Matthew J. Colloff

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

Biodiversity assessment underpins our understanding of ecosystems and determines environmental management decisions on resource use and conservation priorities. Recently, a new discipline – environmental or ecological genomics (ecogenomics) – has emerged from major advances in sequencing technologies, such as pyrosequencing (a technique based on the detection of pyrophosphate during nucleotide incorporation), and enabled extraordinary progress in the way biodiversity can be assessed. Since 2008, numerous high-impact microbial metagenomic sequencing studies, which have relied on both classical and next-generation sequencing, have been published. As a result, many previously unrecognized taxa and biota have been identified, but none of these studies explored eukaryote diversity. Here, we illustrate the power of applying next-generation pyrosequencing to identify and enumerate eukaryote species assemblages in the context of assessing the impacts of human activity on ecosystems.

Resilience of floodplain ecosystems in a semi-arid environment

Implicit to loss of ecosystem resilience is that systems can shift from one stable state to another as a result of disturbance. We present a conceptual model of ecosystem resilience of floodplains and wetlands in semi-arid environments like those of the Murray–Darling Basin. The model is based on a single state characterised by fluctuating wet and dry phases driven by episodic floods and droughts. It might appear that such a single state is inherently unstable, but stability, and the measure of resilience, is conferred by the capacity of floodplains and wetlands to undergo drought and yet return to a functioning wet phase following inundation as well as to undergo flooding and return to the dry phase following flood recession. Floodplains and wetlands are driven by strong, periodic abiotic disturbances and their ecosystem functions and biogeochemical processes are highly rate-limited, spatiotemporally variable and driven by relatively species-poor assemblages of plants and animals adapted to withstand drought and flooding. Extreme drying due to climatic change and over-allocation of water resources represents the primary mechanism via which resilience is lost.

House dust acarofauna and Der p I equivalent in Australia: the relative importance of Dermatophagoides pteronyssinus and Euroglyphus maynei

The acarofauna and Der p I allergen concentrations in dust samples from mattresses and lounge room carpets obtained from 20 homes from two coastal cities, Perth and Bunbury, were determined. All samples were shown to contain mites and the geometric mean numbers of total mites/g of mattress and carpet dust for Perth and Bunbury were 480 and 263, and 585 and 992, respectively. Carpets from both centres had a significantly (P < 0.02) greater mean number of mite species (Perth 9.1, Bunbury 9.0) than mattresses (Perth 5.2, Bunbury 5.7). The predominant mite species were D. pteronyssinus, E. maynei and Tarsonemus spp. D.farinae was found to be absent from all dust samples examined. E. maynei was present in the 10 Bunbury homes and in 50% of the Perth homes, ranging from 0 to 81% of mites identified. The arithmetic mean Der p I concentrations in the mattresses and carpets in Perth and Bunbury were 4.2 and 4.1, and 3.8 and 9.2 μg/per gram of fine dust, respectively, and Der p I concentration correlated with mite counts (r = 0.75; P < 0.001). The concentration of Der p I equivalent per 100 mites was 1.5 μg. The data are consistent with the view that asthmatic patients in Western Australia have significant exposure to a variety of house dust mites and that E. maynei may be clinically significant.

The use ofdomestic steam cleaning for the control of house dust mites

Background Control of dust mites using extremes of temperature is un alternative to the use of acaricides. In ihe past we have attempted control by freezing with liquiid nitrogen. The present paper deals with the opposite exlrcnic, the use of steam.

The abundance of microbial functional genes in grassy woodlands is influenced more by soil nutrient enrichment than by recent weed invasion or livestock exclusion.

ABSTRACT A diverse soil microbial community is involved in nitrogen cycling, and these microbes can be affected by land management practices and weed invasion. We surveyed 20 woodlands with a history of livestock grazing, with livestock recently excluded from 10 sites. We investigated whether soil nutrients were lower when grazing was excluded and higher when exotic grasses dominated the understory. Second, using quantitative real-time PCR, we investigated whether microbial nitrogen functional gene (NFG) abundance was altered with soil nutrient enrichment, livestock exclusion, and exotic grass invasion. The target genes were chiA (decomposition-ammonification), nifH (nitrogen fixation), nirK and narG (denitrification), and bacterial amoA (nitrification). Woodland soils were enriched in phosphorus and nitrogen compared to reference condition sites, but soil nutrients were not lower following livestock exclusion. Total nitrogen and nifH were negatively correlated in grazed woodlands, suggesting that aboveground herbivory reduces the capacity for belowground nitrogen fixation. Woodlands dominated by exotic grasses had higher levels of nitrate, narG, and nirK than those dominated by native grasses. We hypothesize that the increase in potential for denitrification was due to increases in soil nitrate, rather than changes in plant composition. Overall, soil physicochemistry explained more variation in NFG abundance than livestock presence or plant invasion, particularly for chiA and bacterial amoA, with significant relationships between the abundance of all five NFGs and total nitrogen or nitrate. All woodlands investigated had a history of anthropogenic disturbance and nutrification, and soil nutrient levels and the abundance of NFGs are likely to be related to long-term land management practices.

A comparative study of allergenic and potentially allergenic enzymes from Dermatophagoides pteronyssinus, D. farinae and Euroglyphus maynei.

The presence of the enzymatically active allergens equivalent toDer p I (cysteine protease),Der p III (serine protease) and amylase in extracts ofDermatophagoides pteronyssinus, D. farinae andEuroglyphus maynei was determined using appropriate enzymatic techniques. Biochemical equivalents of all three allergens were present in each extract studied. Studies also showed that the mite extracts contained a variety of other biochemically active enzymes including trypsin, chymotrypsin, carboxypeptidase A and B, glucoamylase and lysozyme. Marked differences in the relative concentrations of some of these enzymes in different mite extracts were observed, particularly trypsin and carboxypeptidase A. The enzymes were physicochemically similar to equivalent enzymes from vertebrate and invertebrate sources. Chromatofocusing studies of faecal extracts derived fromD. pteronyssinus andD. farinae showed that several isoforms of each enzyme were present. The data indicated that there were more trypsin isoforms, with pI over a wider range, in extracts prepared fromD. pteronyssinus. Proteases and carbohydrases were also found in extracts prepared from faecally enriched material suggesting that they were endoperitrophic and associated with mite digestion. The data suggest that not only are the group I, III and amylase allergens a consistent feature of most pyroglyphid dust mites but also that other proteases and carbohydrases present in mite faeces are allergenic.

Taxonomy and identification of dust mites

Taxonomy provides the basis for the identity of species, allowing the construction of keys and the reliable, reproducible identification of dust mites for ecologic purposes and other studies. Details are given of nomenclatorial conventions in taxonomy as applied to dust mites, and taxonomically problematic entities are highlighted, such as Blomia kulagini and the sibling species Dermatophagoides farinae and D. microceras. Current keys to dust mites and advances in interactive computer keys are reviewed. An hypothesis of the phylogeny of the family Pyroglyphidae is presented, based on habitat specificity, geographic distribution, and association with birds. The value of predictive classifications based on phylogenies is stressed. Finally, a pictorial key is presented to the mites found in house dust in Scandinavia.

Distribution and abundance of dust mites within homes

The distribution and abundance of dust mites can be modelled on three scales: the microhabitat scale (different habitats within homes), the macrohabitat scale (between homes), and the regional scale. This paper focuses on the first. Those parts of a home in which dust mite populations thrive will tend to be homogeneous in respect of key habitat suitability determinants. The more widespread such determinants, the greater the risk of high mite populations and allergen load. Habitat suitability determinants include an adequate textile substratum, optimal temperature and humidity, and food resources of appropriate quality, as well as other, currently unknown, requirements. Each determinant will have a characteristic distribution within any home, and they can be conceptualized as a series of overlays, or three‐dimensional Venn diagrams, with the areas of overlap representing the most suitable sites for mite survival. That a population of dust mites is focused by constraining biotic and abiotic determinants means that spatial and temporal distribution and abundance are predictable, because the characteristics of the principal foci define optimal conditions for population growth. This concept, known as “focality”, provides a framework for prediction of sites of high density of mite population and allergen exposure, as well as a basis for manipulating the microenvironment for control purposes.

Provisioning of bioavailable carbon between the wet and dry phases in a semi-arid floodplain.

Ecosystem functioning on arid and semi-arid floodplains may be described by two alternate traditional paradigms. The pulse-reserve model suggests that rainfall is the main driver of plant growth and subsequent carbon and energy reserve formation in the soil of arid and semi-arid regions. The flood pulse concept suggests that periodic flooding facilitates the two-way transfer of materials between a river and its adjacent floodplain, but focuses mainly on the period when the floodplain is inundated. We compared the effects of both rainfall and flooding on soil moisture and carbon in a semi-arid floodplain to determine the relative importance of each for soil moisture recharge and the generation of a bioavailable organic carbon reserve that can potentially be utilised during the dry phase. Flooding, not rainfall, made a substantial contribution to moisture in the soil profile. Furthermore, the growth of aquatic macrophytes during the wet phase produced at least an order of magnitude more organic material than rainfall-induced pulse-reserve responses during the dry phase, and remained as recognizable soil carbon for years following flood recession. These observations have led us to extend existing paradigms to encompass the reciprocal provisioning of carbon between the wet and dry phases on the floodplain, whereby, in addition to carbon fixed during the dry phase being important for driving biogeochemical transformations upon return of the next wet phase, aquatic macrophyte carbon fixed during the wet phase is recognized as an important source of energy for the dry phase. Reciprocal provisioning presents a conceptual framework on which to formulate questions about the resistance and ecosystem resilience of arid and semi-arid floodplains in the face of threats like climate change and alterations to flood regimes.

Mites from house dust in Glasgow

Abstract. Glasgows mild, high‐rainfall climate, combined with a deteriorating quality of housing and low standards of living in many parts of the city, makes it a particularly suitable place for thriving populations of house dust mites. The acarofauna in 124 samples of house dust from beds and carpets in seventy‐four homes in Glasgow, Scotland, comprised thirty‐one species of which the most abundant were Dermatophagoid.es pteronyssinus (Trouessart) (64.3%), Glycyphagus domesticus (De Geer) (16.7%), Euroglyphus maynei (Cooreman) (11.6%), Tarsonemus sp. (1.6%), Cheyletus eruditus (Schrank) (1.5%), C.trouessarti Oudemans (0.9%), Tarsonemus fusarii Cooreman (0.8%) and Glycyphagus destructor (Schrank) (0.7%). Mites were present in all the homes surveyed and the mean population density was found to be 97/100 mg of dust (range 2–1210). Over 47% of homes visited showed signs of disrepair associated with damp, especially unmodernized flats in old tenement buildings and 1960s council housing stock, many of which contain deprived occupants. There was a high incidence of hygrophilic species such as Glycyphagus spp., Tarsonemus spp. and Euroglyphus maynei in such homes. Samples from homes of atopic asthmatics were found to contain significantly fewer mites than those from normal volunteers (x2=54.7). This was partly due to the use of house dust mite avoidance measures (e.g. regular vacuum cleaning of mattresses as well as carpets) by some of the asthmatics.