Soil biology encompasses a vast diversity of organisms contributing to soil processes and functions that underpin the delivery of soil ecosystem services. We review the response of soil biology to long-term phosphorus (P) and nitrogen (N) fertiliser application, focusing on trials conducted at Winchmore and Ballantrae Research Stations under sheep grazing. Application of P and N fertiliser increases soil fertility and pasture production and can have impacts on soil biology. Higher earthworm abundance was associated with increasing P, but not N fertiliser application. Microbial biomass or respiration tended to increase with P application but decrease with N application. Both P and N fertiliser decreased fungal biomass. The few microbial functional groups studied also appear responsive to fertilisation. A decline in soil pH may have driven some of these changes and could have been mitigated with lime. Other factors, such as plant composition, may also be important to the soil biology but have received limited attention in these studies. There are currently few indicators that can be used on-farm to assess soil biology. We discuss these as well as measures that can be used in a research context to inform the impacts of fertiliser use on soil biology and its functioning.

The light brown apple moth, Epiphyas postvittana is an invasive, polyphagous pest of horticultural systems around the world. With origins in Australia, the pest has subsequently spread to New Zealand, Hawaii, California and Europe, where it has been found on over 500 plants, including many horticultural crops. We have produced a genomic resource, to understand the biological basis of the polyphagous and invasive nature of this and other lepidopteran pests. The assembled genome sequence encompassed 598 Mb and has an N50 of 301.17 kb, with a BUSCO completion rate of 97.9%. Epiphyas postvittana has 34% of its assembled genome represented as repetitive sequences, with the majority of the known elements made up of longer DNA transposable elements (14.07 Mb) and retrotransposons (LINE 17.83 Mb). Of the 31,389 predicted genes, 28,714 (91.5%) were assigned to 11,438 orthogroups across the Lepidoptera, of which 945 were specific to E. postvittana. Twenty gene families showed significant expansions in E. postvittana, including some likely to have a role in its pest status, such as cytochrome p450s, glutathione-S-transferases and UDP-glucuronosyltransferases. Finally, using a RAD-tag approach, we investigated the population genomics of this pest, looking at its likely patterns of invasion.

The actinidin proteinase family has a striking sequence diversity; isoelectric points range from 3.9 to 9.3. The biological drive for this variation is thought to be actinidin's role as a defense-related protein. In this study we map mutations in the primary sequence onto the 3D structure of the protein and show that the region with the highest diversity is close to the substrate binding groove. Non-conservative substitutions in the active site determine substrate preference and therefore create problems for quantification of actinidin activity. Here we use a peptide substrate library to compare two actinidin isoforms, one from the kiwiberry cultivar 'Hortgem Tahi' (Actinidia arguta), and the other from the familiar kiwifruit cultivar 'Hayward' (Actinidia chinensis var. deliciosa). Among 360 octamer substrates we find one substrate (RVAAGSPI) with the useful property of being readily cleaved by all the functionally active actinidins in a set of A. arguta and A. chinensis var. deliciosa isoforms. In addition, we find that two substrates (LPPKSQPP & ILRDKDNT) have the ability to differentiate different isoforms from a single fruit. We compare actinidins from 'Hayward' and A. arguta for their ability to digest the allergenic gluten peptide (PFPQPQLPY) but find the peptide to be indigestible by all sources of actinidin. The ability to inactivate salivary amylase is shown to be a common trait in Actinidia cultivars due to proteolysis by actinidin and is particularly strong in 'Hortgem Tahi'. A mixture of 10% 'Hortgem Tahi' extract with 90% saliva inactivates 100% of amylase activity within 5 minutes. Conceivably, 'Hortgem Tahi' might lower the glycaemic response in a meal rich in cooked starch.

The objective of this study was to assess barcoding of environmental DNA as a method for monitoring invertebrate ecosystem service providers in soil samples. We selected 26 invertebrate ecosystem service providers that occur in New Zealand kiwifruit or apple orchards and produced mitochondrial cytochrome c oxidase gene subunit I (cytochrome oxidase I) and/or 28S ribosomal DNA sequences for each. Specific barcode primers were designed for each invertebrate ecosystem service provider and tested, along with generic barcoding cytochrome oxidase I primers, for their ability to detect DNA from invertebrate ecosystem service providers that had been added to sterilized and unsterilized soil samples. Although the specific primers accurately detected the invertebrate ecosystem service providers in more than 96% of the samples, the generic cytochrome oxidase I primers detected only 37% of the invertebrate ecosystem service providers added to the sterilized samples and 2.5% in the unsterilized samples. In a field test, we compared metabarcoding with traditional invertebrate trapping methods to detect the invertebrate ecosystem service providers in 10 kiwifruit and 10 apple orchards. All invertebrate ecosystem service providers were collected in traps in at least one orchard, but very few were identified by metabarcoding of soil environmental DNA. Although the specific primers can be used as a tool for monitoring invertebrate ecosystem service providers in soil samples, methodological improvements are needed before metabarcoding of soil environmental DNA can be used to monitor these taxa.

Soil water repellency (SWR) is a common phenomenon observed throughout the world. It has a significant impact on water infiltration, altering soil hydrology and consequently the soil microbial community and nutrient cycling. Despite the importance of this phenomenon, the processes involved in the development and breakdown of SWR are poorly understood. The importance of the microbial community for SWR is becoming increasingly apparent. In this study, relationships between microbial activities and SWR were investigated by utilising the patchy occurrence of SWR to select both repellent and wettable soils in six locations of the east coast of the North Island of New Zealand. Samples were from directly adjacent locations in mid spring and late summer, and a range of soil physico-chemical properties and enzyme activities were measured. The degree and potential persistence of SWR did not change between the two sampling times, whereas actual persistence of SWR increased. Soil moisture decreased between the two times, and although there was an inverse relationship between moisture and actual persistence of SWR in late summer, unexpectedly, it was a positive relationship in spring. Phosphatase, arylsulfatase and polysaccharide degrading enzyme activities increased with increasing SWR, whereas peroxidase activity decreased. The possible effects of increasing temperature and decreasing water content were modelled, and the observed relationships were strengthened. Arylsulfatase activity was strongly correlated with the degree of SWR, as was extractable organic sulfate, suggesting that the breakdown of sulfate-esters within humic material in soil may be involved in the release and accumulation of SWR-inducing hydrophobic compounds.

The effects of soil water repellency (SWR) on runoff and nutrient losses are difficult to isolate. Hydrophobic organic substances coating soil particles can severely delay water infiltration and enhance runoff. We used a portable run-on simulator to investigate the effect of SWR on runoff and nutrient loss. Intact soil slabs, 0.48 m long and 0.19 m wide, were collected from a severely water-repellent Andosol under pasture. One day before simulating 60-min long run-on events with an intensity of 60 mm h−1, superphosphate was applied at a rate of 45 kg P ha−1. The effects of SWR were quantified by comparing runoff volumes and nutrient losses from run-on events conducted with water and a fully wetting aqueous ethanol solution as run-on liquids. Further, through conducting multiple consecutive water run-on events with the same soil slab, the hypothesis, that SWR is lost through the washing off of hydrophobic materials, was tested. Finally, runoff dynamics were visualised by adding a dye to the run-on water. In the first run-on experiment, 88% of the water applied was captured as runoff, while no runoff was observed when aqueous ethanol was used as run-on liquid, providing strong evidence that SWR governed runoff generation from this Andosol. In consecutive water run-on experiments, approximately 23% of the applied P was recovered in the runoff from the first event, while the cumulative P loss over ten consecutive run-on events was around 30% of the applied P. This confirms that nutrient losses were associated with SWR and the occurrence of runoff. After ten consecutive run-on events, the persistence of both actual and potential SWR in areas of the slab that had been wetted were significantly (p < 0.5) reduced. But the persistence of potential SWR of the soil was still classified as severe, suggesting only minor losses of hydrophobic materials from the soil surface. The persistence of potential SWR and the degree of SWR of the dry areas remained more or less unchanged. In accordance with this, visualisation of the wetted areas showed that runoff occurred as rivulets guided by surface topography, rather than as sheet flow, with the wetted area increasing from approximately 20% of the slab in the first event to around one third of the total slab area in the final event. This pattern is reflected in the cumulative pattern of the P losses over the ten events. Consequently, we conclude that SWR should be considered as a factor in hydrological modelling and should be included in models to address appropriately the risk of surface water contamination by solutes exogenously applied to water-repellent soils.

Background: Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. Results: A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Conclusions: Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Green vegetable bugs (GVB) are a pest of kiwifruit and other crops in New Zealand. Because of their similar size and polyphagous diet, they are also a reasonable proxy for the serious agricultural pest, brown marmorated stink bug (BMSB): studying GVB may give us some insights into BMSB prior to its arrival in New Zealand. Using security cameras to monitor GVB eggs, nymphs and adults, we aimed to identify species preying on GVB in a variety of habitats (kiwifruit orchards, vegetable crop field margins and home gardens in Auckland and Te Puke). GVB nymphs and adults were individually tethered using cotton thread glued to their dorsal surfaces, while egg batches were placed in the field on the substrate on which they were laid. We obtained 840 hours of video footage and recorded only 10 predation events. Predators included birds, ants, jumping spiders and harvestmen. When given no choice in the laboratory, we also found praying mantis, hunting and crab spiders would feed on GVB nymphs. Nothing was found to feed on GVB eggs. Although only a few taxa were identified feeding on GVB, most are common in modi ed habitats in New Zealand, and therefore may contribute to the suppression of GVB (and potentially BMSB) populations.

Soil water repellency (SWR) is a phenomenon that can reduce water infiltration into the soil. Generally, the quantity and quality of soil organic matter and the soil moisture content will govern the severity of SWR. The objectives of this study were (i) to characterize SWR for greenhouse and grassland soils using the water drop penetration time (WDPT) test and (ii) to find relationships among the field and laboratory WDPT (WDPTfield and WDPTlab), and the SDM measurements. Two farms that produce vegetables in greenhouses from Japan (Mizuho farm, Miki city, Hyogo) and a beef farm from New Zealand (Tihoi, near Taupo, Waikato) under perennial mixed grass (Lolium perenne L. and Trifolium repens L.) were selected as experimental sites. The New Zealand hillslope site was located on an Andosol. In the greenhouses at the two Japanese sites, vegetables such as spinach (Spinacia oleracea) and spring onion (Allium spp.) were grown on fine-textured Haplic Brown Lowland Soil. The latter soils were fertilized once a season with farm-made compost. Water repellency was measured along a rectangular grid and selected transects. The WDPT was measured using micro-syringe water droplets (50 μL) with five replicates. The WDPTlab and SDM were measured using repacked soil cores. The values of WDPTfield varied widely from non-repellent to extreme SWR. The water repellent soil has observed for grassland soils at pF (= log [−ψ], where ψ is the soil water matric potential in centimeters of H2O) of 3.2 - 4.4 range. The measured WDPTlab showed a linear relationship with the measured SDM (r2 = 0.80). Keywords: Soil water repellency, Water drop penetration time, Soil organic matter, Soil moisture

Recent and Pumice Soils are relatively young, typically only one to three thousand years old. Recent Soils are weakly developed, although they have a distinct topsoil layer. Despite this, they are usually fertile with good water storage capacity and facilitate deep rooting. Pumice Soils, derived from volcanic eruptions, have low soil strength, but like Recent Soils they have good water storage and deep rooting facility. Pumice soils have low fertility because of low levels of some major nutrients and trace elements. However, all soils in this project were fertilised pastures. The two soil orders share many properties, including their susceptibility to soil hydrophobicity, a potential problem for the loss of fertiliser with runoff. We hypothesised that at least some of these common properties may be related to the soils’ biological activity rather than to the soil order.

Soil water repellency (SWR) is a phenomenon which leads to a reduction of wetting and infiltration of soils by water. SWR is a significant problem affecting large areas of land throughout the world, and is found in natural, intensively managed and man-made ecosystems (DeBano 2000). SWR can cause a decrease in plant-available water, reducing agricultural crop production. Coincident with the decreased water absorption is increased surface runoff, which causes nutrient losses for surface applied fertilisers, and soil erosion in extreme cases (Wallis, Scotter et al. 1991). Environmental and edaphic conditions can predispose soils to SWR; some, such as elevated temperature, cause changes in SWR over short time periods (Doerr and Thomas 2000).

Microvilli are conventionally regarded as an extension of the small intestinal absorptive surface, but they are also, as latterly discovered, a launching pad for brush border digestive enzymes. Recent work has demonstrated that motor elements of the microvillus cytoskeleton operate to displace the apical membrane toward the apex of the microvillus, where it vesiculates and is shed into the periapical space. Catalytically active brush border digestive enzymes remain incorporated within the membranes of these vesicles, which shifts the site of BB digestion from the surface of the enterocyte to the periapical space. This process enables nutrient hydrolysis to occur adjacent to the membrane in a pre-absorptive step. The characterization of BB digestive enzymes is influenced by the way in which these enzymes are anchored to the apical membranes of microvilli, their subsequent shedding in membrane vesicles, and their differing susceptibilities to cleavage from the component membranes. In addition, the presence of active intracellular components of these enzymes complicates their quantitative assay and the elucidation of their dynamics. This review summarizes the ontogeny and regulation of BB digestive enzymes and what is known of their kinetics and their action in the peripheral and axial regions of the small intestinal lumen.

Gene silencing through RNA interference (RNAi) has revolutionized the study of gene function, particularly in non-model insects. However, in Lepidoptera (moths and butterflies) RNAi has many times proven to be difficult to achieve. Most of the negative results have been anecdotal and the positive experiments have not been collected in such a way that they are possible to analyze. In this review, we have collected detailed data from more than 150 experiments including all to date published and many unpublished experiments. Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involved in immunity. On the contrary, gene expression in epidermal tissues seems to be most difficult to silence. In addition, gene silencing by feeding dsRNA requires high concentrations for success. Possible causes for the variability of success in RNAi experiments in Lepidoptera are discussed. The review also points to a need to further investigate the mechanism of RNAi in lepidopteran insects and its possible connection to the innate immune response. Our general understanding of RNAi in Lepidoptera will be further aided in the future as our public database at http://insectacentral.org/RNAi will continue to gather information on RNAi experiments.

Yersinia entomophaga MH96 is a native New Zealand soil bacterium that secretes a large ABC-type protein toxin complex, Yen-Tc, similar to those produced by nematode-associated bacteria such as Photorhabdus luminescens. Y. entomophaga displays an exceptionally virulent pathogenic phenotype in sensitive insect species, causing death within 72 h of infection. Because of this phenotype, there is intrinsic interest in the mechanism of action of Yen-Tc, and it also has the potential to function as a novel class of biopesticide. We have identified genes that encode chitinases as part of the toxin complex loci in Y. entomophaga MH96, P. luminescens, Photorhabdus asymbiotica and Xenorhabdus nematophila. Furthermore, we have shown that the secreted toxin complex from Y. entomophaga MH96 includes two chitinases as an integral part of the complex, a feature not described previously in other ABC toxins and possibly related to the severe disease caused by this bacterium. We present here the structure of the Y. entomophaga MH96 Chi1 chitinase, determined by X-ray crystallography to 1.74 Å resolution, and show that a ring of five symmetrically arranged lobes on the surface of the Yen-Tc toxin complex structure, as determined by single-particle electron microscopy, provides a good fit to the Chi1 monomer. We also confirm that the isolated chitinases display endochitinase activity, as does the complete toxin complex.

Toxin complex (Tc) proteins are a class of bacterial protein toxins that form large, multisubunit complexes. Comprising TcA, B, and C components, they are of great interest because many exhibit potent insecticidal activity. Here we report the structure of a novel Tc, Yen-Tc, isolated from the bacterium Yersinia entomophaga MH96, which differs from the majority of bacterially derived Tcs in that it exhibits oral activity toward a broad range of insect pests, including the diamondback moth (Plutella xylostella). We have determined the structure of the Yen-Tc using single particle electron microscopy and studied its mechanism of toxicity by comparative analyses of two variants of the complex exhibiting different toxicity profiles. We show that the A subunits form the basis of a fivefold symmetric assembly that differs substantially in structure and subunit arrangement from its most well characterized homologue, the Xenorhabdus nematophila toxin XptA1. Histopathological and quantitative dose response analyses identify the B and C subunits, which map to a single, surface-accessible region of the structure, as the sole determinants of toxicity. Finally, we show that the assembled Yen-Tc has endochitinase activity and attribute this to putative chitinase subunits that decorate the surface of the TcA scaffold, an observation that may explain the oral toxicity associated with the complex.

The composition of a soil microbial community and the services provided are dependent on soil conditions: pH moisture and oxygen content and nutrient levels. In this study, we examined the biodiversity of a soil under two orchard production management systems, organic and integrated fruit production, looking at the bulk soil and the soil contents of the earthworm, Lumbricus terrestris. Nucleic acids were extracted from the soil; relative gene levels of 16S rRNA for various microbial groups and functional genes of nitrogen metabolism were determined by qPCR. At the DNA level there was no difference between the two bulk soils, and the main difference between soil and gut was an increase in fungi and a decrease in nitrate reductase in the integrated soil. Microbial group composition at the RNA level the bulk soils were again similar, however differences between the bulk and gut soils were greater. Functional genes varied greatly, suggesting that organic soil within the midgut processes more nitrite by dissimilatory reduction than by denitrification, minimising nitrous oxide emissions.