Reassessment of Paleotachina Townsend and Electrotachina Townsend and their removal from?the?Tachinidae (Diptera)

The monotypic genera Paleotachina Townsend, 1921 and Electrotachina Townsend, 1938 were originally described as fossils in amber but were later discovered to be inclusions in copal. Both taxa were originally assigned to the Tachinidae (Diptera) and this placement has continued to the present day. The holotypes of the two type species, P. smithii Townsend and E. smithii Townsend, were examined and the following taxonomic and nomenclatural changes are proposed: Paleotachina is transferred to the Muscidae and placed in synonymy with Aethiopomyia Malloch, 1921, syn. n.; P. smithii Townsend, type species of Paleotachina, is synonymized with Aethiopomyia gigas (Stein, 1906), syn. n.; Electrotachina is transferred to the Sarcophagidae and placed in synonymy with Dolichotachina Villeneuve, 1913, syn. n.; E. smithii Townsend, type species of Electrotachina, is recognized as a valid species of Dolichotachina comb. n. Images of the holotypes of P. smithii and E. smithii are provided and features that have helped place these copal inclusions in their new combinations are discussed.     

Freezing of Nonwoody Plant Tissue: II. Cell Damage and the Fine Structure of Freezing Curves

Increasing pretreatment day temperatures of 20, 30, and 40 C resulted in decreased net photosynthesis in Agropyron smithii (C₃) while in Bouteloua gracilis (C₄) net photosynthesis was increased. The effect on photosynthesis of increasing analysis temperatures was the same as observed by increasing pretreatment temperatures. Resistance of the stomata and boundary layer were less affected by pretreatment temperatures than were the remaining resistances of a physical and chemical nature. Resistances for A. smithii were increased and those for B. gracilis were decreased by increasing pretreatment temperatures. Phenology of the species in the shortgrass prairie is such that A. smithii has its greatest growth activity during the cool portion of the growth season, whereas B. gracilis is most active in the warm portion. Thus, photosynthetic adaptation to temperature is strongly suggested as a strategy for ecosystem utilization by reduction of interspecific competition.     

High Prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae Detected in the Human Gut Using an Improved DNA Detection Protocol

Background

The low and variable prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae DNA in human stool contrasts with the paramount role of these methanogenic Archaea in digestion processes. We hypothesized that this contrast is a consequence of the inefficiencies of current protocols for archaeon DNA extraction. We developed a new protocol for the extraction and PCR-based detection of M. smithii and M. stadtmanae DNA in human stool.

Methodology/Principal Findings

Stool specimens collected from 700 individuals were filtered, mechanically lysed twice, and incubated overnight with proteinase K prior to DNA extraction using a commercial DNA extraction kit. Total DNA was used as a template for quantitative real-time PCR targeting M. smithii and M. stadtmanae 16S rRNA and rpoB genes. Amplification of 16S rRNA and rpoB yielded positive detection of M. smithii in 95.7% and M. stadtmanae in 29.4% of specimens. Sequencing of 16S rRNA gene PCR products from 30 randomly selected specimens (15 for M. smithii and 15 for M. stadtmanae) yielded a sequence similarity of 99–100% using the reference M. smithii ATCC 35061 and M. stadtmanae DSM 3091 sequences.

Conclusions/Significance

In contrast to previous reports, these data indicate a high prevalence of the methanogens M. smithii and M. stadtmanae in the human gut, with the former being an almost ubiquitous inhabitant of the intestinal microbiome.     

A Brazilian Population of the Asexual Fungus-Growing Ant Mycocepurus smithii (Formicidae,Myrmicinae, Attini) Cultivates Fungal Symbionts with Gongylidia-Like Structures

Attine ants cultivate fungi as their most important food source and in turn the fungus is nourished, protected against harmful microorganisms, and dispersed by the ants. This symbiosis evolved approximately 50–60 million years ago in the late Paleocene or early Eocene, and since its origin attine ants have acquired a variety of fungal mutualists in the Leucocoprineae and the distantly related Pterulaceae. The most specialized symbiotic interaction is referred to as “higher agriculture” and includes leafcutter ant agriculture in which the ants cultivate the single species Leucoagaricus gongylophorus. Higher agriculture fungal cultivars are characterized by specialized hyphal tip swellings, so-called gongylidia, which are considered a unique, derived morphological adaptation of higher attine fungi thought to be absent in lower attine fungi. Rare reports of gongylidia-like structures in fungus gardens of lower attines exist, but it was never tested whether these represent rare switches of lower attines to L. gonglyphorus cultivars or whether lower attine cultivars occasionally produce gongylidia. Here we describe the occurrence of gongylidia-like structures in fungus gardens of the asexual lower attine ant Mycocepurus smithii. To test whether M. smithii cultivates leafcutter ant fungi or whether lower attine cultivars produce gongylidia, we identified the M. smithii fungus utilizing molecular and morphological methods. Results shows that the gongylidia-like structures of M. smithii gardens are morphologically similar to gongylidia of higher attine fungus gardens and can only be distinguished by their slightly smaller size. A molecular phylogenetic analysis of the fungal ITS sequence indicates that the gongylidia-bearing M. smithii cultivar belongs to the so-called “Clade 1”of lower Attini cultivars. Given that M. smithii is capable of cultivating a morphologically and genetically diverse array of fungal symbionts, we discuss whether asexuality of the ant host maybe correlated with low partner fidelity and active symbiont choice between fungus and ant mutualists.     

Isolation and Screening of Thermophilic Bacilli from Compost for Electrotransformation and Fermentation: Characterization of Bacillus smithii ET 138 as a New Biocatalyst

Thermophilic bacteria are regarded as attractive production organisms for cost-efficient conversion of renewable resources to green chemicals, but their genetic accessibility is a major bottleneck in developing them into versatile platform organisms. In this study, we aimed to isolate thermophilic, facultatively anaerobic bacilli that are genetically accessible and have potential as platform organisms. From compost, we isolated 267 strains that produced acids from C₅ and C₆ sugars at temperatures of 55°C or 65°C. Subsequently, 44 strains that showed the highest production of acids were screened for genetic accessibility by electroporation. Two Geobacillus thermodenitrificans isolates and one Bacillus smithii isolate were found to be transformable with plasmid pNW33n. Of these, B. smithii ET 138 was the best-performing strain in laboratory-scale fermentations and was capable of producing organic acids from glucose as well as from xylose. It is an acidotolerant strain able to produce organic acids until a lower limit of approximately pH 4.5. As genetic accessibility of B. smithii had not been described previously, six other B. smithii strains from the DSMZ culture collection were tested for electroporation efficiencies, and we found the type strain DSM 4216^T and strain DSM 460 to be transformable. The transformation protocol for B. smithii isolate ET 138 was optimized to obtain approximately 5 × 10³ colonies per μg plasmid pNW33n. Genetic accessibility combined with robust acid production capacities on C₅ and C₆ sugars at a relatively broad pH range make B. smithii ET 138 an attractive biocatalyst for the production of lactic acid and potentially other green chemicals.     

Thelytokous Parthenogenesis in the Fungus-Gardening Ant Mycocepurus smithii (Hymenoptera: Formicidae)

The general prevalence of sexual reproduction over asexual reproduction among organisms testifies to the evolutionary benefits of recombination, such as accelerated adaptation to changing environments and elimination of deleterious mutations. Documented instances of asexual reproduction in groups otherwise dominated by sexual reproduction challenge evolutionary biologists to understand the special circumstances that might confer an advantage to asexual reproductive strategies. Here we report one such instance of asexual reproduction in the ants. We present evidence for obligate thelytoky in the asexual fungus-gardening ant, Mycocepurus smithii, in which queens produce female offspring from unfertilized eggs, workers are sterile, and males appear to be completely absent. Obligate thelytoky is implicated by reproductive physiology of queens, lack of males, absence of mating behavior, and natural history observations. An obligate thelytoky hypothesis is further supported by the absence of evidence indicating sexual reproduction or genetic recombination across the species'' extensive distribution range (Mexico-Argentina). Potential conflicting evidence for sexual reproduction in this species derives from three Mycocepurus males reported in the literature, previously regarded as possible males of M. smithii. However, we show here that these specimens represent males of the congeneric species M. obsoletus, and not males of M. smithii. Mycocepurus smithii is unique among ants and among eusocial Hymenoptera, in that males seem to be completely absent and only queens (and not workers) produce diploid offspring via thelytoky. Because colonies consisting only of females can be propagated consecutively in the laboratory, M. smithii could be an adequate study organism a) to test hypotheses of the population-genetic advantages and disadvantages of asexual reproduction in a social organism and b) inform kin conflict theory.For a Portuguese translation of the abstract, please see Abstract S1.     

No sex in fungus-farming ants or their crops

Asexual reproduction imposes evolutionary handicaps on asexual species, rendering them prone to extinction, because asexual reproduction generates novel genotypes and purges deleterious mutations at lower rates than sexual reproduction. Here, we report the first case of complete asexuality in ants, the fungus-growing ant Mycocepurus smithii, where queens reproduce asexually but workers are sterile, which is doubly enigmatic because the clonal colonies of M. smithii also depend on clonal fungi for food. Degenerate female mating anatomy, extensive field and laboratory surveys, and DNA fingerprinting implicate complete asexuality in this widespread ant species. Maternally inherited bacteria (e.g. Wolbachia, Cardinium) and the fungal cultivars can be ruled out as agents inducing asexuality. M. smithii societies of clonal females provide a unique system to test theories of parent–offspring conflict and reproductive policing in social insects. Asexuality of both ant farmer and fungal crop challenges traditional views proposing that sexual farmer ants outpace coevolving sexual crop pathogens, and thus compensate for vulnerabilities of their asexual crops. Either the double asexuality of both farmer and crop may permit the host to fully exploit advantages of asexuality for unknown reasons or frequent switching between crops (symbiont reassociation) generates novel ant–fungus combinations, which may compensate for any evolutionary handicaps of asexuality in M. smithii.     

Stability of Methanobrevibacter smithii Populations in the Microbial Flora Excreted from the Human Large Bowel

Total anaerobic bacteria and Methanobrevibacter smithii populations were enumerated in fecal specimens from two individuals over 10- and 13-month periods. The ratio of M. smithii to total anaerobic count varied between the individuals, but it was a relatively constant proportion of the large-bowel microbial flora within each individual. Neither a barium enema examination of one subject nor a radical change in the diet of the other had any long-term effect on the methanogen populations.     

Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type

Methane is an undesirable end product of rumen fermentative activity because of associated environmental impacts and reduced host feed efficiency. Our study characterized the rumen microbial methanogenic community in beef cattle divergently selected for phenotypic residual feed intake (RFI) while offered a high-forage (HF) diet followed by a low-forage (LF) diet. Rumen fluid was collected from 14 high-RFI (HRFI) and 14 low-RFI (LRFI) animals at the end of both dietary periods. 16S rRNA gene clone libraries were used, and methanogen-specific tag-encoded pyrosequencing was carried out on the samples. We found that Methanobrevibacter spp. are the dominant methanogens in the rumen, with Methanobrevibacter smithii being the most abundant species. Differences in the abundance of Methanobrevibacter smithii and Methanosphaera stadtmanae genotypes were detected in the rumen of animals offered the LF compared to the HF diet while the abundance of Methanobrevibacter smithii genotypes was different between HRFI and LRFI animals irrespective of diet. Our results demonstrate that while a core group of methanogen operational taxonomic units (OTUs) exist across diet and phenotype, significant differences were observed in the distribution of genotypes within those OTUs. These changes in genotype abundance may contribute to the observed differences in methane emissions between efficient and inefficient animals.     

Monitoring Bacterial Community of Human Gut Microbiota Reveals an Increase in Lactobacillus in Obese Patients and Methanogens in Anorexic Patients

Background

Studies of the bacterial communities of the gut microbiota have revealed a shift in the ratio of Firmicutes and Bacteroidetes in obese patients. Determining the variations of microbial communities in feces may be beneficial for the identification of specific profiles in patients with abnormal weights. The roles of the archaeon Methanobrevibacter smithii and Lactobacillus species have not been described in these studies.

Methods and Findings

We developed an efficient and robust real-time PCR tool that includes a plasmid-based internal control and allows for quantification of the bacterial divisions Bacteroidetes, Firmicutes, and Lactobacillus as well as the methanogen M. smithii. We applied this technique to the feces of 20 obese subjects, 9 patients with anorexia nervosa, and 20 normal-weight healthy controls. Our results confirmed a reduction in the Bacteroidetes community in obese patients (p<0.01). We found a significantly higher Lactobacillus species concentration in obese patients than in lean controls (p = 0.0197) or anorexic patients (p = 0.0332). The M. smithii concentration was much higher in anorexic patients than in the lean population (p = 0.0171).

Conclusions

Lactobacillus species are widely used as growth promoters in the farm industry and are now linked to obesity in humans. The study of the bacterial flora in anorexic patients revealed an increase in M. smithii. This increase might represent an adaptive use of nutrients in this population.     

Distribution of six species of bitterlings in a creek in Fukuoka Prefecture,Japan

Comparative study on the distribution of six species of bitterling in a creek in Fukuoka Prefecture was carried out. The upper part of the creek was fluvial, and the lower part stagnant.Acheilognathus lanceolatus, A. tabira subsp. (b) of Nakamura (1969),A. rhombeus andRhodeus atremius showed wide distribution in the creek throughout their life.A. limbatus seemed to be a fluvial species, andR. ocellatus smithii a lentic species. In the spawning season, however, all the species of bitterling, exceptingR. o. smithii, probably possess a common spawning ground in which mussels occur at a relatively high density. Adult females ofA. lanceolatus, A. tabira subsp. (b) andR. atremius without ripe eggs aggregated in the lower, stagnant parts of the creek. Most juveniles of these species and ofA. rhombeus seemed to grow in the lower part of the creek, and then migrate upward untill their spawning season. No species among the same phylogenetic group has the same set of the life modes (spawning season, spawning sites, aggregation of females without ripe eggs in the lower part of the creek and probability of upstream migration of 0-year-old fish toward spawning sites).     

GENOME RELATIONS AMONG ELYMUS CANADENSIS,ELYMUS TRITICOIDES,ELYMUS DASYSTACHYS,AND AGROPYRON SMITHII

Hand-emasculated Elymus canadensis pollinated by E. triticoides, E. dasystachys, and Agropyron smithii yielded 15, 21, and 1 viable hybrid seeds from 56, 52, and 52 florets, respectively. The 28-chromosome species—E. canadensis, E. triticoides, and E. dasystachys—behaved meiotically as allotetraploids and consistently formed 14 bivalents at metaphase I. Octoploid A. smithii, 2n = 56, averaged 0.41^I, 27.72^II, and 0.03^IV in 87 metaphase-I cells. Agropyron smithii is apparently an allooctoploid or a segmental autoallooctoploid. Meiosis was similar in the E. canadensis X E. triticoides and E. dasystachys hybrids. Chromosome pairing was very low in both hybrids, about two loosely connected open-ended bivalents per cell, and may not represent genuine homologies. The genomes of E. canadensis are distinctly different from those of E. triticoides and E. dasystachys. The E. canadensis X A. smithii hybrid averaged 13.37^I and 14.31^II in 76 metaphase-I cells. More than half of the bivalents were closed at both ends. Inability to distinguish between auto- and allosyndesis resulted in two interpretations of genome relations. Either A. smithii is an alloploid with two of its four genomes similar to those of E. canadensis, or it is a segmental autoalloploid genomically unrelated to E. canadensis. The first interpretation is favored. Agropyron dasystachyum, or one of its close relatives, and E. triticoides are suggested as possible parents of A. smithii.     

Solvent free biocatalytic synthesis of isoniazid from isonicotinamide using whole cell of Bacillus smithii strain IITR6b2

A biocatalytic route for the synthesis of isoniazid, an important first-line antitubercular drug, in aqueous system is presented. The reported bioprocess is a greener method, does not involve any hazardous reagent and takes place under mild reaction conditions. Whole cell amidase of Bacillus smithii strain IITR6b2 having acyltransferase activity was utilized for its ability to transfer acyl group of isonicotinamide to hydrazine–2HCl in aqueous medium. B. smithii strain IITR6b2 possessed 3 folds higher acyltransferase activity as compared to amide hydrolase activity and this ratio was further improved to 4.5 by optimizing concentration of co-substrate hydrazine–2HCl. Various key parameters were optimized and under the optimum reaction conditions of pH (7, phosphate buffer 100 mM), temperature (30 °C), substrate/co-substrate concentration (100/1000 mM) and resting cells concentration (2.0 mg_dcw/ml), 90.4% conversion of isonicotinamide to isoniazid was achieved in 60 min. Under these conditions, a fed batch process for production of isoniazid was developed and resulted in the accumulation of 439 mM of isoniazid with 87.8% molar conversion yield and productivity of 6.0 g/h/g_dcw. These results demonstrated that enzymatic synthesis of isoniazid using whole cells of B. smithii strain IITR6b2 might present an efficient alternative route to the chemical synthesis procedures without the involvement of organic solvent.     

Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses,Salmonella enterica,and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment

The suitability of traditional microbial indicators (i.e., Escherichia coli and enterococci) has been challenged due to the lack of correlation with pathogens and evidence of possible regrowth in the natural environment. In this study, the relationships between alternative microbial indicators of potential human fecal contamination (Bacteroides thetaiotaomicron, Methanobrevibacter smithii, human polyomaviruses [HPyVs], and F+ and somatic coliphages) and pathogens (Salmonella spp., Pseudomonas aeruginosa, rotavirus, astrovirus, norovirus GI, norovirus GII, and adenovirus) were compared with those of traditional microbial indicators, as well as environmental parameters (temperature, conductivity, salinity, pH, dissolved oxygen, total organic carbon, total suspended solids, turbidity, total nitrogen, and total phosphorus). Water samples were collected from surface waters of urban catchments in Singapore. Salmonella and P. aeruginosa had significant positive correlations with most of the microbial indicators, especially E. coli and enterococci. Norovirus GII showed moderately strong positive correlations with most of the microbial indicators, except for HPyVs and coliphages. In general, high geometric means and significant correlations between human-specific markers and pathogens suggest the possibility of sewage contamination in some areas. The simultaneous detection of human-specific markers (i.e., B. thetaiotaomicron, M. smithii, and HPyVs) with E. coli and enterococcus supports the likelihood of recent fecal contamination, since the human-specific markers are unable to regrow in natural surface waters. Multiple-linear-regression results further confirm that the inclusion of M. smithii and HPyVs, together with traditional indicators, would better predict the occurrence of pathogens. Further study is needed to determine the applicability of such models to different geographical locations and environmental conditions.     

Notes on the asteraceae of the Southeastern United States

Nomenclatural innovations are validated inAster, Chrysopsis, Eupatorium,Gaillardia, Helianthus, Prenanthes, Silphium, andSolidago. The genusChrysopsis is maintained as distinct fromHeterotheca, andHelianthus smithii Heiser is reduced to synonymy underH. microcephalus Torr. & Gray.     

THE ORIGIN OF AGROPYRON SMITHII

The hypothesis that North American octoploid Agropyron smithii Rydb., 2n = 56, originated by hybridization between tetraploid Agropyron and Elymus species, followed by chromosome doubling, was tested by observing chromosome pairing in hybrids of A. smithii with an induced amphiploid, 2n = 56, derived from E. canadensis L., 2n = 28, X E. dasystachys Trin., 2n = 28, F₁'s. Chromosome pairing in A. smithii averaged 0.52^I, 27.70^II, 0.01^III, and 0.01^IV in 184 metaphase-I cells; and the amphiploid averaged 1.13^I and 27.44^II in 195 cells. Chromosome pairing in A. smithii X amphiploid hybrids averaged 8.20^I, 23.38^II, 0.34^III, and 0.05^IV in 101 metaphase-I cells. It was concluded that A. smithii was genomically similar to the E. canadensis-E. dasystachys amphiploid. The basic genome formula of the amphiploid is SSHHJJXX, with the SSHH genomes coming from E. canadensis and the JJXX genomes coming from E. dasystachys. Consideration of the morphological, ecological, and reproductive characteristics of all North American species that contain the basic SSHH and JJXX genomes led to the conclusion that A. dasystachyum (Hook.) Scribn., SSHH, and E. triticoides Buckl., JJXX, are the probable progenitors of A. smithii.     

Furanoeremophilanes from Senecio smithii

The investigation of Senecio smithii afforded 17 furanoeremophilanes, six of them being isolated for the first time. Furthermore, two new bisabolon     

Guaianolides from Gochnatia smithii

The structure and stereochemistry of 8α-acetoxy and 8α-tigloyloxy dehydrocostus lactones, two guaianolides isolated from the aerial parts of Gochnatia smithii, were established by chemical and spectroscopic methods.     

Intestinal Methanobrevibacter smithii but not total bacteria is related to diet‐induced weight gain in rats

It is increasingly understood that gastrointestinal (GI) methanogens, including Methanobrevibacter smithii, influence host metabolism.

Objective:

Therefore, we compared M. smithii colonization and weight gain in a rat model under different dietary conditions.

Design and Methods:

Sprague‐Dawley rats were inoculated with M. smithii or vehicle (N = 10/group), fed normal chow until day 112 postinoculation, high‐fat chow until day 182, then normal chow until day 253. Thereafter, five rats from each group were fed high‐fat and normal chow until euthanasia.

Results:

Both groups exhibited M. smithii colonization, which increased following inoculation only for the first 9 days. Change to high‐fat chow correlated with significant increases in weight (P < 0.00001) and stool M. smithii (P < 0.01) in all rats, with stool M. smithi decreasing on return to normal chow. Rats switched back to high‐fat on day 253 further increased weight (P < 0.001) and stool M. smithii (P = 0.039). Euthanasia revealed all animals had higher M. smithii, but not total bacteria, in the small intestine than in the colon. Rats switched back to high‐fat chow had higher M. smithii levels in the duodenum, ileum, and cecum than those fed normal chow; total bacteria did not differ in any bowel segment. Rats which gained more weight had more bowel segments colonized, and the lowest weight recorded was in a rat on high‐fat chow which had minimal M. smithii colonization.

Conclusions:

We conclude that M. smithii colonization occurs in the small bowel as well as in the colon, and that the level and extent of M. smithii colonization is predictive of degree of weight gain in this animal model.     

A phylogenetic groundplan of the specific complex Dactylis glomerata

A phytochemical examination of the specific complex of Dactylis glomerata L. based on flavonoid patterns, has led to a proposed evolutionary scheme. Two phyla are pointed out, originating from diploid ancestors related respectively to D.g. subsp, aschersoniana and D.g. subsp. smithii. The temperate component of the specific complex is monophyletic, derivating from a D.g. subsp, aschersoniana-like diploid ancestor. On the other hand, chemical data support a polyphyletic origin for the geographically mediterranean part of the complex with several subphyla originating from D.g. subsp. aschersoniana-like, smithii-like and secondarily juncinella-like diploids.