Prediction of Potato Tuber Damage by Root-Knot Nematodes using Quantitative DNA Assay of Soil.

Root-knot nematodes (Meloidogyne fallax and M. hapla) cause significant reductions in potato yield by reducing tuber quality. Concentrations of M.

DNA analysis of soil extracts can be used to investigate fine root depth distribution of trees.

Understanding the root distribution of trees by soil coring is time -: consuming as it requires the separation of roots from soil and classification of roots into particular size classes. This labour-intensive process can limit sample throughput and therefore sampling intensity. We investigated the use of quantitative polymerase chain reaction (qPCR) on soil DNA extractions to determine live fine root DNA density (RDD, mg DNA m(-2)) for mango (Mangifera indica) trees.

A DNA-based method for studying root responses to drought in field-grown wheat genotypes.

Root systems are critical for water and nutrient acquisition by crops. Current methods measuring root biomass and length are slow and labour-intensive for studying root responses to environmental stresses in the field. Here, we report the development of a method that measures changes in the root DNA concentration in soil and detects root responses to drought in controlled environment and field trials.

Improved inference of taxonomic richness from environmental DNA.

Accurate estimation of biological diversity in environmental DNA samples using high-throughput amplicon pyrosequencing must account for errors generated by PCR and sequencing. We describe a novel approach to distinguish the underlying sequence diversity in environmental DNA samples from errors that uses information on the abundance distribution of similar sequences across independent samples, as well as the frequency and diversity of sequences within individual samples. We have further refined this approach into a bioinformatics pipeline, Amplicon Pyrosequence Denoising Program (APDP) that is able to process raw sequence datasets into a set of validated sequences in formats compatible with commonly used downstream analyses packages.

Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils.

Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi-arid floodplain would transition towards comprising mainly dry-soil specialist species with increasing drought severity.

Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool.

Determining the source and flow of carbon, energy and nutrients through food webs is essential for understanding ecological connectivity and thus determining the impact of management practices on biodiversity. We combined DNA sequencing, microarrays and stable isotope analyses to test whether this approach would allow us to resolve the carbon flows through food webs in a weir pool on the lower Murray River, a highly impacted, complex and regulated ecosystem in southern Australia. We demonstrate that small fish in the Murray River consume a wide range of food items, but that a significant component of carbon and nitrogen entering the food web during dry periods in summer, but not spring, is derived from nonconventional sources other than in-channel primary producers.

Matching the origin of an invasive weed for selection of a herbivore haplotype for a biological control programme.

The Florida Everglades have been invaded by an exotic weed fern, Lygodium microphyllum. Across its native distribution in the Old World tropics from Africa to Australasia it was found to have multiple location-specific haplotypes. Within this distribution, the climbing fern is attacked by a phytophagous mite, Floracarus perrepae, also with multiple haplotypes.