Academic literature on the topic 'Microbial Resources Management'

Consumers’ increasing interest in sparkling wine has enhanced the global market’s demand. The pro-technological yeasts strains selected for the formulation of microbial starter cultures are a fundamental parameter for exalting the quality and safety of the final product. Nowadays, the management of the employed microbial resource is highly requested by stakeholders, because of the increasing economic importance of this oenological sector. Here, we report an overview of the production processes of sparkling wine and the main characterisation criteria to select Saccharomyces and non-Saccharomyces strains appropriate for the preparation of commercial starter cultures dedicated to the primary and, in particular, the secondary fermentation of sparkling wines. We also focused on the possible uses of selected indigenous strains to improve the unique traits of sparkling wines from particular productive areas. In summary, the sparkling wine industry will get an important advantage from the management of autochthonous microbial resources associated with vineyard/wine microbial diversity.

In agriculture, the wine sector is one of the industries most affected by the sustainability issue. It is responsible for about 0.3% of annual global greenhouse gas emissions from anthropogenic activities. Sustainability in vitiviniculture was firstly linked to vineyard management, where the use of fertilizers, pesticides and heavy metals is a major concern. More recently, the contribution of winemaking, from grape harvest to bottling, has also been considered. Several cellar processes could be improved for reducing the environmental impact of the whole chain, including microbe-driven transformations. This paper reviews the potential of microorganisms and interactions thereof as a natural, environmentally friendly tool to improve the sustainability aspects of winemaking, all along the production chain. The main phases identified as potentially interesting for exploiting microbial activities to lower inputs are: (i) pre-fermentative stages, (ii) alcoholic fermentation, (iii) stage between alcoholic and malolactic fermentation, (iv) malolactic fermentation, (v) stabilization and spoilage risk management, and (vi) by-products and wastewater treatment. The presence of proper yeast or bacterial strains, the management and timing of inoculation of starter cultures, and some appropriate technological modifications that favor selected microbial activities can lead to several positive effects, including (among other) energy savings, reduction of chemical additives such as sulfites, and reuse of certain residues.

The synthesis of a microbial flocculant is strictly controlled by its genetic genes, which may be the result of the expression of flocculant genes in the microbial genome. The whole genome of Klebsiella pneumoniae M1 was sequenced for obtaining the mechanism of flocculant synthesis and exploring the mechanism of flocculant production by flocculant bacteria. Therefore, it provided a basis for molecular genetics and functional genomic analysis of flocculants production bacteria. In this way, the mechanism of flocculant production by flocculating bacteria can be better explored. The whole genome sequence of flocculant strain M1 was determined using advanced second generation (Illumina) and third generation (PacBio) sequencing, which was screened from wheat alcohol wastewater. The genes related to flocculant characteristics produced by strain M1 were analyzed for combining with the analysis of flocculant structure characteristics. According to the de novo assembly, a total of 5,511,794 bp clean reads were generated and assembled into 24 contigs. The GC content was up to 58.39%. The genome contained approximately 5383 genes, but 5348 genes had obvious biological functions. A total of 437 genes were involved in carbohydrate metabolism and had coding genes of five carbohydrate-related enzymes. This result indicated that there were functional genes closely related to polysaccharide production in M1 genome. The main metabolic process of flocculant strain Klebsiella pneumoniae M1 was closely related to the potential pathway of extracellular polysaccharide biosynthesis, in which five kinds of carbohydrate synthase genes were involved.

The increasing demand for qualitative and varietal foods by the consumer society is a big concern for energy production, and utilization of that energy in a judicious manner for sustainable management of resources is a big challenge in the eminent future. Existing resources (land, water, fertilizer, etc.) and their socioeconomic aspects warrant the farming community to adopt alternative strategies aimed at enhancing the use efficiency of inputs and improve the environmental quality. The adaptability of microbes to thrive in different environments has prompted scientists to introduce microbial intervention in the agricultural processes. Bio-priming has the potential to fulfill many objectives of the modern production system with the use of beneficial microorganisms in an eco-friendly manner. Interestingly, it also plays a crucial role in enhancing the nutrient use efficiency of crops. There is rising evidence of a paradigm shift from the use of a single microbe to a consortium approach for efficient rhizosphere engineering in the context of sustainable agriculture. Our understanding of different signaling cascades, rhizosphere chemistry, and other mechanisms of plant–microbial interactions will frame suitable strategies to harness the best ecosystem services including improved resource use efficiency.

Acetic acid bacteria (AAB) are obligate aerobic microorganisms which have large significance in human life. Traditionally, AAB species have been used to produce fermented food and beverages thanks to their ability to oxidize ethanol to acetic acid. Moreover, in the last decades, they have been extensively investigated for other industrial biotechnology applications as the development of processes for highvalue products or biosensors. The potential exploitation of AAB diversity requires the existence of microbial culture collections, which are able to supply not only strains but essential data for fundamental microbial research. Therefore, microbial collections can be helpful to provide critical insights into AAB physiology and metabolism as well as integrate sequence data with transcriptional and functional studies to better define complex traits and develop new potential microbial processes. This article reviews the significance of microbial collections, with an overview of the well-known European Biological Resources Centers (BRCs) collecting AAB, and provides an insight into their cultivability and metabolic activity. It also discusses appropriate techniques in preserving <em>authentic</em> strains, quality control implications, databases and BRC networking as well as connections among collections and stakeholders.

The last 5-10 years has witness a new proven field of research where explanation have been provided to non-cultured microbes. This uncultured microorganisms forms the major group of organisms found in most environment of the Earth. The science of metagenomics makes it possible to investigate resources which can be used to develop new enzymes, genes and several chemical compounds for use in biotechnology. Studies of microorganisms in pure laboratory culture for over a century have led to significant advances into microbial genetics and physiology, biotechnology and molecular biology. The rapid advancement in sequencing technology has brought about drastic reduction cost of sequencing thereby leading to increasing sequencing project been undertaken. This advancement has provided the privilege for the continual use of this sequencing technology to monitor microbes in the environment which before now are not available. While metagenomic applications have been used to consistently have a better understanding of ecology and microbial diversity, it is pertinent to note that its application in environmental monitoring and application is commonly increasing and has been one of the research areas in focus. To this end this article seek to provide a general overview of what metagenmics is, its principle and application in hydrocarbon resource management.

Climate change is widely recognized as one of the most pressing issues confronting humanity today. It is considered to be a direct threat to our food production system including rice. Climate change affects rice production in various ways. The variability in temperature and precipitation increases, predictability of seasonal weather patterns reduces and the frequency and intensity of extreme weather events such as droughts, floods and cyclones increases. In India, the effect of natural disasters on agriculture, including disasters caused by climate change has been gradually growing. It is believed that during the mid and end century India's future rice production is projected to reduced by 2.5 to 5% from the current level. As there is less scope for rice area to grow in the future, any growth in rice production will have to come only from productivity gains. Since climate change is a continuous process, the rice production system requires specific adaptation strategies to prevent rice yield losses and its variability. Therefore, it's critical to understand how climate change affects rice crop and to follow better production practises including crop establishment methods, water management, weed management, nutrient management and microbial resources utilization that make cropping systems more resilient to extreme weather events. The spread of climate resilient production technologies would benefit rice production systems' resilience.

Bois Noir (BN) is a disease of the grapevine yellows (GY) complex associated with ‘Candidatus Phytoplasma solani’ (CaPsol) strains, which causes economic crop losses in viticulture worldwide. The epidemiology of BN is very complex due to the involvement of different herbaceous plants and several insect vectors that transmit CaPsol to grapevine. Therefore, the BN containment is very difficult and require massive efforts for possible spread reduction. The heavy application of chemical insecticides was not successful to control the insect vector presence within the vineyard. The thesis work was framed considering the directives provided by the European council 2009/128/EC regarding the promotion of low use of pesticides in sustainable management approaches. In the present thesis dissertation, CaPsol insect vectors and diseased grapevines were the main targets prioritized for successful containment of BN in organically cultivated vineyards in northern Italy. Since H. obsoletus is the widely distributed insect vector in Europe, the management of the leafhopper population was carefully considered. The use of Vitex agnus-castus as trap plant for H. obsoletus as an indirect control strategy was evaluated. Vitex agnus-castus tended to be a preferred host plant for H. obsoletus, but transmission trials demonstrated its ability to harbor CaPsol and indicated the impossibility of using this plant to avoid BN spread. In addition, the efficacy of different entomopathogenic nematodes and fungi as direct control strategy were evaluated against H. obsoletus nymphs and adults. Their application in a laboratory and semi-field conditions showed a promising killing effect that can be implemented for insect vector control in open field. Due to the very low density of H. obsoletus population in heavily BN infected vineyards questions were raised to figure out the other possible presence of alternative insect vectors. Surveys on Auchenorrhyncha coupled with molecular analyses revealed the presence of numerous putative vectors. Some of them, selected on the basis of their abundance, CaPsol-infection rate and CaPsol strains harbored, went through transmission trials. Eight insects were found able to transmit CaPsol to grapevines. Characterization of the bacterial microbiota associated with H. obsoletus and the alternative insect vectors indicated an interesting perspective regarding the microbial signatures associated with xylem- and phloem-feeding insects, and determinants that could be relevant to establish whether an insect species can be a vector or not, opening up new avenues for developing microbial resource management-based approaches. Moreover, grafting of materials collected from recovered grapevines was conducted in field trials with the aim to evaluate its preventive and curative potentials against BN. Results of symptom observation and CaPsol molecular detection on grafted and non-grafted grapevines showed that grafting of recovered shoots can have a curative effect, increasing the natural recovery. Results obtained in this PhD thesis opened new perspectives to develop integrated sustainable strategies for BN management.

The Water Framework Directive requires reduced environmental impacts from human activities and for the assessment of the non-market benefits of pollution remediation schemes. This policy shift has exacerbated the research problems surrounding the physical, social and economic consequences of the relationship between land use and water quality. This research seeks to quantify the major socio-economic and environmental benefits for people which may arise as riverine pollution is reduced. To achieve these aims this research integrates primary data analyses combining choice experiment techniques with geographical information system based analyses of secondary data concerning the spatial distributions of riverine pollution. Current knowledge on the microbial quality of river water, measured by faecal indicator organism (FIO) concentrations and assessed at catchment scale, is inadequate. This research develops generic regression models to predict base- and high-flow faecal coliform (FC) and enterococci (EN) concentrations, using land cover and population (human and livestock) variables. The resulting models are then used both to predict FIO concentrations in unmonitored watercourses and to evaluate the likely impacts of different land use scenarios, enabling insights into the optimal locations and cost-effective mix of implementation strategies. Valuation experiments frequently conflate respondents’ preferences for different aspects of water quality. This analysis uses stated preference techniques to disaggregate the values of recreation and ecological attributes of water quality, thereby allowing decision makers to better understand the consequences of adopting alternative investment strategies which favour either ecological, recreational or a mix of benefits. The results reveal heterogeneous preferences across society; specifically, latent class analysis identifies three distinct groups, holding significantly different preferences for water quality. From a methodological perspective this research greatly enhances the ongoing synthesis of geographic and economic social sciences and addresses important policy questions which are of interest to a variety of stakeholders, including government departments and the water industry.

During the last decades many studies have been undertaken to investigate life in extreme environments, leading to the discovery of novel organisms and novel habitats previously though to be unapproachable for life. Microbes are key players in a number of ecological processes such as mineral dissolution, soil genesis, plant growth promotion (PGP) and bioremediation of polluted sites and they are the main responsibles for element cycles both in conventional and extreme ecosystems. The biotechnological potential of extremophiles is well recognized, and the aim of this PhD project was to give further insight on the possible exploitation of the microbiome naturally adapted to cope with extreme values of one or more environmental parameters to develop sustainable strategies in agriculture and ecosystem management with a particular focus on arid and saline lands. Mineral-microbe interactions have been studied in detail, particularly regarding the importance of bioweathering bacteria in the ambit of soil fertility promotion in arid lands. Specific sites within the Midtre Lovénbreen glacier moraine (Svalbard, Norway), where pyritic rocks were present, hosted an active acidophilic iron-oxidizing bacterial community involved in the bioweathering of pyrite supplied by the rock disaggregation due to winter freezing. A decreased iron concentration and acidification were observed along the wheathered area departing form the pyrite-rich rock, where the oxidation of ferrous iron led to the accumulation of ferric oxy-hydroxides in the above soil. These ferric compounds were linked to the increase of soil physico-chemical properties that in turn determined a higher water holding capacity (WHC) and nutrient content in the surrounding vegetated area, densely colonized by mosses and small vascular plants. At the outer border of the vegetated area, the rest of the moraine hosted typical first colonizer bacteria, mainly belonging to the class Cyanobacteria, that are capable of nitrogen and carbon fixation. Thus, compared to the rest of the moraine, the enhancement of soil formation processes and plant colonization in the vegetated area was driven by the synergy between acidification and leaching activity of a chemolitotrophic community and the cyanobacteria-mediated primary productivity. A detailed description of the bacterial communities colonizing the weathered area, the vegetated area, and the barren moraine was obtained through the construction of 16S rRNA gene libraries. The statistical ∫-Libshuff analysis indicated these areas as three different ecological niches. The microbiome of the weathered area was dominated by few bacterial taxa due to the low pH value of the biological soil crust (BSC) whereas the vegetated area and the moraine displayed higher biodiversity. The most abundant phylogenetic groups in these BSCs were nevertheless different and in the case of the vegetated area they corresponded to those typical of mature and rhizospheric soils. The ability of microorganisms to interact with minerals is an essential factor that influence plant nutrition by providing nutrients, such as phosphorous, that are generally present in the soils as insoluble forms. The capability to solubilize poorly bioavailable nutrients is one of the PGP activities that have been investigated in the microbiome associated to different plant species living in arid hypersaline soils in Central and South Tunisia (Olea europea and Salicornia spp.) or acid soils located in a volcanic area in Mexico. A large collection of bacterial isolates has been constituted, identified and characterized for the in vitro PGP potential. Halophilic bacteria were isolated from the rhizosphere of Salicornia plants on oligotrophic media enriched with NaCl. The isolates obtained from 15% NaCl enriched media mainly belonged to the Halomonas genus, whereas the bacteria isolated at 10% NaCl showed a higher phylogenetic diversity at the genus level. Most of the bacteria comprised in the halophiles collection exhibited high resistance to drought, temperature and salt stresses. PGP activities were also widespread, especially the ability to produce indol-3-acetic acid (IAA), which promotes lateral roots developement. Furthermore, high percentage of the halophilic bacteria produced ammonium (94%) and were able to solubilize phosphate (64%) while the ability to produce protease, an activity involved in biocontrol processes, was less frequent. The comprehensive study realized on the culturable halophilic fraction of the rhizospheric bacteria associated to Salicornia spp. allowed the identification of 20 isolates as suitable candidate for developing a bacterial inoculum aimed to promote plant growth under saline stress. The diversity of the microbiome inhabiting different fractions of the Olea europea root system was investigated by applying a cultivation-independent method (Denaturing Gradient Gel Electrophoresis). The interior root tissues, the rhizosphere, the root surrounding soil and the bulk soil were colonized by a rich and diverse microbiome, shaped both by interaction with the plant and the environmental parameters of the collection site. Moreover, from these four fractions a bacterial collection was obtained for the screening of ecological and PGP features of culturable bacteria associated to olive tree growing under drought stress. In addition to the abiotic stress resistance, bacterial isolates displayed a variety of PGP activities, such as potential nitrogen fixation, siderophores and exopolysaccharides production and phosphate solubilization. Overall, the obtained dataset highlighted the possibility to use the investigated PGP bacteria associated to olive tree as biofertilizer for supporting olive growth under drought stress. An extremophile plant living at high T (42°C) and low pH (4.1) was collected at El Chichón volcanic system (Mexico). The PGP activities of a collection of rhizobacteria isolated from the plant were explored through in vitro tests. Several strains were able to affect phytohormones balance by the production of indole-3-acetic acid and 1-aminocyclopropane-1-carboxylate (ACC)-deaminase, the latter being involved in the decrease of ethylene level in plants. Remarkable percentage of the isolated bacteria displayed also additional potential PGP activities based on weathering activity. Volcanic habitats can hence be estimated as source of extremophile rhizobacteria potentialy able to help pioneer plants to cope with the severe condition of acidic soils. Microbe-environment interactions have been investigated also in deep hypersaline anoxic basins (DHABs) located in the eastern Mediterranean Sea, model environments to look for bacterial phylotypes specifically adapted to high salinity conditions. Mediterranean DHABs are far below the photic zone and contain brines originated by the dissolution of Messinian evaporites. Compared to other DHABs, Urania has very high concentrations of methane (5.56 mM) and levels of sulfide (up to 16 mM) that make it one of the most sulfidic marine water bodies on Earth. The interface between seawater and the anoxic hypersaline brine of DHABs is an oxic-anoxic interface containing an halocline with layers from seawater to brine typical salinity and is a hot-spot of microbial activity. Methanogenesis activity was detected along the first of the two environmental chemoclines present in the Urania basin and 16S rRNA gene libraries indicated the Euryarchaeota group MSBL1 as the primary candidates for methane production. Cultivation-independent analyses proved that sulfur cycling is a major driver in shaping the microbial communities, though other chemolithoautotrophic processes like manganese oxidation and anaerobic ammonium oxidation (ANAMMOX) are involved. The occurrence of ANAMMOX reaction was verified in other DHABs, namely L’Atalante and Bannock. Labelled dinitrogen gas production in 15N activity test demonstrated that anammox bacteria were active in the chemoclines of both the basins. Fluorescence in situ hybridization and 16S rRNA gene libraries using anammox-specific PCR primers unveiled the presence of the known marine anammox genus ‘Scalindua’, together with putatively novel operational taxonomic units (OTUs) closely affiliated to sequences retrieved in other marine environments where anammox activity were detected. Real Time PCR assay allowed to quantify anammox-related 16S rRNA genes in Bannock basin, which were highly abundant in correspondence of the oxic-anoxic boundary in the salinity range comprised between 6.4 and 12.1%. Cluster analysis of 16S rRNA gene libraries showed that chemoclines of Bannock and L’Atalante basins, having diverse geochemical settings, selected for different anammox phylotypes and that a shift in anammox population could be observed at increasing salinity values. The detection of putative novel phylotypes specifically adapted to peculiar salinity levels represent a key step for designing ad hoc inocula to be used in the remediation of saline wastewaters originated by industrial and agricultural processes. Actually the known freshwater anammox populations could only adapt to salt concentrations up to 3% if salinity is slowly increased, thus the selection of naturally adapted anammox strains would be of primary importance to enhance the exploitation of this process during the removal of nitrogen compounds from wastewater. The occurrence of microbe-plant positive associations was proved in different stressed soils, and their exploitation is likely the most promising approach to avoid or reduce the use of chemical fertilizer and to boost plant growth and crop productivity whitout the use of genetically modified organisms (GMO) in respect of the biodiversity. Similarly, the discovery of novel anammox phylotypes in hypersaline ecosystems shed a new light on the utilization of this functional group of bacteria for the removal of nitrogen from saline wastewaters, a critical step of treatment processes due to the environmental impact of nitrogen compounds and the severe legislation on wastewater discharges.

Waterborne disease is a significant contributor to the global burden of disease, in particular among high-risk populations in developing nations. State-of-the-art methods for the enumeration of microbial pathogens in drinking water sources have important limitations, including high initial cost, 24-48 hour delays in results, high staffing and facility requirements, and training requirements which all become especially problematic in the developing nation context. A number of alternative approaches to microbial water quality testing have been proposed, with the goal of decreasing the required testing time, decreasing overall costs, leveraging appropriate technology approaches, or improving sensitivity or specificity of the water quality testing method. One approach that may offer solutions to some of these limitations involves the deployment of sensor networks using fluorescent spectroscopy to detect intrinsic protein fluorescence in water samples as a proxy for microbial activity. In recent years, a number of researchers have found significant and meaningful correlations between indicator bacteria species and the protein fluorescence of drinking water samples. Additionally, advances in the semiconductor industry could be used to drive down the cost of such sensors. This technology may also be extensible to other water quality parameters, including dissolved organic matter or the presence of fluorescent pollutants. In this thesis, a literature review describes the fundamentals of fluorescence spectroscopy, historical and recent work regarding the fluorescence of the amino acid tryptophan and associated bacterial fluorescence, possible mechanisms for this association, and potential applications of this technology for drinking water quality monitoring and waste water process control. Extensibility of the technology is also discussed. Next, experimental methodology in reproduction of similar results is described. Samples were taken from seven (7) surface water sources and tested using membrane filtration and an off-the-shelf fluorescence spectrometer to help examine the association between the presence of indicator bacteria and the tryptophan fluorescence of the water sample. The results, showing an association of R2 = 0.560, are compared to the results of recent similar experiments. Finally, two prototypes are described, including their design requirements and data from prototype testing. The results of the testing are briefly discussed, and next steps are outlined with the goal of developing a low-cost, in-situ microbial water quality sensor using fluorescence spectroscopy principles.

It has been reported that globally we have achieved Millennium Development Goal (MDG) Target 7C, to halve the proportion of the population without access to safe drinking water; however, there is a major flaw with this statement. While Target 7C calls for access to `safe' drinking water, what is actually being measured and reported is access to an `improved' water source. The World Health Organization (WHO) maintains that they must use this proxy measure because the methods for water quality testing are too expensive and logistically complicated, but by doing so, they may be over reporting safe water coverage. This was shown to be true in Tamatave, Madagascar, where thermotolerant coliforms were detected in water from a type of `improved' source, the Pitcher Pump system. This research looked at several parameters - Pitcher Pump system depth, sampling neighborhood, requirement of pump priming, frequency that the system was repaired, distance from on-site sanitation, and number of users - to see if they were influencing water quality. Of all the parameters tested, only priming was found to be significantly associated with the levels of thermotolerant coliforms detected (Fisher exact test p = 0.03). Using a Mann-Whitney U test, it was shown that the median thermotolerant coliform concentration was significantly higher in primed wells (41.3 cfu/100 ml) than unprimed wells (3.5) (p = 0.01 cfu/100 ml). A pilot study was conducted to look at only the effect of depth and to determine if a depth could be identified that could provide safe drinking water. The result of the pilot study showed that, while thermotolerant coliform concentration did decrease with increasing depth, even at the deepest well of 9.4 m, levels were still above 100 cfu/100 ml. Additional research was conducted to investigate the performance and cost of three test kits for both total coliform and Escherichia coli quantification for water quality analysis in developing countries. IDEXX Colilert Quanti-trays[reg] (Colilert), Micrology Laboratories Coliscan[reg] Membrane Filtration tests (Coliscan MF) and a modified method for 3-M PetrifilmTM Coliform/E. coli plates (modified 3-M) were compared with standard membrane filtration (standard MF) methods under a range of incubation temperature conditions (22.0, 35.0 and 44.5[deg]C). Each test method was also performed by inexperienced volunteers, with the results compared to those of an experienced technician. At non-standard temperatures, Coliscan MF proved to be the most accurate when compared to standard methods, with a significant difference with only total coliforms at 44.5[deg]C. Modified 3-M had the poorest correlation with standard MF over the range of temperatures tested, with significant differences noted for all the temperatures except for E. coli at 44.5[deg]C. Inexperienced university volunteers found Colilert easiest to use, but Coliscan MF produced E. coli results that were most similar to the experts. Coliscan MF was found to have the overall best performance and lowest cost in this study; however, it did produce high numbers of false positive results.

Reliable access to safe drinking water is one necessity for humans to live without concern for major health risks. The overall goal of this research is to improve the public health, through improved drinking water, for communities in the Rakai District in Uganda, directly, and other communities in the world, indirectly, via dissemination of knowledge. This study specifically assessed the knowledge of drinking water quality in regards to public health, their sanitation measures, and water treatment methods for users of Brick by Brick rainwater harvesting tanks in the Rakai District (N = 28) by using a knowledge, attitudes, and practice survey and a sanitary inspection; tested the water quality of the Brick by Brick rainwater harvesting tanks (N = 33) in the Rakai District for physical, chemical, and microbial parameters; and piloted a sustainable treatment technology called the chulli system that uses excess heat from a cookstove to treat water. Twenty of the participants identified contaminated water as a cause of diarrheal disease (N = 28). Participants perceived boiling (1), chlorine (2), and filtering (3) as the best three methods of treating water. The average score for the sanitary inspection was 2.27±2.31, which falls between the low and medium expected risk score categories. Fourteen of the thirty-three samples showed detectable levels of colony forming units for coliforms, and two of the thirty-three samples showed detectable levels of colony forming units for E. coli. A demonstration chulli system was constructed for St. Andrew’s Primary School in Rakai District and operated successfully. The research supports that the chulli system along with proper sanitation measures identified in the sanitary inspections can be a sustainable option for users of Brick by Brick rainwater harvesting tanks in the Rakai District.

Microalgae are considered one of the most promising feedstocks for biofuel production for the future. The most efficient way to produce vast amounts of algal biomass is the use of closed tubular photobioreactors (PBR). The heat requirement for a given system is a major concern since the best algae growth rates are obtained between 25-30 °C, depending on the specific strain. A procedure to determine temperature influence on algal growth rates was developed for a lab-scale PBR system using the species Chlorella. A maximum growth rate of 1.44 doublings per day at 29 °C (optimal temperature) was determined. In addition, a dynamic mathematical model was developed to simulate heating and cooling energy requirements of tubular PBRs for any desired location. Operating the model with hourly weather data as input, heating and cooling loads can be calculated early in the planning stage of a project. Furthermore, the model makes it possible to compare the operation inside a greenhouse to the outdoor operations, and consequently provides fundamental information for an economic feasibility study. The best configuration for a specific location can be evaluated easily. The model was exemplary tested for a hypothetical 100,000 l photobioreactor located in San Luis Obispo, California, U.S.A. Average algae productivity rates of 23% and 67% for outdoor and indoor PBR operations, respectively, were obtained. Actual energy loads (heating and cooling) needed to maintain the PBR at optimal temperature were determined and compared. Sensitivity analyses had been performed for abrupt temperature and solar radiation steps, PBR row distances, ground reflectivities, and ventilation rates of the greenhouse. An optimal row distance of 0.75 m was determined for the specific PBR. The least amount of energy was needed for a ground reflectivity of 20%. The ventilation rate had no major influence on the productivity rate of the system. Results demonstrated the importance of a simulation model as well as the economic impact of a sophisticated heat management system. Energy savings due to an optimized heat management system will eventually increase proficiency of the systems, which will support a new sustainable industry and future developmental potential.

Sanitation, renewable energy, and food security are among the most pressing global development needs of the century, especially for small cities with rapid population growth. Currently, 53% of the world’s population either lacks access to improved sanitation or discharges fecal waste to the environment without treatment. Furthermore, 80% of food consumed in developing regions is produced by 500 million small farms, and while many of them are still rain-fed, irrigated agriculture is increasing. The post-2015 Sustainable Development Goals, recently adopted by the United Nations, include targets to address the water-energy-food nexus. Wastewater reuse in agriculture can be an important solution for these goals, if it is done safely. Globally, 18 – 20 million hectares of agricultural land are irrigated with wastewater, but much is untreated, unregulated, or unsanctioned, causing concerns and uncertainty about health risks. There is a need to better understand pathogen removal in natural and non-mechanized wastewater treatment systems, such as waste stabilization ponds (WSPs) and upflow anaerobic sludge blanket (UASB) reactors, which are commonly used in small cities and towns. Riverbank filtration (RBF) is also a natural technique used by farmers in developing countries to treat surface water polluted with untreated sewage, but pathogen removal in these systems has seldom been assessed in developing countries. The focus of this dissertation is on pathogen removal in natural and non-mechanized wastewater treatment and reuse systems, to evaluate the health implications of water reuse for irrigation, with the following three objectives: 1) assess the current understanding of virus removal in WSP systems through a systematic review of the literature; 2) measure the removal of viruses and their association with particles in systems with WSPs, UASB reactors, or both; and 3) assess the fate and transport of pathogens and fecal indicators in wastewater treatment systems with direct and indirect reuse for irrigation to estimate microbial risks. To advance the understanding of virus removal in WSP systems, a comprehensive analysis of virus removal reported in the literature from 71 different WSP systems revealed only a weak to moderate correlation of virus removal with theoretical hydraulic retention time (HRT). For each log10 reduction of viruses a geometric mean of 14.5 days of retention was required, but the 95th percentile of the data analyzed was 54 days. Also, whereas virus-particle association and subsequent sedimentation has been assumed to be an important removal mechanism for viruses in WSPs, the literature review revealed a lack of evidence to confirm the validity of this assumption. The association of human adenovirus (AdV) with wastewater particles was assessed in five full-scale wastewater treatment systems in Bolivia, Brazil, and the United States (two with only WSPs, two with a UASB reactor and WSPs, and one with only UASB reactors). A mesocosm study was also conducted with WSP water from one of the full-scale systems, and some samples were also analyzed for pepper mild mottle virus (PMMoV), F+ coliphage, culturable enterovirus (EV), norovirus (NoV), and rotavirus (RV). Results indicate that WSPs and UASB reactors affect virus-particle associations in different ways, which may differ for different viruses. In UASB reactor effluent, PMMoV was more associated with particles <180 >µm, showed no indication of settling in subsequent ponds, and appeared to degrade in pond sediments after 5 days. In contrast, AdV in UASB reactor effluent was associated with small and large particles, and in subsequent ponds, particle-associated AdV showed evidence of possible settling or more rapid decay at the water surface. AdV and culturable EV were also more volumetrically-concentrated in UASB reactor sludge than they were in untreated sewage, WSP water, UASB effluent, and WSP sediments, indicating that the reactors may cause these viruses to become entrapped and concentrated in granular sludge. Some viruses may be removed in the sludge, but others exit the reactors in solution and attached to particles. The resuspension of pellets from centrifuged UASB reactor sludge samples in an eluant buffer indicated reversible AdV association with granular sludge, but some associations with particles in solution may not be reversible. The fate and transport of pathogens and fecal indicators was assessed in Bolivia for two WSP systems with direct reuse for irrigation, and one on-farm RBF system used to treat surface water polluted by untreated sewage. In the WSP systems, despite HRTs of 10 days, pathogen and fecal indicator removal was generally ≤1-log10, possibly due to overloading and short-circuiting from sludge accumulation. The RBF system provided removals on the order of 2-log10 for protozoan parasites, 3-log10 or more for viruses, and 4-log10 or more for bacteria. The use of RBF also reduced cumulative estimated health burdens associated with irrigated lettuce. Irrigation of lettuce with untreated river water caused an estimated disease burden that represents 37% of the existing burden from acute diarrhea in Bolivia; when RBF was used, this decreased to only 1.1%, which is not epidemiologically-significant, and complies with the World Health Organization guidelines. Ratios of concentrations of microorganisms in irrigation water to their respective concentrations in soil or crops were calculated, to assess transfer from irrigation water to soil or crops. These ratios (with units mL g-1) were generally < 0.1 mL g-1 for coliphage, between 1 and 100 mL g-1 for Giardia and Cryptosporidium, and generally between 100 and 1,000 mL g-1 for helminth eggs. Higher ratios could indicate more efficient transfer from water to soil or crops, longer persistence in soil or on crops, or slower leaching away from soil or crops. The results from this research demonstrate that pathogen removal in full-scale natural wastewater treatment systems happens via complex mechanisms that vary with respect to pathogen type, treatment systems configuration, and other environmental and operational parameters. Future research and innovation efforts should focus on the use of a combination of natural and non-mechanized technologies, surface-flow systems (e.g., WSPs) and subsurface systems (e.g., RBF), applied at both semi-centralized (e.g., wastewater treatment plant) and decentralized levels (e.g., on farms), to evaluate how this affects the efficiency and resiliency of pathogen removal. Also, future research is needed to further elucidate reasons for the observed differences in virus-particle associations in natural wastewater treatment systems.

Biodiversity in Drylands, the first internationally based synthesis volume in the Long-Term Ecological Research (LTER) Network Series, unifies the concepts of species and landscape diversity with respect to deserts. Within this framework, the book treats several emerging themes, among them: · how animal biodiversity can be supported in deserts · diversity's relation to habitat structure, environmental variability, and species interactions · the relation between spatial scale and diversity · how to use a landscape simulation model to understand diversity · microbial contributions to biodiversity in deserts · species diversity and ecosystem processes · resource partitioning and biodiversity in fractal environments · effects of grazing on biodiversity · reconciliation ecology and the future of conservation management In the face of global change, integration is crucial for dealing with the problem of sustaining biodiversity. This book promises to be a vital resource for students, researchers, and managers interested in integrative species, resource, and landscape diversities.

Over the last decade there has been a dramatic shift in global agricultural practice. The increase in human population, especially in underdeveloped arid and semiarid regions of the world, poses unprecedented challenges to production of an adequate and economically feasible food supply to undernourished populations. Furthermore, the increased living standard in many industrial countries has created a strong demand for high-quality, out-of-season vegetables and fruits as well as for ornamentals such as cut and potted flowers and bedding plants. As a response to these imminent challenges and demands and because of a ban on methyl bromide fumigation of horticultural field soils, soilless greenhouse production systems are regaining increased worldwide attention. Though there is considerable recent empirical and theoretical research devoted to specific issues related to control and management of soilless culture production systems, a comprehensive approach that quantitatively considers all relevant physicochemical processes within the growth substrates is lacking. Moreover, it is common practice to treat soilless growth systems as static, ignoring dynamic changes of important physicochemical and hydraulic properties due to root and microbial growth that require adaptation of management practices throughout the growth period. To overcome these shortcomings, the objectives of this project were to apply thorough physicochemical characterization of commonly used greenhouse substrates in conjunction with state-of-the-art numerical modeling (HYDRUS-3D, PARSWMS) to not only optimize management practices (i.e., irrigation frequency and rates, fertigation, container size and geometry, etc.), but to also “engineer” optimal substrates by mixing organic (e.g., coconut coir) and inorganic (e.g., perlite, pumice, etc.) base substrates and modifying relevant parameters such as the particle (aggregate) size distribution. To evaluate the proposed approach under commercial production conditions, characterization and modeling efforts were accompanied by greenhouse experiments with tomatoes. The project not only yielded novel insights regarding favorable physicochemical properties of advanced greenhouse substrates, but also provided critically needed tools for control and management of containerized soilless production systems to provide a stress-free rhizosphere environment for optimal yields, while conserving valuable production resources. Numerical modeling results provided a more scientifically sound basis for the design of commercial greenhouse production trials and selection of adequate plant-specific substrates, thereby alleviating the risk of costly mistrials.

Objectives: (1) Evaluate Immunocompetence-OTL-containing Chromosomal Regions (ICRs), marked by microsatellites or candidate genes, for magnitude of direct effect and for contribution to relationships among multiple immunocompetence, disease-resistance, and growth traits, in order to estimate epistatic and pleiotropic effects and to predict the potential breeding applications of such markers. (2) Evaluate the interaction of the ICRs with genetic backgrounds from multiple sources and of multiple levels of genetic variation, in order to predict the general applicability of molecular genetic markers across widely varied populations. Background: Diseases cause substantial economic losses to animal producers. Emerging pathogens, vaccine failures and intense management systems increase the impact of diseases on animal production. Moreover, zoonotic pathogens are a threat to human food safety when microbiological contamination of animal products occurs. Consumers are increasingly concerned about drug residues and antibiotic- resistant pathogens derived from animal products. The project used contemporary scientific technologies to investigate the genetics of chicken resistance to infectious disease. Genetic enhancement of the innate resistance of chicken populations provides a sustainable and ecologically sound approach to reduce microbial loads in agricultural populations. In turn, animals will be produced more efficiently with less need for drug treatment and will pose less of a potential food-safety hazard. Major achievements, conclusions and implications:. The PI and co-PIs had developed a refined research plan, aiming at the original but more focused objectives, that could be well-accomplished with the reduced awarded support. The successful conduct of that research over the past four years has yielded substantial new information about the genes and genetic markers that are associated with response to two important poultry pathogens, Salmonella enteritidis (SE) and Escherichia coli (EC), about variation of immunocompetence genes in poultry, about relationships of traits of immune response and production, and about interaction of genes with environment and with other genes and genetic background. The current BARD work has generated a base of knowledge and expertise regarding the genetic variation underlying the traits of immunocompetence and disease resistance. In addition, unique genetic resource populations of chickens have been established in the course of the current project, and they are essential for continued projects. The US laboratory has made considerable progress in studies of the genetics of resistance to SE. Microsatellite-marked chromosomal regions and several specific genes were linked to SE vaccine response or bacterial burden and the important phenomenon of gene interaction was identified in this system. In total, these studies demonstrate the role of genetics in SE response, the utility of the existing resource population, and the expertise of the research group in conducting such experiments. The Israeli laboratories had showed that the lines developed by selection for high or low level of antibody (Ab) response to EC differ similarly in Ab response to several other viral and bacterial pathogens, indicating the existence of a genetic control of general capacity of Ab response in young broilers. It was also found that the 10w-Ab line has developed, possibly via compensatory "natural" selection, higher cellular immune response. At the DNA levels, markers supposedly linked to immune response were identified, as well as SNP in the MHC, a candidate gene responsible for genetic differences in immunocompetence of chickens.