Shaun Nielsen

Shifting paradigms: development of high-efficiency biochar fertilizers based on nano-structures and soluble components

Many biochars have a complex carbon lattice structure with aromatic and aliphatic domains, acidic and basic groups, vacancies, metallic and non-metallic elements, and free radicals. Biochars also have separate mineral oxide, silicate and salt phases, and small and large organic molecules. In the rhizosphere, such constituents can be involved in chemical and biological processes along a soil–microbe–plant continuum, including nutrient cycling, metal chelation and stabilization, redox reactions, and free radical scavenging. It is hypothesized that the greater the amount of these nanoparticles and dissolved components, the greater will be plant and microbial responses. We provide suggestions for developing low-dose, high-efficiency biochar–nanoparticle composites, as well as initial field trial results and detailed characterization of such a biochar–fertilizer composite, to highlight the potential of such biochars.

Effect of exclusive enteral nutrition on the microbiota of children with newly diagnosed Crohn's disease.

Objectives:Exclusive enteral nutrition (EEN) is commonly used to treat pediatric Crohn’s disease (CD). Meta-analysis of pediatric studies that have compared the effect of EEN with other treatments have shown that EEN induces remission in up to 80–85% of patients. We aimed to gain a comprehensive understanding of the effect of EEN on the microbiota of CD patients.Methods:We used 16S rRNA gene and whole-genome high throughout sequencing to determine changes in the fecal microbiota of five CD children, before, during, and after EEN therapy and compared this with five healthy controls.Results:The microbial diversity observed in CD patients tended to be lower than that in controls (CD: 2.25±0.24, controls: 2.75±0.14, P=0.11). In all CD patients, dysbiosis was observed prior to therapy. EEN therapy had a positive effect in all patients, with 80% going into remission. In some patients, the positive effect diminished following the conclusion of EEN therapy. Significantly, the number of operational taxonomic units (OTU) decreased dramatically upon starting EEN and this corresponded with CD remission. Recurrence of CD corresponded with an increase in OTUs. Six families within the Firmicutes were found to correlate with disease activity during and following EEN therapy, a finding that was confirmed by whole-genome high throughput sequencing.Conclusions:Our results demonstrate that EEN leads to common and patient-specific alterations in the microbiota of CD patients, a number of which correlate with disease activity.

Do Cues Matter? Highly Inductive Settlement Cues Don't Ensure High Post-Settlement Survival in Sea Urchin Aquaculture

Increasing settlement and post-settlement survival during the critical transition from planktonic larvae to benthic juveniles will increase efficiency for sea urchin aquaculture. This study investigated the effects of temperature and settlement cues on the settlement and post-settlement survival of the sea urchin Tripneustes gratilla during this phase. The current commercial methodology, which utilises natural biofilm settlement plates, was tested and resulted in low settlement (<2%) and poor post-settlement survival (<1% of settled urchins). In laboratory trials, settlement was high and unaffected by temperatures between 24 and 30°C, but significantly decreased at 33°C. Development of spines, however, was significantly affected by temperatures over 29°C. Mirroring this result, post-settlement survival was optimal between 24–28°C. In laboratory assays, the macroalgae Sargassum linearifolium and Corallina officinalis, and seawater conditioned with these algae, induced significantly higher settlement (>90%) than a natural biofilm (∼25%). The addition of macroalgae-conditioned seawater to natural biofilm significantly increased settlement rates (>85%). Mixed consortia and single strains of bacteria isolated from macroalgae, biofilms and adult conspecifics all induced significant settlement, but at significantly lower rates than macroalgae. No evidence was found that higher rates of settlement to bacteria on macroalgae were generated by a cofactor from the macroalgae. Age of bacterial cultures, culturing bacteria on solid and liquid media and concentration of nutrients in cultures had little effect on settlement rates. Finally, macroalgae-conditioned seawater combined with natural biofilm settlement plates induced significantly higher settlement than to the biofilm plates alone in a commercial scale trial. However, high post-settlement mortality resulted in equivalent survival between treatments after 25 days. This study highlights that settlement studies should extend to post-settlement survival, which remains poor for T. gratilla and is a significant obstacle to increasing efficiency for aquaculture.

A Combination of Biochar–Mineral Complexes and Compost Improves Soil Bacterial Processes, Soil Quality, and Plant Properties

Organic farming avoids the use of synthetic fertilizers and promises food production with minimal environmental impact, however this farming practice does not often result in the same productivity as conventional farming. In recent years, biochar has received increasing attention as an agricultural amendment and by coating it with minerals to form biochar–mineral complex (BMC) carbon retention and nutrient availability can be improved. However, little is known about the potential of BMC in improving organic farming. We therefore investigated here how soil, bacterial and plant properties respond to a combined treatment of BMC and an organic fertilizer, i.e., a compost based on poultry manure. In a pakchoi pot trial, BMC and compost showed synergistic effects on soil properties, and specifically by increasing nitrate content. Soil nitrate has been previously observed to increase leaf size and we correspondingly saw an increase in the surface area of pakchoi leaves under the combined treatment of BMC and composted chicken manure. The increase in soil nitrate was also correlated with an enrichment of bacterial nitrifiers due to BMC. Additionally, we observed that the bacteria present in the compost treatment had a high turnover, which likely facilitated organic matter degradation and a reduction of potential pathogens derived from the manure. Overall our results demonstrate that a combination of BMC and compost can stimulate microbial process in organic farming that result in better vegetable production and improved soil properties for sustainable farming.

Feeding Biochar to Cows: An Innovative Solution for Improving Soil Fertility and Farm Productivity

Addition of biochar produced through thermal decomposition of biomass has been seen as a strategy to improve soils and to sequester carbon (C), but wide scale implementation of the technology requires to devise innovative profitable solutions. To develop biochar utilisation with an integrated system approach, an innovative program was implemented in 2012 on a 53-ha farm in Western Australia to determine the costs and benefits of integrating biochar with animal husbandry and improvement of pastures. Biochar was mixed with molasses and fed directly to cows. The dung-biochar mixture was incorporated into the soil profile by dung beetles. We studied the changes in soil properties over 3 years. Biochar extracted from fresh dung and from the soil to a depth of 40 cm was characterised. A preliminary financial analysis of the costs and benefits of this integrated approach was also undertaken. The preliminary investigation results suggested that this strategy was effective in improving soil properties and increasing returns to the farmer. It was also concluded that the biochar adsorbed nutrients from the cows gut and from the dung. Dung beetles could transport this nutrient-rich biochar into the soil profile. There was little evidence that the recalcitrant component of the biochar was reduced through reactions inside the gut or on/in the soil. Further research is required to quantify the long-term impact of integrating biochar and dung beetles into the rearing of cows.

Micro-fabricated polydimethyl siloxane (PDMS) surfaces regulate the development of marine microbial biofilm communities

This study explored an antifouling (AF) concept based on deployment of microfabricated polydimethyl siloxane (PDMS) surfaces with 1–10 μm periodicity corrugated topographies in temperate marine waters. The effect of the surfaces on the development of microbial biofilms over 28 days and during different seasons, including both summer and winter, was examined using confocal laser scanning microscopy (CLSM) as well as terminal restriction fragment (T-RF) analysis for phylogenetic fingerprinting. The microscale topography significantly impacted biofilm development by altering the attachment pattern and reducing microcolony formation on the 1, 2 and 4 μm PDMS surfaces. Also, field deployments over 28 days showed a significant reduction in biovolume on the 4 and 10 μm PDMS surfaces despite altered environmental conditions. The microfabricated PDMS surfaces further significantly impacted on the community composition of the biofilms, as revealed by changes in T-RF profiles, at different stages of development. Moreover, altered biofilm resistance was demonstrated by exposing pre-established biofilms on 10 μm micro-fabricated surfaces to enhanced flagellate predation by a heterotrophic protist, Rhynchomonas nasuta. Pronounced changes in the overall marine microbial biofilm development as well as community composition warrant exploring substratum modification for marine AF applications.

Predicting the HMA-LMA Status in Marine Sponges by Machine Learning

The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered “HMA indicators” and “LMA indicators.” Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n = 44) and LMA (n = 74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities.

Disrupted progression of the intestinal microbiota with age in children with cystic fibrosis

Cystic fibrosis (CF) is a genetic disorder that leads to formation of thick epithelial secretions in affected organs. Chronic microbial infections associated with thick mucus secretions are the hallmarks of lung disease in CF. Despite similar conditions existing in the gastrointestinal tract, it is much less studied. We therefore examined the microbial communities within the gastrointestinal tract of children with and without CF (either pancreatic sufficient or insufficient) across a range of childhood ages (0.87–17 years). We observed a substantial reduction in the richness and diversity of gut bacteria associated with CF from early childhood (2 years) until late adolescence (17 years). A number of bacteria that establish themselves in the gut of healthy children were unable to do so in children with CF. In contrast, a few bacteria dominated the gut microbiota in children with CF and are unlikely to be beneficial for the metabolic function of the gut. A functioning pancreas (pancreatic sufficient) under a CF lifestyle showed little effect on microbial communities. Our results argue that any attempts to rectify the loss of bacterial diversity and provide normal bacterial function in the gut of CF patients should be conducted no later than early childhood.

The Sponge Microbiome Project

Abstract Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.

Developing More Effective Enhanced Biochar Fertilisers for Improvement of Pepper Yield and Quality

Utilization of biochar at high application rates can increase soil C and crop yields, decrease greenhouse gas emissions and reduce nutrient run-off from soils. However, the high application rate of 10 t ha−1 may not return a profit to the farmer due to the high cost of biochar. In this study biochar was modified through pre-treating the biomass and post-treating with phosphoric acid, minerals and different chemical fertilisers to study the effects of two new enhanced biochar fertilisers on the yield and quality of green pepper in a field experiment with 5 fertilisation treatments and 3 replications. The two new biochar fertilisers significantly (P « 0.05) increased the yield of green pepper (11.33–11.47 t ha−1), compared with the conventional chemical fertiliser (9.72 t ha−1). The biochar fertiliser treatments improved the vitamin C content of green pepper from 236.99 to 278.28 mg kg−1, and also significantly (P < 0.05) reduced the nitrate content from 132.32 to 101.92 mg kg−1, compared with chemical fertiliser. This study indicated that, compared to the use of conventional chemical fertiliser, all of the biochar fertiliser treatments could significantly improve the yield and quality of green pepper.