A bacterial genome in transition - an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus

<p>Abstract</p> <p>Background</p> <p>Insertion sequence (IS) elements are important mediators of genome plasticity and are widespread among bacterial and archaeal genomes. The 1.88 Mbp genome of the obligate intracellular amoeba symbiont <it>Amoebophilus asiaticus </it>contains an unusually large number of transposase genes (n = 354; 23% of all genes).</p> <p>Results</p> <p>The transposase genes in the <it>A. asiaticus </it>genome can be assigned to 16 different IS elements termed ISCaa1 to ISCaa16, which are represented by 2 to 24 full-length copies, respectively. Despite this high IS element load, the <it>A. asiaticus </it>genome displays a GC skew pattern typical for most bacterial genomes, indicating that no major rearrangements have occurred recently. Additionally, the high sequence divergence of some IS elements, the high number of truncated IS element copies (n = 143), as well as the absence of direct repeats in most IS elements suggest that the IS elements of <it>A. asiaticus </it>are transpositionally inactive. Although we could show transcription of 13 IS elements, we did not find experimental evidence for transpositional activity, corroborating our results from sequence analyses. However, we detected contiguous transcripts between IS elements and their downstream genes at nine loci in the <it>A. asiaticus </it>genome, indicating that some IS elements influence the transcription of downstream genes, some of which might be important for host cell interaction.</p> <p>Conclusions</p> <p>Taken together, the IS elements in the <it>A. asiaticus </it>genome are currently in the process of degradation and largely represent reflections of the evolutionary past of <it>A. asiaticus </it>in which its genome was shaped by their activity.</p

A High-Resolution Approach to Mapping Energy Flows through Water Infrastructure Systems

Using data from the water service area of the East Bay Municipal Utility District in Northern California, we develop and discuss a method for assessing, at a high resolution, the energy intensity of water treated and delivered to customers of a major metropolitan water district. This method extends previous efforts by integrating hourly data from supervisory control and data acquisition systems with calculations based on the actual structure of the engineered infrastructure to produce a detailed understanding of energy use in space and time within the territory of a large-scale urban water provider. We found significant variations in the energy intensity of delivered potable water resulting from seasonal and topographic effects. This method enhances our understanding of the energy inputs for potable water systems and can be applied to the entire delivery and postuse water life cycle. A nuanced understanding of water's energy intensity in an urban setting enables more intelligent, targeted efforts to jointly conserve water and energy resources that take seasonal, distance, and elevation effects into account

Estimating the blue water footprint of in-field crop losses: A case study of U.S. potato cultivation

Given the high proportion of water consumption for agriculture, as well as the relatively common occurrence of crop losses in the field, we estimate the amount of water embedded in crops left on the farm. We are particularly interested in understanding losses associated with fruits and vegetables, having a higher level of harvesting selectivity and perishability (and thus, losses) than grain crops. We further refined the study to focus on potatoes, as they represent the largest acreage under cultivation of all fruit and vegetable crops in the U.S. We attempt to get the most complete understanding of pre-harvest and harvest loss data for potatoes by leveraging three centralized data sets collected and managed by the United States Department of Agriculture (USDA). By integrating these three distinct data sets for the five-year period 2012-2016, we are able to estimate water consumption for potato cultivation for total in-field losses by production stage and driver of loss for seven major potato-producing states (representing 77% of total U.S. potato production). Our results suggest that 3.6%-17.9% of potatoes are lost in the field with a total estimated blue water footprint of approximately 84.6 million cubic meters. We also find that the leading driver for crop loss for in-field potato production is harvest sorting and grading, accounting for 84% of total lost production at the farm. We conclude with a discussion of opportunities for improved national level data collection to provide a better understanding of in-field crop losses over time and the resource footprints of these losses

A High-Resolution Approach to Mapping Energy Flows through Water Infrastructure Systems

Using data from the water service area of the East Bay Municipal Utility District in Northern California, we develop and discuss a method for assessing, at a high resolution, the energy intensity of water treated and delivered to customers of a major metropolitan water district. This method extends previous efforts by integrating hourly data from supervisory control and data acquisition systems with calculations based on the actual structure of the engineered infrastructure to produce a detailed understanding of energy use in space and time within the territory of a large-scale urban water provider. We found significant variations in the energy intensity of delivered potable water resulting from seasonal and topographic effects. This method enhances our understanding of the energy inputs for potable water systems and can be applied to the entire delivery and postuse water life cycle. A nuanced understanding of water's energy intensity in an urban setting enables more intelligent, targeted efforts to jointly conserve water and energy resources that take seasonal, distance, and elevation effects into account

Does on-farm food loss prevent waste? Insights from California produce growers

Significant quantities of edible produce are lost at the farm level. Amidst growing concern about the environmental impacts of food loss and waste, advocates have invested in exploring farm-level interventions that might reduce the environmental footprint of food. Farmers are obvious stakeholders in such efforts, yet their voices are often missing from the discussion. Drawing on interviews with 25 fresh produce growers in California, we show how on-farm losses are driven by efforts to mitigate economic risk within food supply chains. Buyers minimize risk by demanding consistent volumes of perfect produce, and growers in turn minimize their financial risks by holding back “imperfect” and surplus food. If food is likely to be rejected further down the chain, growers abandon it on the farm. Using the EPA food recovery hierarchy and the tools of life cycle analysis (LCA), we then compare the environmental impact of farm-level loss to downstream alternatives. While landfill disposal is common at retail and consumer levels, food lost at the farm level is tilled back into the soil or sold as animal feed. We conclude that some on-farm losses may prevent more environmentally harmful “waste,” defined here as landfilled food, further down the supply chain. Our analysis argues for an approach to remedying on-farm food loss that is both ambitious and cautious—one that recognizes the structural causes of loss and that considers how environmental risks can increase as food moves downstream

“A cluster-based spatial analysis of recycling boundaries aligning anaerobic digestion infrastructure with food waste generation in California”

In 2016, California passed Senate Bill (SB) 1383 to reduce short-lived climate pollutants, including methane gas. Towards this end, the law specifically mandates a 75% reduction of organic waste, including food waste (FW), from landfills by 2025. However, current infrastructural capacity to treat this diverted organic waste is limited throughout the state, so new facilities will need to be built to treat these valuable waste flows. The purpose of this study is to investigate ideal size and scale of new facilities that maximize FW treatment and minimize GHG emissions. To do so, this study uses a case study of Los Angeles County to model a decentralized network of small-scale, containerized anerobic digestors (ADs) for treatment of FW in the region. A spatial FW dataset developed for this study is used with a novel iterative-descent clustering model to simulate potential “FW-sheds” of ADs using Geographic Information Systems (GIS). Monte Carlo simulation was used to generate a range of model results and a GHG analysis of FW collection is used to compare systems of two different AD capacities. The results of this analysis show that food waste is ideal for recycling at relatively small spatial scales as hauling burden of FW is reduced in these systems. The proposed infrastructure modeling approach is a first step of developing a zero net energy infrastructural solution that promotes a circular economy of food in direct response to SB 1383 and, more broadly, global climate change

Does on-farm food loss prevent waste? Insights from California produce growers

Significant quantities of edible produce are lost at the farm level. Amidst growing concern about the environmental impacts of food loss and waste, advocates have invested in exploring farm-level interventions that might reduce the environmental footprint of food. Farmers are obvious stakeholders in such efforts, yet their voices are often missing from the discussion. Drawing on interviews with 25 fresh produce growers in California, we show how on-farm losses are driven by efforts to mitigate economic risk within food supply chains. Buyers minimize risk by demanding consistent volumes of perfect produce, and growers in turn minimize their financial risks by holding back “imperfect” and surplus food. If food is likely to be rejected further down the chain, growers abandon it on the farm. Using the EPA food recovery hierarchy and the tools of life cycle analysis (LCA), we then compare the environmental impact of farm-level loss to downstream alternatives. While landfill disposal is common at retail and consumer levels, food lost at the farm level is tilled back into the soil or sold as animal feed. We conclude that some on-farm losses may prevent more environmentally harmful “waste,” defined here as landfilled food, further down the supply chain. Our analysis argues for an approach to remedying on-farm food loss that is both ambitious and cautious—one that recognizes the structural causes of loss and that considers how environmental risks can increase as food moves downstream

The cost-effectiveness of energy savings through water conservation: a utility-scale assessment

It is well-established that water infrastructure systems require energy to treat and deliver water to end-users. This fundamental relationship presents an opportunity to secure energy savings through water conservation. In a previous study, the energy savings linked to a statewide water conservation mandate in California were found comparable in both resource savings as well as cost-effectiveness to the energy savings achieved directly through energy efficiency programs. This study pursues a similar line of inquiry, but at the scale of an individual city as opposed to a statewide assessment. Los Angeles, California, serves as the case study for estimating the energy savings secured through water conservation programs relative to energy efficiency (EE) programs enacted in the study region. We apply three different estimates of energy intensity (EI) for the conversion of water savings to energy savings. These applied EI scenarios are differentiated by scale and system boundary, including: a direct assessment of EI within the water utility service territory, an expanded boundary that includes imported water infrastructure systems, and a broader, top-down estimate for the regional hydrologic zone. Across all scenarios, the estimated energy savings secured through water conservation programs prove to be cost-competitive with the energy efficiency programs enacted by the utility. When using estimates of EI with expanded system boundaries that include the upstream energy embedded in imported water supplies, water conservation becomes a significantly more attractive pathway for saving energy. This outcome underlines the importance of clearly defining the water-energy system boundary of interest, both to determine an accurate EI value, and subsequently, to design and implement cost-effective programs that jointly conserve both water and energy resources