Correlated responses in basal immune function in response to selection for fast development in Drosophila melanogaster.

Often, immunity is invoked in the context of infection, disease and injury. However, an ever alert and robust immune system is essential for maintaining good health, but resource investment into immunity needs to be traded off against allocation to other functions. In this study, we study the consequences of such a trade-off with growth by ascertaining various components of baseline innate immunity in two types of Drosophila melanogaster populations selected for fast development, in combination with either a long effective lifespan (FLJs) or a short effective lifespan (FEJs). We found that distinct immunological parameters were constitutively elevated in both, FLJs and FEJs compared to their ancestral control (JB) populations, and these constitutive elevated immunological parameters were associated with reduced insulin signalling and comparable total gut microbiota. Our results bring into focus the inter-relationship between egg to adult development time, ecdysone levels, larval gut microbiota, insulin signalling, adult reproductive longevity and immune function. We discuss how changes in selection pressures operating on life-history traits can modulate different components of immune system.

Heightened immune surveillance in Drosophila melanogaster populations selected for faster development and extended longevity.

Maximization of life-history traits is under constraints due to both, limitations of resource acquisition and the restricted pathways of resource allocation. Drosophila melanogaster has served as an excellent model organism to not only unravel various trade-offs among life history traits but also numerous aspects of host immune response. Drosophila larvae are semi-aquatic that live, feed and excrete inside the food source-often over-ripe fruits and vegetables that are rich in both commensal and pathogenic microbiota that can impact the larval survival. In this study, we have used six populations of D. melanogaster, three of which are selected for faster pre-adult development and extended adult longevity, and their three ancestral controls, to explore the impact of selection on the basal immune activity in the larval stage. The larvae from selected populations had nearly significantly upregulated plasmatocyte density, significantly higher percent phagocytosis, phagocytic index and higher transcript levels of Tep3, eater and NimC1. Selected populations also had significantly upregulated crystal cell number along with higher transcript of PPO2. Out of seven tested AMPs level, Drosomycin was significantly upregulated in selected populations while Drosocin was significantly higher in control populations. ROS levels were comparable in the selected and control populations. Our results strongly suggest that enhanced basal immune activity during larval stage manages the faster development and could be responsible for comparable larval survival of selected and control populations.

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.

Management of altered metabolic activity in Drosophila model of Huntington's disease by curcumin.

Huntington's disease (HD) is a devastating polyglutamine disorder characterized by extensive neurodegeneration and metabolic abnormalities at systemic, cellular and intracellular levels. Metabolic alterations in HD manifest as abnormal body weight, dysregulated biomolecule levels, impaired adipocyte functions, and defective energy state which exacerbate disease progression and pose acute threat to the health of challenged individuals in form of insulin resistance, cardiovascular disease, and energy crisis. To colossally mitigate disease symptoms, we tested the efficacy of curcumin in Drosophila model of HD. Curcumin is the bioactive component of turmeric (Curcuma longa Linn), well-known for its ability to modulate metabolic activities. We found that curcumin effectively managed abnormal body weight, dysregulated lipid content, and carbohydrate level in HD flies. In addition, curcumin administration lowered elevated reactive-oxygen-species levels in adult adipose tissue of diseased flies, and improved survival and locomotor function in HD flies at advanced disease stage. Altogether, these findings clearly suggest that curcumin efficiently attenuates metabolic derangements in HD flies and can prove beneficial in alleviating the complexities associated with HD.

Fitness consequences of biochemical adaptation in Drosophila melanogaster populations under simultaneous selection for faster pre-adult development and extended lifespan.

In holometabolous insects like Drosophila melanogaster, critical size is an important time point during larval life, for irreversible commitment to metamorphosis. Here, we studied the impact of restricted growth duration in terms of selection for faster pre-adult development in Drosophila melanogaster populations which resulted in the evolution of reduced critical size on adult life history traits. Selection for faster pre-adult development resulted in biochemical adaptation in larval physiology with no compromise in major biomolecules at critical size time point. The flies from the selected populations seem to not only commit to metamorphosis on the attainment of critical size but also seem to channelize resources to reproduction as indicated by similar life-time fecundity of CS and NS flies from selected populations, while the Control CS flies significantly lower life-time fecundity compared to Control NS flies. The flies from selected populations seem to achieve longevity comparable to control flies despite being significantly smaller in size-thus resource constrained due to faster pre-adult development.

Evolution of reduced minimum critical size as a response to selection for rapid pre-adult development in Drosophila melanogaster.

Adult body size in holometabolus insects is directly proportional to the time spent during the larval period. The larval duration can be divided into two parts: (i) pre-critical duration-time required to attain a critical size/critical weight that would result in successful completion of development and metamorphosis even under non-availability of nutrition beyond the time of attainment of critical size, and (ii) post-critical duration-the time duration from the attainment of critical size till pupation. It is of interest to decipher the relative contribution of the two larval growth phases (from the hatching of the egg to the attainment of critical size, and from the attainment of critical size to pupation) to the final adult size. Many studies using Drosophila melanogaster have shown that selecting populations for faster development results in the emergence of small adults. Some of these studies have indirectly reported the evolution of smaller critical size. Using two kinds of D. melanogaster populations, one of which is selected for faster/accelerated pre-adult development and the other their ancestral control, we demonstrate that the final adult size is determined by the time spent as larvae post the attainment of critical size despite having increased growth rate during the second larval instar. Our populations under selection for faster pre-adult development are exhibiting adaptive bailout due to intrinsic food limitation as against extrinsic food limitation in the yellow dung fly.

Wing patterning in faster developing Drosophila is associated with high ecdysone titer and wingless expression.

'Developmental robustness' is the ability of biological systems to maintain a stable phenotype despite genetic, environmental or physiological perturbations. In holometabolous insects, accurate patterning and development is guaranteed by alignment of final gene expression patterns in tissues at specific developmental stage such as molting and pupariation, irrespective of individual rate of development. In the present study, we used faster developing Drosophila melanogaster populations that show reduction of ~22% in egg to adult development time. Flies from the faster developing population exhibit phenotype constancy, although significantly small in size. The reduction in development time in faster developing flies is possibly due to coordination between higher ecdysteroid release and higher expression of developmental genes. The two together might be ensuring appropriate pattern formation and early exit at each development stage in the populations selected for faster pre-adult development compared to their ancestral controls. We report that apart from plasticity in the rate of pattern progression, alteration in the level of gene expression may be responsible for pattern integrity even under reduced development time.

Rapid and solitary production of mono-rhamnolipid biosurfactant and biofilm inhibiting pyocyanin by a taxonomic outlier Pseudomonas aeruginosa strain CR1.

Biosurfactant - Rhamnolipids (RLs) and antibacterial toxin - pyocyanin (PYO) produced by Pseudomonas aeruginosa strains have great potential for biotechnological applications. Generally, RLs are produced as a mixture of di-rhamnolipids (di-RLs) and mono-rhamnolipids (mono-RLs). Mono-RLs possess superior emulsification and antimicrobial properties and are costlier than di-RLs. In this study, a taxonomic outlier P. aeruginosa strain CR1 isolated from rhizosphere soil was explored for mono-RLs and PYO production. Phylogenetically strain CR1 resembles avirulent outlier P. aeruginosa strain ATCC9027, lacks archetypical virulence genes and harbors unique pathways for the synthesis of solely mono-RLs and PYO. Strain CR1 produced RL biosurfactant which efficiently emulsified hydrocarbons, showed hemolysis and inhibited Bacillus subtilis. At 37 °C, strain CR1 exclusively produced 21.77 g L-1 and 19.22 g L-1 rhamnolipid in glycerol amended Luria Bertani (LB) medium and basal medium amended with rice bran oil, respectively after 54 h growth. Besides RL production was unaffected under varying nitrogen sources. Structural characterization using FTIR, TLC, and LC-MS confirmed that strain CR1 exclusively produced mono-RLs, majorly dominated by Rha-C10-C10, Rha-C10-C8, and CH3-Rha-C12:2-C10:1. The compound was stable over a wide pH range (4-12), salinity (25%) and 100 °C indicating its applicability under harsh environmental conditions. In addition, strain CR1 produced 4.5 µg mL-1 PYO, which could efficiently inhibit biofilm formation by Bacillus species. The environmental outlier strain CR1 can be used for the industrial production of biotechnologically important mono-RLs and PYO.

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 ß-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.

Draft Genome Sequence of Deinococcus sp. Strain S9, Isolated from Microbial Mat Deposits of Hot Springs Located atop the Himalayan Ranges at Manikaran, India.

Here, we present the draft genome sequence of Deinococcus sp. strain S9, a red-pigmented and moderately thermophilic bacterium isolated from microbial mat deposits around the hot springs at Manikaran, Himachal Pradesh, India. The draft genome (3.34 Mb) contains 101 contigs with an average GC content of 66.4%.

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.

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.

Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups-rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed ß-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats-freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism's genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe's respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

Altered lipid metabolism in Drosophila model of Huntington's disease.

Huntington's disease (HD) is late-onset, progressive neurodegenerative disorder caused by expansion of polyglutamine (polyQ) repeat within Huntingtin (Htt) protein. In HD patients, energy-related manifestations such as modulation of weight during entire course of disease with energy deficit at terminal stage have been reported, however, underlying reason remains elusive till date. Lipids, carbohydrate and protein constitute a predominant fraction of body's energy reservoir and perturbation in their homeostasis may influence weight. To discern role of these energy molecules in weight alteration, we quantified them in an in vivo transgenic Drosophila model of HD. We document that diseased flies exhibit change in weight due to an altered lipid metabolism, as evident from considerably high lipid levels at the time of disease onset followed by a pathologic decline at end-stage. An alteration in intracellular lipid droplet size suggested altered cellular lipid turnover. Furthermore, diseased flies displayed substantial changes in carbohydrate and protein content. Interestingly, alteration in weight and lipid levels are independent of the feeding pattern in diseased condition and exhibit weak correlation with insulin-like peptide or adipokinetic hormone producing cells. We propose that therapeutic intervention aimed at restoring lipid levels and associated metabolic pathways may improve longevity and quality of patient's life.

Elimination of Arsenophonus and decrease in the bacterial symbionts diversity by antibiotic treatment leads to increase in fitness of whitefly, Bemisia tabaci.

Bemisia tabaci is an invasive agricultural pest with more than 24 genetic groups harboring different bacterial endosymbionts categorized into obligatory and facultative endosymbionts. Arsenophonus is one of the facultative endosymbionts prevalent in B. tabaci of Indian sub-continent. Not much is known about the functional role of this endosymbiont in its host. Some studies have revealed its involvement in virus transmission by B. tabaci, but how it effects the biology of B. tabaci is unknown. In this study, tetracycline was used to eliminate Arsenophonus from B. tabaci to study its effects with regard to development and other fitness parameters. Bacteria specific 16S Polymerase chain reaction (PCR) was used to ascertain Arsenophonus absence with differential effects on other secondary endosymbionts present in B. tabaci. Our results revealed that Arsenophonus negative (A(-)) whiteflies had more fecundity, increased juvenile developmental time, increased nymphal survival and increased adult life span as compared to control (A(+)) whiteflies. Thus, our results demonstrate that A(+) whiteflies have lesser fitness as compared to A(-) whiteflies. These observations give a new insight about the probable role of Arsenophonus in B. tabaci, that need to be explored further.

Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring.

Microbial mats situated at the Manikaran hot springs (>95°C) are characterized by their high arsenic content (140 ppb), qualifying as a stressed niche. Here, we report the annotated draft genome (3.85 Mb) of Cellulosimicrobium sp. strain MM, isolated from these microbial mats, consisting of 3,718 coding sequences, with an average % G+C of 74.4%.

Gender based disruptive selection maintains body size polymorphism in Drosophila melanogaster.

Darwinian fitness in holometabolous insects like the fruit fly Drosophila melanogaster is reported to be positively correlated with body size. If large individuals in a population have higher fitness, then one would expect directional selection to operate leading to uniformly large individuals. However, size polymorphism persists in nature and needs further probing. We assessed the effect of body size on some of the fitness and fitness-related traits in replicate populations of genotypically large, genotypically small and phenotypically small D. melanogaster flies. In this study, the time taken to attain reproductive maturity and copulation duration were independent of fly size. Fecundity and longevity of large females were significantly higher when they partnered genotypically small males than when they were with genotypically larger or phenotypically small males. The increased female longevity when in association with genotypically small males was not due to selective early death of males that would release the female partner from presumed cost of persistent courtship. On the contrary, the genotypically as well as phenotypically small males had significantly higher longevity than large males. The virility of the genotypically small males was not significantly different from that of genotypically large males. Our results clearly show that selection on body size operates in the opposite direction (disruptive selection) for the two genders, thus explaining the persistence of size polymorphisms in the holometabolous insect, Drosophila melanogaster.

Aloe vera or resveratrol supplementation in larval diet delays adult aging in the fruit fly, Drosophila melanogaster.

Longevity extension in Drosophila melanogaster by feeding diet supplemented with chemicals throughout adulthood can cause harmful side effects. We tested the effect of larval diet supplementation with five different concentrations of resveratrol and one concentration of Aloe vera extract on the adult longevity of short-lived D melanogaster populations. Resveratrol and A vera extract supplementation of larval diet extended adult longevity in both the male and female flies without reducing fecundity but by efficient reactive oxygen species scavenging through increased antioxidant enzymes activity and better neuroprotection as indicated by increased locomotor activity in adult males.