Biological control and biomass evaluation of Botrytis cinerea : a thesis presented in partial fulfilment of the requirements for the degree of Master of Applied Science at Massey University

The efficacy of biocontrol agents is often judged by symptom development on inoculated plants. This process can involve long delays, as with Botrytis infection of kiwifruit and an alternative, quicker approach would be useful. When biocontrol is successful, then pathogen biomass is limited hence a means of measuring the biomass of a pathogen on/in a target substrate (plant material) could be used as a tool for rapid estimation of biocontrol efficiency. Two yeast (Enterobacter agglomerans, Enterobacter aerogenes) and two bacteria (Candida sake, Trichosporon pullulans) with an already identified ability to attach to the surface of Botrytis cinerea and to reduce infection in tomato and kiwifruit, were evaluated for control of B. cinerea in bean, lettuce and rose in this study. Potential biological control and efficacy was assessed by measuring lesion size and percentage infection by B. cinerea. An investigation of methods of conidial application of B. cinerea to these crops tissue showed that disease severity and incidence were increased by a high concentration of wet spore application to bean and dry spore application to lettuce and rose tissue. Each application technique was used as the standard technique for biocontrol experiments on the crop on which it was most efficient. Three of the potential BCAs (Enterobacter agglomerans, Enterobacter aerogenes, Trichosporon pullulans) were found to reduce lesion size and percentage infection on all three crops at 20°C. Biological control by bacterial BCAs, Enterobacter agglomerans and Enterobacter aerogenes, were demonstrated by applying them to bean tissue at the time of inoculation with a suspension of 1x108 conidia per ml of B. cinerea. These two bacteria and the yeast, Trichosporon pullulans, showed biological control when applied to lettuce and rose tissue one or two days after inoculation with dry spores of B. cinerea. A potential rapid assessment of biocontrol efficiency of microorganisms has been demonstrated using Laser Scanning Confocal Microscope. A clear image of the fungal hyphae in the host tissue was produced in confocal microscopy by using glutaraldehyde as a fluorescent stain for B. cinerea hyphae. Biomass of B. cinerea at an early stage of infection in bean and lettuce tissues was successfully measured by computer analysis before and after application of yeast and bacterial biocontrol agents. BCAs application in both tissues prevented development of a large biomass of B. cinerea

Characterization of the newly isolated lytic bacteriophages KTN6 and KT28 and their efficacy against Pseudomonas aeruginosa biofilm

We here describe two novel lytic phages, KT28 and KTN6, infecting Pseudomonas aeruginosa, isolated from a sewage sample from an irrigated field near Wroclaw, in Poland. Both viruses show characteristic features of Pbunalikevirus genus within the Myoviridae family with respect to shape and size of head/tail, as well as LPS host receptor recognition. Genome analysis confirmed the similarity to other PB1-related phages, ranging between 48 and 96%. Pseudomonas phage KT28 has a genome size of 66,381 bp and KTN6 of 65,994 bp. The latent period, burst size, stability and host range was determined for both viruses under standard laboratory conditions. Biofilm eradication efficacy was tested on peg-lid plate assay and PET membrane surface. Significant reduction of colony forming units was observed (70-90%) in 24 h to 72 h old Pseudomonas aeruginosa PAO1 biofilm cultures for both phages. Furthermore, a pyocyanin and pyoverdin reduction tests reveal that tested phages lowers the amount of both secreted dyes in 48-72 h old biofilms. Diffusion and goniometry experiments revealed the increase of diffusion rate through the biofilm matrix after phage application. These characteristics indicate these phages could be used to prevent Pseudomonas aeruginosa infections and biofilm formation. It was also shown, that PB1-related phage treatment of biofilm caused the emergence of stable phage-resistant mutants growing as small colony variants

Co-digestion of macroalgae for biogas production: an LCA-based environmental evaluation

Algae represent a favourable and potentially sustainable source of biomass for bioenergy-based industrial pathways in the future. The study, performed on a real pilot plant implemented in Augusta (Italy) within the frame of the BioWALK4Biofuels project, aims to figure out whether seaweed (macroalgae) cultivated in near-shore open ponds could be considered a beneficial aspect as a source of biomass for biogas production within the co-digestion with local agricultural biological waste. The LCA results confirm that the analysed A and B scenarios (namely the algae-based co-digestion scenario and agricultural mix feedstock scenario) present an environmental performance more favourable than that achieved with conventional non-renewable-based technologies (specifically natural gas - Scenario C). Results show that the use of seaweed (Scenario A) represent a feasible solution in order to replace classical biomass used for biofuel production from a land-based feedstock. The improvement of the environmental performances is quantifiable on 10% respect to Scenario B, and 38 times higher than Scenario

Using full-scale duckweed ponds as the finish stage for swine waste treatment with a focus on organic matter degradation

Artigo Publicado em: IWA - Water Science & TechnologyThe rapid increase in the number of swine has caused pronounced environmental impacts worldwide, especially on water resources. As an aggregate, smallholdings have an important role in South American pork production, contributing to the net diffusion of pollution. Thus, duckweed ponds have been successfully used for swine waste polishing, mainly for nutrient removal. Few studies have been carried out to assess organic matter degradation in duckweed ponds. Hence, the present study evaluated the efficiency of two full-scale duckweed ponds for organic matter reduction of swine waste on small pig farms. Duckweed ponds, in series, received the effluent after an anaerobic biodigester and storage pond, with a flow rate of 1 m3 day 1. After 1 year of monitoring, an improvement in effluent quality was observed, with a reduction in biochemical oxygen demand (BOD) and total chemical oxygen demand (tCOD), respectively, of 94.8 and 96.7%, operating at a loading rate of approximately 27 kgBOD ha 1 day 1 and 131 kgCOD ha 1 day 1. Algae inhibition due to duckweed coverage was strongly observed in the pond effluent, where chlorophyll a and turbidity remained below 25 μg L 1 and 10 NTU. Using the study conditions described herein, duckweed ponds were shown to be a suitable technology for swine waste treatment, contributing to the environmental sustainability of rural areas

Influence of temperature and pH on S. bayanus var. uvarum growth; impact of a wine yeast interspecific hybridization on these parameters

The species Saccharomyces bayanus var. uvarum possesses interesting enological characteristics but produces high concentration of volatile fermentative compounds not desirable in Sauvignon blanc wines. Interspecific hybrids between Saccharomyces cerevisiae and S. bayanus var. uvarum were made in order to join the main parental advantages. Two hybrids were selected on the basis of their fermentation characteristics and their karyotypes, i.e. they have a different mitochondrial DNA. In order to produce these hybrids as active dry yeast to be used as starter in winemaking, their optimal environmental conditions for growth, i.e. temperature and pH, were determined as the objective of our work. Using a two-level factorial design it was found that the two parental strains have different optimal temperature but for the two strains, pH does not have a significant influence on growth. The influence of temperature on biomass productivity for hybrid strains were strictly identical, so we suppose that the main genes coding for temperature sensitivity were not contained in mitochondrial DNA, but in nuclear DNA. Moreover the reactions of hybrid strains to the temperature variations were similar to the one of S. bayanus var.uvarum. This latter strain could have a majority of genes responsible of temperature sensitivity dominant in comparison with those of the strain S. cerevisiae

Land Use and Land Cover Mapping in a Changing World

It is increasingly being recognized that land use and land cover changes driven by anthropogenic pressures are impacting terrestrial and aquatic ecosystems and their services, human society, and human livelihoods and well-being. This Special Issue contains 12 original papers covering various issues related to land use and land use changes in various parts of the world (see references), with the purpose of providing a forum to exchange ideas and progress in related areas. Research topics include land use targets, dynamic modelling and mapping using satellite images, pressures from energy production, deforestation, impacts on ecosystem services, aboveground biomass evaluation, and investigations on libraries of legends and classification systems

Estimating exploitable stock biomass for the Maine green sea urchin (Strongylocentrotus droebachiensis) fishery using a spatial statistics approach

The objective of this study was to investigate the spatial patterns in green sea urchin (Strongylocentrotus droebachiensis) density off the coast of Maine, using data from a fishery-independent survey program, to estimate the exploitable biomass of this species. The dependence of sea urchin variables on the environment, the lack of stationarity, and the presence of discontinuities in the study area made intrinsic geostatistics inappropriate for the study; therefore, we used triangulated irregular networks (TINs) to characterize the large-scale patterns in sea urchin density. The resulting density surfaces were modified to include only areas of the appropriate substrate type and depth zone, and were used to calculate total biomass. Exploitable biomass was estimated by using two different sea urchin density threshold values, which made different assumptions about the fishing industry. We observed considerable spatial variability on both small and large scales, including large-scale patterns in sea urchin density related to depth and fishing pressure. We conclude that the TIN method provides a reasonable spatial approach for generating biomass estimates for a fishery unsuited to geostatistics, but we suggest further studies into uncertainty estimation and the selection of threshold density values

Land Use and Land Cover Mapping in a Changing World

It is increasingly being recognized that land use and land cover changes driven by anthropogenic pressures are impacting terrestrial and aquatic ecosystems and their services, human society, and human livelihoods and well-being. This Special Issue contains 12 original papers covering various issues related to land use and land use changes in various parts of the world (see references), with the purpose of providing a forum to exchange ideas and progress in related areas. Research topics include land use targets, dynamic modelling and mapping using satellite images, pressures from energy production, deforestation, impacts on ecosystem services, aboveground biomass evaluation, and investigations on libraries of legends and classification systems

Epilithic biomass in a large gravel-bed river (the Garonne, France): a manifestation of eutrophication?

In order to evaluate the impact of outputs of the city of Toulouse (740 000 inhabitants) on the epilithic communities colonizing pebble banks in the river Garonne, a large gravel-bed river (eighth order), dry mass (DM), ash-free dry mass (AFDM) and chlorophyll-a (chla) epilithic biomass per unit area were measured and autotrophic index (AI) (i.e. ratio AFDM/chla) was calculated at four stations. This river is morphologically characterized by a succession of pools and riffles and by highly fluctuating hydraulic conditions. At the four stations studied (223 km apart), the means of AFDM values varied between 17.1 and 31.1 g m−2 of colonized surface and the chla concentration varied between 112 and 254 mg m−2. However, there were no significant differences in AFDM per unit area between the parts of the river upstream and downstream of the Toulouse area (Mann–Whitney U-test statistic), nor between the four stations (Kruskal–Wallis test statistic), and the AI did not allow the description of changes in periphyton communities between sampling locations. This study showed that epilithic biomass should be considered as the typical microbial community of the river rather than as a manifestation of eutrophication

DeepWheat: Estimating Phenotypic Traits from Crop Images with Deep Learning

In this paper, we investigate estimating emergence and biomass traits from color images and elevation maps of wheat field plots. We employ a state-of-the-art deconvolutional network for segmentation and convolutional architectures, with residual and Inception-like layers, to estimate traits via high dimensional nonlinear regression. Evaluation was performed on two different species of wheat, grown in field plots for an experimental plant breeding study. Our framework achieves satisfactory performance with mean and standard deviation of absolute difference of 1.05 and 1.40 counts for emergence and 1.45 and 2.05 for biomass estimation. Our results for counting wheat plants from field images are better than the accuracy reported for the similar, but arguably less difficult, task of counting leaves from indoor images of rosette plants. Our results for biomass estimation, even with a very small dataset, improve upon all previously proposed approaches in the literature.Comment: WACV 2018 (Code repository: https://github.com/p2irc/deepwheat_WACV-2018