Complete genome sequences of nine Rhodococcus equi phages

We report genomes of nine phages isolated from Actinobacteria Rhodococcus equi NRRL B-16538. Six of these phages belong to actinobacteriophage cluster CR, which otherwise contains Gordonia phages; two form the CF cluster; and one is a singleton. Genome lengths are 62,017-80,980 bp with 63.9%-67.3% GC content.

Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants

While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.

Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny

Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. However, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through (meta)genomic screening and in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant dietary fibers and energy-generating fermentation. Additionally, several members of the specialized adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers. Symbionts from both life stages have the genomic capacity to recycle nitrogen and synthesize amino acids and B-vitamins. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae may aid colony digestion and contribute to colony-wide nitrogen, B-vitamin and energy budgets. In addition, the conserved nature of the digestive capacities among adult-associated symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 45 million years of residency.

Thermally Conductive-Silicone Composites with Thermally Reversible Cross-links

Thermally conductive-silicone composites that contain thermally reversible cross-links were prepared by blending diene- and dienophile-functionalized polydimethylsiloxane (PDMS) with an aluminum oxide conductive filler. This class of thermally conductive-silicones are useful as thermal interface materials (TIMs) within Information Technology (IT) hardware applications to allow rework of valuable components. The composites were rendered reworkable via retro Diels-Alder cross-links when temperatures were elevated above 130 °C and required little mechanical force to remove, making them advantageous over other TIM materials. Results show high thermal conductivity (0.4 W/m·K) at low filler loadings (45 wt %) compared to other TIM solutions (>45 wt %). Additionally, the adhesion of the material was found to be ∼7 times greater at lower temperatures (25 °C) and ∼2 times greater at higher temperatures (120 °C) than commercially available TIMs.

Cephaloticoccus gen. nov., a new genus of 'Verrucomicrobia' containing two novel species isolated from Cephalotes ant guts

Two novel members of the bacterial phylum 'Verrucomicrobia', strains CAG34T and CV41T, were isolated from the guts of Cephalotes rohweri and Cephalotes varians ants, respectively. Strains CAG34T and CV41T were coccoid, Gram-stain-negative, non-motile, and formed cream-coloured colonies on trypticase soy agar. Optimum growth occurred under an atmosphere of 12-20 % O2 and 1 % CO2 for both strains, although strain CV41T could not grow without supplemental CO2. Growth was possible under NaCl concentrations of 0.5-1.5 % (w/v) and temperatures of 23-37 °C for both strains, and pH values of 6.9-7.7 for strain CAG34T and 6.9-7.3 for strain CV41T. The G+C content of the genomic DNA was 60.7 mol% for strain CAG34T and 60.5 mol% for strain CV41T. The major fatty acids for both strains were anteiso-C15 : 0, iso-C14 : 0, C16 : 0, and C16 : 1ω5c. Based on the phylogenetic analysis of 16S rRNA gene sequences, the closest cultivated relative for both strains was the type strain of Opitutus terrae (91.8 % similarity). Hence, strains CAG34T and CV41T are considered to represent a new genus within the 'Verrucomicrobia' family Opitutaceae, for which we propose the name Cephaloticoccus gen. nov. Given that strains CAG34T and CV41T share 97.7 % 16S rRNA gene sequence similarity with each other and are physiologically distinct, we propose to classify the isolates as representing two novel species, Cephaloticoccus primus sp. nov. for strain CAG34T (=NCIMB 15004T =ATCC TSD-38T) and Cephaloticoccus capnophilus sp. nov. for strain CV41T (=NCIMB 15005T =ATCC TSD-39T =DSM 100879T).

Ventosimonas gracilis gen. nov., sp. nov., a member of the Gammaproteobacteria isolated from Cephalotes varians ant guts representing a new family, Ventosimonadaceae fam. nov., within the order 'Pseudomonadales'

Cephalotes 'turtle' ants are known to harbor a core group of gut symbionts, including members belonging to the Gammaproteobacteria. Here, we describe the cultivation and characterization of strain CV58T, a novel member of the Gammaproteobacteria order Pseudomonadales isolated from the guts of the ant Cephalotes varians. Strain CV58T was rod-shaped, Gram-stain-negative, non-motile and formed pale-yellow colonies on trypticase soy agar. Optimum growth occurred under an atmosphere of 4-20 % (v/v) O2. Growth was possible for strain CV58Tat NaCl concentrations of 0-1.5 % (w/v), temperatures of 23-40 °C, and pH values of 5.5-8.5. The G+C content of the genomic DNA was 54.9 mol% and the major fatty acids were C18 : 1ω7c, C16 : 0, C16 : 1ω7c/C16 : 1ω6c, C12 : 0 and C12 : 03OH. The only respiratory quinone detected was ubiquinone-9 (Q-9) and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on phylogenetic analysis of the 16S rRNA gene sequence, strain CV58T shared an 88.3 % nucleotide identity with its closest cultivated neighbor, Pseudomonas putida R43. We believe that this, combined with the housekeeping gene phylogeny, differences in phenotypic characteristics and cellular fatty acid compositions of other cultivated members indicates that strain CV58T represents a novel species occupying a novel genus and family within the order Pseudomonadales. Thus, we propose the name Ventosimonadaceae fam nov., followed by Ventosimonas gracilis gen. nov., sp. nov., to classify strain CV58T (=NCIMB 15011T =DSM 100910T).

Polylactic acid with improved heat deflection temperatures and self-healing properties for durable goods applications

A method to recover fracture toughness after failure and increase thermal properties of polylactic acid (PLA) for use within durable goods applications is presented. Microcapsules were incorporated into PLA to form a composite material in which the microcapsules served the dual purpose of (1) releasing self-healing additives to fracture regions and (2) serving as nucleating agents to improve the PLA composite's thermal tolerance. Self-healing was achieved though embedment of dicyclopentadiene-filled microcapsules and Grubbs' first generation ruthenium metathesis catalyst, the former being autonomically released into damage volumes and undergoing polymerization in the presence of the catalyst. This approach led to up to 84% recovery of the polymer composite's initial fracture toughness. Additionally, PLA's degree of crystallinity and heat deflection temperature were improved by ∼ 11% and ∼ 21 °C, respectively, relative to nonfilled virgin PLA, owing to microcapsule-induced nucleation. The self-healing system developed here overcomes many property limitations of PLA that can potentially lead to its incorporation into various durable goods.

Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4

Five newly isolated mycobacteriophages –Angelica, CrimD, Adephagia, Anaya, and Pixie – have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them – with the exception of TM4 – form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.

Stenoxybacter acetivorans gen. nov., sp. nov., an acetate-oxidizing obligate microaerophile among diverse O2-consuming bacteria from termite guts

In termite hindguts, fermentative production of acetate--a major carbon and energy source for the insect--depends on efficient removal of inwardly diffusing oxygen by microbes residing on and near the hindgut wall. However, little is known about the identity of these organisms or about the substrate(s) used to support their respiratory activity. A cultivation-based approach was used to isolate O(2)-consuming organisms from hindguts of Reticulitermes flavipes. A consistently greater (albeit not statistically significant) number of colonies developed under hypoxia (2% [vol/vol] O(2)) than under air, and the increase coincided with the appearance of morphologically distinct colonies of a novel, rod-shaped, obligately microaerophilic beta-proteobacterium that was <95% similar (based on the 16S rRNA gene sequence) to its closest known relative (Eikenella corrodens). Nearly identical organisms (and/or their 16S rRNA genes) were obtained from geographically separated and genetically distinct populations of Reticulitermes. PCR-based procedures implied that the novel isolates were autochthonous to the hindgut of R. flavipes and comprised ca. 2 to 7% of the hindgut prokaryote community. Representative strain TAM-DN1 utilized acetate and a limited range of other organic and amino acids as energy sources and possessed catalase and superoxide dismutase. On solid medium, the optimal O(2) concentration for growth was about 2%, and no growth occurred with O(2) concentrations above 4% or under anoxia. However, cells in liquid medium could grow with higher O(2) concentrations (up to 16%), but only after proportionately extended lag phases. The genetic and physiological distinctiveness of TAM-DN1 and related strains supports their recognition as a new genus and species, for which the name Stenoxybacter acetivorans gen. nov., sp. nov. is proposed.

Physiological ecology of Stenoxybacter acetivorans, an obligate microaerophile in termite guts

Stenoxybacter acetivorans is a newly described, obligately microaerophilic beta-proteobacterium that is abundant in the acetate-rich hindgut of Reticulitermes. Here we tested the hypotheses that cells are located in the hypoxic, peripheral region of Reticulitermes flavipes hindguts and use acetate to fuel their O(2)-consuming respiratory activity in situ. Physical fractionation of R. flavipes guts, followed by limited-cycle PCR with S. acetivorans-specific 16S rRNA gene primers, indicated that cells of this organism were indeed located primarily among the microbiota colonizing the hindgut wall. Likewise, reverse transcriptase PCR of hindgut RNA revealed S. acetivorans-specific transcripts for acetate-activating enzymes that were also found in cell extracts (acetate kinase and phosphotransacetylase), as well as transcripts of ccoN, which encodes the O(2)-reducing subunit of high-affinity cbb(3)-type cytochrome oxidases. However, S. acetivorans strains did not possess typical enzymes of the glyoxylate cycle (isocitrate lyase and malate synthase A), suggesting that they may use an alternate pathway to replenish tricarboxylic acid cycle intermediates or they obtain such compounds (or their precursors) in situ. Respirometric measurements indicated that much of the O(2) consumption by R. flavipes worker larvae was attributable to their guts, and the potential contribution of S. acetivorans to O(2) consumption by extracted guts was about 0.2%, a value similar to that obtained for other hindgut bacteria examined. Similar measurements obtained with guts of larvae prefed diets to disrupt major members of the hindgut microbiota implied that most of the O(2) consumption observed with extracted guts was attributable to protozoans, a group of microbes long thought to be "strict anaerobes."

New strategies for cultivation and detection of previously uncultured microbes

An integrative approach was used to obtain pure cultures of previously uncultivated members of the divisions Acidobacteria and Verrucomicrobia from agricultural soil and from the guts of wood-feeding termites. Some elements of the cultivation procedure included the following: the use of agar media with little or no added nutrients; relatively long periods of incubation (more than 30 days); protection of cells from exogenous peroxides; and inclusion of humic acids or a humic acid analogue (anthraquinone disulfonate) and quorum-signaling compounds (acyl homoserine lactones) in growth media. The bacteria were incubated in the presence of air and in hypoxic (1 to 2% O(2) [vol/vol]) and anoxic atmospheres. Some bacteria were incubated with elevated concentrations of CO(2) (5% [vol/vol]). Significantly more Acidobacteria were found on isolation plates that had been incubated with 5% CO(2). A simple, high-throughput, PCR-based surveillance method (plate wash PCR) was developed. This method greatly facilitated detection and ultimate isolation of target bacteria from as many as 1,000 colonies of nontarget microbes growing on the same agar plates. Results illustrate the power of integrating culture methods with molecular techniques to isolate bacteria from phylogenetic groups underrepresented in culture.

Down-regulation of androgen receptor expression and inhibition of lacrimal gland cell proliferation by retinoic acid

Androgens and retinoids are known to be involved in control of lacrimal gland function. Because retinoids generally antagonize androgen function it was the purpose of this study to investigate interactions of retinoic acid and androgens in rabbit lacrimal acinar cells in culture by determining effects of retinoic acid on androgen receptor (AR) mRNA expression, AR protein levels and androgen-stimulated cell proliferation. Experiments were conducted using primary rabbit lacrimal acinar cells and a transformed rabbit lacrimal acinar cell line. Exposure of primary lacrimal acinar cells in culture to 10(-10)-10(-6)M all-trans retinoic acid for 4-24hr causes an approximately 50% decrease in AR mRNA expression. Expression of AR protein in primary and transformed rabbit lacrimal acinar cells was confirmed by immunohistochemistry. Exposure of the primary cells to 10(-6)M retinoic acid for 24hr caused a 40% decrease in AR protein levels as determined by measurement of binding of(3) [H]-dihydrotestosterone (DHT) to cells in culture and Scatchard analysis. Exposure to 10(-9)-10(-6)M DHT stimulates proliferation of transformed rabbit lacrimal acinar cells. This effect is receptor mediated since it is blocked by the AR antagonist, flutamide. Proliferation of the lacrimal acinar cells is inhibited by retinoic acid, as compared to control, and retinoic acid also completely inhibits androgen stimulation of cell proliferation. This study supports the hypothesis that androgens play a supportive role in lacrimal gland function. The antagonistic influences of androgens and retinoic acid suggests that, under physiologic conditions there is a balance between the effects of androgens and retinoids in the lacrimal gland. A decrease in androgen levels in a dry eye patient may alter the balance between the effects of these important controllers of gene expression. The antagonistic effect of retinoids on androgens in the lacrimal gland must also be considered when devising pharmaceutical treatments for dye eye.