Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India

Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.

Genome Sequencing Revealed the Biotechnological Potential of an Obligate Thermophile Geobacillus thermoleovorans Strain RL Isolated from Hot Water Spring

In the present study, we report the draft genome sequence of an obligate thermophile Geobacillus thermoleovorans strain RL isolated from Manikaran hot water spring located atop the Himalayan ranges, India. Strain RL grew optimally at 70 °C but not below 45 °C. The draft genome (3.39 Mb) obtained by Illumina sequencing contains 138 contigs with an average G + C content of 52.30%. RAST annotation showed that amino acid metabolism pathways were most dominant followed by carbohydrate metabolism. Genome-wide analysis using NCBI's Prokaryotic Genome Annotation Pipeline revealed that strain RL encodes for a cocktail of industrially important hydrolytic enzymes glycoside hydrolase, α-and β-glucosidase, xylanase, amylase, neopullulanase, pullulanase and lipases required for white biotechnology. In addition, the presence of genes encoding green biocatalyst multicopper polyphenol oxidase (laccase) and an anticancer enzyme l-glutaminase reflects the significance of strain RL in gray and red biotechnology, respectively. Strain RL is a thermophilic multi-enzyme encoding bacterium which could be the source for the recombinant production of biotechnologically significant enzymes. In, addition whole cells of strain RL may be used in bioremediation studies.

Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa

Genomic information for outlier strains of Pseudomonas aeruginosa is exiguous when compared with classical strains. We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. It clustered with the outlier group, hence we scaled up the analyses to understand the differences in environmental and clinical outlier strains. We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. Virulence genotype analysis revealed that strain CR1 lacked hemolytic phospholipase C and D, three genes for LPS biosynthesis and had reduced antibiotic resistance genes when compared with clinical strains. Genes belonging to proteases, bacterial exporters and DNA stabilization were found to be under strong positive selection, thus facilitating pathogenicity and survival of the outliers. The outliers had the complete operon for the production of vibrioferrin, a siderophore present in plant growth promoting bacteria. The competence to acquire multidrug resistance and new virulence factors makes these strains a potential threat. However, we identified major regulatory hubs that can be used as drug targets against both the classical and outlier groups.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.

Laboratory evolution of population stability in Drosophila: constancy and persistence do not necessarily coevolve

1. Despite considerable theoretical work, the evolution of population stability has rarely been investigated empirically. Moreover, it is not clear whether different stability properties of a population evolve together, or independently. 2. We investigate the evolution of two aspects of population stability using laboratory populations of Drosophila melanogaster selected for faster preadult development and early reproduction, and their matched controls. 3. We show that the constancy stability of the selected populations is significantly higher than their controls, confirming a previous observation that population stability can evolve as a by-product of life-history evolution. This enhanced constancy stability is due to a reduced maximal per capita growth rate, brought about by a reduction in fecundity of the selected populations as a result of the trade-off between developmental rate and fecundity. 4. Persistence stability, as reflected by the probability of extinction, does not differ significantly between selected and control populations. 5. We also show how seemingly trivial experimental details, such as the protocol for restarting extinct populations, can interact with life-history traits to alter the manifestation of the stability properties of a population.

Faster development does not lead to correlated evolution of greater pre-adult competitive ability in Drosophila melanogaster

In comparisons across Drosophila species, faster pre-adult development is phenotypically correlated with increased pre-adult competitive ability, suggesting that these two traits may also be evolutionary correlates of one another. However, correlations between traits within- and among- species can differ, and in most cases it is the within-species genetic correlations that are likely to act as constraints on adaptive evolution. Moreover, laboratory studies on Drosophila melanogaster have shown that the suite of traits that evolves in populations subjected to selection for faster development is the opposite of the traits that evolve in populations selected for increased pre-adult competitive ability. This observation led us to propose that, despite having a higher carrying capacity and a reduced minimum food requirement for completing development than controls, D. melanogaster populations subjected to selection for faster development should have lower competitive ability than controls owing to their reduced larval feeding rates and urea tolerance. Here, we describe results from pre-adult competition experiments that clearly show that the faster developing populations are substantially poorer competitors than controls when reared at high density in competition with a marked mutant strain. We briefly discuss these results in the context of different formulations of density-dependent selection theory.

Correction for Shakarad et al. , Faster development does not lead to correlated evolution of greater pre-adult competitive ability in Drosophila melanogaster

Correction for ‘Faster development does not lead to correlated evolution of greater pre-adult competitive ability in Drosophila melanogaster ’ by Mallikarjun Shakarad, N. G. Prasad, Kaustubh Gokhale, Vikram Gadagkar, M. Rajamani and Amitabh Joshi (Biol. Lett. 1 , 91–94. (doi: 10.1098/2004.0261 )).

On p. 91, the Digital Object Identifier should be 10.1098/rsbl.2004.0261.

Variation in adult life history and stress resistance across five species of Drosophila

Dry weight at eclosion, adult lifespan, lifetime fecundity, lipid and carbohydrate content at eclosion, and starvation and desiccation resistance at eclosion were assayed on a long-term laboratory population of Drosophila melanogaster, and one recently wild-caught population each of four other species of Drosophila, two from the melanogaster and two from the immigrans species group. The relationships among trait means across the five species did not conform to expectations based on correlations among these traits inferred from selection studies on D. melanogaster. In particular, the expected positive relationships between fecundity and size/lipid content, lipid content and starvation resistance, carbohydrate (glycogen) content and desiccation resistance, and the expected negative relationship between lifespan and fecundity were not observed. Most traits were strongly positively correlated between sexes across species, except for fractional lipid content and starvation resistance per microgram lipid. For most traits, there was evidence for significant sexual dimorphism but the degree of dimorphism did not vary across species except in the case of adult lifespan, starvation resistance per microgram lipid, and desiccation resistance per microgram carbohydrate. Overall, D. nasuta nasuta and D. sulfurigaster neonasuta (immigrans group) were heavier at eclosion than the melanogaster group species, and tended to have somewhat higher absolute lipid content and starvation resistance. Yet, these two immigrans group species were shorter-lived and had lower average daily fecundity than the melanogaster group species. The smallest species, D. malerkotliana (melanogaster group), had relatively high daily fecundity, intermediate lifespan and high fractional lipid content, especially in females. D. ananassae (melanogaster group) had the highest absolute and fractional carbohydrate content, but its desiccation resistance per microgram carbohydrate was the lowest among the five species. In terms of overall performance, the laboratory population of D. melanogaster was clearly superior, under laboratory conditions, to the other four species if adult lifespan, lifetime fecundity, average daily fecundity, and absolute starvation and desiccation resistance are considered. This finding is contrary to several recent reports of substantially higher adult lifespan and stress resistance in recently wild-caught flies, relative to flies maintained for a long time in discrete-generation laboratory cultures. Possible explanations for these apparent anomalies are discussed in the context of the differing selection pressures likely to be experienced by Drosophila populations in laboratory versus wild environments.

The evolution of population stability as a by-product of life-history evolution

Proposed mechanisms for the evolution of population stability include group selection through longterm persistence, individual selection acting directly on stability determining the demographic parameters, and the evolution of stability as a by-product of life-history evolution. None of these hypotheses currently has clear empirical support. Using two sets of Drosophila melanogaster populations, we provide experimental evidence of stability evolving as a correlated response to selection on traits not directly related to demography. Four populations (FEJs) were selected for faster development and early reproduction for 125 generations, and the other four (JBs) were ancestral controls. All FEJ and JB populations have been maintained on discrete generations at moderate density, thus eliminating differential selection on stability determining demographic parameters. We derived eight small populations from each FEJ and JB population, and subjected four small populations each to either stabilizing or destabilizing food regimes. Census data on these 64 small populations over 20 generations clearly showed that the FEJ populations have significantly less temporal fluctuations in their numbers in both food regimes compared to their controls. This greater stability of the FEJ populations is probably a by-product of the evolution of reduced fecundity and pre-adult survivorship, as a correlated response to selection for rapid development.

K-selection, alpha-selection, effectiveness, and tolerance in competition: density-dependent selection revisited

In the Drosophila literature, selection for faster development and selection for adapting to high density are often confounded, leading, for example, to the expectation that selection for faster development should also lead to higher competitive ability. At the same time, results from experimental studies on evolution at high density do not agree with many of the predictions from classical density-dependent selection theory. We put together a number of theoretical and empirical results from the literature, and some new experimental results on Drosophila populations successfully subjected to selection for faster development, to argue for a broader interpretation of density-dependent selection. We show that incorporating notions of alpha-selection, and the division of competitive ability into effectiveness and tolerance components, into the concept of density-dependent selection yields a formulation that allows for a better understanding of the empirical results. We also use this broader formulation to predict that selection for faster development in Drosophila should, in fact, lead to the correlated evolution of decreased competitive ability, even though it does lead to the evolution of greater efficiency and higher population growth rates at high density when in monotypic culture.

Correlated responses to selection for faster development and early reproduction in Drosophila: the evolution of larval traits

Studies on selection for faster development in Drosophila have typically focused on the trade-offs among development time, adult weight, and adult life span. Relatively less attention has been paid to the evolution of preadult life stages and behaviors in response to such selection. We have earlier reported that four laboratory populations of D. melanogaster selected for faster development and early reproduction, relative to control populations, showed considerably reduced preadult development time and survivorship, dry weight at eclosion, and larval growth rates. Here we study the larval phase of these populations in greater detail. We show here that the reduction in development time after about 50 generations of selection is due to reduced duration of the first and third larval instars and the pupal stage, whereas the duration of the second larval instar has not changed. About 90% of the preadult mortality in the selected populations is due to larval mortality. The third instar larvae, pupae, and freshly eclosed adults of the selected populations weigh significantly less than controls, and this difference appears during the third larval instar. Thereafter, percentage weight loss during the pupal stage does not differ between selected and control populations. The minimum amount of time a larva must feed to subsequently complete development is lower in the selected populations, which also exhibit a syndrome of reduced energy expenditure through reduction in larval feeding rate, larval digging and foraging activity, and pupation height. Comparison of these results with those observed earlier in populations selected for adaptation to larval crowding and faster development under a different protocol from ours reveal differences in the evolved traits that suggest that the responses to selection for faster development are greatly affected by the larval density at which selection acts and on details of the selection pressures acting on the timing of reproduction.

Evolution of faster development does not lead to greater fluctuating asymmetry of sternopleural bristle number in Drosophila

Both strong directional selection and faster development are thought to destabilize development, giving rise to greater fluctuating asymmetry (FA), although there is no strong empirical evidence supporting this assertion. We compared FA in sternopleural bristle number in four populations of Drosophila melanogaster successfully selected for faster development from egg to adult, and in four control populations. The fraction of perfectly symmetric individuals was higher in the selected populations, whereas the FA levels did not differ significantly between selected and control populations, clearly indicating that directional selection for faster development has not led to increased FA in sternopleural bristle number in these populations. This may be because: (i) development time and FA are uncorrelated, (ii) faster development does result in FA, but selection has favoured developmentally stable individuals that can develop fast and still be symmetrical, or (iii) the increased fraction of symmetric individuals in the selected populations is an artifact of reduced body size. Although we cannot discriminate among these explanations, our results suggest that the relationship between development time, FA and fitness may be far more subtle than often thought.

Evolution of reduced pre-adult viability and larval growth rate in laboratory populations of Drosophila melanogaster selected for shorter development time

Four large (n > 1000) populations of Drosophila melanogaster, derived from control populations maintained on a 3 week discrete generation cycle, were subjected to selection for fast development and early reproduction. Egg to eclosion survivorship and development time and dry weight at eclosion were monitored every 10 generations. Over 70 generations of selection, development time in the selected populations decreased by approximately 36 h relative to controls, a 20% decline. The difference in male and female development time was also reduced in the selected populations. Flies from the selected populations were increasingly lighter at eclosion than controls, with the reduction in dry weight at eclosion over 70 generations of selection being approximately 45% in males and 39% in females. Larval growth rate (dry weight at eclosion/development time) was also reduced in the selected lines over 70 generations, relative to controls, by approximately 32% in males and 24% in females. However, part of this relative reduction was due to an increase in growth rate of the controls populations, presumably an expression of adaptation to conditions in our laboratory. After 50 generations of selection had elapsed, a considerable and increasing pre-adult viability cost to faster development became apparent, with viability in the selected populations being about 22% less than that of controls at generation 70 of selection.

Division of labour in a lower termite: the majority of tasks are performed by older workers

Division of labour among workers was investigated in the lower termite, Reticulitermes fukienensisWorkers were separated into three age groups based on size, small workers being the youngest, medium workers intermediate and large workers the oldest. Workers were then compared in behavioural assays for the degree to which they would carry out specific tasks, which included: (1) foraging-related tasks; (2) care of eggs, larvae and the queen; and (3) some other important behaviours including burying corpses, alarm-giving and time spent stationary. All tasks were performed by two or all three of the size-groups of workers. Hence evidence does not support the hypothesis of tasks being discretely allocated among different instars in termites and this having evolved towards the extreme of one caste for every task. The oldest workers (i.e. large workers) carried out the highest frequencies of all tasks investigated. This contrasts with the social Hymenoptera, where younger workers specialize in some tasks (especially brood and queen care). The results suggest a new pattern for social insects for division of labour among workers.Copyright 1997 The Association for the Study of Animal Behaviour1997The Association for the Study of Animal Behaviour