Maureen O'Callaghan

Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions.

Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor [dicyandiamide (DCD)]. We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH(3)) substrate and AOA under low NH(3) substrate conditions.

Effects of selected root exudate components on soil bacterial communities

Low-molecular-weight organic compounds in root exudates play a key role in plant-microorganism interactions by influencing the structure and function of soil microbial communities. Model exudate solutions, based on organic acids (OAs) (quinic, lactic, maleic acids) and sugars (glucose, sucrose, fructose), previously identified in the rhizosphere of Pinus radiata, were applied to soil microcosms. Root exudate compound solutions stimulated soil dehydrogenase activity and the addition of OAs increased soil pH. The structure of active bacterial communities, based on reverse-transcribed 16S rRNA gene PCR, was assessed by denaturing gradient gel electrophoresis and PhyloChip microarrays. Bacterial taxon richness was greater in all treatments than that in control soil, with a wide range of taxa (88-1043) responding positively to exudate solutions and fewer (<24) responding negatively. OAs caused significantly greater increases than sugars in the detectable richness of the soil bacterial community and larger shifts of dominant taxa. The greater response of bacteria to OAs may be due to the higher amounts of added carbon, solubilization of soil organic matter or shifts in soil pH. Our results indicate that OAs play a significant role in shaping soil bacterial communities and this may therefore have a significant impact on plant growth.

Effect of nitrogen and waterlogging on denitrifier gene abundance, community structure and activity in the rhizosphere of wheat

Microbial denitrification plays a key role in determining the availability of soil nitrogen (N) to plants. However, factors influencing the structure and function of denitrifier communities in the rhizosphere remain unclear. Waterlogging can result in root anoxia and increased denitrification, leading to significant N loss from soil and potential nitrous oxide (N(2)O) emissions. This study investigated denitrifier gene abundance, community structure and activity in the rhizosphere of wheat in response to anoxia and N limitation. Denitrifier community structure in the rhizosphere differed from that in bulk soil, and denitrifier gene copy numbers (nirS, nirK, nosZ) and potential denitrification activity were greater in the rhizosphere. Anoxia and N limitation, and in particular a combination of both, reduced the magnitude of this effect on gene abundance (in particular nirS) and activity, with N limitation having greater impact than waterlogging in rhizosphere soil, in contrast to bulk soil where the impact of waterlogging was greater. Increased N supply to anoxic plants improved plant health and increased rhizosphere soil pH, which resulted in enhanced reduction of N(2)O. Both anoxia and N limitation significantly influenced the structure and function of denitrifier communities in the rhizosphere, with reduced root-derived carbon postulated to play an important role.

A model of insect—pathogen dynamics in which a pathogenic bacterium can also reproduce saprophytically

We developed a model of the population dynamic interaction between an insect and a pathogenic bacterium motivated by study of Serratia entomophila, a commercially exploited pathogen of the New Zealand grass grub (Costelytra zealandica). The bacterium is able to reproduce saprophytically, though it competes for saprophytic substrates with non–pathogenic strains, which appear to be superior competitors, probably because they lack a plasmid that carries genes required for pathogenicity. The effect of saprophytism and competition on the invasion criterion (R0), short–term dynamics and long–term dynamics are described. Saprophytism can reduce (possibly to zero) the host threshold at which the pathogen can invade, though this reduction is less when there is competition with non–pathogenic strains. In a model of short–term population dynamics designed to mimic the application of bacteria to a host epizootic, saprophytism enhances the reduction in host density, though again this is tempered by competition with non–pathogens. In the long term, a pathogen that can develop saprophytically can drive its host to extinction in the absence of competition with non–pathogens. When the latter are present, host extinction is prevented. The addition of saprophytic reproduction can stabilize an otherwise unstable host–pathogen model, but we were unable to find a stable equilibrium given the further addition of a wholly saprophytic bacterial strain. The model suggests that enhancing or selecting for saprophytic ability could be a way of improving biological control.

Checklist of naturally occurring entomopathogenic microbes and nematodes in New Zealand

Abstract A checklist of records of naturally occurring insect-pathogenic microbes and nematodes in New Zealand is presented. All records are listed by pathogen group (fungi, bacteria, protozoa, viruses, rickettsia, and nematodes) and also by host insect order and species. Each record is referenced to the original author, and important subsequent references have been included, where appropriate. The checklist should be updated periodically to assist researchers.

Quantum dot nanoparticles affect the reproductive system of Caenorhabditis elegans

Quantum dots (QDs) are an increasingly important class of nanoparticle, but little ecotoxicological data for QDs has been published to date. The effects of mercaptosuccinic acid (MSA)-capped QDs (QDs-MSA) and equivalent concentrations of cadmium (Cd) from cadmium chloride on growth and reproduction of the nematode Caenorhabditis elegans (Rhabditidae) were assessed in laboratory experiments. Growth from larvae to adults of C. elegans was unaffected by exposure to 1 µM fluorescent QDs-MSA, but adults produced more embryos and laid them prematurely. Furthermore, C. elegans exposed to QDs-MSA (1 µM) showed a high percentage of embryo mortality (19.2 ± 0.5, p < 0.001, percentage ± standard deviation) compared with unexposed nematodes (11.6 ± 0.4). An egg-laying defect phenotype was also observed at high frequency in response to 1 µM QDs-MSA exposure (38.3 ± 3.6%, p < 0.01; control 10.0 ± 2.2%). This resulted in a reduced mean life span (20.5 ± 1.1 d, p < 0.05) compared with the control (24.6 ± 1.0 d). Cadmium also caused reduced life span in C. elegans, but a low incidence of egg-laying defects was observed, suggesting that Cd and QDs-MSA affected C. elegans by different mechanisms. Furthermore, egg-laying defects caused by QDs-MSA responded to the addition of the anticonvulsant ethosuximide and to a lesser extent to the neurotransmitter serotonin, suggesting that QDs-MSA might have disrupted motor neurons during the reproduction process.

Occurrence of sep Insecticidal Toxin Complex Genes in Serratia spp. and Yersinia frederiksenii

ABSTRACT Some strains of Serratia entomophila and S. proteamaculans cause amber disease of the grass grub Costelytra zealandica (Coleoptera: Scarabaeidae). Three genes required for virulence, sepABC, are located on a large plasmid, pADAP. Sequence analysis suggests that the sepABC gene cluster may be part of a horizontally mobile region. This study presents evidence for the putative mobility of the sep genes of pADAP. Southern blot analysis showed that orthologues of the sep genes reside on plasmids within S. entomophila, S. liquefaciens, S. proteamaculans, and a plasmid from Yersinia frederiksenii. Three plasmids hybridized to the pADAP sep virulence-associated region but not the pADAP replication and conjugation regions. Subsequent DNA sequence analysis of the Y. frederiksenii sep-like genes, designated tcYF1 and tcYF2, showed that they had 88% and 87% DNA identity to sepA and sepB, respectively. These results indicate that the sep genes are part of a discrete horizontally mobile region.

Links between sulphur oxidation and sulphur-oxidising bacteria abundance and diversity in soil microcosms based on soxB functional gene analysis

Sulphur-oxidising bacteria (SOB) play a key role in the biogeochemical cycling of sulphur in soil ecosystems. However, the ecology of SOB is poorly understood, and there is little knowledge about the taxa capable of sulphur oxidation, their distribution, habitat preferences and ecophysiology. Furthermore, as yet there are no conclusive links between SOB community size or structure and rates of sulphur oxidation. We have developed a molecular approach based on primer design targeting the soxB functional gene of nonfilamentous chemolithotrophic SOB that allows assessment of both abundance and diversity. Cloning and sequencing revealed considerable diversity of known soxB genotypes from agricultural soils and also evidence for previously undescribed taxa. In a microcosm experiment, abundance of soxB genes increased with sulphur oxidation rate in soils amended with elemental sulphur. Addition of elemental sulphur to soil had a significant effect in the soxB gene diversity, with the chemolithotrophic Thiobacillus-like Betaproteobacteria sequences dominating clone libraries 6 days after sulphur application. Using culture-independent methodology, the study provides evidence for links between abundance and diversity of SOB and sulphur oxidation. The methodology provides a new tool for investigation of the ecology and role of SOB in soil sulphur biogeochemistry.

Physicochemical properties of 50 New Zealand pasture soils: a starting point for assessing and managing soil microbial resources

New Zealands pastoral agriculture faces challenges associated with increasing on-farm productivity, while minimizing the environmental footprint of farming. Soil microorganisms mediate a wide range of processes that affect plant production and also have environmental consequences. However, there has been little attempt to manage these in a farming system context. This is primarily because of difficulties in determining what microbiological resources are present in soils, how they link with soil processes and function, and how variation in soil types, climate or farm management practices influence microbial function. We sampled 50 pasture soils from across 11 of New Zealands major soil groups, 10 geographical zones and under different grazing systems (high input dairy units to dry-stock grazing). The environmental and physicochemical properties of the soils were characterized and DNA extracted. The concentrations of elements primarily associated with fertilizer use (phosphorus, nitrogen and sulphur) were all significantly (P< 0.05) higher in dairy-based systems, yet soil carbon was unchanged. The concentration of many properties varied between the soil types, reflecting a combination of their pedogenesis and predominant land use. The amount of DNA in soils was closely related to anaerobically mineralizable nitrogen (P< 0.001), a measure of soil organic matter content, but did not vary with grazing system intensity. The extensive data set for each soil, coupled with DNA originating from the same samples, provides a unique opportunity for a number of ancillary studies to map biological resources in pastures and assess how these are regulated by edaphic and environmental properties.

Influence of culture medium composition, dissolved oxygen concentration and harvesting time on the production of Serratia entomophila, a microbial control agent of the New Zealand grass grub

Abstract The bacterium Serratia entomophila (Enterobacteriaceae) has been developed as a commercially available biopesticide for control of the pasture pest Costelytra zealandica. The influence of culture medium composition, dissolved oxygen (DO) concentration and harvesting time were investigated in order to optimise the production of S. entomophila. In batch fermentations, highest yields were achieved using sucrose (40 g L−1) as the carbon source, followed closely by fructose and molasses. The effect of yeast extract (YE), marmite and bakery yeast as cell growth enhancers was also examined in both batch and fed-batch mode. Culture medium containing 20 g L−1 of YE (fed-batch) produced the highest cell density. No significant effect on cell yield was detected when cultures were supplemented with bakery yeast or marmite. The DO concentration influenced biomass production: a 5-fold increase in cell density was achieved when the concentration of DO was maintained in the range of 20–50% (5.7×1010 CFUs mL−1) in comparison with 1% (1.2×1010 CFUs mL−1). In cultures maintained at 1 and 20% DO concentration, cells harvested from the exponential growth phase survived for less than 2 weeks when stored at 4°C. In contrast, high cell survival (85–100%) was achieved when cells were harvested after they had entered the stationary growth phase. Recommendations are provided for the production of robust, high cell density cultures of S. entomophila.