) highlight successful (and unsuccessful) examples where stress-tolerant soil microbial communities were utilized to improve plant performance; (3) describe the ways in which stress-conditioned soil biota could be deployed in order to assist ecological restoration; and (4) discuss the potential risks and outstanding questions associated with such an approach. 4. If restoration practitioners are able to harness the soil microbiome to improve plant stress tolerance as is currently being explored in agriculture, this could revolutionize methods for the restoration of degraded lands in the Anthropocene

Correction: The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

The authors would like to amend this article based on the discovery that the originally published Acacia ligulata sequence contains assembly errors, which came to light after the publication of the article

Edna metabarcoding of avocado flowers: ‘Hass’ it got potential to survey arthropods in food production systems?

In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, we compared the arthropod communities detected with eDNA metabarcoding of flowers, from an agricultural species (Persea americana—‘Hass’ avocado), with two conventional survey techniques: digital video recording (DVR) devices and pan traps. In total, 80 eDNA flower samples, 96 h of DVRs and 48 pan trap samples were collected. Across the three methods, 49 arthropod families were identified, of which 12 were unique to the eDNA dataset. Environmental DNA metabarcoding from flowers revealed potential arthropod pollinators, as well as plant pests and parasites. Alpha diversity levels did not differ across the three survey methods although taxonomic composition varied significantly, with only 12% of arthropod families found to be common across all three methods. eDNA metabarcoding of flowers has the potential to revolutionize the way arthropod communities are monitored in natural and agro-ecosystems, potentially detecting the response of pollinators and pests to climate change, diseases, habitat loss and other disturbances

Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world\u27s food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security

Evidence that Differences in Fructosamine-3-Kinase Activity May be Associated with the Glycation Gap in Human Diabetes

The phenomenon of a discrepancy between glycated haemoglobin levels and other indicators of average glycaemia may be due to many factors but can be measured as the glycation gap (GGap). This GGap is associated with differences in complications in patients with diabetes and may possibly be explained by dissimilarities in deglycation in turn leading to altered production of Advanced Glycation End (AGE) products. We hypothesised that variations in the level of the deglycating enzyme Fructosamine-3-kinase (FN3K) might be associated with the GGap. We measured erythrocyte FN3K concentrations and enzyme activity in a population dichotomised for a large positive or negative GGap. FN3K protein was higher and we found a striking 3-fold greater activity (323%) at any given FN3K protein level in the erythrocytes of the negative compared with positive GGap groups. This was associated with lower AGE levels in the negative GGap group (79%), lower pro-inflammatory adipokines (Leptin/Adiponectin ratio) (73%) and much lower pro-thrombotic PAI-1 levels (19%). We conclude that FN3K may play a key role in the GGap and thus diabetes complications such that FN3K may be potential predictor of the risk of diabetes complications. Pharmacological modifications of its activity may provide a novel approach to their prevention

Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing

The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool, particularly for otherwise difficult to survey groups such as microbes. However, such approaches for monitoring complex restoration sites such as post-mined landscapes have not yet been tested. Here we examine bacterial and fungal communities across chronosequences of mine site restoration at three locations in Western Australia to determine if there are consistent changes in SMC diversity, community composition and functional capacity. Although we detected directional changes in community composition indicative of microbial recovery, these were inconsistent between locations and microbial taxa (bacteria or fungi). Assessing functional diversity provided greater understanding of changes in site conditions and microbial recovery than could be determined through assessment of community composition alone. These results demonstrate that high-throughput amplicon sequencing of environmental DNA (eDNA) is an effective approach for monitoring the complex changes in SMC following restoration. Future monitoring of mine site restoration using eDNA should consider archiving samples to provide improved understanding of changes in communities over time. Expansion to include other biological groups (e.g. soil fauna) and substrates would also provide a more holistic understanding of biodiversity recovery

Stockpiling disrupts the biological integrity of topsoil for ecological restoration

Purpose: Biotic and abiotic properties of soils can hinder or facilitate ecological restoration, and management practices that impact edaphic factors can strongly influence plant growth and restoration outcomes. Salvaged topsoil is an invaluable resource for mine-site restoration, and a common practice is topsoil transfer from mined areas to restoration sites. However, direct transfer is often not feasible, necessitating storage in stockpiles. We evaluated the effects of topsoil stockpiling on plant performance across diverse ecosystems impacted by mining throughout Western Australia. Methods: We conducted a bioassay experiment using a widespread native Acacia species to assess how topsoil storage might impact plant growth, physiology, and nodulation by N-fixing bacteria using soils from native reference vegetation and stockpiled soils from six mine sites across Western Australia. Results: Plant responses varied across mine sites, but overall plants performed better in soils collected from native vegetation, exhibiting greater biomass, more root nodules, and higher water-use efficiency compared to those grown in stockpiled soils. Soil physiochemistry showed few and minor differences between native soils and stockpiles. Conclusion: Results strongly suggest observed differences in plant performance were biotic in nature. This study highlights the negative effects of topsoil storage on the biological integrity of soil across diverse ecosystems, with important implications for mine-site restoration; our results show that topsoil management can strongly influence plant performance, and stockpiled soils are likely inferior to recently disturbed topsoil for restoration purposes. We also use this study to illustrate the utility of bioassays for assessing soil quality for ecological restoration

Anaesthetic induction and recovery characteristics of a diazepam-ketamine combination compared with propofol in dogs

Induction of anaesthesia occasionally has been associated with undesirable behaviour in dogs. High quality of induction of anaesthesia with propofol has been well described while in contrast variable induction and recovery quality has been associated with diazepam-ketamine. In this study, anaesthetic induction and recovery characteristics of diazepam-ketamine combination with propofol alone were compared in dogs undergoing elective orchidectomy. Thirty-six healthy adult male dogs were used. After habitus scoring (simple descriptive scale [SDS]), the dogs were sedated with morphine and acepromazine. Forty minutes later a premedication score (SDS) was allocated and general anaesthesia was induced using a combination of diazepam-ketamine (Group D/K) or propofol (Group P) and maintained with isoflurane. Scores for the quality of induction, intubation and degree of myoclonus were allocated (SDS). Orchidectomy was performed after which recovery from anaesthesia was scored (SDS) and times to extubation and standing were recorded. Data were analysed using descriptive statistics and Kappa Reliability and Kendall Tau B tests. Both groups were associated with acceptable quality of induction and recovery from anaesthesia. Group P, however, was associated with a poorer quality of induction (p = 0.014), prolonged induction period (p = 0.0018) and more pronounced myoclonus (p = 0.003), but had better quality of recovery (p = 0.000002) and shorter recovery times (p = 0.035) compared with Group D/K. Diazepam-ketamine and propofol are associated with acceptable induction and recovery from anaesthesia. Propofol had inferior anaesthetic induction characteristics, but superior and quicker recovery from anaesthesia compared with diazepam-ketamine.University of Pretoriahttp://www.jsava.co.zaam201