Laura M. Young

Novel myco-like DNA viruses discovered in the faecal matter of various animals

A wide variety of novel single-stranded DNA (ssDNA) viruses have been found in faecal matter of chimpanzees, cows, rodents, bats, badgers, foxes and pigs over the last few years. Using a combination of rolling circle amplification coupled with restriction enzyme digests based approach as well as a next generation sequencing informed approach, we have recovered fourteen full genomes of ssDNA viruses which exhibit genomic features described for members of the recently proposed gemycircularvirus group from a wide variety of mammal and bird faecal samples across New Zealand. The fourteen novel ssDNA viruses (2122-2290nt) encode two major proteins, a replication associated protein (Rep) and a capsid protein (Cp) which are bi-directionally transcribed. Interestingly, the Rep of these novel viruses are similar to gemycircularviruses detected in insects, cassava leaves, and badger faecal matter, the novel viruses share sequence similarities with the mycovirus sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and Rep-like sequences found in fungal genomes. Pairwise sequence similarities between the 14 novel genomes with other related viral isolates (gemycircularviruses) indicated that they share greater than 55.8% genome-wide identity. Additionally, they share between 55% and 59% pairwise identity with putative novel ssDNA virus genomes recently isolated from sewage baminivirus, niminivirus and nephavirus. Based on the similarities to SsHADV-1 and Rep-like sequences found in fungal genomes, these novel gemycircularviruses may infect fungi.

Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand.

In recent years, innovations in molecular techniques and sequencing technologies have resulted in a rapid expansion in the number of known viral sequences, in particular those with circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA genomes. CRESS DNA viruses are present in the virome of many ecosystems and are known to infect a wide range of organisms. A large number of the recently identified CRESS DNA viruses cannot be classified into any known viral families, indicating that the current view of CRESS DNA viral sequence space is greatly underestimated. Animal faecal matter has proven to be a particularly useful source for sampling CRESS DNA viruses in an ecosystem, as it is cost-effective and non-invasive. In this study a viral metagenomic approach was used to explore the diversity of CRESS DNA viruses present in the faeces of domesticated and wild animals in New Zealand. Thirty-eight complete CRESS DNA viral genomes and two circular molecules (that may be defective molecules or single components of multicomponent genomes) were identified from forty-nine individual animal faecal samples. Based on shared genome organisations and sequence similarities, eighteen of the isolates were classified as gemycircularviruses and twelve isolates were classified as smacoviruses. The remaining eight isolates lack significant sequence similarity with any members of known CRESS DNA virus groups. This research adds significantly to our knowledge of CRESS DNA viral diversity in New Zealand, emphasising the prevalence of CRESS DNA viruses in nature, and reinforcing the suggestion that a large proportion of CRESS DNA viruses are yet to be identified.

Back from extinction: Rediscovery of the Canterbury knobbled weevil Hadramphus tuberculatus (Pascoe 1877) (Coleoptera: Curculionidae), with a review of its historical distribution

Abstract The Canterbury knobbled weevil, Hadramphus tuberculatus (Coleoptera: Curculionidae: Molytini), was once widespread in the Canterbury plains, foothills and fringing ranges, ranging from Oxford in the north to Waimate in the south. Habitat degradation, reduction in host plant numbers through grazing and predation by rodents are thought to be responsible for the decline in its numbers and distribution. In December 2004, more than 80 years since the last sighting of H. tuberculatus in 1922, a single individual was found at Burkes Pass Scenic Reserve. This paper records the rediscovery of H. tuberculatus, reviews the historical distribution records for H. tuberculatus, discusses them with respect to changes in host plant habitat in the eastern South Island, and suggests conservation strategies to protect this and other relictual populations that might be found in future.

Ultimate drivers of native biodiversity change in agricultural systems

The ability to address land degradation and biodiversity loss while maintaining the production of plant and animal products is a key global challenge. Biodiversity decline as a result of vegetation clearance, cultivation, grazing, pesticide and herbicide application, and plantation establishment, amongst other factors, has been widely documented in agricultural ecosystems. In this paper we identify six ultimate drivers that underlie these proximate factors and hence determine what native biodiversity occurs in modern agricultural landscapes; (1) historical legacies; (2) environmental change; (3) economy; (4) social values and awareness; (5) technology and knowledge; and (6) policy and regulation. While historical legacies and environmental change affect native biodiversity directly, all six indirectly affect biodiversity by influencing the decisions that land managers make about the way they use their land and water resources. Understanding these drivers is essential in developing strategies for sustaining native biodiversity in agricultural landscapes into the future.