Application of Finite-Time and Control Thermodynamics to Biological Processes at Multiple Scales

An overall synthesis of biology and non-equilibrium thermodynamics remains a challenge at the interface between the physical and life sciences. Herein, theorems from finite-time and control thermodynamics are applied to biological processes to indicate which biological strategies will succeed over different time scales. In general, living systems maximize power at the expense of efficiency during the early stages of their development while proceeding at slower rates to maximize efficiency over longer time scales. The exact combination of yield and power depends upon the constraints on the system, the degrees of freedom in question, and the time scales of the processes. It is emphasized that biological processes are not driven by entropy production but, rather, by <i>informed exergy flow</i>. The entropy production is the generalized friction that is minimized insofar as the constraints allow. Theorems concerning thermodynamic path length and entropy production show that there is a direct tradeoff between the efficiency of a process and the process rate. To quantify this tradeoff, the concepts of <i>compensated heat</i> and <i>waste heat</i> are introduced. Compensated heat is the exergy dissipated, which is necessary for a process to satisfy constraints. Conversely, waste heat is exergy that is dissipated as heat, but does not provide a compensatory increase in rate or other improvement. We hypothesize that it is waste heat that is minimized through natural selection. This can be seen in the strategies employed at several temporal and spatial scales, including organismal development, ecological succession, and long-term evolution. Better understanding the roles of compensated heat and waste heat in biological processes will provide novel insight into the underlying thermodynamic mechanisms involved in metabolism, ecology, and evolution

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

BACKGROUND: Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS , Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity. RESULTS: PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype. CONCLUSION: PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts

The Upper Respiratory Tract as a Microbial Source for Pulmonary Infections in Cystic Fibrosis. Parallels from Island Biogeography

A continuously mixed series of microbial communities inhabits various points of the respiratory tract, with community composition determined by distance from colonization sources, colonization rates, and extinction rates. Ecology and evolution theory developed in the context of biogeography is relevant to clinical microbiology and could reframe the interpretation of recent studies comparing communities from lung explant samples, sputum samples, and oropharyngeal swabs. We propose an island biogeography model of the microbial communities inhabiting different niches in human airways. Island biogeography as applied to communities separated by time and space is a useful parallel for exploring microbial colonization of healthy and diseased lungs, with the potential to inform our understanding of microbial community dynamics and the relevance of microbes detected in different sample types. In this perspective, we focus on the intermixed microbial communities inhabiting different regions of the airways of patients with cystic fibrosis

Variability and host density independence in inductions-based estimates of environmental lysogeny.

Temperate bacterial viruses (phages) may enter a symbiosis with their host cell, forming a unit called a lysogen. Infection and viral replication are disassociated in lysogens until an induction event such as DNA damage occurs, triggering viral-mediated lysis. The lysogen-lytic viral reproduction switch is central to viral ecology, with diverse ecosystem impacts. It has been argued that lysogeny is favoured in phages at low host densities. This paradigm is based on the fraction of chemically inducible cells (FCIC) lysogeny proxy determined using DNA-damaging mitomycin C inductions. Contrary to the established paradigm, a survey of 39 inductions publications found FCIC to be highly variable and pervasively insensitive to bacterial host density at global, within-environment and within-study levels. Attempts to determine the source(s) of variability highlighted the inherent complications in using the FCIC proxy in mixed communities, including dissociation between rates of lysogeny and FCIC values. Ultimately, FCIC studies do not provide robust measures of lysogeny or consistent evidence of either positive or negative host density dependence to the lytic-lysogenic switch. Other metrics are therefore needed to understand the drivers of the lytic-lysogenic decision in viral communities and to test models of the host density-dependent viral lytic-lysogenic switch

The Marine Viromes of Four Oceanic Regions

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness” quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure

Diversity and Population Structure of a Near–shore Marine–sediment Viral Community

Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near–shore marine–sediment viral community. Three–quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double–stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under–represented or absent. This ‘marineness’ suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 104 viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine–sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet

Metagenomic Analyses of an Uncultured Viral Community from Human Feces

Here we present the first metagenomic analyses of an uncultured viral community from human feces, using partial shotgun sequencing. Most of the sequences were unrelated to anything previously reported. The recognizable viruses were mostly siphophages, and the community contained an estimated 1,200 viral genotypes

Power law rank-abundance models for marine phage communities

Metagenomic analyses suggest that the rank–abundance curve for marine phage communities follows a power law distribution. A new type of power law dependence based on a simple model in which a modified version of Lotka–Volterra predator–prey dynamics is sampled uniformly in time is presented. Biologically, the model embodies a kill the winner hypothesis and a neutral evolution hypothesis. The model can match observed power law distributions and uses very few parameters that are readily identifiable and characterize phage ecosystems. The model makes new untested predictions: (1) it is unlikely that the most abundant phage genotype will be the same at different time points and (2) the long-term decay of isolated phage populations follows a power law