Andrew Dopheide

The accurate identification of insects supports conservation, biosecurity and ecological monitoring. However, morphological identification is constrained by taxonomic complexity, undescribed diversity, and limited expertise. DNA barcoding can alleviate some of these challenges and complement morphological identification, if reference data are comprehensive and reliable. We assessed the taxonomic, geographic and elevational coverage of New Zealand insect DNA barcodes using taxonomic names from the New Zealand Organisms Register, published estimates of undescribed species richness, and DNA barcode metadata. Only 18% of described native and exotic insect species currently have DNA barcodes, with higher coverage for exotic (59%) than native species (12%). DNA barcode coverage varies from complete in several single‐species orders to very low in hyperdiverse orders such as Coleoptera (7%) and Diptera (5%), while moderately diverse aquatic orders reach 31%–91% coverage. Low elevation and populated regions are overrepresented in the DNA barcode data, and many species identifications are based on bioinformatic approaches rather than taxonomic or diagnostic expertise. Despite these biases, we propose that a complete national DNA barcode library for described insect species is highly achievable given access to well‐curated insect collections and species name databases for tracking progress. Complete DNA barcoding of undescribed species will be more challenging and will require targeting underrepresented taxa, geographic regions and elevations. Sampling will need to incorporate field surveys with bulk specimen collection, environmental DNA, museomic approaches and expert‐verified identifications. Completing this library will strengthen New Zealand's regional and national‐scale biodiversity monitoring using environmental DNA, with important contributions to biosecurity and conservation outcomes.

Introduction: Forest restoration can be achieved by promoting natural regeneration or planting tree seedlings, but the relative benefits of these widely used approaches are questioned. Soil communities may influence restoration outcomes but are usually ignored by monitoring schemes. Objectives: We investigated whether analyses of multitrophic soil communities and ecosystem functions can usefully complement conventional plant community measurements for assessing current and potential future states of naturally regenerating and planted native forests. Methods: We used DNA metabarcoding to analyze multitrophic soil biodiversity alongside conventional plant community analyses in greater than 20‐year‐old forests of naturally regenerating and planted Leptospermum scoparium (mānuka, Myrtaceae), an important early‐successional tree native to Aotearoa—New Zealand, within two similar sites. Results: Naturally regenerating forests had higher understory native plant cover and sapling wood density, and more saplings of species that dominate old‐growth forests. Planted forests had higher aboveground biomass, richnesses of soil bacteria and protists, and soil pathogen loads. Prokaryote metabolic pathways indicated greater importance of aboveground litter versus belowground plant exudates as soil inputs in planted and naturally regenerating forests, respectively. Soil analyses detected legacy effects of pre‐1860 Māori land use in several plots. Conclusions: Soil biodiversity assessment provided information about past, current, and potential future ecological states that was not apparent from the analysis of aboveground plants alone. Our combined results show that planted forests initially grow faster and sequester more carbon, but naturally regenerating forests might be healthier and able to shift to an old‐growth forest state sooner.

Agathis australis (kauri), the only member of the ancient conifer family Araucariaceae in New Zealand, is colonised by arbuscular mycorrhizal (AM) fungi. The survival of A. australis is threatened by an Oomycota, Phytophthora agathidicida , the causal agent of kauri dieback. Phosphite injections into the trunk are the primary treatment for kauri dieback and have proven effective in reducing disease symptoms. However, the potential impact of phosphite treatment on AM fungal colonisation within A. australis roots and nodules has not been investigated. We conducted a preliminary investigation into whether AM fungi colonise phosphite‐treated trees. Using a combination of microscopy and metabarcoding of AM fungi 18S nuclear ribosomal small subunit genes, we demonstrate that AM fungi colonise the roots and nodules of A. australis trees three to 4 years post‐treatment. Glomeraceae was found to dominate, and AM fungi community composition and colonisation rates were comparable to previously reported values in trees not treated with phosphite. Soil pH, but not date of phosphite treatment or PA infection status, was found to significantly contribute to AM fungal community composition. This work highlights the importance in investigating colonisation events immediately after phosphite treatment of A. australis and a comparison with untreated trees. AM fungi are likely integral for A. australis forests to thrive, thus, ensuring they are protected in the treatment of kauri dieback is essential.

DNA technologies have many advantages for biomonitoring and biodiversity analyses, but these depend on the availability of relevant reference DNA barcodes. To be most useful, a DNA barcode should be linked to a taxonomic name, which can in turn be connected to ecological information. This linking can be achieved by DNA barcoding of taxonomically identified specimens. Museums are a promising source of such specimens, but the DNA in museum specimens is often degraded, necessitating carefully optimised DNA extraction methods. In this issue of Molecular Ecology Resources, Holmquist et al. (2025) present a DNA extraction protocol for museum insect specimens, using in-house formulated Solid Phase Reversible Immobilisation (SPRI) beads. The authors carried out several experiments with statistical evaluation to determine optimal DNA extraction parameters, before testing the protocol on a large and diverse pool of museum-held insect specimens. The result is a low-cost and effective DNA extraction protocol for diverse museum insect specimens.

Leaf surface microbial communities play an important role in forest ecosystems and are known to be affected by environmental and host conditions, including diseases impacting the host. Phytophthora agathidicida is a soil-borne pathogen that causes severe disease (kauri dieback) in one of New Zealand’s endemic trees, Agathis australis (kauri). This research characterised the microbial communities of the A. australis phyllosphere (i.e. leaf surface) using modern molecular techniques and explored the effects of P. agathidicida on those communities. Fresh leaves were collected from trees where P. agathidicida was and was not detected in the soil and characterisation of the leaf surface microbial community was carried out via high-throughput amplicon sequencing of the internal transcribed spacer (ITS) and 16S ribosomal RNA regions. Nutrients in leaf leachates were also measured to identify other possible drivers of microbial diversity. The dominant phyllosphere microbial phylum was Proteobacteria followed by Acidobacteria. The phyllosphere microbial richness of A. agathis associated with P. agathidicida-infected soils was found to be generally lower than where the pathogen was not detected for both prokaryote (bacterial) and fungal phyla. Leaf leachate pH as well as boron and silicon had significant associations with bacterial and fungal community structure. These findings contribute to the development of a comprehensive understanding of A. australis leaf surface microbial communities and the effects of the soil pathogen P. agathidicida on those communities.

The widespread endemic tree Lophomyrtus bullata (ramarama; Myrtaceae) is in serious decline. Lophomyrtus bullata is now considered threatened due to the ongoing spread of Austropuccinia psidii, a rust fungus causing myrtle rust disease. Mycorrhizal communities play an important role in the survival of plant species and have a potential role in disease resistance. Thus, we examined the fungal communities of L.

Inputs of carbon to soil may be used to stimulate microbial growth and immobilize excess nitrogen from sources such as livestock urine. However, the growth responses of microbial taxa to carbon inputs under conditions of excess soil nitrogen remain poorly understood. Using DNA metabarcoding and a field-based soil lysimeter experiment, we characterised the temporal responses (up to 112 days) of bacterial and fungal communities to a simulated bovine urine event plus inputs of labile carbon (sucrose) at two concentrations. Fungal communities were impacted more strongly than bacterial communities by carbon inputs following the simulated urine event, with more variable responses among taxa. Chytridiomycota and Glomeromycota richness were most negatively affected, and Tremellomycetes richness most positively affected, by carbon inputs. A minority of fungal ASVs had greatly increased proportional abundances in response to carbon, while fungal trophic composition became highly dominated by saprotrophs by the experiment end. Bacterial taxa showed consistent trends of declining (to about 14 days) and recovering (to 112 days) richness in response to urine and carbon inputs, but carbon-related evenness and proportional abundance trends varied between taxa. Proportional abundances of Actinobacteria, Bacteroidetes, Betaproteobacteria, and Gammaproteobacteria increased in response to carbon, whereas proportional abundances of Acidobacteria, candidate division WPS-1, Planctomycetes, Deltaproteobacteria, and Verrucomicrobia decreased. These results show that labile carbon inputs to limit nitrate leaching support the recovery of bacterial communities to bovine urine events but may have long-term impacts on fungal community composition and function, with potential consequences for soil food webs, carbon sequestration, and agricultural productivity.

Despite recent advances in high‐throughput DNA sequencing technologies, a lack of locally relevant DNA reference databases limits the potential for DNA‐based monitoring of biodiversity for conservation and biosecurity applications. Museums and national collections represent a compelling source of authoritatively identified genetic material for DNA database development, yet obtaining DNA barcodes from long‐stored specimens may be difficult due to sample degradation. Here we demonstrate a sensitive and efficient laboratory and bioinformatic process for generating DNA barcodes from hundreds of invertebrate specimens simultaneously via the Illumina MiSeq system. Using this process, we recovered full‐length (334) or partial (105) COI barcodes from 439 of 450 (98%) national collection‐held invertebrate specimens. This included full‐length barcodes from 146 specimens which produced low‐yield DNA and no visible PCR bands, and which produced as little as a single sequence per specimen, demonstrating high sensitivity of the process. In many cases, the identity of the most abundant sequences per specimen were not the correct barcodes, necessitating the development of a taxonomy‐informed process for identifying correct sequences among the sequencing output. The recovery of only partial barcodes for some taxa indicates a need to refine certain PCR primers. Nonetheless, our approach represents a highly sensitive, accurate and efficient method for targeted reference database generation, providing a foundation for DNA‐based assessments and monitoring of biodiversity.

Inputs of carbon to soil may be used to stimulate microbial growth and immobilize excess nitrogen from sources such as livestock urine. However, the growth responses of microbial taxa to carbon inputs under conditions of excess soil nitrogen remain poorly understood. Using DNA metabarcoding and a field-based soil lysimeter experiment, we characterised the temporal responses (up to 112 days) of bacterial and fungal communities to a simulated bovine urine event plus inputs of labile carbon (sucrose) at two concentrations. Fungal communities were impacted more strongly than bacterial communities by carbon inputs under simulated urine patch conditions and had more variable responses among taxa. The richness of Chytridiomycota and Glomeromycota were most negatively affected, and Tremellomycetes most positively affected, by carbon inputs. A minority of fungal ASVs had greatly increased abundances in response to carbon, while fungal trophic composition became highly dominated by saprotrophs by the experiment end. Bacterial taxa showed consistent trends of declining (to about 14 days) and recovering (to 112 days) richness in response to urine and carbon inputs, but carbon-related evenness and abundance trends varied between taxa. Actinobacteria, Bacteroidetes, Betaproteobacteria, and Gammaproteobacteria each increased in abundance in response to carbon, whereas Acidobacteria, candidate division WPS-1, Planctomycetes, Deltaproteobacteria, and Verrucomicrobia each decreased in abundance. These results show that labile carbon inputs to limit nitrogenous leaching support the resilience of prokaryote communities to bovine urine events but may have long-term impacts on fungal community composition and function, with potential consequences for soil food webs, carbon sequestration, and agricultural productivity.