Application of an Escherichia coli triple reporter strain for at-line monitoring of single-cell physiology during L-phenylalanine production

Biotechnological production processes are sustainable approaches for the production of biobased components such as amino acids for food and feed industry. Scale-up from ideal lab-scale bioreactors to large-scale processes is often accompanied by loss in productivity. This may be related to population heterogeneities of cells originating from isogenic cultures that arise due to dynamic non-ideal conditions in the bioreactor. To better understand this phenomenon, deeper insights into single-cell physiologies in bioprocesses are mandatory before scale-up. Here, a triple reporter strain (3RP) was developed by chromosomally integrating the fluorescent proteins mEmerald, CyOFP1, and mTagBFP2 into the L-phenylalanine producing Escherichia coli strain FUS4 (pF81_kan) to allow monitoring of growth, oxygen availability, and general stress response of the single cells. Functionality of the 3RP was confirmed in well-mixed lab-scale fed-batch processes with glycerol as carbon source in comparison to the strain without fluorescent proteins, leading to no difference in process performance. Fluorescence levels could successfully reflect the course of related process state variables, revealed population heterogeneities during the transition between different process phases and potentially subpopulations that exhibit superior process performance. Furthermore, indications were found for noise in gene expression as regulation strategy against environmental perturbation.     

snpR: User friendly population genomics for SNP data sets with categorical metadata

The analysis of genomic data can be an intimidating process, particularly for researchers who are not experienced programmers. Commonly used analyses are spread across many programs, each requiring their own specific input formats, and so data must often be repeatedly reorganized and transformed into new formats. Analyses often require splitting data according to metadata variables such as population or family, which can be challenging to manage in large data sets. Here, we introduce snpR, a user-friendly data analysis package in R for processing SNP genomic data. snpR is designed to automate data subsetting and analyses across categorical metadata while also streamlining repeated analyses by integrating approaches contained in many different packages in a single ecosystem. snpR facilitates iterative and efficient analyses centred on a single R object for an entire analysis pipeline.     

Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana

Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global F_ST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.     

RESTRICTED MIGRATION AND THE EVOLUTION OF ALTRUISM

A suggestion that limited migration, i.e., population viscosity, should favor the evolution of altruism has been challenged by recent kin selection models explicitly incorporating restricted migration. It is demonstrated that these models compound two distinct elements of population structure, spatial-genotypic variation and density regulation. These two characteristics are often determined by distinct biological processes. While they may be linked under certain circumstances, this is not invariably true. A simple modification of the migration system employed in these studies decouples migration and population regulation thus favoring inter-group selection. At least in some cases, restricted migration will facilitate the evolution of altruism.     

Stock and recruitment and inversely density-dependent growth of salmon, Salmo salar L., in a Scottish stream

For the 6 years for which detailed data are readily available, estimates of the survival of emergent fry of Atlantic salmon, Salmo salar L., to the first and second autumns at a site on the Shelligan Burn are consistent with the dome-shaped Ricker model with about 11 emergent fry m⁻² maximizing recruitment. The data are not satisfactorily fitted by the asymptotic Beverton and Holt model. A possible mechanism, which results from the observed inversely density-dependent growth, is discussed briefly.     

Seasonal population dynamics of Paraquimpevia tenevvima (Linstow) (Nematoda) in the European eel Anguilla anguilla (Linnaeus) in three localities of southwest England

Seasonal population dynamics of Puraquzmperia tenerrima (Linstow) in the European eel Anguillu anguillu (Linnaeus) have been investigated in three localities in Devon, southwest England. The nematode is common and exhibits very similar seasonal patterns in changes of prevalence and abundance in the three localities. The population increases over winter through to late spring or early summer as the recruitment of the new generation occurs throughout this period. Reproduction of the nematode starts in spring. A sharp decrease of prevalence and abundance accompanies or follows reproduction, and infection levels are very low in autumn and early winter. The dispersion pattern of the nematode varies with the infection levels from over-dispersion in spring and early summer to almost random dispersion in autumn and winter. It is suggested that P. tenerrimu is a common specific parasite of eels, especially in small streams or rivers and that insect larvae or species of crustaceans might serve as intermediate hosts for the nematode.     

THE EFFECT OF HOST PLANT PATCH SIZE VARIATION ON THE POPULATION STRUCTURE OF A SPECIALIST HERBIVORE INSECT,TETRAOPES TETRAOPHTHALMUS

The patchy local distribution of the common milkweed, Asclepias syriaca, organizes populations of a beetle that feeds on it, Tetraopes tetraophthalmus, into numerous local demes. Genetic and ecological characteristics of demes of adult milkweed beetles occupying two naturally occurring size classes of patches, defined as large and small, were studied in order to describe the effect of patch size variation on local population structure. Allele frequency variance in two of three protein polymorphisms was significantly greater in collections of beetles from an array of 13 small patches when compared to collections from an array of 11 large populations. A multivariate measure of variance using information from all 3 genetic markers confirmed that the small patches displayed greater overall genetic differentiation. This was further quantified by computing an F_st value, combined across loci, of 0.018 for the small patches and 0.004 for the large patches. No significant difference between patch size classes in mean allele frequency was detected. Mark and recapture studies of the adults found in five small and four large patches showed the residence times of adults in small patches to be less than half of those found in large patches. This was interpreted as resulting from higher emigration rates from small patches. It is proposed that greater genetic differentiation is found among demes from smaller patches because smaller patches support smaller population sizes and further because smaller patches act as net exporters of migrants while larger patches act as net migrant importers.     

The population biology of tench, Tinea tinea (L.), in two gravel pit lakes

The populations of tench from two gravel pit lakes of contrasting habitat type were studied. The population density of tench from St Peter's Lake, which has abundant aquatic vegetation was 176 individuals ha⁻¹ (102.2 kg ha⁻¹) compared to 0.3 individuals ha⁻¹ (0.5 kg ha⁻¹) in the Main Lake which has very little aquatic vegetation. The results of ageing tench by scales, opercular bones and otoliths were compared; all three structures gave similar results up to 9 years of age, but thereafter there were difficulties in ageing using scales and care was needed in counting annuli. The oldest tench caught was 15 years old. Growth of male and female tench was similar and fitted the von Bertalanffy model; for female tench L_∞ = 573 mm, K =0.122 and for male tench L_∞ = 586 mm, K =0.114. Recruitment was variable and strong year classes occurred in years with warm summers.     

Population ecology of the paddy field-dwelling fish Channa gachua (Günther) (Perciformes, Channidae) in Sri Lanka

A population of Channa gachua in a small irrigation canal that supplies rice fields was studied by monthly sampling over 2 years. The population density was positively correlated with the rainfall and varied from 0.34 to 0.95 individuals m⁻². The growth parameters of the von Bertalanffy growth equation determined on monthly size–frequency data were L_x = 179 mm total length and K =0.50. Overall male to female ratio was 0.82 and there were more females than males in the middle size classes. Spawning occurred throughout the year, but all evidence indicated enhanced breeding during major rainy periods of May to July and October to December. The length at first spawning was 102 mm, which is reached in about 20 months. Fecundity, which varied between 389 and 2130, was positively correlated with gonad weight, body weight and total length. Longevity and natural mortality were estimated as 6 years and l.27 yr⁻¹, respectively. However, 99% of the population appeared to live for only 3 years. The mean biomass, average annual production and turnover ratio of the population were 7.35 g m⁻², 12.06 g m⁻² and 1.64, respectively.