Culture-Independent Investigation of the Microbiome Associated with the Nematode Acrobeloides maximus

Background

Symbioses between metazoans and microbes are widespread and vital to many ecosystems. Recent work with several nematode species has suggested that strong associations with microbial symbionts may also be common among members of this phylu. In this work we explore possible symbiosis between bacteria and the free living soil bacteriovorous nematode Acrobeloides maximus.

Methodology

We used a soil microcosm approach to expose A. maximus populations grown monoxenically on RFP labeled Escherichia coli in a soil slurry. Worms were recovered by density gradient separation and examined using both culture-independent and isolation methods. A 16S rRNA gene survey of the worm-associated bacteria was compared to the soil and to a similar analysis using Caenorhabditis elegans N2. Recovered A. maximus populations were maintained on cholesterol agar and sampled to examine the population dynamics of the microbiome.

Results

A consistent core microbiome was extracted from A. maximus that differed from those in the bulk soil or the C. elegans associated set. Three genera, Ochrobactrum, Pedobacter, and Chitinophaga, were identified at high levels only in the A. maximus populations, which were less diverse than the assemblage associated with C. elegans. Putative symbiont populations were maintained for at least 4 months post inoculation, although the levels decreased as the culture aged. Fluorescence in situ hybridization (FISH) using probes specific for Ochrobactrum and Pedobacter stained bacterial cells in formaldehyde fixed nematode guts.

Conclusions

Three microorganisms were repeatedly observed in association with Acrobeloides maximus when recovered from soil microcosms. We isolated several Ochrobactrum sp. and Pedobacter sp., and demonstrated that they inhabit the nematode gut by FISH. Although their role in A. maximus is not resolved, we propose possible mutualistic roles for these bacteria in protection of the host against pathogens and facilitating enzymatic digestion of other ingested bacteria.     

A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Effects of climate change on the delivery of soil‐mediated ecosystem services within the primary sector in temperate ecosystems: a review and New Zealand case study

Future human well‐being under climate change depends on the ongoing delivery of food, fibre and wood from the land‐based primary sector. The ability to deliver these provisioning services depends on soil‐based ecosystem services (e.g. carbon, nutrient and water cycling and storage), yet we lack an in‐depth understanding of the likely response of soil‐based ecosystem services to climate change. We review the current knowledge on this topic for temperate ecosystems, focusing on mechanisms that are likely to underpin differences in climate change responses between four primary sector systems: cropping, intensive grazing, extensive grazing and plantation forestry. We then illustrate how our findings can be applied to assess service delivery under climate change in a specific region, using New Zealand as an example system. Differences in the climate change responses of carbon and nutrient‐related services between systems will largely be driven by whether they are reliant on externally added or internally cycled nutrients, the extent to which plant communities could influence responses, and variation in vulnerability to erosion. The ability of soils to regulate water under climate change will mostly be driven by changes in rainfall, but can be influenced by different primary sector systems' vulnerability to soil water repellency and differences in evapotranspiration rates. These changes in regulating services resulted in different potentials for increased biomass production across systems, with intensively managed systems being the most likely to benefit from climate change. Quantitative prediction of net effects of climate change on soil ecosystem services remains a challenge, in part due to knowledge gaps, but also due to the complex interactions between different aspects of climate change. Despite this challenge, it is critical to gain the information required to make such predictions as robust as possible given the fundamental role of soils in supporting human well‐being.     

Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis

Introduction  

The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS analysis.     

Plant Species Composition Effects on Belowground Properties and the Resistance and Resilience of the Soil Microflora to a Drying Disturbance

We hypothesised that plant species composition and richness would affect soil chemical and microbial community properties, and that these in turn would affect soil microbial resistance and resilience to an experimentally imposed drying disturbance. We performed a container experiment that manipulated the composition and species richness of common pasture plant species (Trifolium repens, Lolium perenne, and Plantago lanceolata) by growing them in monoculture, and in all the possible two and three-way combinations, along with an unplanted control soil. Experimental units were harvested at four different times over a 16-month period to determine the effect of plant community development and seasonal changes in temperature and moisture on belowground properties. Results showed that plant species composition influenced soil chemistry, soil microbial community properties and soil microbial resistance and resilience. Soil from planted treatments generally showed reduced soil microbial resistance to drying compared to unplanted control soils. Soils from under T. repens showed a higher resistance and resilience than the soils from under P. lanceolata, and a higher resistance than soils from under L. perenne. We suggest that differences across soils in either resource limitation or soil microbial community structure may be responsible for these results. Plant species richness rarely affected soil microbial community properties or soil microbial resistance and resilience, despite having some significant effects on plant community biomass and soil nitrogen contents in some harvests. The effect that treatments had for most variables differed between harvests, suggesting that results can be altered by the stage of plant community development or by extrinsic environmental factors that varied with harvest timing. These results in combination show that soil microbial resistance and resilience was affected by plant community composition, and the time of measurement, but was largely unrelated to plant species richness.     

Gibberellin-like substances and indole type auxins in developing grains of normal- and high-lysine genotypes of barley

Changes in gibberellin-like activity and content of indole type auxins were investigated during grain development of the two high-lysine barley (Hordeum vulgare L.) genotypes Sv 73608 and Risø 1508, and their corresponding normal cultivars Mona and Bomi. A peak in gibberellin-like activity was found in developing grains of the normal cultivars about 18 days after anthesis, whereas the grains of the high-lysine genotypes showed a two to five times higher maximum about 3–4 days later. The auxin content of the cultivar Bomi showed a maximum between the 22nd and the 29th day after anthesis, whereas, throughout their development the grains of the mutant Risø 1508 exhibited only about ¹/10 of the maximum level of auxin found in the grains of Bomi. The normal cultivar Mona also displayed higher contents of auxin than the high-lysine genotypes Sv 73608, particularly at the later stages of grain growth, but the differences in concentration were considerable smaller than for the pair ‘Bomi’—‘Risø 1508’. It is suggested that auxins play an important role in the development of barley grains.     

Wool proteins of New Zealand Romney sheep

Proteins extracted from the wool of 65 Romney ewes were analysed qualitatively by one- and two-dimensional polyacrylamide gel electrophoresis. Romney wool proteins could be classified into the low-sulfur, high-sulfur, and high-tyrosine protein groups described for wool from other breeds. The wool protein pattern of an individual sheep remained constant despite changes in season, age or nutritional status of the sheep, and did not vary between different body positions. There were between-sheep differences in protein pattern, most variation occurring in the high-sulfur protein group. These differences were presumed to reflect genetic differences between the sheep.