Symbiosis in the microbial world: from ecology to genome evolution

© 2018. Published by The Company of Biologists Ltd. The concept of symbiosis – defined in 1879 by de Bary as ‘the living together of unlike organisms’ – has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists’ workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired

Classification of HIV-1 Sequences Using Profile Hidden Markov Models

Accurate classification of HIV-1 subtypes is essential for studying the dynamic spatial distribution pattern of HIV-1 subtypes and also for developing effective methods of treatment that can be targeted to attack specific subtypes. We propose a classification method based on profile Hidden Markov Model that can accurately identify an unknown strain. We show that a standard method that relies on the construction of a positive training set only, to capture unique features associated with a particular subtype, can accurately classify sequences belonging to all subtypes except B and D. We point out the drawbacks of the standard method; namely, an arbitrary choice of threshold to distinguish between true positives and true negatives, and the inability to discriminate between closely related subtypes. We then propose an improved classification method based on construction of a positive as well as a negative training set to improve discriminating ability between closely related subtypes like B and D. Finally, we show how the improved method can be used to accurately determine the subtype composition of Common Recombinant Forms of the virus that are made up of two or more subtypes. Our method provides a simple and highly accurate alternative to other classification methods and will be useful in accurately annotating newly sequenced HIV-1 strains

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

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

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

The estimated impact of California's urban water conservation mandate on electricity consumption and greenhouse gas emissions

In April 2015, the Governor of California mandated a 25% statewide reduction in water consumption (relative to 2013 levels) by urban water suppliers. The more than 400 public water agencies affected by the regulation were also required to report monthly progress towards the conservation goal to the State Water Resources Control Board. This paper uses the reported data to assess how the water utilities have responded to this mandate and to estimate the electricity savings and greenhouse gas (GHG) emissions reductions associated with reduced operation of urban water infrastructure systems. The results show that California succeeded in saving 524 000 million gallons (MG) of water (a 24.5% decrease relative to the 2013 baseline) over the mandate period, which translates into 1830 GWh total electricity savings, and a GHG emissions reduction of 521 000 metric tonnes of carbon dioxide equivalents (MT CO2e). For comparison, the total electricity savings linked to water conservation are approximately 11% greater than the savings achieved by the investor-owned electricity utilities' efficiency programs for roughly the same time period, and the GHG savings represent the equivalent of taking about 111 000 cars off the road for a year. These indirect, large-scale electricity and GHG savings were achieved at costs that were competitive with existing programs that target electricity and GHG savings directly and independently. Finally, given the breadth of the results produced, we built a companion website, called 'H2Open' (https://cwee.shinyapps.io/greengov/), to this research effort that allows users to view and explore the data and results across scales, from individual water utilities to the statewide summary

Vibration therapy versus standard treatment for tennis elbow: A randomized controlled study.

To determine whether a mechanical, high-frequency vibration device (Tenease™) can improve pain and function for the treatment of tennis elbow (TE), compared with standard treatment

Microbial Ecology of Lake Kivu

peer reviewedWe review available data on archaea, bacteria and small eukaryotes in an attempt to provide a general picture of microbial diversity, abundances and microbe-driven processes in Lake Kivu surface and intermediate waters (ca. 0–100 m). The various water layers present contrasting physical and chemical properties and harbour very different microbial communities supported by the vertical redox structure. For instance, we found a clear vertical segregation of archaeal and bacterial assemblages between the oxic and the anoxic zone of the surface waters. The presence of specific bacterial (e.g. Green Sulfur Bacteria) and archaeal (e.g. ammonia-oxidising archaea) communities and the prevailing physico-chemical conditions point towards the redoxcline as the most active and metabolically diverse water layer. The archaeal assemblage in the surface and intermediate water column layers was mainly composed by the phylum Crenarchaeota , by the recently defined phylum Thaumarchaeota and by the phylum Euryarchaeota . In turn, the bacterial assemblage comprised mainly ubiquitous members of planktonic assemblages of freshwater environments (Actinobacteria, Bacteroidetes and Betaproteobacteria among others) and other less commonly retrieved phyla (e.g. Chlorobi, Clostridium and Deltaproteobacteria). The community of small eukaryotes (<5 µm) mainly comprised Stramenopiles , Alveolata , Cryptophyta , Chytridiomycota , Kinetoplastea and Choanoflagellida, by decreasing order of richness. The total prokaryotic abundance ranged between 0.5 × 10^6 and 2.0 × 10^6 cells mL−1 , with maxima located in the 0–20 m layer, while phycoerythrin-rich Synechococcus-like picocyanobacteria populations were comprised between 0.5 × 10^5 and 2.0 × 10^5 cells mL−1 in the same surface layer. Brown-coloured species of Green Sulfur Bacteria permanently developed at 11m depth in Kabuno Bay and sporadically in the anoxic waters of the lower mixolimnion of the main basin. The mean bacterial production was estimated to 336 mg C m−2 day−1 . First estimates of the re-assimilation by bacterioplankton of dissolved organic matter excreted by phytoplankton showed high values of dissolved primary production (ca. 50% of total production). The bacterial carbon demand can totally be fuelled by phytoplankton production. Overall, recent studies have revealed a high microbial diversity in Lake Kivu, and point towards a central role of microbes in the biogeochemical and ecological functioning of the surface layers, comprising the mixolimnion and the upper chemocline