The Escherichia coli transcriptome mostly consists of independently regulated modules

Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome

Agroecosystem energy transitions in the old and new worlds: trajectories and determinants at the regional scale

Energy efficiency in biomass production is a major challenge for a future transition to sustainable food and energy provision. This study uses methodologically consistent data on agroecosystem energy flows and different metrics of energetic efficiency from seven regional case studies in North America (USA and Canada) and Europe (Spain and Austria) to investigate energy transitions in Western agroecosystems from the late nineteenth to the late twentieth centuries. We quantify indicators such as external final energy return on investment (EFEROI, i.e., final produce per unit of external energy input), internal final EROI (IFEROI, final produce per unit of biomass reused locally), and final EROI (FEROI, final produce per unit of total inputs consumed). The transition is characterized by increasing final produce accompanied by increasing external energy inputs and stable local biomass reused. External inputs did not replace internal biomass reinvestments, but added to them. The results were declining EFEROI, stable or increasing IFEROI, and diverging trends in FEROI. The factors shaping agroecosystem energy profiles changed in the course of the transition: Under advanced organic and frontier agriculture of the late nineteenth and early twentieth centuries, population density and biogeographic conditions explained both agroecosystem productivity and energy inputs. In industrialized agroecosystems, biogeographic conditions and specific socio-economic factors influenced trends towards increased agroecosystem specialization. The share of livestock products in a region's final produce was the most important factor determining energy returns on investment

From vineyards to feedlots: a fund-flow scanning of sociometabolic transition in the Vallès County (Catalonia) 1860-1956-1999

We analyse the changes to agricultural metabolism in four municipalities of Vallès County (Catalonia, Iberia) by accounting for their agroecosystemfunds and flows during the socioecological transition from organic to industrial farming between the late nineteenth and twentieth centuries. The choice of three different stages in this transition allows us to observe the transformation of its funds and flows over time, the links established between them and the effect on their energy profiles.We emphasize the relevance of the integration and consistency of agroecosystem funds for energy efficiency in agriculture and their role as underlying historical drivers of this socioecological transition. While readjustment to market conditions and availability and affordability of external inputs are considered the main drivers of the transition, we also highlight the role of societal energy and nutritional transitions. An analysis of advanced organic agriculture c. 1860 reveals the great effort required to reproduce soil fertility and livestock from the internal recirculation of biomass. Meanwhile, a balance between land produce and livestock densities enabled the integration of funds, with a positive impact on energy performance. The adoption of fossil fuels and synthetic fertilizers c. 1956 reduced somewhat the pressure exerted on the land by overcoming the former dependence on local biomass flows to reproduce the agroecosystem. Yet external inputs diminished sustainability. Partial dependence on external markets existed congruently with internal crop diversity and the predominance of organic over industrial farm management. A shift towards animal production and consumption led to a new specialization process c. 1999 that resulted in crop homogenization and agroecological landscape disintegration. The energy returns of this linear feed-food livestock bioconversion declined compared to earlier mixed farming. Huge energy flows driven by a globalized economy ran through this agroecosystem, provoking deep impacts at both a local and external scale

A Net Energy Analysis of the Global Agriculture, Aquaculture, Fishing and Forestry System

The global agriculture, aquaculture, fishing and forestry (AAFF) energy system is subject to three unsustainable trends: (1) the approaching biophysical limits of AAFF; (2) the role of AAFF as a driver of environmental degradation; and (3) the long-term declining energy efficiency of AAFF due to growing dependence on fossil fuels. In response, we conduct a net energy analysis for the period 1971–2017 and review existing studies to investigate the global AAFF energy system and its vulnerability to the three unsustainable trends from an energetic perspective. We estimate the global AAFF system represents 27.9% of societies energy supply in 2017, with food energy representing 20.8% of societies total energy supply. We find that the net energy-return-on-investment (net EROI) of global AAFF increased from 2.87:1 in 1971 to 4.05:1 in 2017. We suggest that rising net EROI values are being fuelled in part by ‘depleting natures accumulated energy stocks’. We also find that the net energy balance of AAFF increased by 130% in this period, with at the same time a decrease in both the proportion of rural residents and also the proportion of the total population working in AAFF—which decreased from 19.8 to 10.3%. However, this comes at the cost of growing fossil fuel dependency which increased from 43.6 to 62.2%. Given the increasing probability of near-term fossil fuel scarcity, the growing impacts of climate change and environmental degradation, and the approaching biophysical limits of global AAFF, ‘Odum’s hoax’ is likely soon to be revealed