Going, Going, Gone The Diminishing Capacity of Museum Specimen Collections to Address Global Change Research: A Case Study on Urban Reptiles.

It has been increasingly popular to use natural history specimens to examine environmental changes. As the current functionality of museum specimens has extended beyond their traditional taxonomic role, there has been a renewed focus on the completeness of biological collections to provide data for current and future research. We used the collections of the Western Australian Museum to answer questions about the change in occurrence of five common reptile species due to the rapid urbanization of Perth. We recorded a significant decline in collection effort from the year 2000 onwards (F = 7.65, p < 0.01) compared to the period 1990-1999. Spatial analysis revealed that only 0.5% of our study region was well sampled, 8.5% were moderately sampled and the majority of the regions (91%) were poorly sampled. By analysing the trend of specimen acquisition from 1950 to 2010, we discovered a significant inconsistency in specimen sampling effort for 13 common reptile species across time and space. A large proportion of past specimens lacked information including the place and time of collection. An increase in investment to museums and an increase in geographically and temporally systematic collecting is advocated to ensure that collections can answer questions about environmental change.

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's 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.

Soil fungal responses to experimental warming and drying in a Mediterranean shrubland.

Implications of a drying and warming climate have been investigated for aboveground vegetation across a range of biomes yet below-ground effects on microorganisms have received considerably less attention, especially in Mediterranean Type Ecosystems (MTE) that are predicted to be negatively impacted by climate change. We experimentally reduced rainfall and increased temperature across two contrasting study sites (deep sand dune vs shallow sand swale) to test how projected future climate conditions may impact soil fungal composition, richness and diversity. We also assessed fungal OTU warming responses and putative functions of 100 most abundant OTUs and 120 OTUs that either increased or decreased based on their presence/absence across treatments. We found a significant effect of study site, treatment and canopy species on fungal composition. Soil fungal diversity increased under warming treatment in swale plots as compared to control plots indicating a positive effect of warming on fungal diversity. In dunes, significantly more OTUs responded to drought than warming treatment. Among the most abundant soil fungal putative functional groups were endophytes, ericoid mycorrhizas, yeasts and ectomycorrhizas consistent with previous studies. Plant pathogens were found to increase across dunes and swales, while ericoid mycorrhizae decreased. In summary, our study revealed that it is critical to understand belowground microbial patterns as a result of climate change treatments for our ability to better predict how ecosystems may respond to global environmental changes in the future.

Diversity of endemic rhizobia on Christmas Island: Implications for agriculture following phosphate mining.

Given that phosphate supplies may diminish and become uneconomic to mine after 2020, there is a compelling need to develop alternative industries to support the population on Christmas Island. Former mine sites could be turned into productive agricultural land, however, large-scale commercial agriculture has never been attempted, and, given the uniqueness of the island, the diversity of rhizobia prior to introducing legumes needed evaluation. Therefore, 84 rhizobia isolates were obtained from nine different hosts, both crop and introduced legumes, located at seven sites across the island. Based on 16S rRNA and recA gene sequence analysis, the isolates grouped into 13 clades clustering within the genus Bradyrhizobium, Ensifer, Cupriavidus and Rhizobium. According to the sequences of their symbiosis genes nodC and nifH, the isolates were classified into 12 and 11 clades, respectively, and clustered closest to tropical or crop legume isolates. Moreover, the symbiosis gene phylogeny and Multi Locus Sequence Analysis gene phylogeny suggested vertical transmission in the Alpha-rhizobia but horizontal transmission within the Beta-rhizobia. Furthermore, this study provides evidence of a large diversity of endemic rhizobia associated with both crop and introduced legumes, and highlights the necessity of inoculation for common bean, chickpea and soybean on the Island.

Reducing the risk of invasive forest pests and pathogens: Combining legislation, targeted management and public awareness.

Intensifying global trade will result in increased numbers of plant pest and pathogen species inadvertently being transported along with cargo. This paper examines current mechanisms for prevention and management of potential introductions of forest insect pests and pathogens in the European Union (EU). Current European legislation has not been found sufficient in preventing invasion, establishment and spread of pest and pathogen species within the EU. Costs associated with future invasions are difficult to estimate but past invasions have led to negative economic impacts in the invaded country. The challenge is combining free trade and free movement of products (within the EU) with protection against invasive pests and pathogens. Public awareness may mobilise the public for prevention and detection of potential invasions and, simultaneously, increase support for eradication and control measures. We recommend focus on commodities in addition to pathways, an approach within the EU using a centralised response unit and, critically, to engage the general public in the battle against establishment and spread of these harmful pests and pathogens.